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Recent Prochlorococcus Related Publications

1. Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1.
   Richter AS, Schleberger C, Backofen R, Steglich C
   Bioinformatics. 2009 Oct 22.
   Pubmed: 19850757
   Abstract
   MOTIVATION: Prochlorococcus possesses the smallest genome of all sequenced photoautotrophs. Although the number of regulatory proteins in the genome is very small, the relative number of small regulatory RNAs is comparable to that of other bacteria. The compact genome size of Prochlorococcus offers an ideal system to search for targets of small RNAs and to refine existing target prediction algorithms. RESULTS: Target predictions for the cyanobacterial small RNA Yfr1 were carried out with IntaRNA in Prochlorococcus MED4. The ultraconserved Yfr1 sequence motif was defined as the putative interaction seed. To study the impact of Yfr1 on its predicted mRNA targets, a reporter system based on green fluorescent protein (GFP) was applied. We show that Yfr1 inhibits the translation of two predicted targets. We used mutation analysis to confirm that Yfr1 directly regulates its targets by an antisense interaction sequestering the ribosome binding site, and to assess the importance of interaction site accessibility. CONTACT: backofen@informatik.uni-freiburg.de, claudia.steglich@biologie.uni-freiburg.de.
2. In search of the main properties of phthalocyanines participating in toxicity against cyanobacteria.
   Jancula D, Marsalek B, Novotna Z, Cerny J, Karaskova M, Rakusan J
   Chemosphere. 2009 Oct 19.
   Pubmed: 19846205
   Abstract
   Phthalocyanines are promising photosensitizers for use in various branches of science including nanotechnology. In the presence of visible light and diatomic oxygen, phthalocyanines can react to produce singlet oxygen ((1)O(2)( *)), which has known inhibitory effects on cellular growth and metabolic activity, although other mechanisms may be involved. The present work focuses on the properties of phthalocyanines (atom charge densities, singlet oxygen production, inhibition effects at various irradiances) contributing to toxicity against the cyanobacteria, Synechococcus nidulans. Our results indicate that positive charge densities at peripheral parts of substituents exhibit greater inhibitory effects against S. nidulans than the amount of singlet oxygen produced, potentially by binding to negatively charged membranes on the cell surface. The weak effect of (1)O(2)( *) was further demonstrated by a 10% increase in phthalocyanine toxicity (the maximal inhibition detected) when the irradiance increased 3-fold from 1200 to 4000lux.
3. The genome and structural proteome of an ocean siphovirus: a new window into the cyanobacterial 'mobilome'
   Sullivan MB, Krastins B, Hughes JL, Kelly L, Chase M, Sarracino D, Chisholm SW
   Environ Microbiol. 2009 Oct 14.
   Pubmed: 19840100
   Abstract
   Summary Prochlorococcus, an abundant phototroph in the oceans, are infected by members of three families of viruses: myo-, podo- and siphoviruses. Genomes of myo- and podoviruses isolated on Prochlorococcus contain DNA replication machinery and virion structural genes homologous to those from coliphages T4 and T7 respectively. They also contain a suite of genes of cyanobacterial origin, most notably photosynthesis genes, which are expressed during infection and appear integral to the evolutionary trajectory of both host and phage. Here we present the first genome of a cyanobacterial siphovirus, P-SS2, which was isolated from Atlantic slope waters using a Prochlorococcus host (MIT9313). The P-SS2 genome is larger than, and considerably divergent from, previously sequenced siphoviruses. It appears most closely related to lambdoid siphoviruses, with which it shares 13 functional homologues. The approximately 108 kb P-SS2 genome encodes 131 predicted proteins and notably lacks photosynthesis genes which have consistently been found in other marine cyanophage, but does contain 14 other cyanobacterial homologues. While only six structural proteins were identified from the genome sequence, 35 proteins were detected experimentally; these mapped onto capsid and tail structural modules in the genome. P-SS2 is potentially capable of integration into its host as inferred from bioinformatically identified genetic machinery int, bet, exo and a 53 bp attachment site. The host attachment site appears to be a genomic island that is tied to insertion sequence (IS) activity that could facilitate mobility of a gene involved in the nitrogen-stress response. The homologous region and a secondary IS-element hot-spot in Synechococcus RS9917 are further evidence of IS-mediated genome evolution coincident with a probable relic prophage integration event. This siphovirus genome provides a glimpse into the biology of a deep-photic zone phage as well as the ocean cyanobacterial prophage and IS element 'mobilome'.
4. Cyanobacteria MT gene SmtA enhance zinc tolerance in Arabidopsis.
   Xu J, Tian YS, Peng RH, Xiong AS, Zhu B, Hou XL, Yao QH
   Mol Biol Rep. 2009 Oct 15.
   Pubmed: 19830591
   Abstract
   Zinc is essential but toxic in excess. A bacterial metallothionein, SmtA from Synechococcus PCC 7942, has high affinity for Zn(2+) and the intracellular exclusively handling of Zn(2+). In this study, we report a functional analysis of SmtA in Arabidopsis thaliana and its response to zinc stress. After high zinc stress, the transgenic plants over-expressing SmtA showed higher survival rate than the wild type. We also found that over-expression of SmtA in Arabidopsis increased the activities of SOD and POD, and enhanced the tolerance to zinc stress. Together, our results indicate that SmtA may play an important role in the response to zinc stress in Arabidopsis.
5. Comparison of bacterioneuston and bacterioplankton dynamics during a phytoplankton bloom in a fjord mesocosm.
   Cunliffe M, Whiteley AS, Newbold L, Oliver A, Schafer H, Murrell JC
   Appl Environ Microbiol. 2009 Sep 25.
   Pubmed: 19783743
   Abstract
   The bacterioneuston is the community of Bacteria present in surface microlayers, the thin surface film that forms the interface between aquatic environments and the atmosphere. In this study we compared bacterial cell abundance and bacterial community structure of the bacterioneuston and the bacterioplankton (from the subsurface water column) during a phytoplankton bloom mesocosm experiment. Bacterial cell abundance, determined by flow cytometry, followed a typical bacterioplankton response to a phytoplankton bloom, with Synechococcus and high nucleic acid (HNA) bacterial cell numbers initially falling, probably due to selective protist grazing. Subsequently HNA and low nucleic acid (LNA) bacterial cells increased in abundance but Synechococcus did not. There was no significant difference between bacterioneuston and bacterioplankton cell abundances during the experiment. Conversely, distinct and consistent differences between the bacterioneuston and the bacterioplankton community structure were observed. This was monitored simultaneously by Bacteria 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). The conserved patterns of community structure observed in all of the mesocosms indicate that the bacterioneuston is distinctive and non-random.
6. [Evolution of gene orders in genomes of cyanobacteria]
   
   Genetika. 2009 Aug;45(8):1036-47.
   Pubmed: 19769292
   Abstract
   Genomes of 23 strains of cyanobacteria were comparatively analyzed using quantitative methods of estimation of gene order similarity. It has been found that reconstructions of phylogenesis of cyanobacteria based on the comparison of the orders of genes in chromosomes and nucleotide sequences appear to be similar. This confirms the applicability of quantitative measures of similarity of gene orders for phylogenetic reconstructions. In the evolution of marine unicellular plankton cyanobacteria, genome rearrangements are fixed with a low rate (about 3% of gene order changes per 1% of 16S rRNA changes), whereas in other groups of cyanobacteria the gene order can change several times more rapidly. The gene orders in genomes of cyanobacteria and chloroplasts preserve a considerable degree of similarity. The closest relatives of chloroplasts among the analyzed cyanobacteria are likely to be strains from hot springs belonging to the genus Synechococcus. Comparative analysis of gene orders and nucleotide sequences strongly suggests that Synechococcus strains from diferent environments (sea, fresh waters, hot springs) are not related and belong to evolutionally distant lines.
7. Low taxa richness of bacterioplankton in high-altitude lakes of the Eastern Tibetan Plateau with predominance of Bacteroidetes and Synechococcus.
   Xing P, Hahn MW, Wu QL
   Appl Environ Microbiol. 2009 Sep 18.
   Pubmed: 19767472
   Abstract
   Plankton samples were collected in six remote freshwater and saline lakes located at altitudes of 3204 to 4718 meter and 1000 km apart within an area of ca. 1 million km(2) on the East Tibetan Plateau to comparatively assess how environmental factors influence the diversity of bacterial communities in high altitude lakes. The composition of bacterioplankton was investigated by analysis of large clone libraries of 16S rRNA genes. Comparison of bacterioplankton diversity estimated for the six Tibetan lakes with reference data previously published for lakes located at lower altitudes indicated relatively low taxa richness in the Tibetan lakes. The estimated average taxa richness in the four Tibetan freshwater lakes was only one-fifth of the average taxa richness estimated for seven low altitude reference lakes. This can neither be explained by low coverage of communities in the Tibetan lakes by the established libraries, nor by differences in habitat size. Furthermore, a comparison of taxonomic composition of bacterioplankton across the six Tibetan lakes revealed low overlaps between their community compositions. About 70.9 % of the OTUs (99% similarity) were specific to single lakes and relatively high percentage (11 %) of sequences were < 95% similar to publicly deposited sequences of cultured or uncultured bacteria. This beta diversity was rather explained by differences in salinity between lakes than by distance effects. Another characteristic of the investigated lakes was the predominance of Cyanobacteria (Synechococcus) and Bacteroidetes. These features of bacterioplankton diversity may reflect specific adaptation of various lineages to the environmental conditions in these high-altitude lakes.
8. Heterologous expression of phosphoenolpyruvate carboxylase enhances the phosphate solubilizing ability of fluorescent pseudomonads by altering the glucose catabolism to improve biomass yield.
   Buch A, Archana G, Naresh Kumar G
   Bioresour Technol. 2009 Sep 18.
   Pubmed: 19767200
   Abstract
   The Synechococcus elongatus PCC 6301 phosphoenolpyruvate carboxylase (ppc) gene was constitutively overexpressed in fluorescent pseudomonads, to increase the supply of oxaloacetate, a crucial anabolic precursor and an intermediate in biosynthesis of organic acids implicated in phosphate (P) solubilization. Pseudomonas fluorescens ATCC 13525, transformed with pAB3 plasmid containing the ppc gene showed a 14-fold increase in PPC activity under P-sufficiency resulting in increased carbon flow through the direct oxidative pathway and reduced metabolic overflow. Under P-limitation, contribution of the direct oxidative pathway significantly increased in P. fluorescens ATCC 13525; however, ppc overexpression enhanced glucose catabolism through intracellular phosphorylative pathway. These results correlated with gluconic, pyruvic and acetic acid levels as well as the activities of key glucose catabolic enzymes. Irrespective of the P-status, ppc overexpression improved biomass yield without altering growth rate, resulting in improved P- solubilizing abilities of P. fluorescens ATCC 13525 as well as of the wheat rhizosphere fluorescent pseudomonads isolates Fp585, P109 and Fp315. Collectively, ppc overexpression reversed the P-status dependent glucose distribution between the direct oxidative and phosphorylative pathways of glucose catabolism in P. fluorescens ATCC 13525 and presents a feasible genetic engineering approach for developing efficient P-solubilizing bacteria.
9. Phosphatidylglycerol depletion affects photosystem II activity in Synechococcus sp. PCC 7942 cells.
   Bogos B, Ughy B, Domonkos I, Laczko-Dobos H, Komenda J, Abasova L, Cser K, Vass I, Sallai A, Wada H, Gombos Z
   Photosynth Res. 2009 Sep 18.
   Pubmed: 19763873
   Abstract
   The role of phosphatidylglycerol (PG) in photosynthetic membranes of cyanobacteria was analyzed in a Synechococcus sp. PCC 7942 mutant produced by inactivating its cdsA gene presumably encoding cytidine 5'-diphosphate-diacylglycerol synthase, a key enzyme in PG synthesis. In a medium supplemented with PG the Synechococcus sp. PCC 7942/DeltacdsA cells grew photoautotrophically. Depletion of PG in the medium resulted (a) in an arrest of cell growth and division, (b) in a suppression of O(2) evolving activity, and (c) in a modification of Chl fluorescence induction curves. Two-dimensional PAGE showed that in the absence of PG (a) the amount of the PSI monomers increased at the expense of the PSI trimers and (b) PSII dimers were decomposed into monomers. [(35)S]methionine labeling confirmed that PG depletion did not block the de novo synthesis of PSII proteins but slowed down the assembly of the newly synthesized D1 protein into PSII core complexes. Retailoring of PG was observed during PG depletion: the exogenously added artificial dioleoyl PG was transformed into photosynthetically more essential PG derivatives. Concomitantly with a decrease in PG content, SQDG content increased, but it could not restore photosynthetic activity.
10. Detailed analysis of the microdiversity of Prochlorococcus populations along a North-South Atlantic Ocean transect.
    Jameson E, Joint I, Mann NH, Muhling M
    Environ Microbiol. 2009 Sep 16.
    Pubmed: 19758347
    Abstract
    Summary In order to understand how environmental factors shape the diversity of Prochlorococcus in the Atlantic Ocean, we have elucidated the microdiversity along a north-south transect. The polymerase chain reaction-restriction fragment length polymorphism analysis of the genetic diversity of rpoC1 gene fragments of Prochlorococcus at 12 sampling sites revealed a latitudinal pattern in Prochlorococcus RFLP-type diversity in the samples collected from two depths. At the depth to which 14% of surface irradiance penetrated, HLII clones dominated the stations closest to the equator. The percentage of HLI clones increased with distance from the equator and LL clones were found only at the most northern and southern stations. In contrast, deeper (1% light depth) water samples did not show any overall trend in Prochlorococcus diversity or clade dominance. Multivariate statistical analyses indicated that Prochlorococcus diversity was linked to water temperature (partially an effect of latitude) and depth (which was linked to light penetration and turbidity). Phylogenetic analysis of the sequences obtained from the 423 different environmental RFLP-types detected in this study indicated that the HLII and HLI populations were composed of a wide range of genetically different clones, while the LL Prochlorococcus clade was less diverse, although half of the samples screened in this study derived from the 1% light depth.
11. The Repertoire and Evolution of ATP-Binding Cassette Systems in Synechococcus and Prochlorococcus.
    Bu L, Xiao J, Lu L, Xu G, Li J, Zhao F, Li X, Wu J
    J Mol Evol. 2009 Sep 16.
    Pubmed: 19756840
    Abstract
    Synechococcus and Prochlorococcus have made great contributions to earth's photosynthetic biomass. ATP-binding cassette (ABC) protein systems have been characterized to play important roles in various physiological functions, including carbon fixation, phosphate assimilation, and vitamin B(12) metabolism. In this study, the repertoire and domain architectures of ABC systems in Synechococcus and Prochlorococcus, as well as their potential evolutionary mechanism, have been surveyed extensively. Comparative analysis revealed an uneven phylogenetic distribution of the ABC systems in these organisms, and in particular that fresh-water Synechococcus strains contain more ABC systems than those of marine ones. Phylogenetic analysis indicated that lineage-specific gene expansion and duplication may be the important forces driving the variability of ABC systems in fresh-water Synechococcus and such an expansion was likely to be relevant to their ecological tolerance. At the domain level, ATP-binding domains in several ABC systems were found to fuse with many additional domains after the divergence from their common ancestor, indicating the versatile functions of ABC systems in cyanobacteria. Subsequently, 19 ABC system families were deduced to be the core set of ABC systems conserved in all marine-living Synechococcus and Prochlorococcus. In conclusion, the comprehensive survey of ABC systems in Synechococcus and Prochlorococcus provides novel insights into their potential evolutionary mechanism and the basis for further investigation of their physiological roles.
12. Glucosylglycerate: a secondary compatible solute common to marine cyanobacteria from nitrogen-poor environments.
    Klahn S, Steglich C, Hess WR, Hagemann M
    Environ Microbiol. 2009 Sep 4.
    Pubmed: 19735283
    Abstract
    Summary The synthesis and accumulation of compatible solutes represent an essential part of the salt acclimation strategy of microorganisms. Glucosylglycerol is considered to be the typical compatible solute among marine cyanobacteria. However, genes that encode enzymes for the synthesis of glucosylglycerol were not detected in the genome sequences of marine picoplanktonic Prochlorococcus strains. Instead, we noticed the presence of genes that putatively encode for glucosylglycerate (GGA) synthesis among Prochlorococcus and most other closely related marine picocyanobacteria. Recombinant proteins from Prochlorococcus marinus SS120 and Synechococcus sp. PCC 7002 exhibited glucosyl-phosphoglycerate synthase (GpgS) activity, and GpgS is a key enzyme of GGA synthesis. GGA accumulation was found to be salt- as well as nitrogen-regulated in the coastal strain Synechococcus sp. PCC 7002. Moreover, GGA was also detected in all picoplanktonic Prochlorococcus and Synechococcus strains harbouring gpgS genes, especially under N-limiting conditions. These results suggest that marine picocyanobacteria acquired the capacity to synthesize the negatively charged compound GGA during their evolution. Our results establish GGA as the fifth most widespread compatible solute among cyanobacteria. Additionally, GGA appears to replace glutamate as an anion to counter monovalent cations in marine picocyanobacteria from N-poor environments.
13. Inorganic and Organic Nitrogen Use by Synechococcus and Diatoms on the West Florida Shelf Measured Using Stable Isotope Probing.
    Wawrik B, Callaghan AV, Bronk DA
    Appl Environ Microbiol. 2009 Sep 4.
    Pubmed: 19734334
    Abstract
    The marine nitrogen (N) cycle is a complex network of biological transformations among different N pools. The linkages among these different reservoirs are often poorly understood. Traditional methods for measuring N uptake rely on bulk community properties and cannot provide taxonomic information. (15)N-based stable isotope probing (SIP), however, is a technique that allows the detection of uptake of individual N sources by specific microorganisms. In this study we applied (15)N-SIP methodology to assess the use of different nitrogen substrates by Synechococcus and diatoms on the west Florida shelf. Seawater was incubated in the presence of (15)N-labeled ammonium, nitrate, urea, glutamic acid, and a mixture of 16 amino acids. DNA was extracted and fractionated using CsCl density gradient centrifugation. Quantitative PCR was used to quantify the amount of Synechococcus and diatom DNA as a function of density, and (15)N tracer techniques were used to measure N uptake rates by the microbial community. Ammonium, nitrate, urea, and dissolved primary amine uptake rates were 0.077, 0.065, 0.013, and 0.055 micromol N L(-1)h(-1) respectively. SIP data indicated that diatoms and Synechococcus were actively incorporating N from (15)N-nitrate, (15)N-ammonium, and (15)N-urea. Synechococcus also incorporated nitrogen from (15)N-glutamate and (15)N-amino acids, but no evidence indicating uptake of labeled amino acids by diatoms was detected. These data suggest that N flow in communities containing Synechococcus and diatoms has more plasticity than the new versus recycled production paradigm might suggest, and that these two phytoplankters should not strictly be viewed as recycled and new producers respectively.
