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.