The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein

SigA (σ(A)) is an essential protein and the primary sigma factor in Mycobacterium tuberculosis (Mtb). However, due to the absence of genetic tools, our understanding of the role and regulation of σ(A) activity and its molecular attributes that help modulate Mtb survival is scant. Here, we generated a conditional gene replacement of σ(A) in Mtb and showed that its depletion results in a severe survival defect in vitro, ex vivo, and in vivo in a murine infection model. Our RNA-seq analysis suggests that σ(A) either directly or indirectly regulates ∼57% of the Mtb transcriptome, including ∼28% of essential genes. Surprisingly, we note that despite having ∼64% similarity with σ(A), overexpression of the primary-like σ factor SigB (σ(B)) fails to compensate for the absence of σ(A), suggesting minimal functional redundancy. RNA-seq analysis of the Mtb σ(B) deletion mutant revealed that 433 genes are regulated by σ(B), of which 283 overlap with the σ(A) transcriptome. Additionally, surface plasmon resonance, in vitro transcription, and functional complementation experiments reveal that σ(A) residues between 132-179 that are disordered and missing from all experimentally determined σ(A)-RNAP structural models are imperative for σ(A) function. Moreover, phosphorylation of σ(A) in the intrinsically disordered N-terminal region plays a regulatory role in modulating its activity. Collectively, these observations and analysis provide a rationale for the centrality of σ(A) for the survival and pathogenicity of this bacillus.