14. Stress responses in Prochlorococcus MIT9313 vs. SS120 involve differential expression of genes encoding proteases ClpP, FtsH and Lon.
    Gomez-Baena G, Rangel OA, Lopez-Lozano A, Garcia-Fernandez JM, Diez J
    Res Microbiol. 2009 Sep 2.
    Pubmed: 19732824
    Abstract
    Prochlorococcus is a marine cyanobacterium responsible for a significant part of global primary production as well as being one of the most abundant organisms on Earth. Protein turnover is an essential and poorly understood aspect of the cyanobacterial response to environmental stresses. In the present work, cultures of the SS120 and MIT9313 strains were subjected to several conditions, and quantitative real time RT-PCR was used to measure changes in the expression of genes encoding three representative ATP-dependent proteases. We found common responses to conditions such as aging. However, the expression pattern under nutrient starvation was strikingly different in the two strains, probably reflecting the different regulatory backgrounds of the two ecotypes here studied.
15. Whole genome amplification and de novo assembly of single bacterial cells.
    Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW
    PLoS One. 2009 Sep 2;4(9):e6864.
    Pubmed: 19724646
    Abstract
    BACKGROUND: Single-cell genome sequencing has the potential to allow the in-depth exploration of the vast genetic diversity found in uncultured microbes. We used the marine cyanobacterium Prochlorococcus as a model system for addressing important challenges facing high-throughput whole genome amplification (WGA) and complete genome sequencing of individual cells. METHODOLOGY/PRINCIPAL FINDINGS: We describe a pipeline that enables single-cell WGA on hundreds of cells at a time while virtually eliminating non-target DNA from the reactions. We further developed a post-amplification normalization procedure that mitigates extreme variations in sequencing coverage associated with multiple displacement amplification (MDA), and demonstrated that the procedure increased sequencing efficiency and facilitated genome assembly. We report genome recovery as high as 99.6% with reference-guided assembly, and 95% with de novo assembly starting from a single cell. We also analyzed the impact of chimera formation during MDA on de novo assembly, and discuss strategies to minimize the presence of incorrectly joined regions in contigs. CONCLUSIONS/SIGNIFICANCE: The methods describe in this paper will be useful for sequencing genomes of individual cells from a variety of samples.
16. Photosystem I gene cassettes are present in marine virus genomes.
    Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, Atamna-Ismaeel N, Pinter RY, Partensky F, Koonin EV, Wolf YI, Nelson N, Beja O
    Nature. 2009 Sep 10;461(7261):258-62. Epub 2009 Aug 26.
    Pubmed: 19710652
    Abstract
    Cyanobacteria of the Synechococcus and Prochlorococcus genera are important contributors to photosynthetic productivity in the open oceans. Recently, core photosystem II (PSII) genes were identified in cyanophages and proposed to function in photosynthesis and in increasing viral fitness by supplementing the host production of these proteins. Here we show evidence for the presence of photosystem I (PSI) genes in the genomes of viruses that infect these marine cyanobacteria, using pre-existing metagenomic data from the global ocean sampling expedition as well as from viral biomes. The seven cyanobacterial core PSI genes identified in this study, psaA, B, C, D, E, K and a unique J and F fusion, form a cluster in cyanophage genomes, suggestive of selection for a distinct function in the virus life cycle. The existence of this PSI cluster was confirmed with overlapping and long polymerase chain reaction on environmental DNA from the Northern Line Islands. Potentially, the seven proteins encoded by the viral genes are sufficient to form an intact monomeric PSI complex. Projection of viral predicted peptides on the cyanobacterial PSI crystal structure suggested that the viral-PSI components might provide a unique way of funnelling reducing power from respiratory and other electron transfer chains to the PSI.
17. A Rubisco Mutant That Confers Growth under a Normally "Inhibitory" Oxygen Concentration.
    Satagopan S, Scott SS, Smith TG, Tabita FR
    Biochemistry. 2009 Sep 1.
    Pubmed: 19705820
    Abstract
    Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) is a globally significant biocatalyst that facilitates the removal and sequestration of CO(2) from the biosphere. Rubisco-catalyzed CO(2) reduction thus provides virtually all of the organic carbon utilized by living organisms. Despite catalyzing the rate-limiting step of photosynthetic and chemoautotrophic CO(2) assimilation, Rubisco is markedly inefficient as the competition between O(2) and CO(2) for the same substrate limits the ability of aerobic organisms to obtain maximum amounts of organic carbon for CO(2)-dependent growth. Random and site-directed mutagenesis procedures were coupled with genetic selection to identify an "oxygen-insensitive" mutant cyanobacterial (Synechococcus sp. strain PCC 6301) Rubisco that allowed for CO(2)-dependent growth of a host bacterium at an oxygen concentration that inhibited growth of the host containing wild-type Synechococcus Rubisco. The mutant substitution, A375V, was identified as an intragenic suppressor of D103V, a negative mutant enzyme incapable of supporting autotrophic growth. Ala-375 (Ala-378 of spinach Rubisco) is a conserved residue in all form I (plant-like) Rubiscos. Structure-function analyses indicate that the A375V substitution decreased the enzyme's oxygen sensitivity (and not CO(2)/O(2) specificity), possibly by rearranging a network of interactions in a fairly conserved hydrophobic pocket near the active site. These studies point to the potential of engineering plants and other significant aerobic organisms to fix CO(2) unfettered by the presence of O(2).
18. Development of paratransgenic Artemia as a platform for control of infectious diseases in shrimp mariculture.
    Subhadra B, Hurwitz I, Fieck A, Rao DV, Subba Rao G, Durvasula R
    J Appl Microbiol. 2009 Jul 13.
    Pubmed: 19702854
    Abstract
    Abstract Aim: To study the accumulation and retention of recombinant proteins in Artemia gut for optimizing paratransgenic disease control in shrimp aquaculture. Methods and Results: Transgenic Escherichia coli expressing fluorescent marker proteins and the transgenic cyanobacterium Synechococcus bacillarus expressing a functional murine single chain antibody, DB3, were fed to Artemia franciscana. Stable expression and retention of several marker molecules (e.g. GFP, DS Red and DB3) up to 10 h after of feeding with E. coli were evident within the gut of Artemia. Engineered strains of S. bacillarus expressing DB3 accumulated within the gut of Artemia with detectable antibody activity for 8-10 h of feeding via ELISA, coincident with the time period of the highest density of transgenic S. bacillarus in the Artemia gut. Conclusions: Artemia fed transgenic bacteria or algae accumulated recombinant proteins for up to 10 h that retained biological activity. Co-delivery of multiple recombinant proteins simultaneously in the gut of Artemia was also demonstrated. Significance and Impact of the Study: Expression of molecules that target infectious agents of mariculture in shrimp via commonly deployed feed organisms such as Artemia could potentially offer powerful new tools in the ongoing global effort to increase food supply.
19. Microbial community genomics in eastern Mediterranean Sea surface waters.
    Feingersch R, Suzuki MT, Shmoish M, Sharon I, Sabehi G, Partensky F, Beja O
    ISME J. 2009 Aug 20.
    Pubmed: 19693100
    Abstract
    Offshore waters of the eastern Mediterranean Sea are one of the most oligotrophic regions on Earth in which the primary productivity is phosphorus limited. To study the unexplored function and physiology of microbes inhabiting this system, we have analyzed a genomic library from the eastern Mediterranean Sea surface waters by sequencing both termini of nearly 5000 clones. Genome recruitment strategies showed that the majority of high-scoring pairs corresponded to genomes from the Alphaproteobacteria (SAR11-like and Rhodobacterales), Cyanobacteria (Synechococcus and high-light adapted Prochlorococcus) and diverse uncultured Gammaproteobacteria. The community structure observed, as evaluated by both protein similarity scores or metabolic potential, was similar to that found in the euphotic zone of the ALOHA station off Hawaii but very different from that of deep aphotic zones in both the Mediterranean Sea and the Pacific Ocean. In addition, a strong enrichment toward phosphate and phosphonate uptake and utilization metabolism was also observed.The ISME Journal advance online publication, 20 August 2009; doi:10.1038/ismej.2009.92.
20. Recombination and microdiversity in coastal marine cyanophages.
    Marston MF, Amrich CG
    Environ Microbiol. 2009 Aug 19.
    Pubmed: 19691502
    Abstract
    Summary Genetic exchange is an important process in bacteriophage evolution. Here, we examine the role of homologous recombination in the divergence of closely related cyanophage isolates from natural marine populations. Four core-viral genes (coliphage T4 homologues g20, g23, g43 and a putative tail fibre gene) and four viral-encoded bacterial-derived genes (psbA, psbD, cobS and phoH) were analysed for 60 cyanophage isolates belonging to five Rhode Island Myovirus (RIM) strains. Phylogenetic analysis of the 60 concatenated sequences revealed well-resolved sequence clusters corresponding to the RIM strain designations. Viral isolates within a strain shared an average nucleotide identity of 99.3-99.8%. Nevertheless, extensive microdiversity was observed within each cyanophage strain; only three of the 60 isolates shared the same nucleotide haplotype. Microdiversity was generated by point mutations, homologous recombination within a strain, and intragenic recombination between RIM strains. Intragenic recombination events between distinct RIM strains were detected most often in host-derived photosystem II psbA and psbD genes, but were also identified in some major capsid protein g23 genes. Within a strain, more variability was observed at the psbA locus than at any of the other seven loci. Although most of the microdiversity within a strain was neutral, some amino acid substitutions were identified, and thus microdiversity within strains has the potential to influence the population dynamics of viral-host interactions.
21. Atomic-resolution structure of reduced cyanobacterial cytochrome c6 with an unusual sequence insertion.
    Bialek W, Krzywda S, Jaskolski M, Szczepaniak A
    FEBS J. 2009 Aug;276(16):4426-36.
    Pubmed: 19678839
    Abstract
    The structure of the reduced form of cytochrome c(6) from the mesophilic cyanobacterium Synechococcus sp. PCC 7002 has been determined at 1.2 A and refined to an R-factor of 0.107. This protein is unique among all known cytochromes c(6), owing to the presence of an unusual seven-residue insertion, KDGSKSL(44-50), which differs from the insertion found in the recently discovered plant cytochromes c(6A). Furthermore, the present protein is unusual because of its very high content (36%) of the smallest residues (glycine and alanine). The structure reveals that the overall fold of the protein is similar to that of other class I c-type cytochromes, despite the presence of the specific insertion. The insertion is located within the most variable region of the cytochrome c(6) sequence, i.e. between helices II and III. The first six residues [KDGSKS(44-49)] form a loop, whereas the last residue, Leu50, extends the N-terminal beginning of helix III. Several specific noncovalent interactions are found inside the insertion, as well as between the insertion and the rest of the protein. The crystal structure contains three copies of the cytochrome c(6) molecule per asymmetric unit, and is characterized by an unusually high packing density, with solvent occupying barely 17.58% of the crystal volume.
22. Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus.
    Ito H, Mutsuda M, Murayama Y, Tomita J, Hosokawa N, Terauchi K, Sugita C, Sugita M, Kondo T, Iwasaki H
    Proc Natl Acad Sci U S A. 2009 Jul 30.
    Pubmed: 19666549
    Abstract
    In the unicellular cyanobacterium Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock under continuous light (LL) conditions. Here, we used high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild-type, kaiABC-null, and kaiC-overexpressor strains under LL and continuous dark (DD) conditions. In the wild-type strains, >30% of transcripts oscillated significantly in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was severely attenuated in kaiABC-null strains. Although it has been proposed that KaiC globally represses gene expression, our analysis revealed that dawn-expressed genes were up-regulated by kaiC-overexpression so that the clock was arrested at subjective dawn. Transfer of cells to DD conditions from LL immediately suppressed expression of most of the genes, while the clock kept even time in the absence of transcriptional feedback. Thus, the Synechococcus genome seems to be primarily regulated by light/dark cycles and is dramatically modified by the protein-based circadian oscillator.
23. Novel cyanophage photosynthetic gene psbA in the floodwater of a Japanese rice field.
    Wang G, Murase J, Asakawa S, Kimura M
    FEMS Microbiol Ecol. 2009 Jul 10.
    Pubmed: 19659578
    Abstract
    The gene psbA, encoding the D1 protein involved in photosynthesis, was recently found in a number of cultured cyanophages infecting marine Synechococcus and Prochlorococcus and in environmental samples from marine and freshwaters. In this study, viral concentrates were prepared by sampling the floodwaters from each of four plots in a Japanese rice field: (1) no fertilizer; (2) P and K chemical fertilizers; (3) N, P and K chemical fertilizers; and (4) chemical fertilizers with compost. Fragments of the cyanophage psbA gene were amplified by PCR from DNA in the viral concentrates, with primers psbA-F and psbA-R. Double denaturing gradient gel electrophoresis was conducted to obtain different psbA clones. Phylogenetic analyses indicated that the majority of the psbA sequences in the floodwater formed two unique groups, with their sequences being more closely related to those from freshwater samples than the sequences obtained from marine waters, suggesting that psbA genes in terrestrial aquatic environments are different from those in marine environments.
24. Whole-genome microarray analyses of Synechococcus-Vibrio interactions.
    Tai V, Paulsen IT, Phillippy K, Johnson DA, Palenik B
    Environ Microbiol. 2009 Jul 30.
    Pubmed: 19659554
    Abstract
    Microbes live in diverse communities yet their physiologies are typically studied in axenic culture. To begin to address this dichotomy, whole-genome microarray analyses were used and revealed that several major metabolic pathways were affected in Synechococcus sp. WH8102, a model phototroph, when grown with Vibrio parahaemolyticus, a model heterotroph. In co-cultures with V. parahaemolyticus, although phosphate was not depleted, Synechococcus sp. WH8102 may have experienced phosphate stress since the expression of phosphate acquisition genes increased and alkaline phosphatase activity was higher than in monocultures. Expression of cell wall synthesis genes and the components of a zinc transporter were also upregulated. In contrast, a ferric uptake regulation (Fur) family gene was downregulated as were genes that encode proteins rich in iron or involved in detoxifying oxygen radicals. Nitrogen use may also have been affected in co-cultures as the gene expression changes share similarities with ammonia-grown Synechococcus. This study demonstrates the multiple impacts that interspecific microbial interactions can have on the physiology of a major primary producer and the importance of investigating microbial physiology from a community perspective.
25. Pigmented Nanoflagellates Grazing on Synechococcus: Seasonal Variations and Effect of Flagellate Size in the Coastal Ecosystem of Subtropical Western Pacific.
    Chan YF, Tsai AY, Chiang KP, Hsieh CH
    Microb Ecol. 2009 Aug 5.
    Pubmed: 19655080
    Abstract
    We investigated seasonal variation of grazing impact of the pigmented nanoflagellates (PNF) with different sizes upon Synechococcus in the subtropical western Pacific coastal waters using grazing experiments with fluorescently labeled Synechococcus (FLS). For total PNF, conspicuous seasonal variations of ingestion rates on Synechococcus were found, and a functional response was observed. To further investigate the impact of different size groups, we separated the PNF into four categories (<3, 3-5, 5-10, and >10 mum). Our results indicated that the smallest PNF (<3 mum PNF) did not ingest FLS and was considered autotrophic. PNF of 3-5 mum in size made up most of the PNF community; however, their ingestion on Synechococcus was too low (0.1-1.9 Syn PNF(-1) h(-1)) to support their growth, and they had to depend on other prey or photosynthesis to survive. The ingestion rate of the 3-5 mum group exhibited no significant seasonal variation; by contrast, the ingestion rates of 5-10 and >10 mum PNFs showed significant seasonal variation. During the warm season, 3-5 mum PNF were responsible for the grazing of 12% of Synechococcus production, 5-10 mum PNF for 48%, and >10 mum PNF for 2%. Taken together, our results demonstrate that the PNF of 3-10 mum consumed most Synechococcus during the warm season and exhibited a significant functional response to the increase in prey concentration.
26. Cyanobacterial psbA gene family: optimization of oxygenic photosynthesis.
    Mulo P, Sicora C, Aro EM
    Cell Mol Life Sci. 2009 Jul 31.
    Pubmed: 19644734
    Abstract
    The D1 protein of Photosystem II (PSII), encoded by the psbA genes, is an indispensable component of oxygenic photosynthesis. Due to strongly oxidative chemistry of PSII water splitting, the D1 protein is prone to constant photodamage requiring its replacement, whereas most of the other PSII subunits remain ordinarily undamaged. In cyanobacteria, the D1 protein is encoded by a psbA gene family, whose members are differentially expressed according to environmental cues. Here, the regulation of the psbA gene expression is first discussed with emphasis on the model organisms Synechococcus sp. and Synechocystis sp. Then, a general classification of cyanobacterial D1 isoforms in various cyanobacterial species into D1(m), D1:1, D1:2, and D1' forms depending on their expression pattern under acclimated growth conditions and upon stress is discussed, taking into consideration the phototolerance of different D1 forms and the expression conditions of respective members of the psbA gene family.
27. Expression of genes involved in nitrogen assimilation and the C/N balance sensing in Prochlorococcus sp. strain SS120.
    Lopez-Lozano A, Gomez-Baena G, Munoz-Marin Mdel C, Rangel OA, Diez J, Garcia-Fernandez JM
    Gene Expr. 2009;14(5):279-89.
    Pubmed: 19630271
    Abstract
    The expression of five genes involved in nitrogen assimilation in cyanobacteria, namely glnA, glsF, icd, ntcA, and glnB, encoding three key enzymes from that pathway (glutamine synthetase, glutamate synthase, isocitrate dehydrogenase) and two regulatory proteins (NtcA and PII), was studied in this work. Their changes under different conditions were analyzed by quantitative real-time RT-PCR. Nutrient limitation induced clear modifications on the expression of most studied genes: lack of nitrogen provoked an initial increase, followed by a marked decrease; in the cases of phosphorus and iron starvation, a general, stronger expression decrease was observed, particularly striking in the case of iron. Darkness and addition of the photosynthethic inhibitors DCMU and DBMIB also had a strong effect on gene expression. Methionine sulfoximine and azaserine, inhibitors of glutamine synthetase and glutamate synthase, respectively, provoked a sharp increase in icd expression. These results, together with previous studies, suggest that 2-oxoglutarate could be the molecule utilized by Prochlorococcus to sense the C/N balance. Besides, our results confirm the different regulation of nitrogen assimilation in Prochlorococcus with regard to other cyanobacteria.
