Comparative RNA-seq analysis of two related pathogenic and non-pathogenic bacterial strains reveals a hidden layer of divergence in the non-coding genome as well as conserved, widespread regulatory structures called ‘Excludons', which mediate regulation through long non-coding antisense RNAs

Christophe Bécavin

Cristel Archambaud

Glaser P

Iris Karunker

J R Mellin

Nina Sesto

Omri Wurtzel

Pascale Cossart

Rotem Sorek

Sarit Edelheit

Molecular Systems Biology

English

PubMed

International audienceListeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein-coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. Our data revealed conservation across most transcripts, but significant divergence between the species in a subset of non-coding RNAs. In L. monocytogenes, we identified 113 small RNAs (33 novel) and 70 antisense RNAs (53 novel), significantly increasing the repertoire of ncRNAs in this species. Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 50 UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such a lasRNA/operon structure, that we named 'excludon', might represent a novel form of regulation in bacteria. Molecular Systems Biology 8: 583; published online 22 May 2012; doi:10.1038/msb.2012.1

Wurtzel, Omri

Sesto, Nina

Mellin, J. R.

Karunker, Iris

Edelheit, Sarit

Becavin, Christophe

Archambaud, Cristel

Cossart, Pascale

Sorek, Rotem

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Comparative transcriptomics of pathogenic and non-pathogenic <em>Listeria</em> species

Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein-coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. Our data revealed conservation across most transcripts, but significant divergence between the species in a subset of non-coding RNAs. In L. monocytogenes, we identified 113 small RNAs (33 novel) and 70 antisense RNAs (53 novel), significantly increasing the repertoire of ncRNAs in this species. Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 50 UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such a lasRNA/operon structure, that we named 'excludon', might represent a novel form of regulation in bacteria. Molecular Systems Biology 8: 583; published online 22 May 2012; doi:10.1038/msb.2012.1

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Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

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Comparative transcriptomics of pathogenic and non‐pathogenic<i>Listeria</i>species

Listeria monocytogenes: a multifaceted model.

OMA 2011: orthology inference among 1000 complete genomes.

https://hal.inrae.fr/hal-02647835v1/file/2012_Wurtzel_Molecular%20Systems%20Biology_1.pdf

Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

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