Abstract
In all studied organisms, a substantial portion of the transcriptome consists of non-coding RNAs that frequently execute regulatory functions. Here, we have compared the primary transcriptomes of the cyanobacteria Synechocystis sp. PCC 6714 and PCC 6803 under 10 different conditions. These strains share 2854 protein-coding genes and a 16S rRNA identity of 99.4%, indicating their close relatedness. Conserved major transcriptional start sites (TSSs) give rise to non-coding transcripts within the sigB gene, from the 5′UTRs of cmpA and isiA, and 168 loci in antisense orientation. Distinct differences include single nucleotide polymorphisms rendering promoters inactive in one of the strains, e.g., for cmpR and for the asRNA PsbA2R. Based on the genome-wide mapped location, regulation and classification of TSSs, non-coding transcripts were identified as the most dynamic component of the transcriptome. We identified a class of mRNAs that originate by read-through from an sRNA that accumulates as a discrete and abundant transcript while also serving as the 5′UTR. Such an sRNA/mRNA structure, which we name ‘actuaton’, represents another way for bacteria to remodel their transcriptional network. Our findings support the hypothesis that variations in the non-coding transcriptome constitute a major evolutionary element of inter-strain divergence and capability for physiological adaptation.
Highlights
Correspondence and requests for materials should be addressed to Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria
We identified a class of mRNAs that originate by read-through from an sRNA that accumulates as a discrete and abundant transcript while serving as the 59UTR
Differential RNA-seq-type transcriptomic analyses are especially powerful, as this technique enables the identification of transcriptional start sites (TSSs) at a genome-wide scale at single-nucleotide resolution and can identify sRNAs as well as transcripts that originate within genes in either orientation
Summary
Correspondence and requests for materials should be addressed to Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria. Based on the genome-wide mapped location, regulation and classification of TSSs, non-coding transcripts were identified as the most dynamic component of the transcriptome. Differential RNA-seq-type transcriptomic analyses (dRNA-seq7) are especially powerful, as this technique enables the identification of TSSs at a genome-wide scale at single-nucleotide resolution and can identify sRNAs as well as transcripts that originate within genes in either orientation. Comparative transcriptomics has proven useful at inferring the dynamics of transcriptional regulation by analysing regulatory responses to different conditions. Such an analysis compared primary transcriptomes of the human pathogen Helicobacter pylori under the midlogarithmic growth phase versus acid stress conditions, mimicking the host environment[7]. PCC 7120 revealed more than 10,000 TSSs active during the differentiation of N2-fixing heterocysts, of which .900 TSSs exhibited minimum www.nature.com/scientificreports fold changes (FCs) of eight, suggesting a large number of unidentified regulators of cell differentiation and N2-fixation[9]
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