Short RNA half-lives in the slow-growing marine cyanobacterium
Steglich C, Lindell
Genome Biol. 2010 May 19;11(5):R54.
BACKGROUND: RNA turnover plays an important role in the gene regulation of
microorganisms and influences their speed of acclimation to environmental
changes. We investigated whole-genome RNA stability of Prochlorococcus, a
relatively slow-growing marine cyanobacterium doubling approximately once a day,
which is extremely abundant in the oceans. RESULTS: Using a combination of
microarrays, quantitative RT-PCR and a new fitting method for determining RNA
decay rates, we found a median half-life of 2.4 min and a median decay rate of
2.6 min for expressed genes - two fold faster than that reported for any
organism. The shortest transcript half-life (33 seconds) was for a gene of
unknown function, while some of the longest (approximately18 min) were for genes
with high transcript levels. Genes organized in operons displayed intriguing
mRNA decay patterns, such as increased stability, and delayed onset of decay
with greater distance from the transcriptional start site. The same phenomenon
was observed on a single probe resolution for genes greater than 2 kb.
CONCLUSION: We hypothesize that the fast turnover relative to the slow
generation time in Prochlorococcus may enable a swift response to environmental
changes through rapid recycling of nucleotides, which could be advantageous in
nutrient poor oceans. Our growing understanding of RNA half-lives will help the
interpretation of the growing bank of metatranscriptomic studies of wild
populations of Prochlorococcus. The surprisingly complex decay patterns of large
transcripts reported here, and the method developed to describe them, will open
new avenues for the investigation and understanding of RNA decay for all
GEO archive Steglich, microarray GEO data for the half-life experiment
containing the cel files and an experimental description.
a table with half-lives and
key suppl data, a key file for the right order of occurrence on the web
page of Genome Biology.