Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen
In this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 ar...
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doaj-416593cae6064d9faedcd8e922edc3422020-11-24T21:38:59ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-03-011010.3389/fmicb.2019.00435442669Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic MethanogenYuanfei Li0Yuqi Li1Wei Jin2Wei Jin3Thomas J. Sharpton4Roderick I. Mackie5Isaac Cann6Isaac Cann7Isaac Cann8Isaac Cann9Yanfen Cheng10Yanfen Cheng11Weiyun Zhu12Weiyun Zhu13Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, ChinaJoint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, ChinaDepartment of Microbiology – Department of Statistics, Oregon State University, Corvallis, OR, United StatesDepartment of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United StatesDepartment of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United StatesDepartment of Microbiology, University of Illinois at Urbana-Champaign, Champaign, IL, United StatesDivision of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United StatesCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United StatesLaboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, ChinaJoint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, ChinaLaboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, ChinaJoint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, ChinaIn this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 are 106.83 Mb, 16.07%, and 23.54%, respectively. Comparison of the fungal monoculture with the methanogen co-culture demonstrated that during the fermentation of glucose, the co-culture initially expressed and then down-regulated a large number of genes encoding both enzymes involved in intermediate metabolism and plant cell wall degradation. However, the number of up-regulated proteins doubled at the late-growth stage in the co-culture. In addition, we provide a mechanistic understanding of the metabolism of this fungus in co-culture with a syntrophic methanogen. Further experiments are needed to explore this interaction during degradation of more complex plant cell wall substrates.https://www.frontiersin.org/article/10.3389/fmicb.2019.00435/fullanaerobic fungusmethanogenmetabolismgenomeRNAseqiTRAQ |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yuanfei Li Yuqi Li Wei Jin Wei Jin Thomas J. Sharpton Roderick I. Mackie Isaac Cann Isaac Cann Isaac Cann Isaac Cann Yanfen Cheng Yanfen Cheng Weiyun Zhu Weiyun Zhu |
spellingShingle |
Yuanfei Li Yuqi Li Wei Jin Wei Jin Thomas J. Sharpton Roderick I. Mackie Isaac Cann Isaac Cann Isaac Cann Isaac Cann Yanfen Cheng Yanfen Cheng Weiyun Zhu Weiyun Zhu Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen Frontiers in Microbiology anaerobic fungus methanogen metabolism genome RNAseq iTRAQ |
author_facet |
Yuanfei Li Yuqi Li Wei Jin Wei Jin Thomas J. Sharpton Roderick I. Mackie Isaac Cann Isaac Cann Isaac Cann Isaac Cann Yanfen Cheng Yanfen Cheng Weiyun Zhu Weiyun Zhu |
author_sort |
Yuanfei Li |
title |
Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen |
title_short |
Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen |
title_full |
Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen |
title_fullStr |
Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen |
title_full_unstemmed |
Combined Genomic, Transcriptomic, Proteomic, and Physiological Characterization of the Growth of Pecoramyces sp. F1 in Monoculture and Co-culture With a Syntrophic Methanogen |
title_sort |
combined genomic, transcriptomic, proteomic, and physiological characterization of the growth of pecoramyces sp. f1 in monoculture and co-culture with a syntrophic methanogen |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Microbiology |
issn |
1664-302X |
publishDate |
2019-03-01 |
description |
In this study, the effects of a syntrophic methanogen on the growth of Pecoramyces sp. F1 was investigated by characterizing fermentation profiles, as well as functional genomic, transcriptomic, and proteomic analysis. The estimated genome size, GC content, and protein coding regions of strain F1 are 106.83 Mb, 16.07%, and 23.54%, respectively. Comparison of the fungal monoculture with the methanogen co-culture demonstrated that during the fermentation of glucose, the co-culture initially expressed and then down-regulated a large number of genes encoding both enzymes involved in intermediate metabolism and plant cell wall degradation. However, the number of up-regulated proteins doubled at the late-growth stage in the co-culture. In addition, we provide a mechanistic understanding of the metabolism of this fungus in co-culture with a syntrophic methanogen. Further experiments are needed to explore this interaction during degradation of more complex plant cell wall substrates. |
topic |
anaerobic fungus methanogen metabolism genome RNAseq iTRAQ |
url |
https://www.frontiersin.org/article/10.3389/fmicb.2019.00435/full |
work_keys_str_mv |
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