28. Metabolic Rhythms of the Cyanobacterium Cyanothece sp. ATCC 51142 Correlate with Modeled Dynamics of Circadian Clock.
    Cerveny J, Nedbal L
    J Biol Rhythms. 2009 Aug;24(4):295-303.
    Pubmed: 19625731
    Abstract
    These experiments aim to reveal the dynamic features that occur during the metabolism of the unicellular, nitrogen fixing cyanobacterium Cyanothece sp. when exposed to diverse circadian forcing patterns (LD 16:8, LD 12:12, LD 8:16, LD 6:6). The chlorophyll concentration grew rapidly from subjective morning when first illuminated to around noon, then remained stable from later in the afternoon and throughout the night. The optical density measured at 735 nm was stable during the morning chlorophyll accumulation, then increased in the early afternoon toward a peak, followed at dusk by a rapid decline toward the late night steady state. The authors propose that these dynamics largely reflect accumulation and subsequent consumption of glycogen granules. This hypothesis is consistent with the sharp peak of respiration that coincides with the putative hydrocarbon catabolism. In the long-day regimen (LD 16:8), these events may mark the transition from the aerobic photosynthetic metabolism to microaerobic nitrogen metabolism that occurs at dusk, and thus cannot be triggered by the darkness that comes later. Rather, control is likely to originate in the circadian clock signaling an approaching night. To explore the dynamics of the link between respiration and circadian oscillations, the authors extrapolated an earlier model of the KaiABC oscillator from Synechococcus elongatus to Cyanothece sp. The measured peak of respiratory activity at dusk correlated strongly in its timing and time width with the modeled peak in accumulation of the KaiB(4) complex, which marks the late afternoon phase of the circadian clock. The authors propose a hypothesis that high levels of KaiB(4) (or of its Cyanothece sp. analog) trigger the glycogen catabolism that is reflected in the experiments in the respiratory peak. The degree of the correlation between the modeled KaiB(4) dynamics and the dynamics of experimentally measured peaks of respiratory activity was further tested during the half-circadian regimen (LD 6:6). The model predicted an irregular pattern of the KaiABC oscillator, quite unlike mechanical or electrical clock pacemakers that are strongly damped when driven at double their endogenous frequency. This highly unusual dynamic pattern was confirmed experimentally, supporting strongly the validity of the circadian model and of the proposed direct link to respiration.
29. Phylogenetic diversity of Synechococcus strains isolated from the East China Sea and the East Sea.
    Choi DH, Noh JH
    FEMS Microbiol Ecol. 2009 Jun 22.
    Pubmed: 19624741
    Abstract
    Abstract Phylogenetic relationships among 33 Synechococcus strains isolated from the East China Sea (ECS) and the East Sea (ES) were studied based on 16S rRNA gene sequences and 16S-23S rRNA gene internal transcribed spacer (ITS) sequences. Pigment patterns of the culture strains were also examined. Based on 16S rRNA gene and ITS sequence phylogenies, the Synechococcus isolates were clustered into 10 clades, among which eight were previously identified and two were novel. Half of the culture strains belonged to clade V or VI. All strains that clustered into novel clades exhibited both phycoerythrobilin and phycourobilin. Interestingly, the pigment compositions of isolates belonging to clades V and VI differed from those reported for other oceanic regions. None of the isolates in clade V showed phycourobilin, whereas strains in clade VI exhibited both phycourobilin and phycoerythrobilin, which is in contrast to previous studies. The presence of novel lineages and the different pigment patterns in the ECS and the ES suggests the possibility that some Synechococcus lineages are distributed only in geographically restricted areas and have evolved in these regions. Therefore, further elucidation of the physiological, ecological, and genetic characteristics of the diverse Synechococcus strains is required to understand their spatial and geographical distribution.
30. Characterization of a metal-independent CAZy family 6 glycosyltransferase from bacteroides ovatus.
    Tumbale P, Brew K
    J Biol Chem. 2009 Jul 21.
    Pubmed: 19622749
    Abstract
    The myriad functions of complex carbohydrates include modulating interactions between bacteria and their eukaryotic hosts. In humans and other vertebrates, variations in the activity of glycosyltransferases of CAZy family 6 generate antigenic variation between individuals and species that facilitates resistance to pathogens. The well-characterized vertebrate glycosyltransferases of this family are multi-domain membrane proteins with C-terminal catalytic domains. Genes for proteins homologous with their catalytic domains are found in at least 9 species of anaerobic commensal bacteria and a cyanophage. While the bacterial proteins are strikingly similar in sequence to the catalytic domains of their eukaryotic relatives, a metal-binding Asp-X-Asp sequence, present in a wide array of metal ion-dependent glycosyl-transferases, is replaced by Asn-X-Asn. We have cloned and expressed one of these proteins from Bacteroides ovatus, a bacterium that is linked to inflammatory bowel disease. Functional characterization shows it to be a metal-independent glycosyltransferase with a 200-fold preference for UDP-GalNAc as substrate relative to UDP-Gal. It efficiently catalyzes the synthesis of oligosaccharides similar to human blood group A and may participate in the synthesis of the bacterial O-antigen. The kinetics for GalNAc transfer to 2'-fucosyl lactose are characteristic of a sequential mechanism, as observed previously for this family. Mutational studies indicate that despite the lack of a metal cofactor there are pronounced similarities in structure-function relationships between the bacterial and vertebrate family 6 GTs. These two groups appear to provide an example of horizontal gene transfer involving vertebrates and prokaryotes.
31. Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades.
    Gupta RS
    Int J Syst Evol Microbiol. 2009 Jul 21.
    Pubmed: 19622649
    Abstract
    A combination of phylogenomic and signature sequence based (or phenetic) approaches was used to understand the evolutionary relationships among cyanobacteria. Phylogenetic trees were constructed for 34 cyanobacteria, whose genomes have been sequenced, based on concatenated sequences for 45 conserved proteins and also the 16S RNA. In parallel, sequence alignments of various proteins were examined to identify conserved indels (i.e. molecular signatures or synapomorphies) that are specific for either all cyanobacteria or their various clades in the phylogenetic trees. Of the >40 molecular signatures described in this work, l5 are specific for all cyanobacteria. The other cyanobacterial clades that can now be identified and circumscribed in molecular terms using these signatures include a deep branching clade (Clade A, corresponds to the subclass Gloebacterophycidae) consisting of Gloebacter violaceus and two diazotrophic Synechococcus strains (JA-3-3Ab and JA2-3-B'a) (15 aa insert in EF-G); a clade comprising of all other cyanobacteria except those from Clade A (18 aa insert in DNA polymerase I (Pol I), 2 aa insert in the DnaX protein, 4 aa insert in TrpRS and a 4-5 aa insert in tryptophan synthase beta subunit); a clade (Clade C, corresponds to the subclass Synechococcophycidae) of various marine unicellular Synechococcus and Prochlorococcus cyanobacteria (12 aa insert in Pol I, 3 aa insert in RpoB, 2 aa insert in KgsA, 6 aa insert in TyrRS, 2 aa insert in tRNA-mG1-transferase and a 1 aa deletion in the RpoC protein); a clade of the Low B/A ecotype Prochlorococcus strains (5 aa deletion in LeuRS and 1 aa insert in the Ffh protein); a clade consisting of the Nostocales species/strains (subclass Nostocophycidae; 4 aa insert in the PetA protein and 5 aa insert in the ribosomal protein S3); a clade of the Chroococcales (1 aa insert in RecA); a clade comprising of the Nostocales, Oscillatoriales and Chroococcales orders (19 aa insert in DnaE, 13 aa insert in GDP-mannose pyrophosphorylase and a 22-27 aa insert in NADP(H)-quinone oxidoreductase subunit D). Two additional conserved indels in the translation initiation factor IF-2 and riboflavin synthase alpha subunit suggest an intermediate placement of the Oscillatoriales in between the Nostocales and Chroococcales orders. The unique presence of these molecular signatures in all available sequences from the indicated groups of cyanobacteria, but not in any other cyanobacteria (or bacteria), indicates that these synapomorphies provide novel and potentially useful means for circumscription of several important taxonomic clades of cyanobacteria in more definitive terms. The species distribution patterns of these synapomorphies also indicate that the plants/plastids homologs are not derived from the Clade A or C cyanobacteria.
32. Spongiibacter tropicus sp. nov., isolated from a Synechococcus culture.
    Hwang CY, Cho BC
    Int J Syst Evol Microbiol. 2009 Jul 15.
    Pubmed: 19605732
    Abstract
    Two Gram-staining-negative, rod-shaped and non-motile strains, designated CL-CB221(T) and CL-CB467, were isolated from a Synechococcus culture derived from surface water of tropical Pacific Ocean. The 16S rRNA gene sequences were identical between the two strains, and it was found that the strains belonged to the class Gammaproteobacteria, with Spongiibacter marinus HAL40b(T) as its closet relative (similarity of 96.3%). Cells of the strains grew optimally at 30-35 degrees C and pH 7-8 in the presence of 3-4% (w/v) NaCl. The major cellular fatty acids were C(18 : 1)omega7c, C(17 : 1)omega8c, C(16 : 0) and C(15 : 0) iso 2-OH and/or C(16 : 1)omega7c. The genomic DNA G+C content was 56.8-57.7 mol%. DNA-DNA hybridization experiments revealed high values (97+/-2%) for relatedness between strains CL-CB221(T) and CL-CB467, and suggested that these two strains constituted a single species. Based on the phylogenetic, chemotaxonomic and phenotypic data presented, it is proposed that strains CL-CB221(T) and CL-CB467 represent a new species of the genus Spongiibacter, for which the name Spongiibacter tropicus sp. nov. is proposed. The type strain is CL-CB221(T) (= KCCM 90065(T) = DSM 19543(T)).
33. Toxicity of copper in natural marine picoplankton populations.
    Debelius B, Forja JM, Delvalls TA, Lubian LM
    Ecotoxicology. 2009 Jul 14.
    Pubmed: 19597988
    Abstract
    Standard microalgae toxicity tests should be able to establish responses in real ecosystems. Natural marine picoplankton samples collected during the months of March, June, August, October 2007 and January 2008, where exposed to 72 h copper toxicity tests. Results analysed by flow cytometry distinguished two groups, with different cytometric characteristics that can match with two of Synechococcus populations. EC(50) values for these two populations resulted low, ranging from 0.62 to 26.28 mug L(-1), this converts copper in a very powerful contaminant and Synechococcus in one of the most sensitive groups of phytoplankton. Differences in EC(50) values for a same population can be related to the month of collection including different initial cellular densities and oceanographic parameters that can affect the picoplankton's tolerance and distribution.
34. Chromatic photoacclimation extends utilisable photosynthetically active radiation in the chlorophyll d-containing cyanobacterium, Acaryochloris marina.
    Duxbury Z, Schliep M, Ritchie RJ, Larkum AW, Chen M
    Photosynth Res. 2009 Jul;101(1):69-75. Epub 2009 Jul 7.
    Pubmed: 19582591
    Abstract
    Chromatic photoacclimation and photosynthesis were examined in two strains of Acaryochloris marina (MBIC11017 and CCMEE5410) and in Synechococcus PCC7942. Acaryochloris contains Chl d, which has an absorption peak at ca 710 nm in vivo. Cultures were grown in one of the three wavelengths (525 nm, 625 nm and 720 nm) of light from narrow-band photodiodes to determine the effects on pigment composition, growth rate and photosynthesis: no growth occurred in 525 nm light. Synechococcus did not grow in 720 nm light because Chl a does not absorb effectively at this long wavelength. Acaryochloris did grow in 720 nm light, although strain MBIC11017 showed a decrease in phycobilins over time. Both Synechococcus and Acaryochloris MBIC11017 showed a dramatic increase in phycobilin content when grown in 625 nm light. Acaryochloris CCMEE5410, which lacks phycobilins, would not grow satisfactorily under 625 nm light. The cells adjusted their pigment composition in response to the light spectral conditions under which they were grown. Photoacclimation and the Q (y) peak of Chl d could be understood in terms of the ecological niche of Acaryochloris, i.e. habitats enriched in near infrared radiation.
35. Structure of Compositionally Simple Lipopolysaccharide from Marine Synechococcus.
    Snyder DS, Brahamsha B, Azadi P, Palenik B
    J Bacteriol. 2009 Jul 6.
    Pubmed: 19581366
    Abstract
    Lipopolysaccharide (LPS) is the first defense against changing environmental factors for many bacteria. Here, we report the first structure of the lipopolysaccharide (LPS) from cyanobacteria based on two strains of marine Synechococcus, WH8102 and CC9311. While enteric LPS contains some of the most complex carbohydrate residues in nature, the full length versions of these cyanobacterial lipopolysaccharides have neither heptose nor 3-deoxy-D-manno-octulosonic acid (Kdo) but instead 4- linked glucose as their main saccharide component with low levels of glucosamine and galacturonic acid also present. MALDI MS of the intact minimal core LPS reveals triacylated and tetraacylated structures having a heterogeneous mix of both hydroxylated and nonhydroxylated fatty acids connected to the diglucosamine backbone, and a predominantly glucose outer core-like region for both strains. WH8102 incorporated rhamnose in the this region as well, contributing to differences in sugar composition and possibly nutritional differences between the strains. In contrast to enteric lipid A which can be liberated from LPS by mild acid hydrolysis, lipid A from these organisms could only be produced by two novel procedures: triethylamine assisted periodate oxidation and acetolysis. The lipid A contains odd chain hydroxylated fatty acids, lacks phosphate and contains a single galacturonic acid. The LPS lacks any LAL (limulus amoebocyte lysate) gelation activity. The highly simplified nature of LPS from these organisms leads us to believe that they may represent either a primordial structure or an adaptation to the relatively higher salt and potentially growth limiting phosphate levels in marine environments.
36. The Rolex and the hour-glass: a simplified circadian clock in Prochlorococcus?
    Mullineaux CW, Stanewsky R
    J Bacteriol. 2009 Jun 26.
    Pubmed: 19561127
    Abstract
    Many cyanobacteria have a sophisticated circadian clock based on an elegant biochemical system requiring only three protein components: KaiA, KaiB and KaiC (3). ...
37. Minimal genomes, maximal productivity: comparative genomics of the photosystem and light-harvesting complexes in the marine cyanobacterium, Prochlorococcus.
    Ting CS, Ramsey ME, Wang YL, Frost AM, Jun E, Durham T
    Photosynth Res. 2009 Jun 26.
    Pubmed: 19557544
    Abstract
    Although Prochlorococcus isolates possess the smallest genomes of any extant photosynthetic organism, this genus numerically dominates vast regions of the world's subtropical and tropical open oceans and has evolved to become an important contributor to global biogeochemical cycles. The sequencing of 12 Prochlorococcus genomes provides a glimpse of the extensive genetic heterogeneity and, thus, physiological potential of the lineage. In this study, we present an up-to-date comparative analysis of major proteins of the photosynthetic apparatus in 12 Prochlorococcus genomes. Our analyses reveal a striking diversity within the Prochlorococcus lineage in the major protein complexes of the photosynthetic apparatus. The heterogeneity that has evolved in the photosynthetic apparatus suggests versatility in strategies for optimizing photosynthesis under conditions of environmental variability and stress. This diversity could be particularly important in ensuring the survival of a lineage whose individuals have evolved minimal genomes and, thus, relatively limited repertoires for responding to environmental challenges.
38. Prochlorococcus: approved for export.
    Johnson ZI, Lin Y
    Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10400-1. Epub 2009 Jun 24.
    Pubmed: 19553202
    
39. Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes.
    Martiny AC, Kathuria S, Berube PM
    Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10787-92. Epub 2009 Jun 23.
    Pubmed: 19549842
    Abstract
    The marine cyanobacterium Prochlorococcus is the most abundant photosynthetic organism in oligotrophic regions of the oceans. The inability to assimilate nitrate is considered an important factor underlying the distribution of Prochlorococcus, and thought to explain, in part, low abundance of Prochlorococcus in coastal, temperate, and upwelling zones. Here, we describe the widespread occurrence of a genomic island containing nitrite and nitrate assimilation genes in uncultured Prochlorococcus cells from marine surface waters. These genes are characterized by low GC content, form a separate phylogenetic clade most closely related to marine Synechococcus, and are located in a different genomic region compared with an orthologous cluster found in marine Synechococcus strains. This sequence distinction suggests that these genes were not transferred recently from Synechococcus. We demonstrate that the nitrogen assimilation genes encode functional proteins and are expressed in the ocean. Also, we find that their relative occurrence is higher in the Caribbean Sea and Indian Ocean compared with the Sargasso Sea and Eastern Pacific Ocean, which may be related to the nitrogen availability in each region. Our data suggest that the ability to assimilate nitrite and nitrate is associated with microdiverse lineages within high- and low-light (LL) adapted Prochlorococcus ecotypes. It challenges 2 long-held assumptions that (i) Prochlorococcus cannot assimilate nitrate, and (ii) only LL adapted ecotypes can use nitrite. The potential for previously unrecognized productivity by Prochlorococcus in the presence of oxidized nitrogen species has implications for understanding the biogeography of Prochlorococcus and its role in the oceanic carbon and nitrogen cycles.
40. Differential grazing of two heterotrophic nanoflagellates on marine Synechococcus strains.
    Zwirglmaier K, Spence E, Zubkov MV, Scanlan DJ, Mann NH
    Environ Microbiol. 2009 Mar 10.
