Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia

Yu Wei Wu, Chijioke Joshua, Stephanie A. Eichorst, John M. Gladden, Blake A. Simmons, Steven W. Singer

研究成果: 雜誌貢獻文章

3 引文 (Scopus)

摘要

Members of the phylum Deinoccocus-Thermus are adapted to grow under extremes of temperature and radiation. Some of these members have broad applications in biotechnology. However, the specific role of members of Deinoccocus-Thermus in plant biomass deconstruction remains largely unknown. Adaptations of thermophilic communities to grow on plant biomass substrates as the sole carbon source have consistently produced consortia with abundant populations affiliated with the Deinoccocus-Thermus. One of these populations was closely related to cultured isolates of Thermus thermophilus, while the second population, termed NIC-1, was distantly related to Truepera radiovictrix. NIC-1 was abundant in adapted cultures grown on xylan-rich substrates, while the T. thermophilus was virtually absent. To begin to understand the origin of this selection, genomic comparisons of xylan and xylose metabolism were undertaken between NIC-1, recovered from the metagenome obtained from an ammonia fiber expansion (AFEX)-pretreated switchgrass-adapted consortium and a T. thermophilus isolate from a related high temperature switchgrass adaptation. While both genomes indicated relatively limited capabilities to hydrolyze xylan, the NIC-1 genome had a putative operon for xylose utilization, while xylose metabolism genes were absent from the T. thermophilus genome. Comparison of multiple T. thermophilus genomes indicated that the genes for xylose metabolism were present on a plasmid in only one strain. Inspection of metagenomic dataset for adapted communities that contain T. thermophilus indicated that the plasmid is present in the T. thermophilus populations but may be lost upon isolation.
原文英語
頁(從 - 到)1031-1038
頁數8
期刊Bioenergy Research
8
發行號3
DOIs
出版狀態已發佈 - 三月 12 2015
對外發佈Yes

指紋

Thermus thermophilus
Thermus
Xylose
xylose
Metabolism
Biomass
Genes
genomics
metabolism
biomass
xylan
genome
Panicum virgatum
plasmids
Substrates
Biotechnology
operon
Ammonia
marker-assisted selection
biotechnology

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Energy (miscellaneous)
  • Renewable Energy, Sustainability and the Environment

引用此文

Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia. / Wu, Yu Wei; Joshua, Chijioke; Eichorst, Stephanie A.; Gladden, John M.; Simmons, Blake A.; Singer, Steven W.

於: Bioenergy Research, 卷 8, 編號 3, 12.03.2015, p. 1031-1038.

研究成果: 雜誌貢獻文章

Wu, Yu Wei ; Joshua, Chijioke ; Eichorst, Stephanie A. ; Gladden, John M. ; Simmons, Blake A. ; Singer, Steven W. / Genomic Analysis of Xylose Metabolism in Members of the Deinoccocus-Thermus Phylum from Thermophilic Biomass-Deconstructing Bacterial Consortia. 於: Bioenergy Research. 2015 ; 卷 8, 編號 3. 頁 1031-1038.
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abstract = "Members of the phylum Deinoccocus-Thermus are adapted to grow under extremes of temperature and radiation. Some of these members have broad applications in biotechnology. However, the specific role of members of Deinoccocus-Thermus in plant biomass deconstruction remains largely unknown. Adaptations of thermophilic communities to grow on plant biomass substrates as the sole carbon source have consistently produced consortia with abundant populations affiliated with the Deinoccocus-Thermus. One of these populations was closely related to cultured isolates of Thermus thermophilus, while the second population, termed NIC-1, was distantly related to Truepera radiovictrix. NIC-1 was abundant in adapted cultures grown on xylan-rich substrates, while the T. thermophilus was virtually absent. To begin to understand the origin of this selection, genomic comparisons of xylan and xylose metabolism were undertaken between NIC-1, recovered from the metagenome obtained from an ammonia fiber expansion (AFEX)-pretreated switchgrass-adapted consortium and a T. thermophilus isolate from a related high temperature switchgrass adaptation. While both genomes indicated relatively limited capabilities to hydrolyze xylan, the NIC-1 genome had a putative operon for xylose utilization, while xylose metabolism genes were absent from the T. thermophilus genome. Comparison of multiple T. thermophilus genomes indicated that the genes for xylose metabolism were present on a plasmid in only one strain. Inspection of metagenomic dataset for adapted communities that contain T. thermophilus indicated that the plasmid is present in the T. thermophilus populations but may be lost upon isolation.",
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AU - Simmons, Blake A.

AU - Singer, Steven W.

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AB - Members of the phylum Deinoccocus-Thermus are adapted to grow under extremes of temperature and radiation. Some of these members have broad applications in biotechnology. However, the specific role of members of Deinoccocus-Thermus in plant biomass deconstruction remains largely unknown. Adaptations of thermophilic communities to grow on plant biomass substrates as the sole carbon source have consistently produced consortia with abundant populations affiliated with the Deinoccocus-Thermus. One of these populations was closely related to cultured isolates of Thermus thermophilus, while the second population, termed NIC-1, was distantly related to Truepera radiovictrix. NIC-1 was abundant in adapted cultures grown on xylan-rich substrates, while the T. thermophilus was virtually absent. To begin to understand the origin of this selection, genomic comparisons of xylan and xylose metabolism were undertaken between NIC-1, recovered from the metagenome obtained from an ammonia fiber expansion (AFEX)-pretreated switchgrass-adapted consortium and a T. thermophilus isolate from a related high temperature switchgrass adaptation. While both genomes indicated relatively limited capabilities to hydrolyze xylan, the NIC-1 genome had a putative operon for xylose utilization, while xylose metabolism genes were absent from the T. thermophilus genome. Comparison of multiple T. thermophilus genomes indicated that the genes for xylose metabolism were present on a plasmid in only one strain. Inspection of metagenomic dataset for adapted communities that contain T. thermophilus indicated that the plasmid is present in the T. thermophilus populations but may be lost upon isolation.

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