Unknown,Transcriptomics,Genomics,Proteomics

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The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome

ABSTRACT: RNA-Seq technique was used to obtain the transcriptome map of Prochlorococcus MED4, including operons, untranslated regions, non-coding RNAs, and novel genes. Genome-wide expression profiles revealed that three factors contribute to core genome stabilization. First, a negative correlation between gene expression levels and protein evolutionary rates was observed. Highly expressed genes were overrepresented in the core genome but not in the flexible genome. Gene necessity was determined as a second powerful constraint on genome evolution through functional enrichment analysis. Third, quick mRNA turnover may increase corresponding proteinsM-bM-^@M-^Y fidelity among genes that were abundantly expressed. Together, these factors influence core genome stabilization during MED4 genome evolution. The cells were cultured on Pro99 medium for a certain time course (1, 3, 4, 8, and 10 days); or transferred to AMP (Artificial Medium for Prochlorococcus) with 6 mM or 24 mM sodium bicarbonate for 5 or 10 hours.

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

SUBMITTER: Bang Wang

PROVIDER: E-GEOD-49517 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome.

Wang Bang B Lu Lina L Lv Hexin H Jiang Huifeng H Qu Ge G Tian Chaoguang C Ma Yanhe Y

BMC microbiology 20140118

<h4>Background</h4>Gene gain and loss frequently occurs in the cyanobacterium Prochlorococcus, a phototroph that numerically dominates tropical and subtropical open oceans. However, little is known about the stabilization of its core genome, which contains approximately 1250 genes, in the context of genome streamlining. Using Prochlorococcus MED4 as a model organism, we investigated the constraints on core genome stabilization using transcriptome profiling.<h4>Results</h4>RNA-Seq technique was u ...[more]

PMID: 24438106

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Project description: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.

Dataset Information

The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome

Publications

The transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome.

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