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

Frontiers in Microbiology
Yichang LiuVeronica Guariglia-Oropeza

Abstract

Among Listeria monocytogenes' four alternative σ factors, σB controls the largest regulon. As σB-dependent transcription of some genes may be masked by overlaps among regulons, and as some σB-dependent genes are expressed only under very specific conditions, we hypothesized that the σB regulon is not yet fully defined. To further extend our understanding of the σB regulon, we used RNA-seq to identify σB-dependent genes in an L. monocytogenes strain that expresses σB 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 σB-dependent transcription units (TUs) comprising 201 genes preceded by σB-dependent promoters. Of these 105 TUs, 7 TUs comprising 15 genes had not been identified previously as σB-dependent. An additional 23 genes not reported previously as σB-dependent were identified in 9 previously recognized σB-dependent TUs. Overall, 38 of these 201 genes had not been identified previously as members of the L. monocytogenes σB regulon. These newly identified σB-dependent genes encod...Continue Reading

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Citations

Sep 6, 2019·Microbiology and Molecular Biology Reviews : MMBR·Ahmed GaballaKathryn J Boor
Feb 11, 2020·Frontiers in Microbiology·Martin Laage Kragh, Lisbeth Truelstrup Hansen
Sep 26, 2019·Frontiers in Microbiology·Atsadang BoonmeeSoraya Chaturongakul
Feb 6, 2021·World Journal of Microbiology & Biotechnology·Hoai T Tran, Carla Y Bonilla

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Datasets Mentioned

BETA
GSE94284

Methods Mentioned

BETA
PCR
cDNA library construction
RNA-seq
electrophoresis
salt stress
ChIP-seq

Software Mentioned

BaySeq
GOseq
BLAST
Bayseq package for R
WebLogo
samtools
Photoshop

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