Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

D'haeseleer, Patrik, Gladden, John M., Allgaier, Martin, Chain, Patrik S. G., Tringe, Susannah G., Malfatti, Stephanie A., Aldrich, Joshua T., Nicora, Carrie D., Robinson, Errol W., Pasa-Tolic, Ljiljana, Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2013) Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Plos One, 8 7: e68465.1-e68465.11. doi:10.1371/journal.pone.0068465

Author D'haeseleer, Patrik
Gladden, John M.
Allgaier, Martin
Chain, Patrik S. G.
Tringe, Susannah G.
Malfatti, Stephanie A.
Aldrich, Joshua T.
Nicora, Carrie D.
Robinson, Errol W.
Pasa-Tolic, Ljiljana
Hugenholtz, Philip
Simmons, Blake A.
Singer, Steven W.
Title Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
Journal name Plos One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2013-07
Year available 2013
Sub-type Article (original research)
DOI 10.1371/journal.pone.0068465
Open Access Status DOI
Volume 8
Issue 7
Start page e68465.1
End page e68465.11
Total pages 11
Place of publication San Francisco, United States
Publisher Public Library of Science (PLoS)
Collection year 2014
Language eng
Abstract Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the little-studied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify >3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.
Keyword Complete Genome Sequence
Eubacterium Rhodothermus-Marinus
Comparative-Analysis System
Sample Preparation Method
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Australian Centre for Ecogenomics
Official 2014 Collection
School of Chemistry and Molecular Biosciences
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Citation counts: TR Web of Science Citation Count  Cited 17 times in Thomson Reuters Web of Science Article | Citations
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