Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function σ factor σ rC from Mycobacterium tuberculosis

σ factors are transcriptional regulatory proteins that bind to the RNA polymerase and dictate gene expression. The extracytoplasmic function σ factors (ECF) govern the environment dependent regulation of transcription. ECF factors have two domains σ⊂2 and σ⊂4 that recognize the -10 and -35 promoter elements. However, unlike the primary sσ factor σ^rA, the ECF factors lack σ⊂3, a region that helps in the recognition of the extended -10 element and σ⊂1.1, a domain involved in the auto-inhibition of σ^rA in the absence of core RNA polymerase. Mycobacterium tuberculosis σ^rC is an ECF factor that is essential for the pathogenesis and virulence of M. tuberculosis in the mouse and guinea pig models of infection. However, unlike other ECF factors, σ^rC does not appear to have a regulatory anti-σ factor located in the same operon. We also note that Mycobacterium tuberculosis σ^rC differs from the canonical ECF factors as it has an N-terminal domain comprising of 126 amino acids that precedes the σ^rC⊂2 and σ^rC⊂4 domains. In an effort to understand the regulatory mechanism of this protein, the crystal structures of the σ^rC⊂2 and σ^rC⊂4 domains of σ^rC were determined. These promoter recognition domains are structurally similar to the corresponding domains of σ^rA despite the low sequence similarity. Fluorescence experiments using the intrinsic tryptophan residues of σ^rC⊂2 as well as surface plasmon resonance measurements reveal that the σ^rC⊂2 and σ^rC⊂4 domains interact with each other. Mutational analysis suggests that the Pribnow box binding region of σ^rC⊂2 is involved in this inter-domain interaction. Interaction between the promoter recognition domains in M. tuberculosis σ^rC are thus likely to regulate the activity of this protein even in the absence of an anti-σ factor.

Thakur, K., Joshi, A., Gopal, B. (2006) Structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function σ factor σ rC from Mycobacterium tuberculosis. J. Biol. Chem. 282:4711-8.

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