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PLoS One. 2014 Jul 3;9(7):e99221. doi: 10.1371/journal.pone.0099221. eCollection 2014.

Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.

Author information

1
Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
2
Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.
3
Microbial Ecology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom.
4
Architecture et Fonction des Macromolecules Biologiques, Aix-Marseille University and Centre National de la Recherche Scientifique (CNRS), Marseille, France.
5
University of Queensland Diamantina Institute, Woolloongabba, Queensland, Australia; Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America.
6
The French National Institute for Agricultural Research (INRA), UR454 Unité de Microbiologie, Saint-Genès-Champanelle, France.
7
Department of Animal and Range Sciences, Montana State University, Bozeman, Montana, United States of America.
8
The Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America; Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America.

Abstract

BACKGROUND:

A 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 FINDINGS:

Here, 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/SIGNIFICANCE:

Our 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.

PMID:
24992679
PMCID:
PMC4081043
DOI:
10.1371/journal.pone.0099221
[Indexed for MEDLINE]
Free PMC Article

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