Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus
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gb-2010-11-5-r54.pdf
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Author(s)
Steglich, Claudia
Lindell, Debbie
Futschik, Matthias
Rector, Trent
Steen, Robert
Chisholm, Sallie (Penny)
Date Issued
May 2010
Journal
Genome Biology
Publisher
BioMed Central Ltd
Citation
Steglich, Claudia et al. “Short RNA Half-lives in the Slow-growing Marine Cyanobacterium Prochlorococcus.” Genome Biology 11.5 (2010): R54.
Version
Final published version
Abstract
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 minutes and a median decay rate of 2.6 minutes for expressed genes - twofold 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 (approximately 18 minutes) 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. Conclusions 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 us interpret 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 organisms.
MIT Department
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
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DOI of Published Version
https://doi.org/10.1186/gb-2010-11-5-r54
