Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 8:583

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
Molecular Systems Biology (Impact Factor: 10.87). 05/2012; 8(1):583. DOI: 10.1038/msb.2012.11
Source: PubMed


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 5' 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.

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Available from: Christophe Becavin, Oct 08, 2015
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    • "The LntA-mediated stimulation of type III-IFN responses might support localized pro-bacterial conditions, as was proposed for IFN-I responses (Toledo-Arana et al. 2009; Dussurget et al. 2014). In addition to suggesting a role for non-coding RNA in virulence of L. monocytogenes, new findings (Wurtzel et al. 2012) identified a recurrent organization, called excludon, where transcription of long RNAs, antisense to transcripts encoding proteins, represses expression of overlapping genes whose functions are opposite. "
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    ABSTRACT: The review recapitulate the current knowledge on the roles and importance of non-coding RNAs (ncRNAs) and small RNAs in bacteria. Many new RNAs have been described either in Gram positive and Gram negative bacteria, and in particular RNAs involved in pathogenesis and tolerance to stresses. The review recapitulate the current knowledge on the roles and importance of non-coding RNAs (ncRNAs) and small RNAs in bacteria. Several cases of regulating and signaling RNAs are presented either in Gram positive and Gram negative bacteria, with a focus on bacterial RNAs involved in pathogenesis and stress responses. Examples of small RNAs and their mechanisms of action, transcriptional and post-transcriptional regulation, induction of new genes, increased stability of their targets or their destination to the degradation pathway.
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    • "Another reported excludon (anti0424) is most likely involved in regulating central metabolic pathways in L. monocytogenes. As it spans two divergently oriented genes encoding for enzymes necessary for the usage of different carbon utilization, it might represent a possibility for a selective switching between those pathways (Wurtzel et al., 2012). "
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    ABSTRACT: Listeria monocytogenes is a Gram-positive human-pathogen bacterium that served as an experimental model for investigating fundamental processes of adaptive immunity and virulence. Recent novel technologies allowed the identification of several hundred non-coding RNAs (ncRNAs) in the Listeria genome and provided insight into an unexpected complex transcriptional machinery. In this review, we discuss ncRNAs that are encoded on the opposite strand of the target gene and are therefore termed antisense RNAs (asRNAs). We highlight mechanistic and functional concepts of asRNAs in L. monocytogenes and put these in context of asRNAs in other bacteria. Understanding asRNAs will further broaden our knowledge of RNA-mediated gene regulation and may provide targets for diagnostic and antimicrobial development.
    Frontiers in Cellular and Infection Microbiology 09/2014; 4:135. DOI:10.3389/fcimb.2014.00135 · 3.72 Impact Factor
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    • "As seen above, cis-regulatory element functions are suggested by their locations relative to known ORFs. Although not greatly exploited in mycobacterial species, bioinformatics tools such as TargetRNA have been used in Salmonella and Listeria pathogens to predict sRNA interactions in silico (Tjaden, 2008; Wurtzel et al., 2012; Yu and Schneiders, 2012). Still, experimental methods are necessary to confirm these suggested interactions. "
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    ABSTRACT: Mycobacteria represent a class of powerful pathogens, including those causing tuberculosis and leprosy, which continue to be worldwide health challenges. In the last 20 years, an abundance of non-coding, small RNAs (sRNAs) have been discovered in model bacteria and gained significant attention as regulators of cellular responses, including pathogenesis. Naturally, a search in mycobacteria followed, revealing over 200 sRNAs thus far. Characterization of these sRNAs is only beginning, but differential expression under environmental stresses suggests relevance to mycobacterial pathogenesis. This review provides a comprehensive overview of the current knowledge of sRNAs in mycobacteria, including historical perspective and techniques used for identification and characterization.
    Frontiers in Cellular and Infection Microbiology 07/2014; 4:96. DOI:10.3389/fcimb.2014.00096 · 3.72 Impact Factor
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