AUTHOR=Liu Yichang , Orsi Renato H. , Boor Kathryn J. , Wiedmann Martin , Guariglia-Oropeza Veronica 

TITLE=Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σB

JOURNAL=Frontiers in Microbiology

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.01910

DOI=10.3389/fmicb.2017.01910

ISSN=1664-302X

ABSTRACT=<p>Among <italic>Listeria monocytogenes'</italic> four alternative σ factors, σ<sup>B</sup> controls the largest regulon. As σ<sup>B</sup>-dependent transcription of some genes may be masked by overlaps among regulons, and as some σ<sup>B</sup>-dependent genes are expressed only under very specific conditions, we hypothesized that the σ<sup>B</sup> regulon is not yet fully defined. To further extend our understanding of the σ<sup>B</sup> regulon, we used RNA-seq to identify σ<sup>B</sup>-dependent genes in an <italic>L. monocytogenes</italic> strain that expresses σ<sup>B</sup> following rhamnose induction, and in which genes encoding the other alternative sigma factors have been deleted. Analysis of RNA-seq data with multiple bioinformatics approaches, including a sliding window method that detects differentially transcribed 5′ untranslated regions (UTRs), identified 105 σ<sup>B</sup>-dependent transcription units (TUs) comprising 201 genes preceded by σ<sup>B</sup>-dependent promoters. Of these 105 TUs, 7 TUs comprising 15 genes had not been identified previously as σ<sup>B</sup>-dependent. An additional 23 genes not reported previously as σ<sup>B</sup>-dependent were identified in 9 previously recognized σ<sup>B</sup>-dependent TUs. Overall, 38 of these 201 genes had not been identified previously as members of the <italic>L. monocytogenes</italic> σ<sup>B</sup> regulon. These newly identified σ<sup>B</sup>-dependent genes encode proteins annotated as being involved in transcriptional regulation, oxidative and osmotic stress response, and in metabolism of energy, carbon and nucleotides. In total, 18 putative σ<sup>B</sup>-dependent promoters were newly identified. Interestingly, a number of genes previously identified as σ<sup>B</sup>-dependent did not show significant evidence for σ<sup>B</sup>-dependent transcription in our experiments. Based on promoter analyses, a number of these genes showed evidence for co-regulation by σ<sup>B</sup> and other transcriptional factors, suggesting that some σ<sup>B</sup>-dependent genes require additional transcriptional regulators along with σ<sup>B</sup> for transcription. Over-expression of a single alternative sigma factor in the absence of all other alternative sigma factors allowed us to: (i) identify new σ<sup>B</sup>-dependent functions in <italic>L. monocytogenes</italic>, such as regulation of genes involved in 1,2-propanediol utilization (LMRG_00594-LMRG_00611) and biosynthesis of pyrimidine nucleotides (LMRG_00978-LMRG_00985); and (ii) identify new σ<sup>B</sup>-dependent genes involved in stress response and pathogenesis functions. These data further support that σ<sup>B</sup> not only regulates stress response functions, but also plays a broad role in <italic>L. monocytogenes</italic> homeostasis and resilience.</p>