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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 Laboratory (NREL), Golden, CO (United States); Oak Ridge National Laboratory (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:
Journal Article: 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. https://doi.org/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. 2016. "Dramatic performance of Clostridium thermocellum explained by its wide range of cellulase modalities". United States. https://doi.org/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},
url = {https://www.osti.gov/biblio/1244830}, journal = {Science Advances},
issn = {2375-2548},
number = 2,
volume = 2,
place = {United States},
year = {Fri Feb 05 00:00:00 EST 2016},
month = {Fri Feb 05 00:00:00 EST 2016}
}

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Cited by: 74 works
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Works referenced in this record:

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Fungal cellulases and complexed cellulosomal enzymes exhibit synergistic mechanisms in cellulose deconstruction
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High Ethanol Titers from Cellulose by Using Metabolically Engineered Thermophilic, Anaerobic Microbes
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Improving activity of minicellulosomes by integration of intra- and intermolecular synergies
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Cellulosomes: plant-cell-wall-degrading enzyme complexes
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Major characteristics of the cellulolytic system of Clostridium thermocellum coincide with those of the purified cellulosome
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Biological lignocellulose solubilization: comparative evaluation of biocatalysts and enhancement via cotreatment
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IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
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Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
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Microbial enzyme systems for biomass conversion: emerging paradigms
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Clostridium thermocellum cellulosomal genes are regulated by extracytoplasmic polysaccharides via alternative sigma factors
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Cellodextrin and Laminaribiose ABC Transporters in Clostridium thermocellum
journal, October 2008


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


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
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A defined growth medium with very low background carbon for culturing Clostridium thermocellum
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Protease inhibitors in bacteria: an emerging concept for the regulation of bacterial protein complexes?
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Distinct Affinity of Binding Sites for S-Layer Homologous Domains in Clostridium thermocellum and Bacillus anthracis Cell Envelopes
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Cellulosomes—Structure and Ultrastructure
journal, December 1998


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


Natural paradigms of plant cell wall degradation
journal, June 2009


The cellulosome of Clostridium cellulolyticum
journal, September 2005


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Cellulosomics of the cellulolytic thermophile Clostridium clariflavum
journal, January 2014


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


Works referencing / citing this record:

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


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


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


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


Regulation of biomass degradation by alternative σ factors in cellulolytic clostridia
journal, July 2018


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


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


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


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


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


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


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


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


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


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


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


Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum
journal, June 2016


Efficient whole-cell-catalyzing cellulose saccharification using engineered Clostridium thermocellum
journal, May 2017


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


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


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


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


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


The Cellulosome Paradigm in An Extreme Alkaline Environment
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