Rumen Cellulosomics: Divergent Fiber-Degrading Strategies Revealed by Comparative Genome-Wide Analysis of Six Ruminococcal Strains

Abstract

BackgroundA complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels.Methodology/Principal FindingsHere, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37).Conclusions/SignificanceOur comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.

Nanoscale Engineering of Designer Cellulosomes

“…[53,54] A large effort in comparative genomics was able to identify highly-conserved, functionally-indispensable modules and residues. [55,56] Since the heterogeneity and flexibility of the full-length cellulases and cellulosomes are impediments to crystallization, small angle X-ray scattering (SAXS) measurements have helped to confirm the overall architecture of the cellulosome. [57] Recent advances in instrumentation and automation (in particular, the routine use of synchrotron radia-tion, exploitation of anomalous diffraction methods in protein crystallography, and adaptation of beam lines to perform SAXS on proteins in solution) provide more sophisticated experi-mental techniques to study these challenging and intricate cellulolytic assemblies.…”

“…Mechanical forces can conceivably play a very important role in the cellulosome physiology; in the first instance the bacteria is a mesoscopic object ("microscopic" in biological jargon) and as such is not only subjected to Brownian motion, like molecules in solution, but will additionally feel longer-range hydrodynamic forces (e.g., in a turbulent cow stomach or capillary flow gradients in moist soil). [56] Under these conditions maximum holding strength and maximum catalytic efficiency seems to be needed. It is therefore not surprising that the mechanical strengths measured in cellulosome studies are among the highest found so far in biological systems.…”

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome

“…We, therefore, selected the rumen microbiome for its highly complex nature, together with its main functionality of plant cell wall deconstruction (Qi et al, 2010;Mizrahi, 2013;Dassa et al, 2014). This gap of knowledge stems from the fact that these complexes have been mainly studied in cultivated isolated microorganisms.…”

Dinâmica do microbioma ruminal de ovinos (<i>Ovis aries</i>) e sua relação com a degradação de biomassa

“…Este grupo de microrganismos possui bactérias especializadas na degradação da parede celular vegetal, apresentando um sistema complexo multi-enzimático chamado celulossoma (DASSA et al, 2014). A bactéria anaeróbica…”