Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex

The sigma(70) family alternative sigma(I) factors and their cognate anti-sigma(I) factors are widespread in Clostridia and Bacilli and play a role in heat stress response, virulence, and polysaccharide sensing. Multiple sigma(I)/anti-sigma(I) factors exist in some lignocellulolytic clostridial species, specifically for regulation of components of a multienzyme complex, termed the cellulosome. The sigma(I) and anti-sigma(I) factors are unique, because the C-terminal domain of sigma(I) (SigI(C)) and the N-terminal inhibitory domain of anti-sigma(I) (RsgI(N)) lack homology to known proteins. Here, we report structure and interaction studies of a pair of sigma(I) and anti-sigma(I) factors, SigI1 and RsgI1, from the cellulosome-producing bacterium, Clostridium thermocellum. In contrast to other known anti-sigma factors that have N-terminal helical structures, RsgI(N) has a beta-barrel structure. Unlike other anti-sigma factors that bind both sigma(2) and sigma(4) domains of the sigma factors, RsgI(N) binds SigI(C) specifically. Structural analysis showed that SigI(C) contains a positively charged surface region that recognizes the promoter -35 region, and the synergistic interactions among multiple interfacial residues result in the specificity displayed by different sigma(I)/anti-sigma(I) pairs. We suggest that the sigma(I)/anti-sigma(I) factors represent a distinctive mode of sigma(I)/anti-sigma complex formation, which provides the structural basis for understanding the molecular mechanism of the intricate sigma(I)/anti-sigma(I) system.