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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    • "Reads from the bisulfite strand-specific libraries were used to estimate antisense transcripts (asRNA) length according to the coverage they produced for the phage genome. Reads from the 5′-end libraries were used for determining transcriptional start sites across the phage genome, and were analyzed as previously described (Wurtzel et al., 2012a) with some minor modifications (Supplementary Text). Regions upstream of these transcriptional start sites were scanned for promoter motifs. "
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    • "In the last decade, several high throughput screens have been utilized to identify P. aeruginosa effectors involved in infection, for instance using: (i) microarrays and RNA-Sequencing to monitor bacterial gene expression during infection of eukaryotic host cells (Wolfgang et al., 2003; Chugani and Greenberg, 2007; Wurtzel et al., 2012; Skurnik et al., 2013), (ii) bacterial mutant libraries to identify virulence-attenuated strains (Feinbaum et al., 2012), (iii) a set of target genes to evaluate their toxicity when produced in yeast (Arnoldo et al., 2008), (iv) high-throughput sequencing of transposon libraries to identify the contribution of individual genes to the fitness of organisms in different environments (Skurnik et al., 2013), (v) mass spectrometry identification of secretomes (Russell et al., 2012), or (vi) bioinformatic approaches (Jehl et al., 2011; Burstein et al., 2015). However, despite the high throughput of these approaches, new P. aeruginosa effectors are still regularly revealed (Sana et al., 2012; Russell et al., 2013; Faure et al., 2014; Burstein et al., 2015) and many others certainly remain to be discovered. "
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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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