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Title: Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities

Abstract

Clostridium thermocellum is the most efficient microorganism for solubilizing lignocellulosic biomass known to date. Its high cellulose digestion capability is attributed to efficient cellulases consisting of both a free-enzyme system and a tethered cellulosomal system wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins to generate large protein complexes attached to the bacterial cell wall. This study demonstrates that C. thermocellum also uses a type of cellulosomal system not bound to the bacterial cell wall, called the “cell-free” cellulosomal system. The cell-free cellulosome complex can be seen as a “long range cellulosome” because it can diffuse away from the cell and degrade polysaccharide substrates remotely from the bacterial cell. The contribution of these two types of cellulosomal systems in C. thermocellum was elucidated by characterization of mutants with different combinations of scaffoldin gene deletions. The primary scaffoldin, CipA, was found to play the most important role in cellulose degradation by C. thermocellum, whereas the secondary scaffoldins have less important roles. Additionally, the distinct and efficient mode of action of the C. thermocellum exoproteome, wherein the cellulosomes splay or divide biomass particles, changes when either the primary or secondary scaffolds are removed, showing that the intact wild-typemore » cellulosomal system is necessary for this essential mode of action. This new transcriptional and proteomic evidence shows that a functional primary scaffoldin plays a more important role compared to secondary scaffoldins in the proper regulation of CAZyme genes, cellodextrin transport, and other cellular functions.« less

Authors:
 [1];  [2];  [1];  [3];  [1];  [1];  [4];  [4];  [5];  [1]; ;  [4];  [4];  [5];  [6];  [1];  [1]
  1. National Renewable Energy Lab. (NREL), Golden, CO (United States); BioEnergy Science Center, Oak Ridge, TN (United States)
  2. BioEnergy Science Center, Oak Ridge, TN (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
  3. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  4. BioEnergy Science Center, Oak Ridge, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  5. BioEnergy Science Center, Oak Ridge, TN (United States); Dartmouth College, Hanover, NH (United States)
  6. The Weizmann Institute of Science, Rehovot (Israel)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
Sponsoring Org.:
USDOE Office of Science (SC); USDOE Bioenergy Science Center (BESC)
OSTI Identifier:
1244830
Alternate Identifier(s):
OSTI ID: 1286890
Report Number(s):
NREL/JA-2700-65384
Journal ID: ISSN 2375-2548
Grant/Contract Number:  
AC36-08GO28308; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Science Advances
Additional Journal Information:
Journal Volume: 2; Journal Issue: 2; Journal ID: ISSN 2375-2548
Publisher:
AAAS
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; cell biology; biomass; biofuels; cellulases; cellulosomes; 60 APPLIED LIFE SCIENCES

