Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>

ABSTRACT Ruminococcus bromii is a dominant member of the human gut microbiota that plays a key role in releasing energy from dietary starches that escape digestion by host enzymes via its exceptional activity against particulate “resistant” starches. Genomic analysis of R. bromii shows that it is hi...

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Autores principales: Xiaolei Ze, Yonit Ben David, Jenny A. Laverde-Gomez, Bareket Dassa, Paul O. Sheridan, Sylvia H. Duncan, Petra Louis, Bernard Henrissat, Nathalie Juge, Nicole M. Koropatkin, Edward A. Bayer, Harry J. Flint
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Publicado: American Society for Microbiology 2015
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spelling oai:doaj.org-article:2a363ea495f24b07a2f9cf311e4aa5d82021-11-15T15:41:31ZUnique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>10.1128/mBio.01058-152150-7511https://doaj.org/article/2a363ea495f24b07a2f9cf311e4aa5d82015-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01058-15https://doaj.org/toc/2150-7511ABSTRACT Ruminococcus bromii is a dominant member of the human gut microbiota that plays a key role in releasing energy from dietary starches that escape digestion by host enzymes via its exceptional activity against particulate “resistant” starches. Genomic analysis of R. bromii shows that it is highly specialized, with 15 of its 21 glycoside hydrolases belonging to one family (GH13). We found that amylase activity in R. bromii is expressed constitutively, with the activity seen during growth with fructose as an energy source being similar to that seen with starch as an energy source. Six GH13 amylases that carry signal peptides were detected by proteomic analysis in R. bromii cultures. Four of these enzymes are among 26 R. bromii proteins predicted to carry dockerin modules, with one, Amy4, also carrying a cohesin module. Since cohesin-dockerin interactions are known to mediate the formation of protein complexes in cellulolytic ruminococci, the binding interactions of four cohesins and 11 dockerins from R. bromii were investigated after overexpressing them as recombinant fusion proteins. Dockerins possessed by the enzymes Amy4 and Amy9 are predicted to bind a cohesin present in protein scaffoldin 2 (Sca2), which resembles the ScaE cell wall-anchoring protein of a cellulolytic relative, R. flavefaciens. Further complexes are predicted between the dockerin-carrying amylases Amy4, Amy9, Amy10, and Amy12 and two other cohesin-carrying proteins, while Amy4 has the ability to autoaggregate, as its dockerin can recognize its own cohesin. This organization of starch-degrading enzymes is unprecedented and provides the first example of cohesin-dockerin interactions being involved in an amylolytic system, which we refer to as an “amylosome.” IMPORTANCE Fermentation of dietary nondigestible carbohydrates by the human colonic microbiota supplies much of the energy that supports microbial growth in the intestine. This activity has important consequences for health via modulation of microbiota composition and the physiological and nutritional effects of microbial metabolites, including the supply of energy to the host from short-chain fatty acids. Recent evidence indicates that certain human colonic bacteria play keystone roles in degrading nondigestible substrates, with the dominant but little-studied species Ruminococcus bromii displaying an exceptional ability to degrade dietary resistant starches (i.e., dietary starches that escape digestion by host enzymes in the upper gastrointestinal tract because of protection provided by other polymers, particle structure, retrogradation, or chemical cross-linking). In this report, we reveal the unique organization of the amylolytic enzyme system of R. bromii that involves cohesin-dockerin interactions between component proteins. While dockerins and cohesins are fundamental to the organization of cellulosomal enzyme systems of cellulolytic ruminococci, their contribution to organization of amylases has not previously been recognized and may help to explain the starch-degrading abilities of R. bromii.Xiaolei ZeYonit Ben DavidJenny A. Laverde-GomezBareket DassaPaul O. SheridanSylvia H. DuncanPetra LouisBernard HenrissatNathalie JugeNicole M. KoropatkinEdward A. BayerHarry J. FlintAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 6, Iss 5 (2015)
institution DOAJ
collection DOAJ
language EN
topic Microbiology
QR1-502
spellingShingle Microbiology
QR1-502
Xiaolei Ze
Yonit Ben David
Jenny A. Laverde-Gomez
Bareket Dassa
