Mycobacterial SigA and SigB Cotranscribe Essential Housekeeping Genes during Exponential Growth

Mycobacterial σ(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 ΔsigB deletion mutants of Mycobacteriumsmegmatis, M. abscessus, and M. tuberculosis to rifampin (RIF) and uncovered an additional constitutive role of σ(B) during exponential growth of mycobacteria that complements the function of the primary sigma factor, σ(A). Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, σ(B) binds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed σ(A)-FLAG demonstrated that at least 61 promoter sites are recognized by both σ(A) and σ(B). These results together suggest that RNA polymerase holoenzymes containing either σ(A) or σ(B) 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 σ(A) restores the RIF tolerance of the ΔsigB mutant to that of the wild type, concomitantly ruling out a specialized role of σ(B) in RIF tolerance. Although the properties of mycobacterial σ(B) parallel those of Escherichiacoli σ(38) in its ability to transcribe a subset of housekeeping genes, σ(B) presents a clear departure from the E. coli paradigm, wherein the cellular levels of σ(38) are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing σ(70) (E.σ(70)).