Abstract
The bacterial cellulosome is an extracellular, multi-enzyme machinery, which efficiently depolymerizes plant biomass by degrading plant cell wall polysaccharides. Several cellulolytic bacteria have evolved various elaborate modular architectures of active cellulosomes. We present here a genome-wide analysis of a dozen mesophilic clostridia species, including both well-studied and yet-undescribed cellulosome-producing bacteria. We first report here, the presence of cellulosomal elements, thus expanding our knowledge regarding the prevalence of the cellulosomal paradigm in nature. We explored the genomic organization of key cellulosome components by comparing the cellulosomal gene clusters in each bacterial species, and the conserved sequence features of the specific cellulosomal modules (cohesins and dockerins), on the background of their phylogenetic relationship. Additionally, we performed comparative analyses of the species-specific repertoire of carbohydrate-degrading enzymes for each of the clostridial species, and classified each cellulosomal enzyme into a specific CAZy family, thus indicating their putative enzymatic activity (e.g., cellulases, hemicellulases, and pectinases). Our work provides, for this large group of bacteria, a broad overview of the blueprints of their multi-component cellulosomal complexes. The high similarity of their scaffoldin clusters and dockerin-based recognition residues suggests a common ancestor, and/or extensive horizontal gene transfer, and potential cross-species recognition. In addition, the sporadic spatial organization of the numerous dockerin-containing genes in several of the genomes, suggests the importance of the cellulosome paradigm in the given bacterial species. The information gained in this work may be utilized directly or developed further by genetically engineering and optimizing designer cellulosome systems for enhanced biotechnological biomass deconstruction and biofuel production.
Highlights
The plant cell wall forms a complex structure of cellulose fibers embedded into a colloidal mixture of hemicellulose, pectin, and lignin [1]
For profiling the cellulosomal system of each genome, we focused on its specific properties: the number of scaffoldins and dockerin-containing proteins which are potentially coded; the nature of the cellulosomal protein modules; and genomic organization and sequence conservation of genes coding for cellulosomal components
In early work, selected anaerobic mesophilic bacteria were found to exhibit distinctive characteristics consistent with the production of cellulosomes [41,61]. The list of such bacteria was later extended in additional studies by the sequencing of scaffoldin genes in other mesophilic cellulolytic clostridia [37,39]
Summary
The plant cell wall forms a complex structure of cellulose fibers embedded into a colloidal mixture of hemicellulose, pectin, and lignin [1]. Cellulolytic microorganisms are prevalent in natural lignocellulose-containing habitats abundant in plant cell walls, such as soil, wood, rumen, and termite guts, or in man-made sewage sludge or compost piles [2,3,4]. They employ various strategies to efficiently hydrolyze cellulose and hemicellulose of wood and plants into simple hexose and pentose sugars that will be directed to their carbohydrate metabolism and cell construction [5]. The major scaffoldin generally mediates the attachment of the complex to both the cellulosic substrate, via a carbohydrate-binding module (CBM), and the cell surface, via divergent type of cohesin–dockerin integration into an anchoring protein
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