Listeria monocytogenes sRNA transcriptome
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Project description:Small non-coding RNAs (sRNAs) are widespread effectors of post-transcriptional gene regulation in bacteria. Currently extensive information exists on the sRNAs of Listeria monocytogenes (Lm) expressed during growth in extracellular environments. We used deep sequencing of cDNAs obtained from fractioned RNA (<500nt) isolated from extracellularly growing bacteria and from Lm-infected macrophages to catalog the sRNA repertoire during intracellular bacterial growth. Here we report on the discovery of 150 regulatory RNAs of which 71 have never been previously described. A total of 29 regulatory RNAs, including small non-coding antisense RNAs, are specifically expressed intracellularly. We validated highly expressed sRNAs by Northern blotting and demonstrated by the construction and characterization of isogenic mutants of rli31, rli33-1 and rli50 for intracellular expressed sRNA candidates, that their expression is required for efficient growth of bacteria in macrophages. All three mutants were attenuated when assessed for growth in mouse and insect models of infection. Comparative genomic analysis revealed the presence of lineage specific sRNAs and the absence of sRNA loci in genomes of naturally-occurring infection-attenuated bacteria, with additional loss in non-pathogenic listerial genomes. Our analyses reveal extensive sRNA expression as an important feature of bacterial regulation during intracellular growth.
2011-07-21 | E-MTAB-329 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level changes in Listeria monocytogenes LO28 delta-lhrC1-5 mutant, compared to the wild type strain. The lhrC1-5 genes encode the regulatory sRNAs LhrC1-5. The microarray studied the gene expression of unstressed cells and cells exposed to cefuroxime for 30 min. The lhrC1-5 mutant employed in this study is further described in Sievers et al. (2014) A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB. Nucleic Acids Res. 42:9383-98.
2015-05-19 | GSE68996 | GEO
Project description:These studies were designed to examine the acute Listeria monocytogenes transcriptional response to mammalian (porcine) bile.
2011-04-12 | GSE28507 | GEO
Project description:Investigation of whole genome gene expression level changes in Listeria monocytogenes LO28 delta-lhrC1-5 mutant, compared to the wild type strain. The lhrC1-5 genes encode the regulatory sRNAs LhrC1-5. The microarray studied the gene expression of unstressed cells and cells exposed to cefuroxime for 30 min. The lhrC1-5 mutant employed in this study is further described in Sievers et al. (2014) A multicopy sRNA of Listeria monocytogenes regulates expression of the virulence adhesin LapB. Nucleic Acids Res. 42:9383-98. A twelve chip study using RNA extracted from 6 different cultures of L. monocytogenes LO28 delta-lhrC1-5 (three unstressed and three stressed cultures) and 6 different cultures of L. monocytognes LO28 wild-type (three unstressed cultures and three stressed cultures).
2015-05-19 | E-GEOD-68996 | biostudies-arrayexpress
Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator CtsR, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DctsR log phase cells were compared to both wt and ictsR-mcsA log phase cells grown with 0.5mM IPTG to identify CtsR-dependent genes.We identified 62 CtsR-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression either between ΔctsR and wt or between ΔctsR and ictsR-mcsA. Keywords: Listeria monocytogenes, CtsR regulon, log phase
2007-10-14 | GSE7514 | GEO
Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes. We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression between ΔhrcA and wt. Combined with microarray analysis, Hidden Markov Model searches show HrcA directly repress at least 8 genes. Keywords: Listeria monocytogenes, HrcA regulon, stationary phase
2007-11-03 | GSE7517 | GEO
Project description:Listeria monocytogenes strain 10403S has been studied extensively for stress response activity toward multiple stressors (acid, osmotic, cold, high temperature, etc.) as well as multiple stress regulons (SigB, CtsR, HrcA, etc.). Here we aimed to determine the transcriptional response of Listeria monocytogenes in early log phase towards the strong oxidative stress imposed by ClO2. The elucidation of such a response allows for further a more completel understanding of the mechanism of inactivation by sanitizers, specifically ClO2.
2014-03-07 | GSE48187 | GEO
Project description:In recent years, more than 60 small RNAs (sRNAs) have been identified in the gram-positive human pathogen Listeria monocytogenes, but their putative roles and mechanisms of action remain largely unknown. The sRNA LhrA was recently shown to be a post-transcriptional regulator of a single gene, lmo0850, which encodes a small protein of unknown function. LhrA controls the translation and degradation of the lmo0850 mRNA by an antisense mechanism, and it depends on the RNA chaperone Hfq for efficient binding to its target. In the present study, we sought to gain more insight into the functional role of LhrA in L. monocytogenes. To this end, we determined the effects of LhrA on global-wide gene expression. We observed that nearly 300 genes in L. monocytogenes are either positively or negatively affected by LhrA. Among these genes, we identified lmo0302 and chiA as direct targets of LhrA, thus establishing LhrA as a multiple target regulator. Lmo0302 encodes a hypothetical protein with no known function, whereas chiA encodes one of two chitinases present in L. monocytogenes. We show here that LhrA acts as a post-transcriptional regulator of lmo0302 and chiA by interfering with ribosome recruitment, and we provide evidence that both LhrA and Hfq act to down-regulate the expression of lmo0302 and chiA. Furthermore, in vitro binding experiments show that Hfq stimulates the base pairing of LhrA to chiA mRNA. Finally, we demonstrate that LhrA has a negative effect on the chitinolytic activity of L. monocytogenes. In marked contrast to this, we found that Hfq has a stimulating effect on the chitinolytic activity, suggesting that Hfq plays multiple roles in the complex regulatory pathways controlling the chitinases of L. monocytogenes.
2011-01-26 | GSE26818 | GEO
Project description:Several Toll-like receptors are activated by Listeria monocytogenes infection, resulting in the activation of MyD88 dependent signaling pathway. However, the negative role of MyD88 in gene expresson is unclear. To address this, we performed microarray analysis of mRNAs from WT or MyD88-/- peritoneal macrophages infected with Listeria monocytogenes.
2014-06-29 | GSE52115 | GEO
Project description: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 (TSS) 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 sRNAs and 70 asRNAs, significantly increasing the repertoire of non coding RNAs in this species. Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 5M-bM-^@M-^Y UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such lasRNA/operon structure, termed "excludon", might represent a novel form of regulation in bacteria. Construction of consensus TSS-maps in Listeria monocytogenes and Listeria innocua by applying 5'-end sequencing on samples in different conditions and genetic backgrounds.
2012-05-01 | E-GEOD-36060 | biostudies-arrayexpress