Citation Formats

Xu, Qi, Resch, Michael G., Podkaminer, Kara, Yang, Shihui, Baker, John O., Donohoe, Bryon S., Wilson, Charlotte, Klingeman, Dawn M., Olson, Daniel G., Decker, Stephen R., Richard J. Giannone, Hettich, Robert L., Brown, Steven D., Lynd, Lee R., Bayer, Edward A., Himmel, Michael E., and Bomble, Yannick J. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. United States: N. p., 2016. Web. doi:10.1126/sciadv.1501254.
Xu, Qi, Resch, Michael G., Podkaminer, Kara, Yang, Shihui, Baker, John O., Donohoe, Bryon S., Wilson, Charlotte, Klingeman, Dawn M., Olson, Daniel G., Decker, Stephen R., Richard J. Giannone, Hettich, Robert L., Brown, Steven D., Lynd, Lee R., Bayer, Edward A., Himmel, Michael E., & Bomble, Yannick J. Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities. United States. doi:10.1126/sciadv.1501254.
Xu, Qi, Resch, Michael G., Podkaminer, Kara, Yang, Shihui, Baker, John O., Donohoe, Bryon S., Wilson, Charlotte, Klingeman, Dawn M., Olson, Daniel G., Decker, Stephen R., Richard J. Giannone, Hettich, Robert L., Brown, Steven D., Lynd, Lee R., Bayer, Edward A., Himmel, Michael E., and Bomble, Yannick J. Fri . "Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities". United States. doi:10.1126/sciadv.1501254. https://www.osti.gov/servlets/purl/1244830.
@article{osti_1244830,
title = {Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities},
author = {Xu, Qi and Resch, Michael G. and Podkaminer, Kara and Yang, Shihui and Baker, John O. and Donohoe, Bryon S. and Wilson, Charlotte and Klingeman, Dawn M. and Olson, Daniel G. and Decker, Stephen R. and Richard J. Giannone and Hettich, Robert L. and Brown, Steven D. and Lynd, Lee R. and Bayer, Edward A. and Himmel, Michael E. and Bomble, Yannick J.},
abstractNote = {Clostridium thermocellum is the most efficient microorganism for solubilizing lignocellulosic biomass known to date. Its high cellulose digestion capability is attributed to efficient cellulases consisting of both a free-enzyme system and a tethered cellulosomal system wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins to generate large protein complexes attached to the bacterial cell wall. This study demonstrates that C. thermocellum also uses a type of cellulosomal system not bound to the bacterial cell wall, called the “cell-free” cellulosomal system. The cell-free cellulosome complex can be seen as a “long range cellulosome” because it can diffuse away from the cell and degrade polysaccharide substrates remotely from the bacterial cell. The contribution of these two types of cellulosomal systems in C. thermocellum was elucidated by characterization of mutants with different combinations of scaffoldin gene deletions. The primary scaffoldin, CipA, was found to play the most important role in cellulose degradation by C. thermocellum, whereas the secondary scaffoldins have less important roles. Additionally, the distinct and efficient mode of action of the C. thermocellum exoproteome, wherein the cellulosomes splay or divide biomass particles, changes when either the primary or secondary scaffolds are removed, showing that the intact wild-type cellulosomal system is necessary for this essential mode of action. This new transcriptional and proteomic evidence shows that a functional primary scaffoldin plays a more important role compared to secondary scaffoldins in the proper regulation of CAZyme genes, cellodextrin transport, and other cellular functions.},
doi = {10.1126/sciadv.1501254},
journal = {Science Advances},
number = 2,
volume = 2,
place = {United States},
year = {2016},
month = {2}
}

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Works referenced in this record:

The Cellulosomes: Multienzyme Machines for Degradation of Plant Cell Wall Polysaccharides
journal, October 2004


Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction
journal, January 2013

  • Resch, Michael G.; Donohoe, Bryon S.; Baker, John O.
  • Energy & Environmental Science, Vol. 6, Issue 6
  • DOI: 10.1039/c3ee00019b

Natural paradigms of plant cell wall degradation
journal, June 2009


Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress
journal, January 2012


DAnTE: a statistical tool for quantitative analysis of -omics data
journal, May 2008


The cellulosome of Clostridium cellulolyticum
journal, September 2005


Caldicellulosiruptor Core and Pangenomes Reveal Determinants for Noncellulosomal Thermophilic Deconstruction of Plant Biomass
journal, May 2012

  • Blumer-Schuette, S. E.; Giannone, R. J.; Zurawski, J. V.
  • Journal of Bacteriology, Vol. 194, Issue 15
  • DOI: 10.1128/JB.00266-12

Cellulosomics of the cellulolytic thermophile Clostridium clariflavum
journal, January 2014

  • Artzi, Lior; Dassa, Bareket; Borovok, Ilya
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-100

Global Gene Expression Patterns in Clostridium thermocellum as Determined by Microarray Analysis of Chemostat Cultures on Cellulose or Cellobiose
journal, December 2010

  • Riederer, Allison; Takasuka, Taichi E.; Makino, Shin-ichi
  • Applied and Environmental Microbiology, Vol. 77, Issue 4
  • DOI: 10.1128/AEM.02008-10

Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production
journal, February 2007

  • Himmel, M. E.; Ding, S.-Y.; Johnson, D. K.
  • Science, Vol. 315, Issue 5813, p. 804-807
  • DOI: 10.1126/science.1137016

A Novel Acetivibrio cellulolyticus Anchoring Scaffoldin That Bears Divergent Cohesins
journal, August 2004


Thermophilic lignocellulose deconstruction
journal, May 2014

  • Blumer-Schuette, Sara E.; Brown, Steven D.; Sander, Kyle B.
  • FEMS Microbiology Reviews, Vol. 38, Issue 3
  • DOI: 10.1111/1574-6976.12044

Cellulosomes—Structure and Ultrastructure
journal, December 1998

  • Bayer, Edward A.; Shimon, Linda J. W.; Shoham, Yuval
  • Journal of Structural Biology, Vol. 124, Issue 2-3
  • DOI: 10.1006/jsbi.1998.4065

