Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparative genome-wide identification of transcriptional start sites in two environmentally relevant cyanobacteria reveals unexpected diversity in the transcriptome architecture

ABSTRACT: Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present the comprehensive comparison of the structure and composition of the transcriptomes of two closely related Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We used large-scale strand-specific cDNA sequencing, microarray RNA profiling and computational analyses to characterize the transcriptomes of Prochlorococcus sp. MED4 and Prochlorococcus sp. MIT9313, representatives of the two major ecotypes adapted to high and low light conditions, respectively. We present genome-wide maps of transcriptional start sites (TSS) for both organisms. Our data suggest antisense transcription for three quarters of all genes. A direct comparison revealed very little conservation in the use of TSS and the nature of non-coding transcripts between both strains. We conclude that the major transcriptional output from these highly streamlined genomes consists of antisense RNA and that a hitherto unrecognized high degree of variability exists in the transcriptional architecture of these rapidly evolving prokaryotes. Furthermore, we detected extremely short 5M-bM-^@M-^Y untranslated regions with a median length of only 27 nt and 29 nt for MED4 and MIT9313, respectively, and noticed the absence of the Shine-Dalgarno motif, which is suggestive of alternative mechanisms for the initiation of translation. For 8 % of all protein-coding genes, the median length to the initiator codon is 10 nt or shorter, suggesting that leaderless translation and ribosomal protein S1-dependent translation constitute the primary avenues for protein synthesis in Prochlorococcus. Prochlorococcus cells were either grown under standard growth conditions or various stress conditions (darkness, high light, iron or nitrogen depletion, cold or heat stress). Stress conditions were subsequently pooled and hybridized on one microarray.

ORGANISM(S): Prochlorococcus marinus subsp. pastoris str. CCMP1986

SUBMITTER: Karsten Voigt

PROVIDER: E-GEOD-53065 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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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Comparative genome-wide identification of transcriptional start sites in two environmentally relevant cyanobacteria reveals unexpected diversity in the transcriptome architecture

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