Mycobacterial SigA and SigB cotranscribe essential housekeeping genes during exponential growth

Abstract

Mycobacterial βB 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 Mycobacterium smegmatis, M. abscessus, and M. tuberculosis to rifampin (RIF) and uncovered an additional constitutive role of βB during exponential growth of mycobacteria that complements the function of the primary sigma factor, βA. Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, βB binds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed βA-FLAG demonstrated that at least 61 promoter sites are recognized by both βA and βB. These results together suggest that RNA polymerase holoenzymes containing either βA or βB 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 βA restores the RIF tolerance of the ΔsigB mutant to that of the wild type, concomitantly ruling out a specialized role of βB in RIF tolerance. Although the properties of mycobacterial βB parallel those of Escherichia coli β38 in its ability to transcribe a subset of housekeeping genes, βB presents a clear departure from the E. coli paradigm, wherein the cellular levels of β38 are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing β70 (E.β70). IMPORTANCE All mycobacteria encode a group II sigma factor, βB, closely related to the group I principal housekeeping sigma factor, βA. 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 βB that complements the function of βA in logarithmically growing cells. These findings implicate a novel and dynamic partnership between βA and βB 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.