DanteR: an extensible R-based tool for quantitative analysis of -omics data
journal, July 2012


High Ethanol Titers from Cellulose by Using Metabolically Engineered Thermophilic, Anaerobic Microbes
journal, September 2011

  • Argyros, D. Aaron; Tripathi, Shital A.; Barrett, Trisha F.
  • Applied and Environmental Microbiology, Vol. 77, Issue 23, p. 8288-8294
  • DOI: 10.1128/AEM.00646-11

A conserved motif in S-layer proteins is involved in peptidoglycan binding in Thermus thermophilus.
journal, August 1996


The functional repertoire of prokaryote cellulosomes includes the serpin superfamily of serine proteinase inhibitors
journal, June 2006


Improving activity of minicellulosomes by integration of intra- and intermolecular synergies
journal, January 2013


Cellulosomes: plant-cell-wall-degrading enzyme complexes
journal, July 2004

  • Doi, Roy H.; Kosugi, Akihiko
  • Nature Reviews Microbiology, Vol. 2, Issue 7
  • DOI: 10.1038/nrmicro925

Microbial Cellulose Utilization: Fundamentals and Biotechnology
journal, September 2002

  • Lynd, L. R.; Weimer, P. J.; van Zyl, W. H.
  • Microbiology and Molecular Biology Reviews, Vol. 66, Issue 3, p. 506-577
  • DOI: 10.1128/MMBR.66.3.506-577.2002

Major characteristics of the cellulolytic system of Clostridium thermocellum coincide with those of the purified cellulosome
journal, January 1985


Biological lignocellulose solubilization: comparative evaluation of biocatalysts and enhancement via cotreatment
journal, January 2016

  • Paye, Julie M. D.; Guseva, Anna; Hammer, Sarah K.
  • Biotechnology for Biofuels, Vol. 9, Issue 1
  • DOI: 10.1186/s13068-015-0412-y

The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons
journal, January 2014

  • Hong, Wei; Zhang, Jie; Feng, Yingang
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-80

IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
journal, August 2009

  • Ma, Ze-Qiang; Dasari, Surendra; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 8, Issue 8
  • DOI: 10.1021/pr900360j

Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
journal, January 2013

  • Wilson, Charlotte M.; Yang, Shihui; Rodriguez, Miguel
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-131

Microbial enzyme systems for biomass conversion: emerging paradigms
journal, March 2010

  • Himmel, Michael E.; Xu, Qi; Luo, Yonghua
  • Biofuels, Vol. 1, Issue 2
  • DOI: 10.4155/bfs.09.25

Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors
journal, October 2010

  • Nataf, Y.; Bahari, L.; Kahel-Raifer, H.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 43
  • DOI: 10.1073/pnas.1012175107

Cellodextrin and Laminaribiose ABC Transporters in Clostridium thermocellum
journal, October 2008

  • Nataf, Y.; Yaron, S.; Stahl, F.
  • Journal of Bacteriology, Vol. 191, Issue 1
  • DOI: 10.1128/JB.01190-08

Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass
journal, January 2013

  • Wilson, Charlotte M.; Rodriguez, Miguel; Johnson, Courtney M.
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-179

Genome-wide analysis of Acetivibrio cellulolyticus provides a blueprint of an elaborate cellulosome system
journal, January 2012


MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis
journal, February 2007

  • Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 6, Issue 2
  • DOI: 10.1021/pr0604054

A defined growth medium with very low background carbon for culturing Clostridium thermocellum
journal, February 2012

  • Holwerda, Evert K.; Hirst, Kyle D.; Lynd, Lee R.
  • Journal of Industrial Microbiology & Biotechnology, Vol. 39, Issue 6
  • DOI: 10.1007/s10295-012-1091-3

Cellulose, cellulases and cellulosomes
journal, October 1998


Role of the CipA Scaffoldin Protein in Cellulose Solubilization, as Determined by Targeted Gene Deletion and Complementation in Clostridium thermocellum
journal, November 2012

  • Olson, D. G.; Giannone, R. J.; Hettich, R. L.
  • Journal of Bacteriology, Vol. 195, Issue 4
  • DOI: 10.1128/JB.02014-12

