Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth

Mycobacterial sigma B 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 Delta sigB deletion mutants of Mycobacterium smegmatis, M. abscessus, and M. tuberculosis to rifampin (RIF) and uncovered an additional constitutive role of sigma(B) during exponential growth of mycobacteria that complements the function of the primary sigma factor, sigma(A). Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, sigma(B) binds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed sigma(A)-FLAG demonstrated that at least 61 promoter sites are recognized by both sigma(A) and sigma(B). These results together suggest that RNA polymerase holoenzymes containing either sigma(A) or sigma(B) transcribe housekeeping genes in exponentially growing mycobacteria. The RIF sensitivity of the.sigB 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 sigma(A) restores the RIF tolerance of the Delta sigB mutant to that of the wild type, concomitantly ruling out a specialized role of sigma(B) in RIF tolerance. Although the properties of mycobacterial sigma(B) parallel those of Escherichia coli sigma(38) in its ability to transcribe a subset of housekeeping genes, sigma(B) presents a clear departure from the E. coli paradigm, wherein the cellular levels of sigma(38) are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing sigma(70) (E.sigma(70)). IMPORTANCE All mycobacteria encode a group II sigma factor, sigma(B), closely related to the group I principal housekeeping sigma factor, sigma(A). 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 sigma(B) that complements the function of sigma(A) in logarithmically growing cells. These findings implicate a novel and dynamic partnership between sigma(A) and sigma(B) 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.