    Pubmed: 19508559
    Abstract
    Summary Grazing of heterotrophic nanoflagellates on marine picophytoplankton presents a major mortality factor for this important group of primary producers. However, little is known of the selectivity of the grazing process, often merely being thought of as a general feature of cell size and motility. In this study, we tested grazing of two heterotrophic nanoflagellates, Paraphysomonas imperforata and Pteridomonas danica, on strains of marine Synechococcus. Both nanoflagellates proved to be selective in their grazing, with Paraphysomonas being able to grow on 5, and Pteridomonas on 11, of 37 Synechococcus strains tested. Additionally, a number of strains (11 for Paraphysomonas, 9 for Pteridomonas) were shown to be ingested, but not digested (and thus did not support growth of the grazer). Both the range of prey strains that supported growth as well as those that were ingested but not digested was very similar for the two grazers, suggesting a common property of these prey strains that lent them susceptible to grazing. Subsequent experiments on selected Synechococcus strains showed a pronounced difference in grazing susceptibility between wild-type Synechococcus sp. WH7803 and a spontaneous phage-resistant mutant derivative, WH7803PHR, suggesting that cell surface properties of the Synechococcus prey are an important attribute influencing grazing vulnerability.
41. Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution.
    Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ
    Environ Microbiol. 2009 Jun 7.
    Pubmed: 19508343
    Abstract
    The vast majority of cyanophages isolated to date are cyanomyoviruses, a group related to bacteriophage T4. Comparative genome analysis of five cyanomyoviruses, including a newly sequenced cyanophage S-RSM4, revealed a 'core genome' of 64 genes, the majority of which are also found in other T4-like phages. Subsequent comparative genomic hybridization analysis using a pilot microarray showed that a number of 'host' genes are widespread in cyanomyovirus isolates. Furthermore, a hyperplastic region was identified between genes g15-g18, within a highly conserved structural gene module, which contained a variable number of inserted genes that lacked conservation in gene order. Several of these inserted genes were host-like and included ptoX, gnd, zwf and petE encoding plastoquinol terminal oxidase, 6-phosphogluconate dehydrogenase, glucose 6-phosphate dehydrogenase and plastocyanin respectively. Phylogenetic analyses suggest that these genes were acquired independently of each other, even though they have become localized within the same genomic region. This hyperplastic region contains no detectable sequence features that might be mechanistically involved with the acquisition of host-like genes, but does appear to be a site specifically associated with the acquisition process and may represent a novel facet of the evolution of marine cyanomyoviruses.
42. The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria.
    Gierga G, Voss B, Hess WR
    RNA Biol. 2009 Jul 1;6(3).
    Pubmed: 19502815
    Abstract
    Sequence signatures, predicted secondary structures and experimental data suggest the Yfr2 family of non-coding RNAs (ncRNAs) to be present in nearly all cyanobacteria sequenced to date. The common features of the family members include a central consensus element (CCE), 5'-RKT SGA AAC WHG GHM ASA M-3', predicted to form a 12 nt single stranded region plus a short helical region consisting of three base pairs and one unpaired nucleotide that is either bulging or the begin of a short internal loop. Yfr2 family members are 63 to 100 nucleotides in size and they share a conserved region at the 5' end, starting with 5'-GUGAGGA-3' or a closely related motif. The genes for ncRNAs of this family are suggested to exist in highly variable copy numbers in the individual genomes, with up to nine copies in some marine Synechococcus.
43. Photoheterotrophic microbes in the Arctic Ocean in summer and winter.
    Cottrell MT, Kirchman DL
    Appl Environ Microbiol. 2009 Jun 5.
    Pubmed: 19502441
    Abstract
    Photoheterotrophic microbes, which are capable of utilizing dissolved organic materials (DOM) and harvesting light energy, include coccoid cyanobacteria (Synechococcus and Prochlorococcus), aerobic anoxygenic phototrophic (AAP) bacteria, and proteorhodopsin (PR)-containing bacteria. Our knowledge of photoheterotrophic microbes is largely incomplete, especially in high latitude waters such as the Arctic Ocean where photoheterotrophs may have special ecological relationships and distinct biogeochemical impacts due to extremes in day length and seasonal ice cover. These microbes were examined by epifluorescence microscopy, flow cytometry, and quantitative PCR (QPCR) assays for proteorhodopsin and a gene diagnostic of AAP bacteria (pufM). The abundance of AAP bacteria and PR-containing bacteria decreased from summer to winter in parallel with a 3-fold decrease in the total prokaryotic community. In contrast, Synechococcus did not decrease in winter, suggesting that their growth was supported by organic substrates. Results from QPCR assays revealed no substantial shifts in community structure of AAP bacteria and PR-containing bacteria. However, Arctic PR genes were different from those found at lower latitudes, and surprisingly not similar to those in Antarctic coastal waters. Photoheterotrophic microbes appear to compete successfully with strict heterotrophs during winter darkness below the ice, but AAP bacteria and PR-containing bacteria do not behave as superior competitors during summer.
44. Coastal strains of marine Synechococcus exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to open ocean strains.
    Stuart RK, Dupont CL, Johnson DA, Paulsen IT, Palenik B
    Appl Environ Microbiol. 2009 Jun 5.
    Pubmed: 19502430
    Abstract
    Copper appears to be influencing the distribution and abundance of phytoplankton in marine environments, and cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity. Using growth assays, on phylogenetically divergent clades, we found that coastal strains of marine Synechococcus were more tolerant to copper shock than open ocean strains. Global transcriptional response to two levels of copper shock were determined in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a common reduction in photosynthetic-related gene transcripts. Contrastingly, the open ocean strain showed a general stress response whereas the coastal strain exhibited a more specifically oxidative or heavy metal acclimation response, that may be conferring tolerance. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus strains may in part be a result of a generally increased ability to sense and respond in a more stress-specific manner.
45. Biochemical evidence for a timing mechanism in Prochlorococcus.
    Axmann IM, Duhring U, Seeliger L, Arnold A, Vanselow JT, Kramer A, Wilde A
    J Bacteriol. 2009 Jun 5.
    Pubmed: 19502405
    Abstract
    Organisms coordinate biological activities into daily cycles using an internal circadian clock. The circadian oscillator proteins KaiA, KaiB and KaiC are widely believed to underlie 24-h oscillations of gene expression in cyanobacteria. However, a group of very abundant cyanobacteria, namely marine Prochlorococcus, lost the third oscillator component, KaiA, during evolution. We demonstrate here that the remaining Kai proteins fulfill their known biochemical functions, although KaiC is hyperphosphorylated by default in this system. These data provide biochemical support for the observed evolutionary reduction of the clock locus in Prochlorococcus, and are consistent with a model in which a less robust mechanism than the well-characterized KaiABC protein clock of Synechococcus is sufficient for biological timing in the very stable environment that Prochlorococcus inhabits.
46. Ecological genomics of marine picocyanobacteria.
    Scanlan DJ, Ostrowski M, Mazard S, Dufresne A, Garczarek L, Hess WR, Post AF, Hagemann M, Paulsen I, Partensky F
    Microbiol Mol Biol Rev. 2009 Jun;73(2):249-99.
    Pubmed: 19487728
    Abstract
    Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45 degrees N to 40 degrees S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.
47. Mutations at pipX suppress lethality of PII deficient mutants of Synechococcus elongatus sp. PCC 7942.
    Espinosa J, Castells MA, Laichoubi KB, Contreras A
    J Bacteriol. 2009 May 29.
    Pubmed: 19482921
    Abstract
    The PII proteins are found in all three domains of life as key integrators of signals reflecting the nitrogen and carbon balance. Genetic inactivation of PII proteins is typically associated with severe growth defects or lethality. However, the molecular basis of these defects depends on the specific functions of the proteins with which PII proteins interact to regulate nitrogen metabolism in different organisms. In Synechococcus elongatus sp. PCC 7942, where PII forms complexes with the NtcA coactivator PipX, attempts to engineer PII deficient strains failed in a wild type background, but were successful in pipX null mutants. Consisting with the idea that PII is essential to counteract the activity of PipX, four different spontaneous mutations in the pipX gene were found in cultures in which glnB had been genetically inactivated.
48. Whole genome assembly from 454 sequencing output via modified DNA graph concept.
    Blazewicz J, Bryja M, Figlerowicz M, Gawron P, Kasprzak M, Kirton E, Platt D, Przybytek J, Swiercz A, Szajkowski L
    Comput Biol Chem. 2009 Jun;33(3):224-30. Epub 2009 May 3.
    Pubmed: 19477687
    Abstract
    Recently, 454 Life Sciences Corporation proposed a new biochemical approach to DNA sequencing (the 454 sequencing). It is based on the pyrosequencing protocol. The 454 sequencing aims to give reliable output at a low cost and in a short time. The produced sequences are shorter than reads produced by classical methods. Our paper proposes a new DNA assembly algorithm which deals well with such data and outperforms other assembly algorithms used in practice. The constructed SR-ASM algorithm is a heuristic method based on a graph model, the graph being a modified DNA graph proposed for DNA sequencing by hybridization procedure. Other new features of the assembly algorithm are, among others, temporary compression of input sequences, and a new and fast multiple alignment heuristics taking advantage of the way the output data for the 454 sequencing are presented and coded. The usefulness of the algorithm has been proved in tests on raw data generated during sequencing of the whole 1.84Mbp genome of Prochlorococcus marinus bacteria and also on a part of chromosome 15 of Homo sapiens. The source code of SR-ASM can be downloaded from http://bio.cs.put.poznan.pl/ in the section 'Current research'--> 'DNA Assembly'. Among publicly available assemblers our algorithm appeared to generate the best results, especially in the number of produced contigs and in the lengths of the contigs with high similarity to the genome sequence.
49. CaCO nucleation by cyanobacteria: laboratory evidence for a passive, surface-induced mechanism.
    Obst M, Wehrli B, Dittrich M
    Geobiology. 2009 May 19.
    Pubmed: 19476505
    Abstract
    Calcite nucleation on the surface of cyanobacteria of the Synechococcus leopoliensis strain PCC 7942 was investigated to assess the influence of photosynthetic uptake of inorganic carbon and active ion exchange processes across the cell membrane on the nucleation and precipitation mechanisms. We performed long-term precipitation experiments at a constant CO(2) level in ambient air by adding suspensions of previously washed cyanobacteria to solutions of NaHCO(3)/CaCl(2) which were supersaturated with respect to calcite. Induction times between 4 and 110 h were measured over a range of saturation states, Omega, between 8 and 4. The kinetics of CaCO(3) nucleation was compared between experiments: (i) with ongoing photosynthesis, (ii) with cells metabolizing but not undergoing photosynthetic uptake of inorganic carbon and (iii) in darkness without photosynthesis. No significant differences were observed between the three treatments. The results reveal that under low nutrient concentrations and permanent CO(2) supply, photosynthetic uptake of inorganic carbon predominantly uses CO(2) and consequently does not directly influence the nucleation process of CaCO(3) at the surface of S. leopoliensis. Furthermore, ion exchange processes did not affect the kinetics, indicating a passive nucleation process wherein the cell surface or extracellular polymers provided preferential sites for mineral nucleation. The catalyzing effect of the cyanobacteria on calcite nucleation was equivalent to a approximately 18% reduction in the specific interfacial free energy of the calcite nuclei. This result and the ubiquitous abundance of cyanobacteria suggest that this process may have an impact on local and global carbon cycling.
50. Amoebic grazing of freshwater Synechococcus strains rich in phycocyanin.
    Dillon A, Parry JD
    FEMS Microbiol Ecol. 2009 Apr 25.
    Pubmed: 19453737
    Abstract
    Abstract Fifteen strains of naked amoebae were presented with 19 strains of Synechococcus on an agar surface. After 14 days of incubation, each of the 285 combinations yielded one of three responses. 42.1% of combinations showed clearing (digestion) of the Synechococcus (C), 56.5% of combinations showed no clearing of the Synechococcus (N) while 1.4% of combinations showed partial clearing of the Synechococcus (P). In general, the Synechococcus strains showed variability in their susceptibility to digestion by the amoebae and the amoebae showed variability in their ability to digest the Synechococcus strains. There was no evidence for amoebae actively selecting profitable prey and equivalent-sized Synechococcus strains were ingested at the same rate, irrespective of their fate. There was some evidence of 'size-selective' grazing in that amoebae ingested the smaller Synechococcus strains at higher rates than the larger strains. However, there was no correlation between prey size and their ultimate fate. These data suggest that amoebae are not selective with regard to the ingestion of synechococci, but that 'selection' occurs at the digestion stage, i.e. whether the synechococci are digested or not.
51. Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean.
    Schattenhofer M, Fuchs BM, Amann R, Zubkov MV, Tarran GA, Pernthaler J
    Environ Microbiol. 2009 Apr 30.
    Pubmed: 19453607
    Abstract
    Summary Members of the prokaryotic picoplankton are the main drivers of the biogeochemical cycles over large areas of the world's oceans. In order to ascertain changes in picoplankton composition in the euphotic and twilight zones at an ocean basin scale we determined the distribution of 11 marine bacterial and archaeal phyla in three different water layers along a transect across the Atlantic Ocean from South Africa (32.9 degrees S) to the UK (46.4 degrees N) during boreal spring. Depth profiles down to 500 m at 65 stations were analysed by catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and automated epifluorescence microscopy. There was no obvious overall difference in microbial community composition between the surface water layer and the deep chlorophyll maximum (DCM) layer. There were, however, significant differences between the two photic water layers and the mesopelagic zone. SAR11 (35 +/- 9%) and Prochlorococcus (12 +/- 8%) together dominated the surface waters, whereas SAR11 and Crenarchaeota of the marine group I formed equal proportions of the picoplankton community below the DCM (both approximately 15%). However, due to their small cell sizes Crenarchaeota contributed distinctly less to total microbial biomass than SAR11 in this mesopelagic water layer. Bacteria from the uncultured Chloroflexi-related clade SAR202 occurred preferentially below the DCM (4-6%). Distinct latitudinal distribution patterns were found both in the photic zone and in the mesopelagic waters: in the photic zone, SAR11 was more abundant in the Northern Atlantic Ocean (up to 45%) than in the Southern Atlantic gyre ( approximately 25%), the biomass of Prochlorococcus peaked in the tropical Atlantic Ocean, and Bacteroidetes and Gammaproteobacteria bloomed in the nutrient-rich northern temperate waters and in the Benguela upwelling. In mesopelagic waters, higher proportions of SAR202 were present in both central gyre regions, whereas Crenarchaeota were clearly more abundant in the upwelling regions and in higher latitudes. Other phylogenetic groups such as the Planctomycetes, marine group II Euryarchaeota and the uncultured clades SAR406, SAR324 and SAR86 rarely exceeded more than 5% of relative abundance.
52. A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment.
    Tzahor S, Man-Aharonovich D, Kirkup BC, Yogev T, Berman-Frank I, Polz MF, Beja O, Mandel-Gutfreund Y
    BMC Genomics. 2009 May 16;10(1):229.
    Pubmed: 19445709
    Abstract
    ABSTRACT: BACKGROUND: Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the photosystem II reaction center (psbA and psbD) were found in cyanophage genomes. This phenomenon suggested that the horizontal transfer of these genes may be involved in increasing phage fitness. To date, a very small percentage of marine bacteria and phages has been cultured. Thus, mapping genomic data extracted directly from the environment to its taxonomic origin is necessary for a better understanding of phage-host relationships and dynamics. RESULTS: To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM) with a codon usage position specific scoring matrix (cuPSSM). Our method has been applied successfully to classify core-photosystem-II gene fragments, including partial sequences coming directly from the ocean, to seven different taxonomic classes. Applying the method on a large set of DNA and RNA psbA clones from the Mediterranean Sea, we studied the distribution of cyanobacterial psbA genes and transcripts in their natural environment. Using our approach, we were able to simultaneously examine taxonomic and ecological distributions in the marine environment. CONCLUSION: The ability to accurately classify the origin of individual genes and transcripts coming directly from the environment is of great importance in studying marine ecology. The classification method presented in this paper could be applied further to classify other genes amplified from the environment, for which training data is available.
53. Enhanced citric acid biosynthesis in Pseudomonas fluorescens ATCC 13525 by overexpression of Escherichia coli citrate synthase gene.
    Buch AD, Archana G, Naresh Kumar G
    Microbiology. 2009 May 14.
    Pubmed: 19443543
    Abstract
    Citric acid secretion by fluorescent pseudomonads has a distinct significance in microbial phosphate solubilization. The role of citrate synthase in citric acid biosynthesis and glucose catabolism in pseudomonads was investigated by overexpressing E. coli gltA gene in Pseudomonas fluorescens ATCC 13525. The resultant ~2 fold increase in citrate synthase activity in Pf (AB7) enhanced the intracellular and extracellular citric acid yields during the stationary phase, by ~2 and 26 fold, respectively, as compared to the control; without affecting the growth rate, glucose depletion rate and biomass yield. Reduced glucose consumption was parallel with increased gluconic acid production due to an increase in glucose dehydrogenase activity. While the extracellular acetic acid yield increased in Pf (AB7); the reduced pyruvic acid secretion correlated with increase in pyruvate carboxylase activity, suggesting an increased demand for anabolic precursor oxaloacetate. Activities of other key enzymes glucose-6-phosphate dehydrogenase and isocitrate dehydrogenase remained unaltered while contribution of phosphoenolpyruvate carboxylase and isocitrate lyase to the glucose catabolism was negligible. Moreover, Pf (AB7) demonstrated an enhanced P-solubilizing ability as compared to the control. Co-expression of Synechococcus elongatus PCC 6301 phosphoenolpyruvate carboxylase and E. coli gltA genes in P. fluorescens ATCC 13525, so as to supplement oxaloacetate for citrate biosynthesis, neither significantly affected citrate biosynthesis nor caused any other physiological and biochemical change, despite ~1.3 and 5 fold increase in citrate synthase and phosphoenolpyruvate carboxylase activities, respectively. Thus, our results demonstrate that citrate synthase is rate-limiting in enhancing citrate biosynthesis in P. fluorescens ATCC 13525. Significantly low extracellular citrate levels as compared to the intracellular levels in Pf (AB7) suggested a probable limitation of efficient citrate transport.
54. A single origin of the photosynthetic organelle in different Paulinella lineages.
    Yoon HS, Nakayama T, Reyes-Prieto A, Andersen RA, Boo SM, Ishida K, Bhattacharya D
    BMC Evol Biol. 2009 May 13;9:98.
