Rumen cellulosomics

divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains

Bareket Dassa, Ilya Borovok, Vered Ruimy-Israeli, Raphael Lamed, Harry J Flint, Sylvia H Duncan, Bernard Henrissat, Pedro Coutinho, Mark Morrison, Pascale Mosoni, Carl J Yeoman, Bryan A White, Edward A Bayer

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Article numbere99221
Number of pages14
JournalPloS ONE
Volume9
Issue number7
Early online date3 Jul 2014
DOIs
Publication statusPublished - 3 Jul 2014

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Ruminococcus
Rumen
Biomass
rumen
Cellulosomes
Genome Components
Genes
Genome
Bacteria
Herbivory
genome
Biofuels
Fibers
Plant Cells
Ruminants
Computational Biology
Ruminococcus albus
Ruminococcus flavefaciens
Cell Wall
Digestion

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Rumen cellulosomics : divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. / Dassa, Bareket; Borovok, Ilya; Ruimy-Israeli, Vered; Lamed, Raphael; Flint, Harry J; Duncan, Sylvia H; Henrissat, Bernard; Coutinho, Pedro; Morrison, Mark; Mosoni, Pascale; Yeoman, Carl J; White, Bryan A; Bayer, Edward A.

In: PloS ONE, Vol. 9, No. 7, e99221, 03.07.2014.

Research output: Contribution to journalArticle

Dassa, B, Borovok, I, Ruimy-Israeli, V, Lamed, R, Flint, HJ, Duncan, SH, Henrissat, B, Coutinho, P, Morrison, M, Mosoni, P, Yeoman, CJ, White, BA & Bayer, EA 2014, 'Rumen cellulosomics: divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains', PloS ONE, vol. 9, no. 7, e99221. https://doi.org/10.1371/journal.pone.0099221
Dassa, Bareket ; Borovok, Ilya ; Ruimy-Israeli, Vered ; Lamed, Raphael ; Flint, Harry J ; Duncan, Sylvia H ; Henrissat, Bernard ; Coutinho, Pedro ; Morrison, Mark ; Mosoni, Pascale ; Yeoman, Carl J ; White, Bryan A ; Bayer, Edward A. / Rumen cellulosomics : divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains. In: PloS ONE. 2014 ; Vol. 9, No. 7.
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AU - Duncan, Sylvia H

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AB - 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.

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