The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing

Clostridium thermocellum is actively being developed as a microbial platform to produce biofuels and chemicals from renewable plant biomass. An attractive feature of this bacterium is its ability to efficiently degrade lignocellulose using surface-displayed cellulosomes, large multi-protein complexes that house different types of cellulase enzymes. Clostridium thermocellum tailors the enzyme composition of its cellulosome using nine membrane-embedded anti-sigma factors (RsgI1-9), which are thought to sense different types of extracellular carbohydrates and then elicit distinct gene expression programs via cytoplasmic sigma factors. Here we show that the RsgI9 anti-sigma factor interacts with cellulose via a C-terminal bi-domain unit. A 2.0 angstrom crystal structure reveals that the unit is constructed from S1C peptidase and NTF2-like protein domains that contain a potential binding site for cellulose. Small-angle X-ray scattering experiments of the intact ectodomain indicate that it adopts a bi-lobed, elongated conformation. In the structure, a conserved RsgI extracellular (CRE) domain is connected to the bi-domain via a proline-rich linker, which is expected to project the carbohydrate-binding unit similar to 160 angstrom from the cell surface. The CRE and proline-rich elements are conserved in several other C. thermocellum anti-sigma factors, suggesting that they will also form extended structures that sense carbohydrates.