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Title: A parts list for fungal cellulosomes revealed by comparative genomics

Abstract

Cellulosomes are large, multi-protein complexes that tether plant biomass degrading enzymes together for improved hydrolysis1. These complexes were first described in anaerobic bacteria where species specific dockerin domains mediate assembly of enzymes onto complementary cohesin motifs interspersed within non-catalytic protein scaffolds1. The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic protein-scale pathways2,3. For decades, analogous structures have been reported in the early branching anaerobic fungi, which are known to assemble by sequence divergent non-catalytic dockerin domains (NCDD)4. However, the enzyme components, modular assembly mechanism, and functional role of fungal cellulosomes remain unknown5,6. Here, we describe the comprehensive set of proteins critical to fungal cellulosome assembly, including novel, conserved scaffolding proteins unique to the Neocallimastigomycota. High quality genomes of the anaerobic fungi Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis were assembled with long-read, single molecule technology to overcome their repeat-richness and extremely low GC content. Genomic analysis coupled with proteomic validation revealed an average 320 NCDD-containing proteins per fungal strain that were overwhelmingly carbohydrate active enzymes (CAZymes), with 95 large fungal scaffoldins identified across 4 genera that contain a conserved amino acid sequence repeat that binds to NCDDs. Fungal dockerin andmore » scaffoldin domains have no similarity to their bacterial counterparts, yet several catalytic domains originated via horizontal gene transfer with gut bacteria. Though many catalytic domains are shared with bacteria, the biocatalytic activity of anaerobic fungi is expanded by the inclusion of GH3, GH6, and GH45 enzymes in the enzyme complexes. Collectively, these findings suggest that the fungal cellulosome is an evolutionarily chimeric structure – an independently evolved fungal complex that co-opted useful activities from bacterial neighbors within the gut microbiome.« less

Authors:
; ; ; ORCiD logo; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »; ORCiD logo; ; « less
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1367380
Report Number(s):
PNNL-SA-120227
Journal ID: ISSN 2058-5276; 48080; KP1704020
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Nature Microbiology
Additional Journal Information:
Journal Volume: 2; Journal ID: ISSN 2058-5276
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Haitjema, Charles H., Gilmore, Sean P., Henske, John K., Solomon, Kevin V., de Groot, Randall, Kuo, Alan, Mondo, Stephen J., Salamov, Asaf A., LaButti, Kurt, Zhao, Zhiying, Chiniquy, Jennifer, Barry, Kerrie, Brewer, Heather M., Purvine, Samuel O., Wright, Aaron T., Hainaut, Matthieu, Boxma, Brigitte, van Alen, Theo, Hackstein, Johannes H. P., Henrissat, Bernard, Baker, Scott E., Grigoriev, Igor V., and O'Malley, Michelle A. A parts list for fungal cellulosomes revealed by comparative genomics. United States: N. p., 2017. Web. doi:10.1038/nmicrobiol.2017.87.
Haitjema, Charles H., Gilmore, Sean P., Henske, John K., Solomon, Kevin V., de Groot, Randall, Kuo, Alan, Mondo, Stephen J., Salamov, Asaf A., LaButti, Kurt, Zhao, Zhiying, Chiniquy, Jennifer, Barry, Kerrie, Brewer, Heather M., Purvine, Samuel O., Wright, Aaron T., Hainaut, Matthieu, Boxma, Brigitte, van Alen, Theo, Hackstein, Johannes H. P., Henrissat, Bernard, Baker, Scott E., Grigoriev, Igor V., & O'Malley, Michelle A. A parts list for fungal cellulosomes revealed by comparative genomics. United States. doi:10.1038/nmicrobiol.2017.87.
Haitjema, Charles H., Gilmore, Sean P., Henske, John K., Solomon, Kevin V., de Groot, Randall, Kuo, Alan, Mondo, Stephen J., Salamov, Asaf A., LaButti, Kurt, Zhao, Zhiying, Chiniquy, Jennifer, Barry, Kerrie, Brewer, Heather M., Purvine, Samuel O., Wright, Aaron T., Hainaut, Matthieu, Boxma, Brigitte, van Alen, Theo, Hackstein, Johannes H. P., Henrissat, Bernard, Baker, Scott E., Grigoriev, Igor V., and O'Malley, Michelle A. Fri . "A parts list for fungal cellulosomes revealed by comparative genomics". United States. doi:10.1038/nmicrobiol.2017.87.
@article{osti_1367380,
title = {A parts list for fungal cellulosomes revealed by comparative genomics},
author = {Haitjema, Charles H. and Gilmore, Sean P. and Henske, John K. and Solomon, Kevin V. and de Groot, Randall and Kuo, Alan and Mondo, Stephen J. and Salamov, Asaf A. and LaButti, Kurt and Zhao, Zhiying and Chiniquy, Jennifer and Barry, Kerrie and Brewer, Heather M. and Purvine, Samuel O. and Wright, Aaron T. and Hainaut, Matthieu and Boxma, Brigitte and van Alen, Theo and Hackstein, Johannes H. P. and Henrissat, Bernard and Baker, Scott E. and Grigoriev, Igor V. and O'Malley, Michelle A.},
abstractNote = {Cellulosomes are large, multi-protein complexes that tether plant biomass degrading enzymes together for improved hydrolysis1. These complexes were first described in anaerobic bacteria where species specific dockerin domains mediate assembly of enzymes onto complementary cohesin motifs interspersed within non-catalytic protein scaffolds1. The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic protein-scale pathways2,3. For decades, analogous structures have been reported in the early branching anaerobic fungi, which are known to assemble by sequence divergent non-catalytic dockerin domains (NCDD)4. However, the enzyme components, modular assembly mechanism, and functional role of fungal cellulosomes remain unknown5,6. Here, we describe the comprehensive set of proteins critical to fungal cellulosome assembly, including novel, conserved scaffolding proteins unique to the Neocallimastigomycota. High quality genomes of the anaerobic fungi Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis were assembled with long-read, single molecule technology to overcome their repeat-richness and extremely low GC content. Genomic analysis coupled with proteomic validation revealed an average 320 NCDD-containing proteins per fungal strain that were overwhelmingly carbohydrate active enzymes (CAZymes), with 95 large fungal scaffoldins identified across 4 genera that contain a conserved amino acid sequence repeat that binds to NCDDs. Fungal dockerin and scaffoldin domains have no similarity to their bacterial counterparts, yet several catalytic domains originated via horizontal gene transfer with gut bacteria. Though many catalytic domains are shared with bacteria, the biocatalytic activity of anaerobic fungi is expanded by the inclusion of GH3, GH6, and GH45 enzymes in the enzyme complexes. Collectively, these findings suggest that the fungal cellulosome is an evolutionarily chimeric structure – an independently evolved fungal complex that co-opted useful activities from bacterial neighbors within the gut microbiome.},
doi = {10.1038/nmicrobiol.2017.87},
journal = {Nature Microbiology},
issn = {2058-5276},
number = ,
volume = 2,
place = {United States},
year = {2017},
month = {5}
}

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