    Pubmed: 19439085
    Abstract
    BACKGROUND: Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines of photosynthesis are plastids (e.g., chloroplast in plants) that evolved from cyanobacteria through primary endosymbiosis. Our knowledge of plastid evolution, however, remains limited because the primary endosymbiosis occurred more than a billion years ago. In this context, the thecate "green amoeba" Paulinella chromatophora is remarkable because it very recently (i.e., minimum age of approximately 60 million years ago) acquired a photosynthetic organelle (termed a "chromatophore"; i.e., plastid) via an independent primary endosymbiosis involving a Prochlorococcus or Synechococcus-like cyanobacterium. All data regarding P. chromatophora stem from a single isolate from Germany (strain M0880/a). Here we brought into culture a novel photosynthetic Paulinella strain (FK01) and generated molecular sequence data from these cells and from four different cell samples, all isolated from freshwater habitats in Japan. Our study had two aims. The first was to compare and contrast cell ultrastructure of the M0880/a and FK01 strains using scanning electron microscopy. The second was to assess the phylogenetic diversity of photosynthetic Paulinella to test the hypothesis they share a vertically inherited plastid that originated in their common ancestor. RESULTS: Comparative morphological analyses show that Paulinella FK01 cells are smaller than M0880/a and differ with respect to the number of scales per column. There are more distinctive, multiple fine pores on the external surface of FK01 than in M0880/a. Molecular phylogenetic analyses using multiple gene markers demonstrate these strains are genetically distinct and likely comprise separate species. The well-supported monophyly of the Paulinella chromatophora strains analyzed here using plastid-encoded 16S rRNA suggests strongly that they all share a common photosynthetic ancestor. The strain M0880/a is most closely related to Japanese isolates (Kanazawa-1, -2, and Kaga), whereas FK01 groups closely with a Kawaguchi isolate. CONCLUSION: Our results indicate that Paulinella chromatophora comprises at least two distinct evolutionary lineages and likely encompasses a broader taxonomic diversity than previously thought. The finding of a single plastid origin for both lineages shows these taxa to be valuable models for studying post-endosymbiotic cell and genome evolution.
55. CO2 Uptake and Fixation by a Thermoacidophilic Microbial Community Attached to Precipitated Sulfur in a Geothermal Spring.
    Boyd ES, Leavitt WD, Geesey GG
    Appl Environ Microbiol. 2009 May 8.
    Pubmed: 19429558
    Abstract
    Carbon fixation at temperatures above 73 degrees C, the upper limit for photosynthesis, is carried out by chemosynthetic thermophiles. Yellowstone National Park (YNP), Wyoming possesses many thermal features that, while too hot for photosynthesis, presumably support chemosynthetic-based carbon fixation. To our knowledge, in situ rates of chemosynthetic reactions at these high temperatures in YNP or other high temperature terrestrial geothermal springs have not yet been reported. A microbial community attached to precipitated elemental sulfur (S degrees floc) at the source of Dragon Spring (73 degrees C, pH 3.1) in Norris Geyser Basin, YNP exhibited a maximum rate of CO2 uptake of 21.3 +/- 11.9 microg C 10(7) cells(-1) h(-1). When extrapolated over the estimated total quantity of S degrees floc at the spring's source, the S degrees floc-associated microbial community accounted for the uptake of 121 mg C h(-1) at this site. On a per cell basis, the rate was higher than that calculated for a photosynthetic mat microbial community dominated by Synechococcus spp. in alkaline springs at comparable temperatures. A portion of the carbon taken up as CO2 by the S degrees floc-associated biomass was recovered in the cellular nucleic acid pool, demonstrating that uptake was coupled to fixation. The most abundant sequences in a 16S rRNA clone library of the S degrees floc-associated community were related to chemolithoautotrophic Hydrogenobaculum strains previously isolated from springs in Norris Geyser Basin. These microorganisms likely contributed to the uptake and fixation of CO2 in this geothermal habitat.
56. Identification and quantification of water-soluble metabolites by cryoprobe-assisted nuclear magnetic resonance spectroscopy applied to microbial fermentation.
    Carrieri D, McNeely K, De Roo AC, Bennette N, Pelczer I, Dismukes GC
    Magn Reson Chem. 2009 May 5.
    Pubmed: 19415773
    Abstract
    We highlight a range of cryoprobe-assisted NMR methods for studying metabolite production by cyanobacteria, which should be valuable for a wide range of biological applications requiring ultrasensitivity and precise concentration determination over a large dynamic range. Cyroprobe-assisted (1)H and (13)C NMR have been applied to precise determination of metabolic products excreted during autofermentation in two cyanobacterial species: filamentous Arthrospira (Spirulina) maxima CS-328 and unicellular Synechococcus sp. PCC 7002. Several fermentative end products were identified and quantified in concentrations ranging from 50 to 3000 microM in cell-free media (a direct measurement of native-like samples) with less than 5.5% relative error in under 10 min of acquisition per sample with the assistance of an efficient water-suppression protocol. Relaxation times (T1) of these metabolites in aqueous ((1)H(2)O) solution were measured and found to vary by nearly threefold, necessitating generation of individual calibration curves for each species for highest precision. However, using a 4.5 x longer overall recycle delay between scans, the metabolite concentrations can be predicted within 25% error by calibrating only to a single calibration standard (succinate); other metabolites are then calculated on the basis of their signal integrals and known proton degeneracies. Precise ratios of concentrations of (13)C-labeled versus unlabeled metabolites were determined from integral ratios of (1)H peaks that exhibit (13)C--(1)H J-couplings and independently confirmed by direct measurement of areas of corresponding (13)C resonances. (13)C NMR was used to identify and quantify production of osmolytes, trehalose, and glucosylglycerol by A. maxima. Copyright (c) 2009 John Wiley & Sons, Ltd.
57. Translocation of green fluorescent protein to cyanobacterial periplasm using ice nucleation protein.
    Chungjatupornchai W, Fa-aroonsawat S
    J Microbiol. 2009 Apr;47(2):187-92. Epub 2009 May 2.
    Pubmed: 19412603
    Abstract
    The translocation of proteins to cyanobacterial cell envelope is made complex by the presence of a highly differentiated membrane system. To investigate the protein translocation in cyanobacterium Synechococcus PCC 7942 using the truncated ice nucleation protein (InpNC) from Pseudomonas syringae KCTC 1832, the green fluorescent protein (GFP) was fused in frame to the carboxyl-terminus of InpNC. The fluorescence of GFP was found almost entirely as a halo in the outer regions of cells which appeared to correspond to the periplasm as demonstrated by confocal laser scanning microscopy, however, GFP was not displayed on the outermost cell surface. Western blotting analysis revealed that InpNC-GFP fusion protein was partially degraded. The N-terminal domain of InpNC may be susceptible to protease attack; the remaining C-terminal domain conjugated with GFP lost the ability to direct translocation across outer membrane and to act as a surface display motif. The fluorescence intensity of cells with periplasmic GFP was approximately 6-fold lower than that of cells with cytoplasmic GFP. The successful translocation of the active GFP to the periplasm may provide a potential means to study the property of cyanobacterial periplasmic substances in response to environmental changes in a non-invasive manner.
58. Spectral characteristic of fluorescence induction in a model cyanobacterium, Synechococcus sp. (PCC 7942).
    Kana R, Prasil O, Komarek O, Papageorgiou GC, Govindjee G
    Biochim Biophys Acta. 2009 Apr 30.
    Pubmed: 19410552
    Abstract
    We present results of a new method allowing three-dimensional time-wavelength displays of changes in the intensity of variable fluorescence observed in photosynthetic organisms at room temperature. The method allowed us to measure contributions of individual chromophores to fluorescence spectra at various times of fluorescence induction (FI). The method was applied to a freshwater cyanobacterium, Synechococcus sp. (PCC 7942). Analysis of our experimental results provides the following new conclusions: (i) The main chlorophyll (Chl) a emission band at ~685 nm that originates in photosystem (PS) II exhibits typical fast (OPS) and slow (SMT) FI kinetics with both orange (622 nm) and blue (464 nm) excitation. (ii) Similar kinetics are exhibited for its far-red emission satellite band centered at ~745 nm, where the PS II contribution predominates. (iii) The OPS-SMT kinetics can be observed also for the far-red emission at ~710 nm (for blue irradiation) that originates from Chl a of PS I. (iv) A significant OPS-SMT-type kinetics of C-phycocyanin emission at ~650 nm are observed with the blue light excitation, but not with orange light excitation where the signal rose only slightly to a maximum. However, in both the cases an induction of F650 (and F710) occurred, that cannot be caused by an admixture of the F685 fluorescence. This is the first report of light-inducible and dark-reversible changes of phycobilin fluorescence in vivo. We discuss possible interpretations of this new observation.
59. N-Acetyl-l-Glutamate Kinase (NAGK) from Oxygenic Phototrophs: P(II) Signal Transduction across Domains of Life Reveals Novel Insights in NAGK Control.
    Beez S, Fokina O, Herrmann C, Forchhammer K
    J Mol Biol. 2009 May 3.
    Pubmed: 19409905
    Abstract
    N-Acetyl-l-glutamate kinase (NAGK) catalyzes the first committed step in arginine biosynthesis in organisms that perform the cyclic pathway of ornithine synthesis. In eukaryotic and bacterial oxygenic phototrophs, the activity of NAGK is controlled by the P(II) signal transduction protein. Recent X-ray analysis of NAGK-P(II) complexes from a higher plant (Arabidopsis thaliana) and a cyanobacterium (Synechococcus elongatus) revealed that despite several differences, the overall structure of the complex is highly similar. The present study analyzes the functional conservation of P(II)-mediated NAGK regulation in plants and cyanobacteria to distinguish between universal properties and those that are specific for the different phylogenetic lineages. This study shows that plant and cyanobacterial P(II) proteins can mutually regulate the NAGK enzymes across the domains of life, implying a high selective pressure to conserve P(II)-NAGK interaction over more than 1.2 billion years of separate evolution. The non-conserved C-terminus of S. elongatus NAGK was identified as an element, which strongly enhances arginine inhibition and is responsible for most of the differences between S. elongatus and A. thaliana NAGK with respect to arginine sensitivity. Both P(II) proteins relieve arginine inhibition of NAGK, and in both lineages, P(II)-mediated relief from arginine inhibition is antagonized by 2-oxoglutarate. Together, these properties highlight the conserved role of P(II) as a signal integrator of the C/N balance sensed as 2-oxoglutarate to regulate arginine synthesis in oxygenic phototrophs.
60. Crystallization and preliminary X-ray analysis of glutathione transferases from cyanobacteria.
    Feil SC, Tang J, Hansen G, Gorman MA, Wiktelius E, Stenberg G, Parker MW
    Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 May 1;65(Pt 5):475-7. Epub 2009 Apr 24.
    Pubmed: 19407380
    Abstract
    Glutathione S-transferases (GSTs) are a group of multifunctional enzymes that are found in animals, plants and microorganisms. Their primary function is to remove toxins derived from exogenous sources or the products of metabolism from the cell. Mammalian GSTs have been extensively studied, in contrast to bacterial GSTs which have received relatively scant attention. A new class of GSTs called Chi has recently been identified in cyanobacteria. Chi GSTs exhibit a high glutathionylation activity towards isothiocyanates, compounds that are normally found in plants. Here, the crystallization of two GSTs are presented: TeGST produced by Thermosynechococcus elongates BP-1 and SeGST from Synechococcus elongates PCC 6301. Both enzymes formed crystals that diffracted to high resolution and appeared to be suitable for further X-ray diffraction studies. The structures of these GSTs may shed further light on the evolution of GST catalytic activity and in particular why these enzymes possess catalytic activity towards plant antimicrobial compounds.
61. Gracilimonas tropica gen. nov., sp. nov., isolated from a Synechococcus culture.
    Choi DH, Zhang GI, Noh JH, Kim WS, Cho BC
    Int J Syst Evol Microbiol. 2009 May;59(Pt 5):1167-72.
    Pubmed: 19406813
    Abstract
    An irregular, long, rod-shaped marine bacterium, designated CL-CB462(T), was isolated from a Synechococcus culture, which was established from surface water from the tropical Pacific Ocean. The physiological and biochemical features, fatty acid profile and phylogenetic position based on 16S rRNA gene sequences were investigated for the novel strain. Phylogenetic analysis of the 16S rRNA gene sequence showed that the closest relatives of strain CL-CB462(T) were Balneola vulgaris and Balneola alkaliphila. Strain CL-CB462(T) formed a robust clade with members of the genus Balneola in all phylogenetic trees constructed by three different methods. However, the 16S rRNA gene sequence similarity was very low (91.3-91.5 % similarity) and phenotypic and physiological features could clearly differentiate strain CL-CB462(T) from the genus Balneola. Cells of the novel strain were non-motile and spore-forming. The strain was able to grow at 1-20 % (w/v) (optimum of 3-6 %) sea salt concentration, at temperatures of 20-40 degrees C and between pH 6 and 10. The fatty acids were dominated by 15 : 0 iso (41.2 %) and 17 : 1omega9c iso (21.4 %). The DNA G+C content was 42.7 mol%. Based on polyphasic evidence, strain CL-CB462(T) was considered to represent a new genus. The name Gracilimonas tropica gen. nov., sp. nov. is proposed for the type strain of the type species (CL-CB462(T)=KCCM 90063(T)=DSM 19535(T)).
62. Statistical Analysis of Microarray Data with Replicated Spots: A Case Study with Synechococcus WH8102.
    Thomas EV, Phillippy KH, Brahamsha B, Haaland DM, Timlin JA, Elbourne LD, Palenik B, Paulsen IT
    Comp Funct Genomics. 2009:950171. Epub 2009 Apr 23.
    Pubmed: 19404483
    Abstract
    Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting biological outcome of this experiment is the indication of the extent to which the phosphorus regulatory system of this cyanobacterium affects the expression of multiple genes beyond those strictly involved in phosphorus acquisition.
63. ApcD is necessary for efficient energy transfer from phycobilisomes to photosystem I and helps to prevent photoinhibition in the cyanobacterium Synechococcus sp. PCC 7002.
    Dong C, Tang A, Zhao J, Mullineaux CW, Shen G, Bryant DA
    Biochim Biophys Acta. 2009 Apr 24.
    Pubmed: 19397890
    Abstract
    Phycobilisomes (PBS) are the major light-harvesting, protein-pigment complexes in cyanobacteria and red algae. PBS absorb and transfer light energy to photosystem (PS) II as well as PS I, and the distribution of light energy from PBS to the two photosystems is regulated by light conditions through a mechanism known as state transitions. In this study the quantum efficiency of excitation energy transfer from PBS to PS I in the cyanobacterium Synechococcus sp. PCC 7002 was determined, and the results showed that energy transfer from PBS to PS I is extremely efficient. The results further demonstrated that energy transfer from PBS to PS I occurred directly and that efficient energy transfer was dependent upon the allophycocyanin-B alpha subunit, ApcD. In the absence of ApcD, cells were unable to perform state transitions and were trapped in state 1. Action spectra showed that light energy transfer from PBS to PS I was severely impaired in the absence of ApcD. An apcD mutant grew more slowly than the wild type in light preferentially absorbed by phycobiliproteins and was more sensitive to high light intensity. On the other hand, a mutant lacking ApcF, which is required for efficient energy transfer from PBS to PS II, showed greater resistance to high light treatment. Therefore, state transitions in cyanobacteria have two roles: (1) they regulate light energy distribution between the two photosystems; and (2) they help to protect cells from the effects of light-energy excess at high light intensities.
64. Visualization of BrdU-labelled DNA in cyanobacterial cells by Hilbert differential contrast transmission electron microscopy.
    Nitta K, Nagayama K, Danev R, Kaneko Y
    J Microsc. 2009 May;234(2):118-23.
    Pubmed: 19397740
    Abstract
    We have attempted to observe the native shape of DNA in rapidly frozen whole cyanobacterial cells through 5-bromo-2-deoxyuridine (BrdU) incorporation and visualization with a Hilbert differential contrast transmission electron microscopy (HDC TEM). The incorporation of BrdU into the DNA of Synechococcus elongatus PCC 7942 was confirmed with fluorescently labelled anti-BrdU antibodies and through EDX analysis of ultra-thin sections. HDC TEM observed cells that had incorporated BrdU into their DNA exhibited electron dense areas at the location corresponding to fluorescently labelled BrdU. Since various strings and strands were observed in high contrast with the HDC TEM, we conclude that the method promises to allow us to identify and understand bulk structural changes of the in vivo DNA and the nucleoid through observation at high resolution.
65. A novel allele of kaiA shortens circadian period and strengthens interaction of oscillator components in the cyanobacterium Synechococcus elongatus PCC 7942.
    Chen Y, Kim YI, Mackey SR, Holtman CK, Liwang A, Golden SS
    J Bacteriol. 2009 Apr 24.
    Pubmed: 19395479
    Abstract
    The basic circadian oscillator of the unicellular fresh water cyanobacterium Synechococcus elongatus PCC 7942, the model organism for cyanobacterial circadian clocks, consists of only three protein components: KaiA, KaiB and KaiC. These proteins, all of which are homomultimers, periodically interact to form large protein complexes with stoichiometries that depend on the phosphorylation state of KaiC. KaiA stimulates KaiC autophosphorylation through direct physical interactions. Screening a library of S. elongatus transposon mutants for circadian clock phenotypes uncovered an atypical short-period mutant that carries a kaiA insertion. Genetic and biochemical analyses showed that the short-period phenotype is caused by the truncation of KaiA by three amino acid residues at its C-terminus. The disruption of a negative element upstream of the kaiBC promoter was another consequence of the insertion of the transposon; when not associated with a truncated kaiA allele, this mutation extended the circadian period. The circadian rhythm of KaiC phosphorylation was conserved in these mutants, but with some modifications in the rhythmic pattern of KaiC phosphorylation, such as the ratio of phosphorylated to unphosphorylated KaiC and the relative phase of the circadian phosphorylation peak. The results showed that there is no correlation between the phasing of the KaiC phosphorylation pattern and the rhythm of gene expression, measured as bioluminescence from luciferase reporter genes. The interaction between KaiC and the truncated KaiA was stronger than normal, as shown by fluorescence anisotropy analysis. Our data suggest that the KaiA-KaiC interaction and the circadian pattern of KaiC autophosphorylation are both important for determining the period, but not the relative phasing, of circadian rhythms in S. elongatus.
66. Analysis of dissolved microcystins in surface water samples from Kovada Lake, Turkey.
    Gurbuz F, Metcalf JS, Karahan AG, Codd GA
    Sci Total Environ. 2009 Apr 21.
