Alternative σⁱ/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 (SigIC) and the N-terminal inhibitory domain of anti-σ^I (RsgIN) 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, RsgIN has a β-barrel structure. Unlike other anti-σ factors that bind both σ2 and σ4 domains of the σ factors, RsgIN binds SigIC specifically. Structural analysis showed that SigIC contains a positively charged surface region that recognizes the promoter -35 region, and the synergistic interactions amongmultiple 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.