Microarray Projects
Light Sensing
- Genome-Wide Analysis of Light Sensing In Prochlorococcus
Authors: Steglich C, Futschik M, Rector T, Steen R, Chisholm SW
Browse Data: Here
Abstract:
Prochlorococcus MED4 has, with a total of only 1,716 annotated
protein-coding genes, the most compact genome of a free-living
photoautotroph. Although light quality and quantity play an important role
in regulating the growth rate of this organism in its natural habitat, the
majority of known light-sensing proteins are absent from its genome. To
explore the potential for light sensing in this phototroph, we measured
its global gene expression pattern in response to different light
qualities and quantities by using high-density Affymetrix microarrays.
Though seven different conditions were tested, only blue light elicited a
strong response. In addition, hierarchical clustering revealed that the
responses to high white light and blue light were very similar and
different from that of the lower-intensity white light, suggesting that
the actual sensing of high light is mediated via a blue-light receptor.
Bacterial cryptochromes seem to be good candidates for the blue-light
sensors. The existence of a signaling pathway for the redox state of the
photosynthetic electron transport chain was suggested by the presence of
genes that responded similarly to red and blue light as well as genes that
responded to the addition of DCMU
[3-(3,4-dichlorophenyl)-1,1-N-N'-dimethylurea], a specific inhibitor of
photosystem II-mediated electron transport.
Download: Paper's Supplementary Data
Pubmed: 16980454
Nitrogen Availability
- Global Gene Expression of Prochlorococcus Ecotypes In Response To Changes In Nitrogen Availability
Authors: Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW
Browse Data: Here
Abstract:
Nitrogen (N) often limits biological productivity in the oceanic gyres
where Prochlorococcus is the most abundant photosynthetic organism. The
Prochlorococcus community is composed of strains, such as MED4 and
MIT9313, that have different N utilization capabilities and that belong to
ecotypes with different depth distributions. An interstrain comparison of
how Prochlorococcus responds to changes in ambient nitrogen is thus
central to understanding its ecology. We quantified changes in MED4 and
MIT9313 global mRNA expression, chlorophyll fluorescence, and photosystem
II photochemical efficiency (Fv/Fm) along a time series of increasing N
starvation. In addition, the global expression of both strains growing in
ammonium-replete medium was compared to expression during growth on
alternative N sources. There were interstrain similarities in N regulation
such as the activation of a putative NtcA regulon during N stress. There
were also important differences between the strains such as in the
expression patterns of carbon metabolism genes, suggesting that the two
strains integrate N and C metabolism in fundamentally different ways.
Download: Paper's Supplementary Data
Pubmed: 17016519
Phage Infection
- Genome-Wide Expression Dynamics of A Marine Virus and Host Reveal Features of Co-Evolution
Authors: Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW
Browse Data: Here
Abstract:
Interactions between bacterial hosts and their viruses (phages) lead to
reciprocal genome evolution through a dynamic co-evolutionary process.
Phage-mediated transfer of host genes--often located in genome
islands--has had a major impact on microbial evolution. Furthermore, phage
genomes have clearly been shaped by the acquisition of genes from their
hosts. Here we investigate whole-genome expression of a host and phage,
the marine cyanobacterium Prochlorococcus MED4 and the T7-like cyanophage
P-SSP7, during lytic infection, to gain insight into these co-evolutionary
processes. Although most of the phage genome was linearly transcribed over
the course of infection, four phage-encoded bacterial metabolism genes
formed part of the same expression cluster, even though they are
physically separated on the genome. These genes--encoding photosystem II
D1 (psbA), high-light inducible protein (hli), transaldolase (talC) and
ribonucleotide reductase (nrd)--are transcribed together with phage DNA
replication genes and seem to make up a functional unit involved in energy
and deoxynucleotide production for phage replication in resource-poor
oceans. Also unique to this system was the upregulation of numerous genes
in the host during infection. These may be host stress response genes
and/or genes induced by the phage. Many of these host genes are located in
genome islands and have homologues in cyanophage genomes. We hypothesize
that phage have evolved to use upregulated host genes, leading to their
stable incorporation into phage genomes and their subsequent transfer back
to hosts in genome islands. Thus activation of host genes during infection
may be directing the co-evolution of gene content in both host and phage
genomes.
Download: Paper's Supplementary Data
Pubmed: 17805294
Phosphate Starvation
- Phosphate Acquisition Genes In Prochlorococcus Ecotypes: Evidence For Genome-Wide Adaptation
Authors: Martiny AC, Coleman ML, Chisholm SW
Browse Data: Here
Abstract:
The cyanobacterium Prochlorococcus is the numerically dominant phototroph
in the oligotrophic oceans. This group consists of multiple ecotypes that
are physiologically and phylogenetically distinct and occur in different
abundances along environmental gradients. Here we examine adaptations to
phosphate (P) limitation among ecotypes. First, we used DNA microarrays to
identify genes involved in the P-starvation response in two strains
belonging to different ecotypes, MED4 (high-light-adapted) and MIT9313
(low-light-adapted). Most of the up-regulated genes under P starvation
were unique to one strain. In MIT9313, many ribosomal genes were
down-regulated, suggesting a general stress response in this strain. We
also observed major differences in regulation. The P-starvation-induced
genes comprise two clusters on the chromosome, the first containing the P
master regulator phoB and most known P-acquisition genes and the second,
absent in MIT9313, containing genes of unknown function. We examined the
organization of the phoB gene cluster in 11 Prochlorococcus strains
belonging to diverse ecotypes and found high variability in gene content
that was not congruent with rRNA phylogeny. We hypothesize that this
genome variability is related to differences in P availability in the
oceans from which the strains were isolated. Analysis of a metagenomic
library from the Sargasso Sea supports this hypothesis; most
Prochlorococcus cells in this low-P environment contain the P-acquisition
genes seen in MED4, although a number of previously undescribed gene
combinations were observed.
Download: Paper's Supplementary Data
Pubmed: 16895994
Genomes