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.

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