Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition

Sarah Morais, Yonit Ben David, Lizi Bensoussan, Sylvia H. Duncan, Nicole M. Koropatkin, Eric C. Martens, Harry J. Flint, Edward A. Bayer

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Abstract

Ruminococcus champanellensis is considered a keystone species in the human gut that degrades microcrystalline cellulose efficiently and contains the genetic elements necessary for cellulosome production. The basic elements of its cellulosome architecture, mainly cohesin and dockerin modules from scaffoldins and enzyme-borne dockerins, have been characterized recently. In this study, we cloned, expressed and characterized all of the glycoside hydrolases that contain a dockerin module. Among the 25 enzymes: 10 cellulases, 4 xylanases, 3 mannanases, 2 xyloglucanases, 2 arabinofuranosidases, 2 arabinanases and one β-glucanase were assessed for their comparative enzymatic activity on their respective substrates. The dockerin specificities of the enzymes were examined by ELISA, and 80 positives out of 525 possible interactions were detected. Our analysis reveals a fine-tuned system for cohesin-dockerin specificity and the importance of diversity among the cohesin-dockerin sequences. Our results imply that cohesin-dockerin pairs are not necessarily assembled at random among the same specificity types, as generally believed for other cellulosome-producing bacteria, but reveal a more organized cellulosome architecture. Moreover our results highlight the importance of the cellulosome paradigm for cellulose and hemicellulose degradation by R. champanellensis in the human gut.
Original languageEnglish
Pages (from-to)542-556
Number of pages15
JournalEnvironmental Microbiology
Volume18
Issue number2
Early online date14 Oct 2015
DOIs
Publication statusPublished - Feb 2016

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cellulosome
Cellulosomes
Ruminococcus
digestive system
enzyme
Bacteria
bacterium
cellulose
bacteria
Enzymes
enzymes
keystone species
alpha-N-arabinofuranosidase
beta-mannosidase
Cellulases
cellulases
Glycoside Hydrolases
xylanases
substrate
degradation

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Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition. / Morais, Sarah; David, Yonit Ben; Bensoussan, Lizi; Duncan, Sylvia H.; Koropatkin, Nicole M.; Martens, Eric C.; Flint, Harry J.; Bayer, Edward A.

In: Environmental Microbiology, Vol. 18, No. 2, 02.2016, p. 542-556.

Research output: Contribution to journalArticle

Morais, Sarah ; David, Yonit Ben ; Bensoussan, Lizi ; Duncan, Sylvia H. ; Koropatkin, Nicole M. ; Martens, Eric C. ; Flint, Harry J. ; Bayer, Edward A. / Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition. In: Environmental Microbiology. 2016 ; Vol. 18, No. 2. pp. 542-556.
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title = "Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition",
abstract = "Ruminococcus champanellensis is considered a keystone species in the human gut that degrades microcrystalline cellulose efficiently and contains the genetic elements necessary for cellulosome production. The basic elements of its cellulosome architecture, mainly cohesin and dockerin modules from scaffoldins and enzyme-borne dockerins, have been characterized recently. In this study, we cloned, expressed and characterized all of the glycoside hydrolases that contain a dockerin module. Among the 25 enzymes: 10 cellulases, 4 xylanases, 3 mannanases, 2 xyloglucanases, 2 arabinofuranosidases, 2 arabinanases and one β-glucanase were assessed for their comparative enzymatic activity on their respective substrates. The dockerin specificities of the enzymes were examined by ELISA, and 80 positives out of 525 possible interactions were detected. Our analysis reveals a fine-tuned system for cohesin-dockerin specificity and the importance of diversity among the cohesin-dockerin sequences. Our results imply that cohesin-dockerin pairs are not necessarily assembled at random among the same specificity types, as generally believed for other cellulosome-producing bacteria, but reveal a more organized cellulosome architecture. Moreover our results highlight the importance of the cellulosome paradigm for cellulose and hemicellulose degradation by R. champanellensis in the human gut.",
author = "Sarah Morais and David, {Yonit Ben} and Lizi Bensoussan and Duncan, {Sylvia H.} and Koropatkin, {Nicole M.} and Martens, {Eric C.} and Flint, {Harry J.} and Bayer, {Edward A.}",
note = "Acknowledgements This research was supported by the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel, and by a grant (No. 1349) to EAB from the Israel Science Foundation (ISF). Additional support was obtained from the establishment of an Israeli Center of Research Excellence (I-CORE Center No. 152/11) managed by the Israel Science Foundation. The authors also appreciate the support of the European Union, Area NMP.2013.1.1-2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project Number: 604530 and an ERA-IB Consortium (EIB.12.022), acronym FiberFuel. In addition, EAB is grateful for a grant from the F. Warren Hellman Grant for Alternative Energy Research in Israel in support of alternative energy research in Israel administered by the Israel Strategic Alternative Energy Foundation (I-SAEF). HJF acknowledges support from BBSRC Grant No BB/L009951/1, from the Scottish Government Food, Land and People program, and from the Society for Applied Microbiology. Thanks are due to Fergus Nicol and Louise Cantlay for proteomic analysis. EAB is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry.",
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AU - David, Yonit Ben

AU - Bensoussan, Lizi

AU - Duncan, Sylvia H.

AU - Koropatkin, Nicole M.

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N1 - Acknowledgements This research was supported by the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel, and by a grant (No. 1349) to EAB from the Israel Science Foundation (ISF). Additional support was obtained from the establishment of an Israeli Center of Research Excellence (I-CORE Center No. 152/11) managed by the Israel Science Foundation. The authors also appreciate the support of the European Union, Area NMP.2013.1.1-2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project Number: 604530 and an ERA-IB Consortium (EIB.12.022), acronym FiberFuel. In addition, EAB is grateful for a grant from the F. Warren Hellman Grant for Alternative Energy Research in Israel in support of alternative energy research in Israel administered by the Israel Strategic Alternative Energy Foundation (I-SAEF). HJF acknowledges support from BBSRC Grant No BB/L009951/1, from the Scottish Government Food, Land and People program, and from the Society for Applied Microbiology. Thanks are due to Fergus Nicol and Louise Cantlay for proteomic analysis. EAB is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic Chemistry.

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AB - Ruminococcus champanellensis is considered a keystone species in the human gut that degrades microcrystalline cellulose efficiently and contains the genetic elements necessary for cellulosome production. The basic elements of its cellulosome architecture, mainly cohesin and dockerin modules from scaffoldins and enzyme-borne dockerins, have been characterized recently. In this study, we cloned, expressed and characterized all of the glycoside hydrolases that contain a dockerin module. Among the 25 enzymes: 10 cellulases, 4 xylanases, 3 mannanases, 2 xyloglucanases, 2 arabinofuranosidases, 2 arabinanases and one β-glucanase were assessed for their comparative enzymatic activity on their respective substrates. The dockerin specificities of the enzymes were examined by ELISA, and 80 positives out of 525 possible interactions were detected. Our analysis reveals a fine-tuned system for cohesin-dockerin specificity and the importance of diversity among the cohesin-dockerin sequences. Our results imply that cohesin-dockerin pairs are not necessarily assembled at random among the same specificity types, as generally believed for other cellulosome-producing bacteria, but reveal a more organized cellulosome architecture. Moreover our results highlight the importance of the cellulosome paradigm for cellulose and hemicellulose degradation by R. champanellensis in the human gut.

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