Protease inhibitors in bacteria: an emerging concept for the regulation of bacterial protein complexes?
journal, June 2006


    Works referencing / citing this record:

    Unraveling essential cellulosomal components of the (Pseudo)Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes
    journal, May 2019

    • Zhivin-Nissan, Olga; Dassa, Bareket; Morag, Ely
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1447-2

    Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment
    journal, July 2016

    • Wurch, Louie; Giannone, Richard J.; Belisle, Bernard S.
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms12115

    Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization
    journal, July 2019

    • Wang, Ying; Leng, Ling; Islam, Md Khairul
    • International Journal of Molecular Sciences, Vol. 20, Issue 13
    • DOI: 10.3390/ijms20133354

    Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics
    journal, April 2018

    • Whitham, Jason M.; Moon, Ji-Won; Rodriguez, Miguel
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-018-1095-y

    Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells
    journal, February 2017

    • Dumitrache, Alexandru; Klingeman, Dawn M.; Natzke, Jace
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/srep43583

    The LacI family protein GlyR3 co-regulates the celC operon and manB in Clostridium thermocellum
    journal, June 2017

    • Choi, Jinlyung; Klingeman, Dawn M.; Brown, Steven D.
    • Biotechnology for Biofuels, Vol. 10, Issue 1
    • DOI: 10.1186/s13068-017-0849-2

    Identification of endoxylanase XynE from Clostridium thermocellum as the first xylanase of glycoside hydrolase family GH141
    journal, September 2017


    Unique genetic cassettes in a Thermoanaerobacterium contribute to simultaneous conversion of cellulose and monosugars into butanol
    journal, March 2018


    The effects of micronutrient deficiencies on bacterial species from the human gut microbiota
    journal, May 2017


    Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides
    journal, June 2019


    Unraveling essential cellulosomal components of the (Pseudo)Bacteroides cellulosolvens reveals an extensive reservoir of novel catalytic enzymes
    journal, May 2019

    • Zhivin-Nissan, Olga; Dassa, Bareket; Morag, Ely
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1447-2

    Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization
    journal, July 2019

    • Wang, Ying; Leng, Ling; Islam, Md Khairul
    • International Journal of Molecular Sciences, Vol. 20, Issue 13
    • DOI: 10.3390/ijms20133354

    Unique organization and unprecedented diversity of the Bacteroides (Pseudobacteroides) cellulosolvens cellulosome system
    journal, September 2017


    Cellulosomes localise on the surface of membrane vesicles from the cellulolytic bacterium Clostridium thermocellum
    journal, June 2019

    • Ichikawa, Shunsuke; Ogawa, Satoru; Nishida, Ayami
    • FEMS Microbiology Letters, Vol. 366, Issue 12
    • DOI: 10.1093/femsle/fnz145

    Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides
    journal, December 2016

    • Artzi, Lior; Bayer, Edward A.; Moraïs, Sarah
    • Nature Reviews Microbiology, Vol. 15, Issue 2
    • DOI: 10.1038/nrmicro.2016.164

    An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme
    journal, July 2018

    • Sammond, Deanne W.; Kastelowitz, Noah; Donohoe, Bryon S.
    • Biotechnology for Biofuels, Vol. 11, Issue 1
    • DOI: 10.1186/s13068-018-1178-9

    Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei
    journal, August 2018

    • Blackler, Ryan J.; López-Guzmán, Arturo; Hager, Fiona F.
    • Nature Communications, Vol. 9, Issue 1
    • DOI: 10.1038/s41467-018-05471-3

    Cellulosic ethanol production via consolidated bioprocessing by a novel thermophilic anaerobic bacterium isolated from a Himalayan hot spring
    journal, March 2017

    • Singh, Nisha; Mathur, Anshu S.; Tuli, Deepak K.
    • Biotechnology for Biofuels, Vol. 10, Issue 1
    • DOI: 10.1186/s13068-017-0756-6

    Characterization of a leukocidin identified in Staphylococcus pseudintermedius
    journal, September 2018


    Inducing effects of cellulosic hydrolysate components of lignocellulose on cellulosome synthesis in Clostridium thermocellum
    journal, June 2018


    Multiple levers for overcoming the recalcitrance of lignocellulosic biomass
    journal, January 2019

    • Holwerda, Evert K.; Worthen, Robert S.; Kothari, Ninad
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1353-7

    Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides
    journal, June 2019