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

Wurtzel, Omri; Sesto, Nina; Mellin, J. R.; Karunker, Iris; Edelheit, Sarit; Bécavin, Christophe; Archambaud, Cristel; Cossart, Pascale; Sorek, Rotem

doi:10.1038/msb.2012.11

Cited by 263 publications

(334 citation statements)

References 50 publications

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“…Coordinate regulation of overlapping transcripts from divergently transcribed genes has been described in S. aureus and Listeria monocytogenes (11,25). Lasa et al (9) reported involvement of RNase III in the formation of short RNA fragments (∼22 nt) mapping to overlapping transcripts.…”

Section: Discussionmentioning

confidence: 99%

The double-stranded transcriptome of Escherichia coli

Lybecker

Zimmermann

Bilusic

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

103

146

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Advances in high-throughput transcriptome analyses have revealed hundreds of antisense RNAs (asRNAs) for many bacteria, although few have been characterized, and the number of functional asRNAs remains unknown. We have developed a genomewide high-throughput method to identify functional asRNAs in vivo. Most mechanisms of gene regulation via asRNAs require an RNA-RNA interaction with its target RNA, and we hypothesized that a functional asRNA would be found in a double strand (dsRNA), duplexed with its cognate RNA in a single cell. We developed a method of isolating dsRNAs from total RNA by immunoprecipitation with a ds-RNA specific antibody. Total RNA and immunoprecipitated dsRNA from Escherichia coli RNase III WT and mutant strains were deep-sequenced. A statistical model was applied to filter for biologically relevant dsRNA regions, which were subsequently categorized by location relative to annotated genes. A total of 316 potentially functional asRNAs were identified in the RNase III mutant strain and are encoded primarily opposite to the 5′ ends of transcripts, but are also found opposite ncRNAs, gene junctions, and the 3′ ends. A total of 21 sense/antisense RNA pairs identified in dsRNAs were confirmed by Northern blot analyses. Most of the RNA steady-state levels were higher or detectable only in the RNase III mutant strain. Taken together, our data indicate that a significant amount of dsRNA is formed in the cell, that RNase III degrades or processes these dsRNAs, and that dsRNA plays a major role in gene regulation in E. coli.T he advent and development of high-throughput sequencing technologies has uncovered the presence of widespread antisense transcription in many bacteria, with the number of annotated genes associated with antisense RNA (asRNA) differing greatly among bacterial species (1, 2). asRNAs are encoded on the DNA strand opposite an annotated gene and overlap a portion of a gene or the entire gene, or span multiple genes with perfect complementarity. asRNAs range in size from tens to thousands of nucleotides. Although numerous chromosomally encoded asRNAs have been identified, few have been confirmed by traditional methods or functionally characterized. Raghavan et al. (3) reported that few asRNAs are conserved between Escherichia coli and Salmonella enterica, and that the predicted promoter sequences of the asRNAs are not conserved between these species, suggesting that most asRNA transcripts are products of spurious transcription and are not biologically functional RNAs.The majority of functionally characterized asRNAs are found on plasmids, phages, and transposons (4, 5). The mode of regulation by asRNAs can be classified according to molecular mechanism as transcription interference, transcription attenuation, alteration of transcript stability, and translation inhibition (1, 2, 6). With the exception of transcription interference, a physical RNA-RNA interaction between the sense RNAs and asRNAs is necessary for all of these mechanisms, requiring that both RNAs be expressed in the same...

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Section: Discussionmentioning

confidence: 99%

The double-stranded transcriptome of Escherichia coli

Lybecker

Zimmermann

Bilusic

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

103

146

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“…In both Listeria monocytogenes and Staphylococcus aureus a subset of asRNAs are dependent on the alternative sigma factor SigB, suggesting these transcripts are regulated and functional. 20,22 In a recent report, 67 bona fide asRNAs were co-immunoprecipitated with the RNA chaperone Hfq in E. coli. 7 Hfq is often required for the function of trans-encoded sRNAs in Gram-negative bacteria, but its role in gene regulation via cis-encoded asRNAs was not previously reported.…”

Section: Evidence For Functional Asrnasmentioning

confidence: 99%

Pervasive transcription: detecting functional RNAs in bacteria

2014

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“…The first noncoding RNAs (ncRNAs) in L. monocytogenes were identified by coimmunoprecipitation with Hfq, a small RNA-binding protein required for the activity of small regulatory RNAs in prokaryotes [21] and by an in silico-based approaches [22]. Since then, the use of high-density tiling arrays and RNA deep sequencing provided a picture of the whole L. monocytogenes transcriptome in multiple conditions, allowing the discovery of many regulatory RNAs [23][24][25][26][27][28] and the annotation of hundreds of regulatory RNAs in L.…”

Section: Unconventional Mechanisms Regulating Bacterial Gene Expressimentioning

confidence: 99%

“…An excludon typically consists of two divergent transcriptional units overlapped by a long asRNA that inhibits the expression of one of the two divergent operons, but whose distal part harbors information as an mRNA, activating therefore the expression of the other operon ( Figure 3C). The first excludon discovered was the mogR locus in L. monogytogenes and excludons are conserved in other Listeria species 11 and also in a more distantly related bacterium Clostridium difficile [28]. It is highly possible that excludons exist not only in bacteria, but also in other organisms.…”

mentioning

confidence: 99%

“…High-resolution transcriptome of L. monocytogenes highlighted a class of very long asRNAs (lasRNAs) which display a dual function as both asRNA and mRNA and encoded by an "excludon" [27,28]. An excludon typically consists of two divergent transcriptional units overlapped by a long asRNA that inhibits the expression of one of the two divergent operons, but whose distal part harbors information as an mRNA, activating therefore the expression of the other operon ( Figure 3C).…”

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confidence: 99%

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How the Study of Listeria Monocytogenes has Led to New Concepts in Biology

Rolhion

Cossart

2017

Future Microbiol.

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The opportunistic intracellular bacterial pathogen Listeria monocytogenes has in 30 years emerged as an exceptional bacterial model system in infection biology. Research on this bacterium has provided considerable insight into how pathogenic bacteria adapt to mammalian hosts, invade eukaryotic cells, move intracellularly, interfere with host cell functions and disseminate within tissues. It also contributed to unveil features of normal host cells pathways and unsuspected functions of previously known cellular proteins. This review provides an updated overview of our knowledge on this pathogen. In many examples, findings on Listeria monocytogenes provided the basis for new concepts in bacterial regulation, cell biology and infection processes.

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Comparative transcriptomics of pathogenic and non‐pathogenic Listeria species

Cited by 263 publications

References 50 publications

The double-stranded transcriptome of Escherichia coli

The double-stranded transcriptome of Escherichia coli

Pervasive transcription: detecting functional RNAs in bacteria

How the Study of Listeria Monocytogenes has Led to New Concepts in Biology

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