Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth

ABSTRACT Mycobacterial σB belongs to the group II family of sigma factors, which are widely considered to transcribe genes required for stationary-phase survival and the response to stress. Here we explored the mechanism underlying the observed hypersensitivity of ΔsigB deletion mutants of Mycobacte...

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Autores principales:	Kelley Hurst-Hess, Rajesh Biswas, Yong Yang, Paulami Rudra, Erica Lasek-Nesselquist, Pallavi Ghosh
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	ChIP-Seq Mycobacterium rifampin sigB sigma factor Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/34c0ae62b5184153931a5ddce77a94f6
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spelling	oai:doaj.org-article:34c0ae62b5184153931a5ddce77a94f62021-11-15T15:55:24ZMycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth10.1128/mBio.00273-192150-7511https://doaj.org/article/34c0ae62b5184153931a5ddce77a94f62019-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00273-19https://doaj.org/toc/2150-7511ABSTRACT Mycobacterial σB belongs to the group II family of sigma factors, which are widely considered to transcribe genes required for stationary-phase survival and the response to stress. Here we explored the mechanism underlying the observed hypersensitivity of ΔsigB deletion mutants of Mycobacteriumsmegmatis, M. abscessus, and M. tuberculosis to rifampin (RIF) and uncovered an additional constitutive role of σB during exponential growth of mycobacteria that complements the function of the primary sigma factor, σA. Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, σB binds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed σA-FLAG demonstrated that at least 61 promoter sites are recognized by both σA and σB. These results together suggest that RNA polymerase holoenzymes containing either σA or σB transcribe housekeeping genes in exponentially growing mycobacteria. The RIF sensitivity of the ΔsigB mutant possibly reflects a decrease in the effective housekeeping holoenzyme pool, which results in susceptibility of the mutant to lower doses of RIF. Consistent with this model, overexpression of σA restores the RIF tolerance of the ΔsigB mutant to that of the wild type, concomitantly ruling out a specialized role of σB in RIF tolerance. Although the properties of mycobacterial σB parallel those of Escherichiacoli σ38 in its ability to transcribe a subset of housekeeping genes, σB presents a clear departure from the E. coli paradigm, wherein the cellular levels of σ38 are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing σ70 (E.σ70). IMPORTANCE All mycobacteria encode a group II sigma factor, σB, closely related to the group I principal housekeeping sigma factor, σA. Group II sigma factors are widely believed to play specialized roles in the general stress response and stationary-phase transition in the bacteria that encode them. Contrary to this widely accepted view, we show an additional housekeeping function of σB that complements the function of σA in logarithmically growing cells. These findings implicate a novel and dynamic partnership between σA and σB in maintaining the expression of housekeeping genes in mycobacteria and can perhaps be extended to other bacterial species that possess multiple group II sigma factors.Kelley Hurst-HessRajesh BiswasYong YangPaulami RudraErica Lasek-NesselquistPallavi GhoshAmerican Society for MicrobiologyarticleChIP-SeqMycobacteriumrifampinsigBsigma factorMicrobiologyQR1-502ENmBio, Vol 10, Iss 3 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	ChIP-Seq Mycobacterium rifampin sigB sigma factor Microbiology QR1-502
spellingShingle	ChIP-Seq Mycobacterium rifampin sigB sigma factor Microbiology QR1-502 Kelley Hurst-Hess Rajesh Biswas Yong Yang Paulami Rudra Erica Lasek-Nesselquist Pallavi Ghosh Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
description	ABSTRACT Mycobacterial σB belongs to the group II family of sigma factors, which are widely considered to transcribe genes required for stationary-phase survival and the response to stress. Here we explored the mechanism underlying the observed hypersensitivity of ΔsigB deletion mutants of Mycobacteriumsmegmatis, M. abscessus, and M. tuberculosis to rifampin (RIF) and uncovered an additional constitutive role of σB during exponential growth of mycobacteria that complements the function of the primary sigma factor, σA. Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, σB binds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed σA-FLAG demonstrated that at least 61 promoter sites are recognized by both σA and σB. These results together suggest that RNA polymerase holoenzymes containing either σA or σB transcribe housekeeping genes in exponentially growing mycobacteria. The RIF sensitivity of the ΔsigB mutant possibly reflects a decrease in the effective housekeeping holoenzyme pool, which results in susceptibility of the mutant to lower doses of RIF. Consistent with this model, overexpression of σA restores the RIF tolerance of the ΔsigB mutant to that of the wild type, concomitantly ruling out a specialized role of σB in RIF tolerance. Although the properties of mycobacterial σB parallel those of Escherichiacoli σ38 in its ability to transcribe a subset of housekeeping genes, σB presents a clear departure from the E. coli paradigm, wherein the cellular levels of σ38 are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing σ70 (E.σ70). IMPORTANCE All mycobacteria encode a group II sigma factor, σB, closely related to the group I principal housekeeping sigma factor, σA. Group II sigma factors are widely believed to play specialized roles in the general stress response and stationary-phase transition in the bacteria that encode them. Contrary to this widely accepted view, we show an additional housekeeping function of σB that complements the function of σA in logarithmically growing cells. These findings implicate a novel and dynamic partnership between σA and σB in maintaining the expression of housekeeping genes in mycobacteria and can perhaps be extended to other bacterial species that possess multiple group II sigma factors.
format	article
author	Kelley Hurst-Hess Rajesh Biswas Yong Yang Paulami Rudra Erica Lasek-Nesselquist Pallavi Ghosh
author_facet	Kelley Hurst-Hess Rajesh Biswas Yong Yang Paulami Rudra Erica Lasek-Nesselquist Pallavi Ghosh
author_sort	Kelley Hurst-Hess
title	Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
title_short	Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
title_full	Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
title_fullStr	Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
title_full_unstemmed	Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth
title_sort	mycobacterial siga and sigb cotranscribe essential housekeeping genes during exponential growth
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/34c0ae62b5184153931a5ddce77a94f6
work_keys_str_mv	AT kelleyhursthess mycobacterialsigaandsigbcotranscribeessentialhousekeepinggenesduringexponentialgrowth AT rajeshbiswas mycobacterialsigaandsigbcotranscribeessentialhousekeepinggenesduringexponentialgrowth AT yongyang mycobacterialsigaandsigbcotranscribeessentialhousekeepinggenesduringexponentialgrowth AT paulamirudra mycobacterialsigaandsigbcotranscribeessentialhousekeepinggenesduringexponentialgrowth AT ericalaseknesselquist mycobacterialsigaandsigbcotranscribeessentialhousekeepinggenesduringexponentialgrowth AT pallavighosh mycobacterialsigaandsigbcotranscribeessentialhousekeepinggenesduringexponentialgrowth
_version_	1718427207169212416

Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth

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