Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.
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...
Guardado en:
| Autores principales: | , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2013
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/dbf50186b0d4430fade2773ef57f26c7 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:dbf50186b0d4430fade2773ef57f26c7 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:dbf50186b0d4430fade2773ef57f26c72021-11-18T09:03:51ZProteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass.1932-620310.1371/journal.pone.0068465https://doaj.org/article/dbf50186b0d4430fade2773ef57f26c72013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23894306/?tool=EBIhttps://doaj.org/toc/1932-6203Thermophilic 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.Patrik D'haeseleerJohn M GladdenMartin AllgaierPatrik S G ChainSusannah G TringeStephanie A MalfattiJoshua T AldrichCarrie D NicoraErrol W RobinsonLjiljana Paša-TolićPhilip HugenholtzBlake A SimmonsSteven W SingerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68465 (2013) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Patrik D'haeseleer John M Gladden Martin Allgaier Patrik S G Chain Susannah G Tringe Stephanie A Malfatti Joshua T Aldrich Carrie D Nicora Errol W Robinson Ljiljana Paša-Tolić Philip Hugenholtz Blake A Simmons Steven W Singer Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. |
| description |
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. |
| format |
article |
| author |
Patrik D'haeseleer John M Gladden Martin Allgaier Patrik S G Chain Susannah G Tringe Stephanie A Malfatti Joshua T Aldrich Carrie D Nicora Errol W Robinson Ljiljana Paša-Tolić Philip Hugenholtz Blake A Simmons Steven W Singer |
| author_facet |
Patrik D'haeseleer John M Gladden Martin Allgaier Patrik S G Chain Susannah G Tringe Stephanie A Malfatti Joshua T Aldrich Carrie D Nicora Errol W Robinson Ljiljana Paša-Tolić Philip Hugenholtz Blake A Simmons Steven W Singer |
| author_sort |
Patrik D'haeseleer |
| title |
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. |
| title_short |
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. |
| title_full |
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. |
| title_fullStr |
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. |
| title_full_unstemmed |
Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. |
| title_sort |
proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2013 |
| url |
https://doaj.org/article/dbf50186b0d4430fade2773ef57f26c7 |
| work_keys_str_mv |
AT patrikdhaeseleer proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT johnmgladden proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT martinallgaier proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT patriksgchain proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT susannahgtringe proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT stephanieamalfatti proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT joshuataldrich proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT carriednicora proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT errolwrobinson proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT ljiljanapasatolic proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT philiphugenholtz proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT blakeasimmons proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass AT stevenwsinger proteogenomicanalysisofathermophilicbacterialconsortiumadaptedtodeconstructswitchgrass |
| _version_ |
1718420993839464448 |