Listeria monocytogenes σ ^B Has a Small Core Regulon and a Conserved Role in Virulence but Makes Differential Contributions to Stress Tolerance across a Diverse Collection of Strains

Refinement of the Listeria monocytogenes σB regulon through quantitative proteomic analysis

“…opuCC (i) is also preceded by a putative s B -dependent promoter and (ii) belongs to the four-gene opuC operon that has been identified in (Fraser et al, 2003;Sue et al, 2003). lmo0265, which had a significant P c value and a FC of 8.0 reported in the Oliver et al (2010) microarray study, did not show evidence for differential expression in the two other array studies (Ollinger et al, 2009;Raengpradub et al, 2008), which used an EGD-e array that had an lmo0265 probe with low (71 %) homology to the 10403S lmo0265 gene, likely leading to a false-negative result in these two studies.…”

“…A meta-analysis of three published microarray studies was performed to identify genes that showed differential transcript levels between the L. monocytogenes parent strain 10403S and an isogenic DsigB strain. Two of these studies used 10403S and an isogenic DsigB strain (Oliver et al, 2010;Raengpradub et al, 2008), while one study (Ollinger et al, 2009) used an L. monocytogenes 10403S prfA* strain, which constitutively expresses an active form of the virulence gene transcriptional activator PrfA, and an isogenic prfA*DsigB strain. Two of these studies (Ollinger et al, 2009;Raengpradub et al, 2008) used the same set of microarray probes, which were designed based on the genome sequence of strain EGD-e, while the other study (Oliver et al, 2010) used a set of microarray probes designed based on four different genomes.…”

“…In this study .200 genes were identified as having significant s B effects with FC ¢1.5 between the parent and mutant strain. In addition, Oliver et al (2010) used microarray analyses to compare transcript levels in parent and DsigB mutant strain pairs representing L. monocytogenes lineages I, II, IIIA and IIIB; lineages IIIA and IIIB have recently been reclassified as lineages III and IV (Ward et al, 2008). In L. monocytogenes 10403S, a lineage II strain, 252 genes were found to be significantly positively regulated by s B in stationary phase cells, with a FC ¢1.5.…”

“…Overall, the studies detailed above show that s B in L. monocytogenes is responsible for positive regulation of a large regulon with .100 genes, with a considerable number of these genes directly regulated by s B , as supported by identification of s B consensus promoters upstream of many of these genes (Abram et al, 2008a;Oliver et al, 2009Oliver et al, , 2010Raengpradub et al, 2008); however, a comprehensive analysis that formally integrates data on the s B regulon from multiple studies has been missing so far. Increasing evidence further suggests that s B also makes important contributions to gene regulation in L. monocytogenes via mechanisms other than direct regulation of a gene or operon through s B -dependent transcription from an upstream promoter, including, but not limited to, regulation of non-coding RNAs (ncRNAs), which can regulate gene expression at both the transcriptional and post-transcriptional stage (Mellin & Cossart, 2012;Nielsen et al, 2008;Oliver et al, 2009;Toledo-Arana et al, 2009).…”

“…The other proteins with lower expression levels were Lmo0427 (fructose-specific PTS system IIB component), Lmo0484 (haem-degrading monooxygenase, IsdG) and Lmo2648 (similar to phosphotriesterase), which showed FC of 21.56, 21.53 and 21.60, respectively. The genes encoding these six proteins also had significant P c values in the microarray meta-analysis and displayed negative FC ranging from 21.6 to 21.1 in three (lmo2648; lmo1998; lmo2002) or two (lmo0484; lmo0427; lmo1997) microarray studies in DsigB stationary phase cells (Oliver et al, 2010;Ollinger et al, 2009;Raengpradub et al, 2008). No genes were identified as negatively regulated by s B in the RNA-Seq study (Oliver et al, 2009).…”