Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system

Abstract

BackgroundMicrobial degradation of plant cell walls and its conversion to sugars and other byproducts is a key step in the carbon cycle on Earth. In order to process heterogeneous plant-derived biomass, specialized anaerobic bacteria use an elaborate multi-enzyme cellulosome complex to synergistically deconstruct cellulosic substrates. The cellulosome was first discovered in the cellulolytic thermophile, Clostridium thermocellum, and much of our knowledge of this intriguing type of protein composite is based on the cellulosome of this environmentally and biotechnologically important bacterium. The recently sequenced genome of the cellulolytic mesophile, Acetivibrio cellulolyticus, allows detailed comparison of the cellulosomes of these two select cellulosome-producing bacteria.ResultsComprehensive analysis of the A. cellulolyticus draft genome sequence revealed a very sophisticated cellulosome system. Compared to C. thermocellum, the cellulosomal architecture of A. cellulolyticus is much more extensive, whereby the genome encodes for twice the number of cohesin- and dockerin-containing proteins. The A. cellulolyticus genome has thus evolved an inflated number of 143 dockerin-containing genes, coding for multimodular proteins with distinctive catalytic and carbohydrate-binding modules that play critical roles in biomass degradation. Additionally, 41 putative cohesin modules distributed in 16 different scaffoldin proteins were identified in the genome, representing a broader diversity and modularity than those of Clostridium thermocellum. Although many of the A. cellulolyticus scaffoldins appear in unconventional modular combinations, elements of the basic structural scaffoldins are maintained in both species. In addition, both species exhibit similarly elaborate cell-anchoring and cellulosome-related gene- regulatory elements.ConclusionsThis work portrays a particularly intricate, cell-surface cellulosome system in A. cellulolyticus and provides a blueprint for examining the specific roles of the various cellulosomal components in the degradation of complex carbohydrate substrates of the plant cell wall by the bacterium.

Cell-surface Attachment of Bacterial Multienzyme Complexes Involves Highly Dynamic Protein-Protein Anchors

“…The residues that participate in dockerin recognition are mostly invariant in the three cohesins (data not shown), suggesting that ScaC can accommodate three ScaB proteins via the recognition of the C-terminal dockerin module. In addition, a second A. cellulolyticus protein termed ScaJ, accession number WP_010243813, contains a single N-terminal cohesin module that shares extensive similarity with the ScaC cohesins, primarily at the residues important for protein recognition (13,19). ScaJ also contains a C-terminal SLH domain, which suggests that, like ScaC, it constitutes an anchoring scaffoldin with the ability to recognize a single ScaB molecule.…”

“…1) (9). The recent sequencing of the A. cellulolyticus CD2 genome identified numerous additional cellulosomal components, gene regulatory elements, and cell anchoring modules (identified by the presence of dockerins or cohesins), suggestive of a much more elaborate and sophisticated cellulosome system than originally observed (13). Analysis of the genome uncovered 41 putative cohesin modules distributed among 16 scaffoldins (including ScaA, ScaB, ScaC, and ScaD), some of which have both cohesins and dockerins in the same polypeptide chain.…”

“…Analysis of the genome uncovered 41 putative cohesin modules distributed among 16 scaffoldins (including ScaA, ScaB, ScaC, and ScaD), some of which have both cohesins and dockerins in the same polypeptide chain. All of the identified scaffoldins, with the exception of ScaI, appear to contain a signal peptide, suggesting that these proteins are secreted (13). The genome of A. cellulolyticus encodes 143 dockerin-containing proteins, which is about twice the number of such proteins in clostridial bacteria, but fewer than the 220 cellulosomal proteins encoded by the Ruminococcus flavefaciens FD-1 genome (13,14).…”

Three cellulosomal xylanase genes inClostridium thermocellum are regulated by both vegetative SigA (σA) and alternative SigI6 (σI6) factors

“…1B) [38]. The recently published genomes of Clostridium clariflavum [30] and Acetivibrio cellulolyticus [19] revealed similar putative biomass-sensing systems containing carbohydrate binding module (CBM) modules of families 3, 35, 42 and also PA14.…”

Structure–function analyses generate novel specificities to assemble the components of multienzyme bacterial cellulosome complexes

“…ScaB is the first example of a cellulosomal adaptor protein (10) (Figure 1) (10). The genome sequence of A. cellulolyticus CD2 revealed numerous additional cellulosomal components, gene regulatory elements and cell anchoring modules (identified by the presence of signature Docs or Cohs sequences), suggestive of a much more elaborate and sophisticated cellulosome system than originally observed (13). In total 143 Doc-containing A. cellulolyticus proteins were identified.…”