Alternative σ(I)/anti-σ(I) factors represent a unique form of bacterial σ/anti-σ complex

The σ(70) family alternative σ(I) factors and their cognate anti-σ(I) factors are widespread in Clostridia and Bacilli and play a role in heat stress response, virulence, and polysaccharide sensing. Multiple σ(I)/anti-σ(I) factors exist in some lignocellulolytic clostridial species, specifically for regulation of components of a multienzyme complex, termed the cellulosome. The σ(I) and anti-σ(I) factors are unique, because the C-terminal domain of σ(I) (SigI(C)) and the N-terminal inhibitory domain of anti-σ(I) (RsgI(N)) lack homology to known proteins. Here, we report structure and interaction studies of a pair of σ(I) and anti-σ(I) factors, SigI1 and RsgI1, from the cellulosome-producing bacterium, Clostridium thermocellum. In contrast to other known anti-σ factors that have N-terminal helical structures, RsgI(N) has a β-barrel structure. Unlike other anti-σ factors that bind both σ(2) and σ(4) domains of the σ 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 σ(I)/anti-σ(I) pairs. We suggest that the σ(I)/anti-σ(I) factors represent a distinctive mode of σ/anti-σ complex formation, which provides the structural basis for understanding the molecular mechanism of the intricate σ(I)/anti-σ(I) system.