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Exoproteomes of marine cyanobacteria grown under different regimes to detect their pili production; analysed by LC-MS/MS

ABSTRACT: Exoproteomes generated from Synechococcus sp. WH7803 and Prochlorococcus sp. MIT9313 cultures grown under different nutrient, light and temperature conditions. The aim was to see how the production of the pili were affected. Exoproteomes of marine Prochlorococcus under different growth regimes analysed by LC-MS/MS

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Prochlorococcus Sp.

TISSUE(S): Cell Culture

SUBMITTER: Joseph Christie-Oleza

LAB HEAD: Joseph A. Christie-Oleza

PROVIDER: PXD018395 | Pride | 2021-02-24

REPOSITORIES: Pride

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			Action	DRS
	OT_190712_17_MS19-171_Pro_PCR_1.raw	Raw
	OT_190712_17_MS19-171_Pro_PCR_2.raw	Raw
	OT_190712_17_MS19-171_Pro_Pro99_HLHT_1.raw	Raw
	OT_190712_17_MS19-171_Pro_Pro99_HLHT_2.raw	Raw
	OT_190712_17_MS19-171_Pro_Pro99_HLLT_1.raw	Raw

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Project description:RNA decay was measured in Prochlorococcus after inhibition of transcription by rifampicin using customized Affymetrix gene expression arrays. 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. Using a combination of microarrays, quantitative RT-PCR and a new algorithm 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 â 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 (ca. 18 min) were for highly expressed genes. 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. We hypothesize that the fast turnover relative to 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 inform on the modelling of cell processes and help 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. Prochlorococcus cells were treated with rifampicin, which prevents initiation of new transcripts. Cells were harvested at 0 min (before rifampicin addition), 2.5 min, 5 min, 10 min, 20 min, 40 min and 60 min after rifampicin addition.

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Exoproteomes of marine cyanobacteria grown under different regimes to detect their pili production; analysed by LC-MS/MS

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