Paul O. Sheridan
Sylvia H. Duncan
Petra Louis
Bernard Henrissat
Nathalie Juge
Nicole M. Koropatkin
Edward A. Bayer
Harry J. Flint
Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>
description ABSTRACT Ruminococcus bromii is a dominant member of the human gut microbiota that plays a key role in releasing energy from dietary starches that escape digestion by host enzymes via its exceptional activity against particulate “resistant” starches. Genomic analysis of R. bromii shows that it is highly specialized, with 15 of its 21 glycoside hydrolases belonging to one family (GH13). We found that amylase activity in R. bromii is expressed constitutively, with the activity seen during growth with fructose as an energy source being similar to that seen with starch as an energy source. Six GH13 amylases that carry signal peptides were detected by proteomic analysis in R. bromii cultures. Four of these enzymes are among 26 R. bromii proteins predicted to carry dockerin modules, with one, Amy4, also carrying a cohesin module. Since cohesin-dockerin interactions are known to mediate the formation of protein complexes in cellulolytic ruminococci, the binding interactions of four cohesins and 11 dockerins from R. bromii were investigated after overexpressing them as recombinant fusion proteins. Dockerins possessed by the enzymes Amy4 and Amy9 are predicted to bind a cohesin present in protein scaffoldin 2 (Sca2), which resembles the ScaE cell wall-anchoring protein of a cellulolytic relative, R. flavefaciens. Further complexes are predicted between the dockerin-carrying amylases Amy4, Amy9, Amy10, and Amy12 and two other cohesin-carrying proteins, while Amy4 has the ability to autoaggregate, as its dockerin can recognize its own cohesin. This organization of starch-degrading enzymes is unprecedented and provides the first example of cohesin-dockerin interactions being involved in an amylolytic system, which we refer to as an “amylosome.” IMPORTANCE Fermentation of dietary nondigestible carbohydrates by the human colonic microbiota supplies much of the energy that supports microbial growth in the intestine. This activity has important consequences for health via modulation of microbiota composition and the physiological and nutritional effects of microbial metabolites, including the supply of energy to the host from short-chain fatty acids. Recent evidence indicates that certain human colonic bacteria play keystone roles in degrading nondigestible substrates, with the dominant but little-studied species Ruminococcus bromii displaying an exceptional ability to degrade dietary resistant starches (i.e., dietary starches that escape digestion by host enzymes in the upper gastrointestinal tract because of protection provided by other polymers, particle structure, retrogradation, or chemical cross-linking). In this report, we reveal the unique organization of the amylolytic enzyme system of R. bromii that involves cohesin-dockerin interactions between component proteins. While dockerins and cohesins are fundamental to the organization of cellulosomal enzyme systems of cellulolytic ruminococci, their contribution to organization of amylases has not previously been recognized and may help to explain the starch-degrading abilities of R. bromii.
format article
author Xiaolei Ze
Yonit Ben David
Jenny A. Laverde-Gomez
Bareket Dassa
Paul O. Sheridan
Sylvia H. Duncan
Petra Louis
Bernard Henrissat
Nathalie Juge
Nicole M. Koropatkin
Edward A. Bayer
Harry J. Flint
author_facet Xiaolei Ze
Yonit Ben David
Jenny A. Laverde-Gomez
Bareket Dassa
Paul O. Sheridan
Sylvia H. Duncan
Petra Louis
Bernard Henrissat
Nathalie Juge
Nicole M. Koropatkin
Edward A. Bayer
Harry J. Flint
author_sort Xiaolei Ze
title Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>
title_short Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>
title_full Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>
title_fullStr Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>
title_full_unstemmed Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic <italic toggle="yes">Firmicutes</italic> Bacterium <named-content content-type="genus-species">Ruminococcus bromii</named-content>
title_sort unique organization of extracellular amylases into amylosomes in the resistant starch-utilizing human colonic <italic toggle="yes">firmicutes</italic> bacterium <named-content content-type="genus-species">ruminococcus bromii</named-content>
publisher American Society for Microbiology
publishDate 2015
url https://doaj.org/article/2a363ea495f24b07a2f9cf311e4aa5d8
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