Single Binding Mode Integration of Hemicellulose-degrading Enzymes via Adaptor Scaffoldins in Ruminococcus flavefaciens Cellulosome

Abstract

Edited by Gerald HartThe assembly of one of Nature's most elaborate multienzyme complexes, the cellulosome, results from the binding of enzymeborne dockerins to reiterated cohesin domains located in a noncatalytic primary scaffoldin. Generally, dockerins present two similar cohesin-binding interfaces that support a dual binding mode. The dynamic integration of enzymes in cellulosomes, afforded by the dual binding mode, is believed to incorporate additional flexibility in highly populated multienzyme complexes. Ruminococcus flavefaciens, the primary degrader of plant structural carbohydrates in the rumen of mammals, uses a portfolio of more than 220 different dockerins to assemble the most intricate cellulosome known to date. A sequence-based analysis organized R. flavefaciens dockerins into six groups. Strikingly, a subset of R. flavefaciens cellulosomal enzymes, comprising dockerins of groups 3 and 6, were shown to be indirectly incorporated into primary scaffoldins via an adaptor scaffoldin termed ScaC. Here, we report the crystal structure of a group 3 R. flavefaciens dockerin, Doc3, in complex with ScaC cohesin. Doc3 is unusual as it presents a large cohesin-interacting surface that lacks the structural symmetry required to support a dual binding mode. In addition, dockerins of groups 3 and 6, which bind exclusively to ScaC cohesin, display a conserved mechanism of protein recognition that is similar to Doc3. Groups 3 and 6 dockerins are predominantly appended to hemicellulose-degrading enzymes. Thus, single binding mode dockerins interacting with adaptor scaffoldins exemplify an evolutionary pathway developed by R. flavefaciens to recruit hemicellulases to the sophisticated cellulosomes acting in the gastrointestinal tract of mammals.Plant cell wall polysaccharides, primarily cellulose and hemicellulose, are the most abundant organic molecules produced in Nature, thus constituting a major reservoir of carbon and energy (1). The intricate organization of structural carbohydrates in plant cell walls and their inherent heterogeneity pose significant constraints to polysaccharide degradation, which usually requires a wide array of catalytic activities acting cooperatively (2, 3). In highly competitive anaerobic environments, such as the rumen of mammals, enzymatic systems that recycle the carbon stored in plant cell walls are organized in high molecular mass multienzyme complexes termed cellulosomes (4, 5). Molecular integration of microbial biocatalysts into these extremely elaborate nanomachines results from the binding of enzyme-borne dockerin modules (Doc) 3 to reiterated cohesin domains (Coh) located in large non-catalytic scaffoldins, a mechanism that promotes enzyme synergy and stability. In addition, recruitment of cellulosomes to the bacterial cell surface via divergent Coh-Doc interactions allows the immediate uptake of released sugars, which are used by microbes as an energy source.Ruminococcus flavefaciens is a Gram-positive, anaerobic bacterium of the Firmicutes phylum and the only species in the...

Target highlights from the first post‐PSI CASP experiment (CASP12, May–August 2016)

“…Based on primary sequence similarity, R. flavefaciens dockerins are classified in different groups. Recent studies have shown that groups 3 and 6 R. flavefaciens Docs display a single‐binding mode for their target Cohs, that is, binding occurs in one orientation only . Intriguingly, Group 1 Docs also do not seem to possess the internal sequence symmetry required to support the dual‐binding mode.…”

Assembly of Ruminococcus flavefaciens cellulosome revealed by structures of two cohesin-dockerin complexes

“…flavefaciens ScaC group 3 Coh (ref. 12 ; Figure S2 ). The structure of Rf CohScaB3, whether unbound or in complex with Rf Doc1a, was essentially identical (rmsd ~0.37 Å).…”

“…This contrasts with the interface of the recently described R . flavefaciens Rf CohScaC-Doc3 complex where the two Doc3 helices (helix 1 and helix 3) make similar contributions to CohScaC recognition 12 . In Rf CohScaC-Doc3, CohScaC’s α-helix located between β-strands 4 and 5, which is absent in Rf CohScaB3 and Rf CohScaA , is elevated in relation to the 8-3-6-5 plane allowing the entire Coh surface to be in closer proximity to both Doc α-helices.…”

“…These Docs were classified into group 4 and group 2. Finally, hemicellulases containing group 3 or 6 Docs bind to the adaptor scaffoldin ScaC, whose group 1 Doc locks onto the Cohs in ScaA or ScaB Cohs 1–4 12 , 13 . The ScaA Doc is the only member of group 5 and binds exclusively to ScaB Cohs 5–9.…”

Estudos estruturais de dockerinas e cohesinas em <i>Ruminococcus flavefaciens</i> e sua aplicação no desenvolvimento de matrizes auto montáveis de proteínas

“…Curiosamente, a cohesina de ScaC se situa mais próxima a cohesinas de tipo-I nas árvores de filogenia, a despeito de suas semelhanças funcionais e estruturais com o tipo-II. 13 Existem ainda algumas estruturas disponíveis de cohesinas de tipo-III desacompanhadas de dockerinas, com outras peculiaridades, que corroboram a inexistência de um consenso com relação a características do tipo III, visto que há uma diferença grande de similaridade entre seus membros. Nas 223 dockerinas de FD-1 essa similaridade varia de 20 a 98%.…”