ArticleThe ISME journal2014
Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity.
Article in The ISME journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 91 citations in OpenAlex.
- Phosphoproteomics reveals essential regulatory roles of phosphorylation in marine oligotrophic bacteria.Marine life science & technology · 2026Article
- A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments.Microbiology and molecular biology reviews : MMBR · 2023Review
- Nitrogen-regulated antisense transcription in the adaptation to nitrogen deficiency inPNAS nexus · 2023Article
- Acclimation and stress response ofFrontiers in microbiology · 2022Article
- Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria.Bio-protocol · 2020Article
- A framework for the computational prediction and analysis of non-coding RNAs in microbial environmental populations and their experimental validation.The ISME journal · 2020Article
- Prevalence of small base-pairing RNAs derived from diverse genomic loci.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- The power of cooperation: Experimental and computational approaches in the functional characterization of bacterial sRNAs.Molecular microbiology · 2020Review
- Synergic Effects of Temperature and Irradiance on the Physiology of the MarineFrontiers in microbiology · 2020Article
- Interplay and Targetome of the Two Conserved Cyanobacterial sRNAs Yfr1 and Yfr2 in Prochlorococcus MED4.Scientific reports · 2019Article
- Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes.Nucleic acids research · 2018Article
- A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria.Nucleic acids research · 2018Article
- The GntR family transcriptional regulator PMM1637 regulates the highly conserved cyanobacterial sRNA Yfr2 in marine picocyanobacteria.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!Microbiology spectrum · 2018Review
- Widespread Antisense Transcription in Prokaryotes.Microbiology spectrum · 2018Review
- Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.The ISME journal · 2018Article
- The primary transcriptome of the fast-growing cyanobacteriumBiotechnology for biofuels · 2018Article
- Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells.The ISME journal · 2017Article
- Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species.Genome biology and evolution · 2017Article
- Termination factor Rho: From the control of pervasive transcription to cell fate determination in Bacillus subtilis.PLoS genetics · 2017Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5' untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine-Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.
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