    Pubmed: 19395066
    Abstract
    Dissolved (extracellular) microcystin (MC) concentrations were determined at 3 sampling stations on Lake Kovada, Turkey. The dominant species of cyanobacteria found in August and September of 2006 were Microcystis aeruginosa, Synechococcus sp., Phormidium limosum, Phormidium formosa and Planktothrix limnetica. MC concentrations in water were measured by ELISA and MC variants were examined by HPLC-PDA. Quantitative analysis by HPLC indicated that five MC variants (MC-LR, -RR, -LA, -LW, -LF) were identified in water samples from Kovada Lake. The maximum concentration of dissolved MC-LW was 98.9 microg l(-1) in October. MC-LR was only detected in May at a concentration of 0.5 microg l(-1). The cross reactivity of the antibody (MC10E7) to variants such as MC-LA MC-LW & MC-LF was low. Hence the results determined by ELISA were lower than those determined by HPLC in September and October samples due to differences in the specificity of the antibody to MC variants. Total extraceullar MCs was quantified by ELISA and ranged from 0.73 to 48.5 microg MC-LR equivalents l(-1), which in some cases exceeded the WHO provisional Guideline Value for MC-LR in drinking water. This study confirms that the lakes of Turkey should be monitored for toxic cyanobacteria and for MCs to avoid or reduce the potential exposure of people to these health hazards.
67. Genetic diversity and temporal variation of the marine Synechococcus community in the subtropical coastal waters of Hong Kong.
    Jing H, Zhang R, Pointing SB, Liu H, Qian P
    Can J Microbiol. 2009 Mar;55(3):311-8.
    Pubmed: 19370074
    Abstract
    The phylogenetic diversity of the marine Synechococcus community in the subtropical coastal waters of Hong Kong, China, was examined through intergenic transcribed spacer clone libraries. All the sequences obtained fell within both marine cluster A (MC-A) and B (MC-B), with MC-A phylotypes dominating throughout the year. Distinct phylogenetic lineages specific to Hong Kong waters were detected from both MC-A and MC-B. The highest Synechococcus community diversity occurred in December, but the highest Synechococcus abundance occurred in August. On the other hand, both the abundance and diversity of Synechococcus showed a minimum in February. The remarkable seasonal variations of Synechococcus diversity observed were likely the result of the changes of hydrographic condition modulated by monsoons. Principal component analysis revealed that the in situ abiotic water characteristics, especially salinity and water turbidity, explained much of the variability of the marine Synechococcus population diversity in Hong Kong coastal waters. In addition, the temporal changes of Synechococcus abundance were largely driven by water temperature.
68. Phylogenetic Analysis Indicates Evolutionary Diversity and Environmental Segregation of Marine Podovirus DNA Polymerase Gene Sequences.
    Labonte J, Reid KE, Suttle CA
    Appl Environ Microbiol. 2009 Apr 10.
    Pubmed: 19363063
    Abstract
    The distribution of viral genotypes in the oceans, and their evolutionary relatedness, remains poorly constrained. This paper presents data on the genetic diversity and evolutionary relationships of 1.2 kb DNA polymerase (pol) gene fragments from podoviruses. A newly designed set of PCR primers was used to amplify DNA directly from coastal sediment and water samples collected from inlets adjacent to the Strait of Georgia, British Columbia, Canada, and from the NE Gulf of Mexico. Restriction fragment length polymorphism analysis of 160 cloned PCR products revealed 29 distinct operational taxonomic units (OTUs), with OTUs within a site typically being more similar than those among sites. Phylogenetic analysis of the DNA pol gene fragments demonstrated high similarity between some environmental sequences and sequences from the marine podoviruses Roseophage SIO1 and Cyanophage P60, while others were not closely related to sequences from cultured phage. Interrogation of the CAMERA database for sequences from metagenomics data demonstrated that the amplified sequences were representative of the diversity of podovirus pol sequences found in marine samples. Our results indicate high genetic diversity within marine podovirus communities within a close geographic region and demonstrate that the diversity of environmental polymerase gene sequences for podoviruses is far more extensive than previously recognized.
69. Temporal variation of Synechococcus clades at a coastal Pacific Ocean monitoring site.
    Tai V, Palenik B
    ISME J. 2009 Apr 9.
    Pubmed: 19360028
    Abstract
    Marine cyanobacteria from the genus Synechococcus are found throughout the world's oceans and are important contributors to global primary productivity and carbon cycling. Cultured isolates and environmental DNA clone libraries of Synechococcus have demonstrated the diversity of these microbes. However, the natural distribution of this diversity through space and time and the ecological significance of their distribution are still poorly understood. To understand the seasonal dynamics of Synechococcus diversity, we have developed a quantitative PCR strategy using the gene encoding as a subunit of DNA-dependent RNA polymerase (rpoC1) and applied it to a 3-year time series of surface samples from the Scripps Institution of Oceanography pier (La Jolla, CA, USA), a coastal site in the northeastern Pacific Ocean. Synechococcus from clades I and IV were dominant throughout the time series and correlated with total Synechococcus abundance. The relative abundance of these two dominant clades showed evidence of a seasonal cycle. Synechococcus from clade IV were typically more abundant, but those from clade I dominated during periods just before the annual spring bloom of Synechococcus. Synechococcus from clades II and III were absent during spring and early summer, but appeared at low abundances in late summer and winter possibly due to changes in circulation in the Southern California Bight. As the first long-term time series describing Synechococcus population diversity, these temporal dynamics were used to interpret the genetic/genomic diversity observed in the environment and the potential factors regulating their distribution.The ISME Journal advance online publication, 9 April 2009; doi:10.1038/ismej.2009.35.
70. Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus.
    Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, Rector T, Steen R, McNulty N, Thompson LR, Chisholm SW
    PLoS ONE. 2009;4(4):e5135. Epub 2009 Apr 8.
    Pubmed: 19352512
    Abstract
    The marine cyanobacterium Prochlorococcus MED4 has the smallest genome and cell size of all known photosynthetic organisms. Like all phototrophs at temperate latitudes, it experiences predictable daily variation in available light energy which leads to temporal regulation and partitioning of key cellular processes. To better understand the tempo and choreography of this minimal phototroph, we studied the entire transcriptome of the cell over a simulated daily light-dark cycle, and placed it in the context of diagnostic physiological and cell cycle parameters. All cells in the culture progressed through their cell cycles in synchrony, thus ensuring that our measurements reflected the behavior of individual cells. Ninety percent of the annotated genes were expressed, and 80% had cyclic expression over the diel cycle. For most genes, expression peaked near sunrise or sunset, although more subtle phasing of gene expression was also evident. Periodicities of the transcripts of genes involved in physiological processes such as in cell cycle progression, photosynthesis, and phosphorus metabolism tracked the timing of these activities relative to the light-dark cycle. Furthermore, the transitions between photosynthesis during the day and catabolic consumption of energy reserves at night- metabolic processes that share some of the same enzymes--appear to be tightly choreographed at the level of RNA expression. In-depth investigation of these patterns identified potential regulatory proteins involved in balancing these opposing pathways. Finally, while this analysis has not helped resolve how a cell with so little regulatory capacity, and a 'deficient' circadian mechanism, aligns its cell cycle and metabolism so tightly to a light-dark cycle, it does provide us with a valuable framework upon which to build when the Prochlorococcus proteome and metabolome become available.
71. Exciton Delocalization and Transport in Photosystem I of Cyanobacteria Synechococcus elongates: Simulation Study of Coherent Two-Dimensional Optical Signals.
    Abramavicius D, Mukamel S
    J Phys Chem B. 2009 Apr 7.
    Pubmed: 19351124
    Abstract
    Electronic excitations and the optical properties of the photosynthetic complex PSI are analyzed using an effective exciton model developed by Vaitekonis et al. [Photosynth. Res. 2005, 86, 185]. States of the reaction center, the linker states, the highly delocalized antenna states and the red states are identified and assigned in absorption and circular dichroism spectra by taking into account the spectral distribution of density of exciton states, exciton delocalization length, and participation ratio in the reaction center. Signatures of exciton cooperative dynamics in nonchiral and chirality-induced two-dimensional (2D) photon-echo signals are identified. Nonchiral signals show resonances associated with the red, the reaction center, and the bulk antenna states as well as transport between them. Spectrally overlapping contributions of the linker and the delocalized antenna states are clearly resolved in the chirality-induced signals. Strong correlations are observed between the delocalized antenna states, the linker states, and the RC states. The active space of the complex covering the RC, the linker, and the delocalized antenna states is common to PSI complexes in bacteria and plants.
72. Vertical partitioning and expression of primary metabolic genes in a thermophilic microbial mat.
    Lau MC, Pointing SB
    Extremophiles. 2009 Apr 4.
    Pubmed: 19347567
    Abstract
    A thermophilic microbial mat with a relatively simple morphological composition was used to study the expression of key metabolic genes between mat layers. Mats comprised Roseiflexus castenholzii, Synechococcus sp., a Sphingomonas-like proteobacterial taxon and an unidentified member of the Thermotogae as determined by 16S rRNA phylotypes. The diversity of expressed loci for key genes involved in oxygenic photosynthesis (cbbL), anoxygenic photosynthesis (pufM) and nitrogen fixation (nifH) was assessed. The cyanobacterial surface layer supported two cbbL transcripts, with closest phylogenetic affinity to those from the cyanobacterium Synechococcus sp. and a proteobacterium Nitrobacter sp. This indicates that both photoautotrophic and chemolithoautotrophic carbon dioxide fixation may occur in this mat layer. Lower layers did not support cbbL transcripts. Anoxygenic photosynthesis was indicated by a single pufM transcript with closest affinity to that of R. castenholzii. Expression occurred in all layers beneath the cyanobacterial surface layer. Expression of a single nifH transcript with closest affinity to a proteobacterial nitrogenase occurred in samples throughout all mat layers.
73. Current trends in high throughput proteomics in cyanobacteria.
    Ow SY, Wright PC
    FEBS Lett. 2009 Apr 2.
    Pubmed: 19345218
    Abstract
    Advancements in genome sequencing and high throughput proteomics of cyanobacterial strains led to 13 published reports, from a small number of laboratories. These successful studies focused on Synechocystis, Nostoc and Anabaena strains, prochlorococcus, and halotolerant Euhalothece. The implications of emerging quantitative aspects developed and applied in these large-scale studies are assessed in the wake of advanced cyanobacterial research. Furthermore, contributions from traditional and early high throughput analysis of cyanobacterial proteomics are compared and summarised. Finally, opinions are provided to link both the trends and the future challenges. This review aims to push the synergy between proteomics and cyanobacterial research to improve both the technical and biological significance.
74. Physical and genetic characterization of an outer membrane protein (OmpM1) containing an N-terminal S-layer-like homology domain from the phylogenetically Gram-positive gut anaerobe Mitsuokella multacida.
    Kalmokoff ML, Austin JW, Cyr TD, Hefford MA, Teather RM, Selinger LB
    Anaerobe. 2009 Jan 20.
    Pubmed: 19344649
    Abstract
    Thin sectioning and freeze-fracture-etch of the ovine ruminal isolate Mitsuokella multacida strain 46/5(2) revealed a Gram-negative envelope ultra-structure consisting of a peptidoglycan wall overlaid by an outer-membrane. Sodium-dodecyl-sulfate-polyacrylamide gel electrophoretic (SDS-PAGE) analysis of whole cells, cell envelopes and Triton X-100 extracted envelopes in combination with thin-section and N-terminal sequence analyses demonstrated that the outer-membrane contained two major proteins (45 and 43kDa) sharing identical N-termini (A-A-N-P-F-S-D-V-P-A-D-H-W-A-Y-D). A gene encoding a protein with a predicted N-terminus identical to those of the 43 and 45kDa outer membrane proteins was cloned. The 1290bp open reading frame encoded a 430 amino acid polypeptide with a predicted molecular mass of 47492 Da. Cleavage of a predicted 23 amino acid leader sequence would yield a protein with a molecular mass of 45232 Da. Mass spectroscopic analysis confirmed that the cloned gene (ompM1) encoded the 45kDa outer membrane protein. The N-terminus of the mature OmpM1 protein (residues 24 to 70) shared homology with surface-layer homology (SLH) domains found in a wide variety of regularly structured surface-layers (S-layers). However, the outer-membrane locale, resistance to denaturation by SDS and high temperatures and the finding that the C-terminal residue was a phenylalanine suggested that ompM1 encoded a porin. Threading analysis in combination with the identification of membrane spanning domains indicated that the C-terminal region of OmpM1 (residues 250 - 430) likely forms a 16-strand beta-barrel and appears to be related to the unusual N-terminal SLH-domain-containing beta-barrel-porins previously described in the Cyanobacteria Synechococcus PCC6301.
75. Microarray analysis of phosphate regulation in the marine cyanobacterium Synechococcus sp. WH8102.
    Tetu SG, Brahamsha B, Johnson DA, Tai V, Phillippy K, Palenik B, Paulsen IT
    ISME J. 2009 Apr 2.
    Pubmed: 19340084
    Abstract
    Primary productivity of open ocean environments, such as those inhabited by marine picocyanobacteria, is often limited by low inorganic phosphate (P). To observe how these organisms cope with P starvation, we constructed a full genome microarray for Synechococcus sp. WH8102 and compared differences in gene expression under P-replete and P-limited growth conditions, including both early P stress, during extracellular alkaline phosphatase induction, and late P stress. A total of 36 genes showed significant upregulation (>log(2) fold) whereas 23 genes were highly downregulated at the early time point; however, these changes in expression were maintained during late P stress for only 5 of the upregulated genes. Knockout mutants were constructed for genes SYNW0947 and SYNW0948, comprising a two-component regulator hypothesized to have a key function in regulating P metabolism. A high degree of overlap in the sets of genes affected by P stress conditions and in the knockout mutants supports this hypothesis; however, there is some indication that other regulators may be involved in this response in Synechococcus sp. WH8102. Consistent with what has been observed in many other cyanobacteria, the Pho regulon of this strain is comprised largely of genes for alkaline phosphatases, P transport or P metabolism. Interestingly, however, the exact composition and arrangement of the Pho regulon appears highly variable in marine cyanobacteria.The ISME Journal advance online publication, 2 April 2009; doi:10.1038/ismej.2009.31.
76. Chimeric nitrogenase-like enzymes of (bacterio)chlorophyll biosynthesis.
    Watzlich D, Brocker MJ, Uliczka F, Ribbe M, Virus S, Jahn D, Moser J
    J Biol Chem. 2009 Mar 30.
    Pubmed: 19336405
    Abstract
    The nitrogenase-like light-independent protochlorophyllide oxidoreductase (DPOR) is involved in chlorophyll biosynthesis. Bacteriochlorophyll formation additionally requires the structurally related chlorophyllide oxidoreductase (COR). During catalysis homodimeric subunit BchL(2) or ChlL(2) of DPOR transfers electrons to the corresponding heterotetrameric catalytic subunit (BchNB)(2) or (ChlNB)(2). Analogously, subunit BchX(2) of COR enzymes delivers electrons to subunit (BchYZ)(2). Various chimeric DPOR enzymes formed between recombinant subunits (BchNB)(2) and BchL(2) from Chlorobaculum tepidum or (ChlNB)(2) and ChlL(2) from Prochlorococcus marinus and Thermosynechococcus elongatus were found enzymatically active indicating a conserved docking surface for the interaction of both DPOR protein subunits. Biotin label transfer experiments revealed the interaction of P. marinus ChlL(2) with both subunits, ChlN and ChlB of the (ChlNB)(2) tetramer. Based on these findings and on structural information from the homologous nitrogenase system a site-directed mutagenesis approach yielded ten DPOR mutants for the characterization of amino acid residues involved in protein-protein-interaction. Surface exposed residues Tyr(127) of subunit ChlL, Leu(70) and Val(107) of subunit ChlN and Gly(66) of subunit ChlB were found essential for P. marinus DPOR activity. Next, the BchL(2) or ChlL(2) part of DPOR was exchanged with electron-transferring BchX(2) subunits of COR and NifH(2) of nitrogenase. Active chimeric DPOR was generated via combination of BchX(2) from C. tepidum or Roseobacter denitrificans with (BchNB)(2) from C. tepidum. No DPOR activity was observed for the chimeric enzyme consisting of NifH(2) from Azotobacter vinelandii in combination with (BchNB)(2) from C. tepidum or (ChlNB)(2) from P. marinus and T. elongatus, respectively.
77. Identification and Structural Analysis of a Novel Carboxysome Shell Protein with Implications for Metabolite Transport.
    Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA
    J Mol Biol. 2009 Mar 27.
    Pubmed: 19328811
    Abstract
    Bacterial microcompartments (BMCs) are polyhedral bodies composed entirely of proteins that function as organelles in bacteria; they promote subcellular processes by encapsulating and co-localizing targeted enzymes with their substrates. The best-characterized BMC is the carboxysome, a central part of the carbon-concentrating mechanism that greatly enhances carbon fixation in cyanobacteria and some chemoautotrophs. Here we report the first structural insights into the carboxysome of Prochlorococcus, the numerically dominant cyanobacterium in the world's oligotrophic oceans. Bioinformatic methods, substantiated by analysis of gene expression data, were used to identify a new carboxysome shell component, CsoS1D, in the genome of Prochlorococcus strain MED4; orthologs were subsequently found in all cyanobacteria. Two independent crystal structures of Prochlorococcus MED4 CsoS1D reveal three features not seen in any BMC-domain protein structure solved to date. First, CsoS1D is composed of a fused pair of BMC domains. Second, this double-domain protein trimerizes to form a novel pseudohexameric building block for incorporation into the carboxysome shell, and the trimers further dimerize, forming a two-tiered shell building block. Third, and most strikingly, the large pore formed at the 3-fold axis of symmetry appears to be gated. Each dimer of trimers contains one trimer with an open pore and one whose pore is obstructed due to side-chain conformations of two residues that are invariant among all CsoS1D orthologs. This is the first evidence of the potential for gated transport across the carboxysome shell and reveals a new type of building block for BMC shells.
78. Colimitation of a freshwater herbivore by sterols and polyunsaturated fatty acids.
    Martin-Creuzburg D, Sperfeld E, Wacker A
    Proc Biol Sci. 2009 Feb 20.
