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Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.

D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW - PLoS ONE (2013)

Bottom Line: Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations.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.

View Article: PubMed Central - PubMed

Affiliation: Joint BioEnergy Institute, Emeryville, California, United States of America. patrikd@llnl.gov

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.

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Normalized protein abundance within each of the three proteome fractions, by phylogenetic bins.
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pone-0068465-g002: Normalized protein abundance within each of the three proteome fractions, by phylogenetic bins.

Mentions: The proteins were assigned to specific bins based on comparison to the metagenomic data. In all three fractions, proteins assigned to the Gemmatimonadetes, Paenibacillus and Thermus bins were >50% of the total estimated protein abundance (Figure 2). While among the most abundant bins in the metagenome, proteins assigned to Rhodothermus seem to be much less prevalent in the proteome, accounting for only 4–10% of the proteome fractions. Statistical analysis of the proteome (see Materials and Methods) revealed that proteins in the Thermus bin were dominant in the suspended and the fiber-attached fractions, but underrepresented in the supernatant fraction. In contrast, proteins from the Paenibacillus bin were especially overrepresented in the supernatant fraction, constituting >26% of the proteome. Proteins from the Sphaerobacter bin, which was among the minor bins in the metagenome, were overrepresented in the supernatant.


Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.

D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Paša-Tolić L, Hugenholtz P, Simmons BA, Singer SW - PLoS ONE (2013)

Normalized protein abundance within each of the three proteome fractions, by phylogenetic bins.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3716776&req=5

pone-0068465-g002: Normalized protein abundance within each of the three proteome fractions, by phylogenetic bins.
Mentions: The proteins were assigned to specific bins based on comparison to the metagenomic data. In all three fractions, proteins assigned to the Gemmatimonadetes, Paenibacillus and Thermus bins were >50% of the total estimated protein abundance (Figure 2). While among the most abundant bins in the metagenome, proteins assigned to Rhodothermus seem to be much less prevalent in the proteome, accounting for only 4–10% of the proteome fractions. Statistical analysis of the proteome (see Materials and Methods) revealed that proteins in the Thermus bin were dominant in the suspended and the fiber-attached fractions, but underrepresented in the supernatant fraction. In contrast, proteins from the Paenibacillus bin were especially overrepresented in the supernatant fraction, constituting >26% of the proteome. Proteins from the Sphaerobacter bin, which was among the minor bins in the metagenome, were overrepresented in the supernatant.

Bottom Line: Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations.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.

View Article: PubMed Central - PubMed

Affiliation: Joint BioEnergy Institute, Emeryville, California, United States of America. patrikd@llnl.gov

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.

Show MeSH