Dataset Information

Quantitative proteomics shows extensive remodelling induced by N limitation in Prochlorococcus sp. SS120 C4PR_LIV

ABSTRACT: Prochlorococcus is the most abundant photosynthetic organism on Earth, contributing significantly to the global primary production and playing a prominent role in biogeochemical cycles. Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes of the proteome is necessary to gain fundamental insights into such response. Here we study the effects of extreme nitrogen limitation, a feature of the oligotrophic oceans inhabited by this organism.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Prochlorococcus Marinus Subsp. Marinus Str. Ccmp1375

TISSUE(S): Photosynthetic Cell

SUBMITTER: Guadalupe Gomez Baena

LAB HEAD: Robert J. Beynon

PROVIDER: PXD005745 | Pride | 2017-05-03

REPOSITORIES: Pride

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Publications

Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcusmarinus SS120.

Domínguez-Martín Maria Agustina MA Gómez-Baena Guadalupe G Díez Jesús J López-Grueso Maria José MJ Beynon Robert J RJ García-Fernández José Manuel JM

mSystems 20170530 3

Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate ...[more]

PMID: 28593196

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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.

Dataset Information

Quantitative proteomics shows extensive remodelling induced by N limitation in Prochlorococcus sp. SS120 C4PR_LIV

Publications

Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in <i>Prochlorococcus</i><i>marinus</i> SS120.

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