    Pubmed: 19324803
    Abstract
    Empirical data providing evidence for a colimitation of an herbivore by two or more essential nutrients are scarce, particularly in regard to biochemical resources. Here, a graphical model is presented, which describes the growth of an herbivore in a system with two potentially limiting resources. To verify this model, life-history experiments were conducted with the herbivore Daphnia magna feeding on the picocyanobacterium Synechococcus elongatus, which was supplemented with increasing amounts of cholesterol either in the presence or the absence of saturating amounts of eicosapentaenoic acid (EPA). For comparison, D. magna was raised on diets containing different proportions of S. elongatus and the cholesterol- and EPA-rich eukaryotic alga Nannochloropsis limnetica. Somatic and population growth of D. magna on a sterol- and EPA-deficient diet was initially constrained by the absence of sterols. With increased sterol availability, a colimitation by EPA became apparent and when the sterol requirements were met, the growth-limiting factor was shifted from a limitation by sterols to a limitation by EPA. These data imply that herbivores are frequently limited by two or more essential nutrients simultaneously. Hence, the concept of colimitation has to be incorporated into models assessing nutrient-limited growth kinetics of herbivores to accurately predict demographic changes and population dynamics.
79. Biocomputational prediction of non-coding RNAs in model cyanobacteria.
    Voss B, Georg J, Schon V, Ude S, Hess WR
    BMC Genomics. 2009 Mar 23;10:123.
    Pubmed: 19309518
    Abstract
    BACKGROUND: In bacteria, non-coding RNAs (ncRNA) are crucial regulators of gene expression, controlling various stress responses, virulence, and motility. Previous work revealed a relatively high number of ncRNAs in some marine cyanobacteria. However, for efficient genetic and biochemical analysis it would be desirable to identify a set of ncRNA candidate genes in model cyanobacteria that are easy to manipulate and for which extended mutant, transcriptomic and proteomic data sets are available. RESULTS: Here we have used comparative genome analysis for the biocomputational prediction of ncRNA genes and other sequence/structure-conserved elements in intergenic regions of the three unicellular model cyanobacteria Synechocystis PCC6803, Synechococcus elongatus PCC6301 and Thermosynechococcus elongatus BP1 plus the toxic Microcystis aeruginosa NIES843. The unfiltered numbers of predicted elements in these strains is 383, 168, 168, and 809, respectively, combined into 443 sequence clusters, whereas the numbers of individual elements with high support are 94, 56, 64, and 406, respectively. Removing also transposon-associated repeats, finally 78, 53, 42 and 168 sequences, respectively, are left belonging to 109 different clusters in the data set. Experimental analysis of selected ncRNA candidates in Synechocystis PCC6803 validated new ncRNAs originating from the fabF-hoxH and apcC-prmA intergenic spacers and three highly expressed ncRNAs belonging to the Yfr2 family of ncRNAs. Yfr2a promoter-luxAB fusions confirmed a very strong activity of this promoter and indicated a stimulation of expression if the cultures were exposed to elevated light intensities. CONCLUSION: Comparison to entries in Rfam and experimental testing of selected ncRNA candidates in Synechocystis PCC6803 indicate a high reliability of the current prediction, despite some contamination by the high number of repetitive sequences in some of these species. In particular, we identified in the four species altogether 8 new ncRNA homologs belonging to the Yfr2 family of ncRNAs. Modelling of RNA secondary structures indicated two conserved single-stranded sequence motifs that might be involved in RNA-protein interactions or in the recognition of target RNAs. Since our analysis has been restricted to find ncRNA candidates with a reasonable high degree of conservation among these four cyanobacteria, there might be many more, requiring direct experimental approaches for their identification.
80. The biosynthetic pathway for myxol-2' fucoside (myxoxanthophyll) in the cyanobacterium Synechococcus sp. strain PCC 7002.
    Graham JE, Bryant DA
    J Bacteriol. 2009 Mar 20.
    Pubmed: 19304845
    Abstract
    Synechococcus sp. strain PCC 7002 produces a variety of carotenoids, which predominantly comprise dicylic beta-carotene and two dicyclic xanthophylls, zeaxanthin and synechoxanthin. However, this cyanobacterium also produces a monocyclic myxoxanthophyll, which was identified as myxol-2'-fucoside. Compared to the carotenoid glycosides produced by diverse microorganisms, cyanobacterial myxoxanthophyll and closely related compounds are unusual because they are glycosylated on the 2'-OH rather than on the 1'-OH position of the psi-end of the molecule. In this study the genes encoding two enzymes that modify the psi-end of myxoxanthophyll were identified in Synechococcus sp. strain PCC 7002. Mutational and biochemical studies showed that open reading frame SynPCC7002_A2032 encodes a 1'-hydroxylase, renamed cruF, and that open reading frame SynPCC7002_A2031 encodes a 2'-O-glycosyl transferase, renamed cruG. The enzymatic activity of CruF was verified by chemical characterization of the carotenoid products synthesized when cruF was expressed in a lycopene-producing strain of Escherichia coli. Database searches showed that homologs of CruF and CruG occur in the genomes of all sequenced cyanobacterial strains that are known to produce myxol or the acylic xanthophyll, oscillaxanthin. The genomes of many other bacteria that produce hydroxylated carotenoids but do not contain crtC homologs also encode cruF orthologs. Based upon observable intermediates, a complete biosynthetic pathway for myxoxanthophyll is proposed. This study expands the suite of enzymes available for metabolic engineering of carotenoid biosynthetic pathways for biotechnological applications.
81. Nitrite transport activity of the ABC-type cyanate transporter of the cyanobacterium Synechococcus elongatus.
    Maeda SI, Omata T
    J Bacteriol. 2009 Mar 13.
    Pubmed: 19286804
    Abstract
    In addition to the ATP-binding cassette (ABC)-type nitrate/nitrite-bispecific transporter, which has high affinity for both substrates (Km approximately 1 microM), Synechococcus elongatus has an active nitrite transport system with an apparent Km (NO2(-)) value of 20 microM. We found that this activity depends on the cynABD genes, encoding a putative cyanate (NCO(-)) ABC-type transporter. Accordingly, nitrite transport by CynABD was competitively inhibited by cyanate with a Ki (NCO(-)) value of 0.025 microM. The transporter was induced under the conditions of nitrogen deficiency, and the induced cells showed a Vmax value of 11-13 micromol per mg of chlorophyll per hour for cyanate or nitrite, which could supply approximately 30% of the amount of nitrogen required for optimum growth. Its relative specificity for the substrates and the regulation at transcriptional and post-translational levels suggested that the physiological role of the bispecific cyanate/nitrite transporter in S. elongatus is to allow nitrogen-deficient cells to assimilate low concentrations of cyanate in medium. Its contribution to nitrite assimilation was significant in a mutant lacking the ABC-type nitrate/nitrite transporter, suggesting a possible role of CynABD in nitrite assimilation by the cyanobacterial species that lack other high-affinity mechanism(s) for nitrite transport.
82. Detection of UVBR-sensitive and -tolerant bacteria in surface waters of the western North Pacific.
    Kataoka T, Hodoki Y, Suzuki K, Saito H, Higashi S
    J Photochem Photobiol B. 2009 Feb 20.
    Pubmed: 19285879
    Abstract
    In order to evaluate the effects of solar ultraviolet radiation (UVR) on eubacterial community composition, we examined the tolerance of eubacterial phylotypes to solar UV radiation in surface waters of the western North Pacific during September 2005. Bromodeoxyuridine (BrdU), a halogenated thymine analogue, was used for labeling newly synthesized DNA in proliferating cells. Thymine dimers (TD), which are specifically formed in DNA by biologically harmful ultraviolet B radiation (UVBR; 280-315nm), were also applied to detect UVB damaged genomes selectively. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) on the labeled samples revealed that UVBR-resistant cells showing active synthesis of DNA without accumulating TD, varied among phylotypes. In addition, UVBR-sensitive band positions with TD indicated inter-specific variations in sensitivity to UVBR. Phylogenetic analysis revealed that 12 DNA sequences were classified into eight phylogenetic groups: three Roseobacter, one Sphingomonas, two Gammaproteobacteria, one Actinobacteria, one Synechococcus, two Prochlorococcus, one plastid and one another group. A UVBR-resistant phylotype was affiliated to Erythrobacter sp. (previously designated as Sphingomonas sp.), which was distributed in warmer waters from the south of Oyashio to Kuroshio regions. A UVBR-sensitive phylotype was affiliated to Pseudoalteromonas sp. in Gammaproteobacteria. Dominant heterotrophic eubacteria were composed of both sensitive and resistant phylotypes. This is the first report on TD accumulated eubacterial phylotypes in oceanic surface waters.
83. Toxicity of atmospheric aerosols on marine phytoplankton.
    Paytan A, Mackey KR, Chen Y, Lima ID, Doney SC, Mahowald N, Labiosa R, Post AF
    Proc Natl Acad Sci U S A. 2009 Mar 9.
    Pubmed: 19273845
    Abstract
    Atmospheric aerosol deposition is an important source of nutrients and trace metals to the open ocean that can enhance ocean productivity and carbon sequestration and thus influence atmospheric carbon dioxide concentrations and climate. Using aerosol samples from different back trajectories in incubation experiments with natural communities, we demonstrate that the response of phytoplankton growth to aerosol additions depends on specific components in aerosols and differs across phytoplankton species. Aerosol additions enhanced growth by releasing nitrogen and phosphorus, but not all aerosols stimulated growth. Toxic effects were observed with some aerosols, where the toxicity affected picoeukaryotes and Synechococcus but not Prochlorococcus. We suggest that the toxicity could be due to high copper concentrations in these aerosols and support this by laboratory copper toxicity tests preformed with Synechococcus cultures. However, it is possible that other elements present in the aerosols or unknown synergistic effects between these elements could have also contributed to the toxic effect. Anthropogenic emissions are increasing atmospheric copper deposition sharply, and based on coupled atmosphere-ocean calculations, we show that this deposition can potentially alter patterns of marine primary production and community structure in high aerosol, low chlorophyll areas, particularly in the Bay of Bengal and downwind of South and East Asia.
84. Horizontal gene transfer in cyanobacterial signature genes.
    Yerrapragada S, Siefert JL, Fox GE
    Methods Mol Biol. 2009;532:339-66.
    Pubmed: 19271195
    Abstract
    Comparison of 15 phylogenetically diverse cyanobacterial genomes identified an updated list of 183 signature genes that are widely found in cyanobacteria but absent in non-cyanobacterial species. These signature genes comprise the unique portion of the core cyanobacterial phenotype, and their absence from other lineages implies that if they arose by horizontal gene transfer (HGT), it likely occurred before the last shared cyanobacterial ancestor. A remaining issue is whether or not these signature genes would be relatively immune to HGT within the cyanobacterial lineage. Phylogenetic trees for each signature gene were constructed and compared to cyanobacterial groupings based on 16S rRNA sequences, with clear incongruence considered indicative of HGT. Approximately 18% of the signature genes exhibited such anomalies, indicating that the incidence of inter-lineage HGT has been significant. A preliminary analysis of intra-lineage transfer was conducted using four Synechococcus/Prochlorococcus species. In this case, it was found that 13% of the signature genes had likely been involved in within group HGT. In order to compare this level of likely HGT to other gene types, the analysis was extended to 1380 genes shared by the four Synechococcus/Prochlorococcus species. Successful HGT events appear to be most frequent among genes involved in photosynthesis/respiration and genes of unknown function, many of which are signature genes. This is consistent with the hypothesis that genes that most directly effect competition and adaptation of similar species in neighboring niches would be most usefully transferred. Such genes may be more easily integrated into a new genomic environment due to close similarities in regulatory circuits. In summary, signature genes are not immune from HGT and in fact may be favored candidates for HGT among closely related cyanobacterial strains.
85. Determination of phytoplankton composition using absorption spectra.
    Martinez-Guijarro R, Romero I, Paches M, Del Rio JG, Marti CM, Gil G, Ferrer-Riquelme A, Ferrer J
    Talanta. 2009 May 15;78(3):814-9. Epub 2009 Jan 23.
    Pubmed: 19269434
    Abstract
    Characterisation of phytoplankton communities in aquatic ecosystems is a costly task in terms of time, material and human resources. The general objective of this paper is not to replace microscopic counts but to complement them, by fine-tuning a technique using absorption spectra measurements that reduces the above-mentioned costs. Therefore, the objective proposed in this paper is to assess the possibility of achieving a qualitative determination of phytoplankton communities by classes, and also a quantitative estimation of the number of phytoplankton cells within each of these classes, using spectrophotometric determination. Samples were taken in three areas of the Spanish Mediterranean coast. These areas correspond to estuary systems that are influenced by both continental waters and Mediterranean Sea waters. 139 Samples were taken in 7-8 stations per area, at different depths in each station. In each sample, the absorption spectrum and the phytoplankton classes (Bacyllariophyceae (diatoms), Cryptophyceae, Clorophyceae, Chrysophyceae, Prasynophyceae, Prymnesophyceae, Euglenophyceae, Cyanophyceae, Dynophyceae and the Synechococcus sp.) were determined. Data were analysed by means of the Partial Least Squares (PLS) multivariate statistical technique. The absorbances obtained between 400 and 750 nm were used as the independent variable and the cell/l of each phytoplankton class was used as the dependent variable, thereby obtaining models which relate the absorbance of the sample extract to the phytoplankton present in it. Good results were obtained for diatoms (Bacillarophyceae), Chlorophyceae and Cryptophyceae.
86. Biogeography of photosynthetic light-harvesting genes in marine phytoplankton.
    Bibby TS, Zhang Y, Chen M
    PLoS ONE. 2009;4(2):e4601. Epub 2009 Feb 25.
    Pubmed: 19240807
    Abstract
    BACKGROUND: Photosynthetic light-harvesting proteins are the mechanism by which energy enters the marine ecosystem. The dominant prokaryotic photoautotrophs are the cyanobacterial genera Prochlorococcus and Synechococcus that are defined by two distinct light-harvesting systems, chlorophyll-bound protein complexes or phycobilin-bound protein complexes, respectively. Here, we use the Global Ocean Sampling (GOS) Project as a unique and powerful tool to analyze the environmental diversity of photosynthetic light-harvesting genes in relation to available metadata including geographical location and physical and chemical environmental parameters. METHODS: All light-harvesting gene fragments and their metadata were obtained from the GOS database, aligned using ClustalX and classified phylogenetically. Each sequence has a name indicative of its geographic location; subsequent biogeographical analysis was performed by correlating light-harvesting gene budgets for each GOS station with surface chlorophyll concentration. CONCLUSION/SIGNIFICANCE: Using the GOS data, we have mapped the biogeography of light-harvesting genes in marine cyanobacteria on ocean-basin scales and show that an environmental gradient exists in which chlorophyll concentration is correlated to diversity of light-harvesting systems. Three functionally distinct types of light-harvesting genes are defined: (1) the phycobilisome (PBS) genes of Synechococcus; (2) the pcb genes of Prochlorococcus; and (3) the iron-stress-induced (isiA) genes present in some marine Synechococcus. At low chlorophyll concentrations, where nutrients are limited, the Pcb-type light-harvesting system shows greater genetic diversity; whereas at high chlorophyll concentrations, where nutrients are abundant, the PBS-type light-harvesting system shows higher genetic diversity. We interpret this as an environmental selection of specific photosynthetic strategy. Importantly, the unique light-harvesting system isiA is found in the iron-limited, high-nutrient low-chlorophyll region of the equatorial Pacific. This observation demonstrates the ecological importance of isiA genes in enabling marine Synechococcus to acclimate to iron limitation and suggests that the presence of this gene can be a natural biomarker for iron limitation in oceanic environments.
87. Structure and function of a novel type of ATP-dependent CLP protease.
    Andersson FI, Tryggvesson A, Sharon M, Diemand AV, Classen M, Best C, Schmidt R, Schelin J, Stanne TM, Bukau B, Robinson CV, Witt S, Mogk A, Clarke AK
    J Biol Chem. 2009 Feb 23.
    Pubmed: 19237538
    Abstract
    The Clp protease is conserved among eubacteria and most eukaryotes, and uses ATP to drive protein substrate unfolding and translocation into a chamber of sequestered proteolytic active sites. The main constitutive Clp protease in photosynthetic organisms has evolved into a functionally essential and structurally intricate enzyme. The model Clp protease from the cyanobacterium Synechococcus consists of the HSP100 molecular chaperone ClpC and a mixed proteolytic core comprised of two distinct subunits, ClpP3 and ClpR. We have purified the ClpP3/R complex, the first for a Clp proteolytic core comprised of heterologous subunits. The ClpP3/R complex has unique functional and structural features, consisting of twin heptameric rings each with an identical ClpP33ClpR4 configuration. As predicted by its lack of an obvious catalytic triad, the ClpR subunit is shown to be proteolytically inactive. Interestingly, extensive modification to ClpR to restore proteolytic activity to this subunit showed that its presence in the core complex is not rate-limiting for the overall proteolytic activity of the ClpCP3/R protease. Altogether, the ClpP3/R complex shows remarkable similarities to the 20S core of the proteasome, revealing a far greater degree of convergent evolution than previously thought between the development of the Clp protease in photosynthetic organisms and that of the eukaryotic 26S proteasome.
88. Detection and expression of the phosphonate transporter gene phnD in marine and freshwater picocyanobacteria.
    Ilikchyan IN, McKay RM, Zehr JP, Dyhrman ST, Bullerjahn GS
    Environ Microbiol. 2009 Feb 9.
    Pubmed: 19220397
    Abstract
    Summary We describe a PCR-based assay designed to detect expression of the phosphonate assimilation gene phnD from picocyanobacteria. The phnD gene encodes the phosphonate binding protein of the ABC-type phosphonate transporter, present in many of the picocyanobacterial genome sequences. Detection of phnD expression can indicate a capacity of picoplankton to utilize phosphonates, a refractory form of phosphorus that can represent 25% of the high-molecular-weight dissolved organic phosphorus pool in marine systems. Primer sets were designed to specifically amplify phnD sequences from marine and freshwater Synechococcus spp., Prochlorococcus spp. and environmental samples from the ocean and Laurentian Great Lakes. Quantitative RT-PCR from cultured marine Synechococcus sp. strain WH8102 and freshwater Synechococcus sp. ARC-21 demonstrated induction of phnD expression in P-deficient media, suggesting that phn genes are regulated coordinately with genes under phoRB control. Last, RT-PCR of environmental RNA samples from the Sargasso Sea and Pacific Ocean detected phnD expression from the endemic picocyanobacterial population. Synechococcus spp. phnD expression yielded a depth-dependent pattern following gradients of P bioavailability. By contrast, the Prochlorococcus spp. primers revealed that in all samples tested, phnD expression was constitutive. The method described herein will allow future studies aimed at understanding the utilization of naturally occurring phoshonates in the ocean as well as monitoring the acquisition of synthetic phosphonate herbicides (e.g. glyphosate) by picocyanobacteria in freshwaters.
89. Formation of Multilayered Photosynthetic Biofilms in an Alkaline Thermal Spring in Yellowstone National Park, WY, USA.
    Boomer SM, Noll KL, Geesey GG, Dutton BE
    Appl Environ Microbiol. 2009 Feb 13.
    Pubmed: 19218404
    Abstract
    In this study, glass rods suspended at the air-water interface in the runoff channel of Fairy Geyser, Yellowstone National Park, WY were used as a substratum to promote the development of biofilms that resembled multilayered mat communities in the splash zone at the geyser's source. This approach enabled the establishment of the temporal relationship between the appearance of Cyanobacteria, which ultimately formed the outer green layer, and the development of a red underlayer containing Roseiflexus-like Chloroflexi. This is the first study to define time-dependent successional events involved in the development of different colored layers within microbial mats associated with many thermal features in Yellowstone National Park. Initial (1 mo) biofilms were localized below the air-water interface (60-70 degrees C) and the majority of retrieved bacterial sequences were similar to Synechococcus and Thermus. Biofilms then shifted, becoming established at and above the air-water interface after 3 mo. During winter sampling (6-8 mo), distinct red-orange microcolonies were observed, consistent with the appearance of Roseiflexus-like sequences and bacteriochlorophyll a pigment signatures. Additionally, populations of Cyanobacteria diversified to include both unicellular and filamentous cell and sequence types. Distinct green and red layers were observed at 13 mo. Planctomycetes-like sequences were also retrieved in high abundance from final biofilm layers and winter samples. Finally, biomass associated with geyser vent water contained Roseiflexus-like sequences, in addition to other high abundance sequence types retrieved from biofilm samples, supporting the idea that geothermal water serves as an inoculum for these habitats.
90. Detection of an L-amino acid dehydrogenase activity in Synechocystis sp. PCC 6803.
    Schriek S, Kahmann U, Staiger D, Pistorius EK, Michel KP
    J Exp Bot. 2009 Feb 12.
    Pubmed: 19213808
    Abstract
    The protein Slr0782 from Synechocystis sp. PCC 6803, which has similarity to L-amino acid oxidase from Synechococcus elongatus PCC 6301 and PCC 7942, has been characterized in part. Immunoblot blot analysis showed that Slr0782 is mainly thylakoid membrane-associated. Moreover, expression of slr0782 mRNA and Slr0782 protein were analyzed and an activity assay was developed. Utilizing toluene-permeabilized cells, an L-arginine-stimulated O(2) uptake became detectable in Synechocystis sp. PCC 6803. Besides oxidizing the basic L-amino acids L-arginine, L-lysine, L-ornithine, and L-histidine, a number of other L-amino acids were also substrates, while D-amino acids were not. The best substrate was L-cysteine, and the second best was L-arginine. The L-arginine-stimulated O(2) uptake was inhibited by cations. The inhibition by o-phenanthroline and salicylhydroxamic acid suggested the presence of a transition metal besides FAD in the enzyme. Moreover, it is shown that inhibitors of the respiratory electron transport chain, such as KCN and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, also inhibited the L-arginine-stimulated O(2) uptake, suggesting that Slr0782 functions as an L-arginine dehydrogenase, mediating electron transfer from L-arginine into the respiratory electron transport chain utilizing O(2) as electron acceptor via cytochrome oxidase. The results imply that Slr0782 is an additional substrate dehydrogenase being able to interact with the electron transport chain of the thylakoid membrane.
91. Dark-to-light transition in Synechococcus sp. PCC 7942 cells studied by fluorescence kinetics assesses plastoquinone redox poise in the dark and photosystem II fluorescence component and dynamics during state 2 to state 1 transition.
    Tsimilli-Michael M, Stamatakis K, Papageorgiou GC
    Photosynth Res. 2009 Feb 11.
    Pubmed: 19205920
    Abstract
    We investigated the dark-to-light transition in Synechococcus sp. PCC 7942 cells by a detailed analysis of fluorescence transients induced by strong red light. The transients, recorded with high data-acquisition, revealed all the steps of the fast (OJIP; 10(-5)-1 s) and slow phase (PSM(T); 1-10(3) s), kinetically distinguished with precision. Focusing on the OJIP-rise, we show, for the first time, how the variable to initial fluorescence ratio and the relative height of J-level can serve as indexes of the plastoquinone redox poise and the established state in the dark; hence, differences among cyanobacteria can be recognised in a simple way. Applying intermittent illumination (20-s light pulses separated by 10-s dark intervals) to induce dark-to-light transition and analysing the individual transients, we establish a method by which we determine the fluorescence component not originating from photosystem (PS) II and we assess PSII dynamics during state 2 to state 1 transition. The development of photochemical and non-photochemical quenching is also discussed, as well as evidences favouring the mobile antenna model.
92. Stability and lability of circadian period of gene expression in the cyanobacterium Synechococcus elongatus.
    Clerico EM, Cassone VM, Golden SS
    Microbiology. 2009 Feb;155(Pt 2):635-41.
    Pubmed: 19202112
    Abstract
    Molecular aspects of the circadian clock in the cyanobacterium Synechococcus elongatus have been described in great detail. Three-dimensional structures have been determined for the three proteins, KaiA, KaiB and KaiC, that constitute a central oscillator of the clock. Moreover, a temperature-compensated circadian rhythm of KaiC phosphorylation can be reconstituted in vitro with the addition of KaiA, KaiB and ATP. These data suggest a relatively simple circadian system in which a single oscillator provides temporal information for all downstream processes. However, in vivo the situation is more complex, and additional components contribute to the maintenance of a normal period, the resetting of relative phases of circadian oscillations, and the control of rhythms of gene expression. We show here that two well-studied promoters in the S. elongatus genome report different circadian periods of expression under a given set of conditions in wild-type as well as mutant genetic backgrounds. Moreover, the period differs between these promoters with respect to modulation by light intensity, growth phase, and the presence or absence of a promoter-recognition subunit of RNA polymerase. These data contrast sharply with the current clock model in which a single Kai-based oscillator governs circadian period. Overall, these findings suggest that complex interactions among the circadian oscillator, perhaps other oscillators, and other cellular machinery result in a clock that is plastic and sensitive to the environment and to the physiological state of the cell.
93. Diversity and abundance of photosynthetic sponges in temperate Western Australia.
    Lemloh ML, Fromont J, Brummer F, Usher KM
    BMC Ecol. 2009 Feb 5;9(1):4.
    Pubmed: 19196460
    Abstract
    ABSTRACT: BACKGROUND: Photosynthetic sponges are important components of reef ecosystems around the world, but are poorly understood. It is often assumed that temperate regions have low diversity and abundance of photosynthetic sponges, but to date no studies have investigated this question. The aim of this study was to compare the percentages of photosynthetic sponges in temperate Western Australia (WA) with previously published data on tropical regions, and to determine the abundance and diversity of these associations in a range of temperate environments. RESULTS: We sampled sponges on 5 m belt transects to determine the percentage of photosynthetic sponges and identified at least one representative of each group of symbionts using 16S rDNA sequencing together with microscopy techniques. Our results demonstrate that photosynthetic sponges are abundant in temperate WA, with an average of 63% of sponge individuals hosting high levels of photosynthetic symbionts and 11% with low to medium levels. These percentages of photosynthetic sponges are comparable to those found on tropical reefs and may have important implications for ecosystem function on temperate reefs in other areas of the world. A diverse range of symbionts sometimes occurred within a small geographic area, including the three "big" cyanobacterial clades, Oscillatoria spongeliae, "Candidatus Synechococcus spongiarum" and Synechocystis species, and it appears that these clades all occur in a wide range of sponges. Additionally, spongin-permeating red algae occurred in at least 7 sponge species. This study provides the first investigation of the molecular phylogeny of rhodophyte symbionts in sponges. CONCLUSIONS: Photosynthetic sponges are abundant and diverse in temperate WA, with comparable percentages of photosynthetic to non-photosynthetic sponges to tropical zones. It appears that there are three common generalist clades of cyanobacterial symbionts of sponges which occur in a wide range of sponges in a wide range of environmental conditions.
94. Use of Stable Isotope-Labelled Cells To Identify Active Grazers of Picocyanobacteria In Ocean Surface Waters
    Frias-Lopez J, Thompson A, Waldbauer J, Chisholm SW
    Environ Microbiol. 2009 Feb;11(2):512-25.
    Pubmed: 19196281
    Abstract
    Prochlorococcus and Synechococcus are the two most abundant marine cyanobacteria. They represent a significant fraction of the total primary production of the world oceans and comprise a major fraction of the prey biomass available to phagotrophic protists. Despite relatively rapid growth rates, picocyanobacterial cell densities in open-ocean surface waters remain fairly constant, implying steady mortality due to viral infection and consumption by predators. There have been several studies on grazing by specific protists on Prochlorococcus and Synechococcus in culture, and of cell loss rates due to overall grazing in the field. However, the specific sources of mortality of these primary producers in the wild remain unknown. Here, we use a modification of the RNA stable isotope probing technique (RNA-SIP), which involves adding labelled cells to natural seawater, to identify active predators that are specifically consuming Prochlorococcus and Synechococcus in the surface waters of the Pacific Ocean. Four major groups were identified as having their 18S rRNA highly labelled: Prymnesiophyceae (Haptophyta), Dictyochophyceae (Stramenopiles), Bolidomonas (Stramenopiles) and Dinoflagellata (Alveolata). For the first three of these, the closest relative of the sequences identified was a photosynthetic organism, indicating the presence of mixotrophs among picocyanobacterial predators. We conclude that the use of RNA-SIP is a useful method to identity specific predators for picocyanobacteria in situ, and that the method could possibly be used to identify other bacterial predators important in the microbial food-web.
95. Iron Stress Genes In Marine Synechococcus and The Development of A Flow Cytometric Iron Stress Assay
    Rivers AR, Jakuba RW, Webb EA
    Environ Microbiol. 2009 Feb;11(2):382-96.
    Pubmed: 19196270
    Abstract
    Marine Synechococcus are frequently found in environments where iron (Fe) is a limiting nutrient. To understand their capacity to respond to Fe stress, we screened picoplankton genomes and the Global Ocean Survey metagenome for known Fe stress genes. Many open ocean strains of Synechococcus lack most known genes for Fe stress, while coastal and upwelling strains contain many, suggesting that maintaining multiple Fe limitation compensation strategies is not a selective advantage in the open ocean. All genomes contained iron deficiency-induced protein A (IdiA) and its complementary Fe(3+) transport proteins. The ubiquity of IdiA was exploited to develop an in situ Fe stress bioassay based on immunolabelling and flow cytometry. As a test of field applicability, we used the assay on natural Synechococcus populations from one station in the Costa Rica Upwelling Dome where total Fe ranged from <0.08 to 0.14 nM in the upper water column. The bioassay found Fe stress in 5-54% of the population. Based on our findings, we believe that when reactive strains are present this assay can reveal environmental and clade-specific differences in the response of Synechococcus to Fe stress.
96. Coastal Synechococcus Metagenome Reveals Major Roles For Horizontal Gene Transfer and Plasmids In Population Diversity
    Palenik B, Ren Q, Tai V, Paulsen IT
    Environ Microbiol. 2009 Feb;11(2):349-59.
    Pubmed: 19196269
    Abstract
    The extent to which cultured strains represent the genetic diversity of a population of microorganisms is poorly understood. Because they do not require culturing, metagenomic approaches have the potential to reveal the genetic diversity of the microbes actually present in an environment. From coastal California seawater, a complex and diverse environment, the marine cyanobacteria of the genus Synechococcus were enriched by flow cytometry-based sorting and the population metagenome was analysed with 454 sequencing technology. The sequence data were compared with model Synechococcus genomes, including those of two coastal strains, one isolated from the same and one from a very similar environment. The natural population metagenome had high sequence identity to most genes from the coastal model strains but diverged greatly from these genomes in multiple regions of atypical trinucleotide content that encoded diverse functions. These results can be explained by extensive horizontal gene transfer presumably with large differences in horizontally transferred genetic material between different strains. Some assembled contigs showed the presence of novel open reading frames not found in the model genomes, but these could not yet be unambiguously assigned to a Synechococcus clade. At least three distinct mobile DNA elements (plasmids) not found in model strain genomes were detected in the assembled contigs, suggesting for the first time their likely importance in marine cyanobacterial populations and possible role in horizontal gene transfer.
97. Occurrence of phosphate acquisition genes in Prochlorococcus cells from different ocean regions.
    Martiny AC, Huang Y, Li W
    Environ Microbiol. 2009 Jan 23.
    Pubmed: 19187282
    Abstract
    Summary The cyanobacterium Prochlorococcus is the numerically dominant phototroph in oligotrophic parts of the oceans. Recently, it was shown that the distribution of phosphate acquisition genes did not match the 16S rRNA phylogeny among isolates from this group but rather appeared related to phosphate availability where the strains had been isolated. To further understand adaptation to phosphate limitation in Prochlorococcus, the distribution of phosphate acquisition genes was investigated in different ocean regions and related to local ortho-phosphate concentration. In regions characterized by less than 0.1 muM phosphate, most Prochlorococcus cells contain genes involved in phosphate uptake, regulation and utilization of organic phosphates. In contrast, most of these genes are absent in regions with more than 0.1 muM phosphate with the exception of genes involved in transport of phosphate (phoE and pstABCS) and three genes of unknown function. This pattern of phosphate acquisition genes showed no significant correspondence to the distribution of rRNA phylotypes. In addition, it was demonstrated that several genes in a separate genomic island were commonly present in low-P sites while absent in high-P sites. Overall, this study further demonstrates a linkage between environmental conditions in the ocean and genome content of Prochlorococcus.
98. Phycourobilin in trichromatic phycocyanin from oceanic cyanobacteria is formed post-translationally by a phycoerythrobilin lyase-isomerase.
    Blot N, Wu XJ, Thomas JC, Zhang J, Garczarek L, Bohm S, Tu JM, Zhou M, Ploscher M, Eichacker L, Partensky F, Scheer H, Zhao KH
    J Biol Chem. 2009 Jan 31.
    Pubmed: 19182270
    Abstract
    Most cyanobacteria harvest light with large antenna complexes called phycobilisomes. The diversity of their pigment-protein components, the phycobiliproteins, contributes to optimize the photosynthetic capacity of these microorganisms. Phycobiliprotein biosynthesis, which involves several post-translational modifications including covalent attachment of the linear tetrapyrrolic chromophores (phycobilins) to apoproteins, begins to be well understood. However, the biosynthesis of the blue-absorbing phycourobilin (lambda(max) ~495 nm) remained unknown. The free chromophore was never found, although it is the major pigment of cyanobacteria living in oceanic areas where blue-green light penetrates deeply into the water column. We describe a unique trichromatic phycocyanin, R-PC V, extracted from phycobilisomes of Synechococcus sp. strain WH8102. It is evolutionarily remarkable as the only pigment known so far that absorbs the whole wavelength range between 450 and 650 nm. R-PC V carries a phycourobilin chromophore on its alpha-subunit and this can be considered an extreme case of adaptation to blue light. We also discovered the enzyme responsible for its biosynthesis. The monomeric RpcG, catalyzes binding of the green-absorbing phycoerythrobilin at cysteine-alpha84 with concomitant isomerization to phycourobilin. This reaction is analogous to formation of the orange-absorbing phycoviolobilin from the red-absorbing phycocyanobilin that is catalyzed by the heterodimeric lyase-isomerase PecE/F in some freshwater cyanobacteria. The fused lyase, RpcG, and PecE/F are mutually interchangeable in vitro but not in vivo. The novel R-PC V probably optimizes rod-core energy transfer in phycobilisomes, and thereby adaptation of a major phytoplankton group to the blue-green light prevailing in oceanic waters.
99. Carrying photosynthesis genes increases ecological fitness of cyanophage in silico.
    Hellweger FL
    Environ Microbiol. 2009 Jan 23.
    Pubmed: 19175665
    Abstract
    Several viruses infecting marine cyanobacteria carry photosynthesis genes (e.g. psbA, hli) that are expressed, yield proteins (D1, HLIP) and help maintain the cell's photosynthesis apparatus during the latent period. This increases energy and speeds up virus production, allowing for a reduced latent period (a fitness benefit), but it also increases the DNA size, which slows down new virus production and reduces burst size (a fitness cost). How do these genes affect the net ecological fitness of the virus? Here, this question is explored using a combined systems biology and systems ecology ('systems bioecology') approach. A novel agent-based model simulates individual cyanobacteria cells and virus particles, each with their own genes, transcripts, proteins and other properties. The effect of D1 and HLIP proteins is explicitly considered using a mechanistic photosynthesis component. The model is calibrated to the available database for Prochlorococcus ecotype MED4 and podovirus P-SSP7. Laboratory- and field-scale in silico survival, competition and evolution (gene packaging error) experiments with wild type and genetically engineered viruses are performed to develop vertical survival and fitness profiles, and to determine the optimal gene content. The results suggest that photosynthesis genes are nonessential, increase fitness in a manner correlated with irradiance, and that the wild type has an optimal gene content.
100. A small heat-shock protein confers stress tolerance and stabilizes thylakoid membrane proteins in cyanobacteria under oxidative stress.
     Sakthivel K, Watanabe T, Nakamoto H
     Arch Microbiol. 2009 Jan 24.
     Pubmed: 19169670
     Abstract
     Small heat-shock proteins are molecular chaperones that bind and prevent aggregation of nonnative proteins. They also associate with membranes. In this study, we show that the small heat-shock protein HspA plays a protective role under oxidative stress in the cyanobacterium Synechococcus elongatus strain ECT16-1, which constitutively expresses HspA. Compared with the reference strain ECT, ECT16-1 showed much better growth and viability in the presence of hydrogen peroxide. Under the peroxide stress, pigments in thylakoid membrane, chlorophyll, carotenoids, and phycocyanins, were continuously reduced in ECT, but in ECT16-1 they decreased only during the first 24 h of stress; thereafter no further reduction was observed. For comparison, we analyzed a wild type and an hspA deletion strain from Synechocystis sp. PCC 6803 and found that lack of hspA significantly affected the viability of the cell and the pigment content in the presence of methyl viologen, suggesting that HspA stabilizes membrane proteins such as the photosystems and phycobilisomes from oxidative damage. In vitro pull down assays showed a direct interaction of HspA with components of phycobilisomes. These results show that HspA and small heat-shock proteins in general play an important role in the acclimation to oxidative stress in cyanobacteria.