Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it>
<p>Abstract</p> <p>Background</p> <p><it>Rhodoferax ferrireducens </it>is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2009-09-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/447 |
| _version_ | 1818344406406660096 |
|---|---|
| author | Daugherty Sean Kothari Sagar Huot Heather Shrivastava Susmita Ismail Wael DeBoy Robert Mahadevan Radhakrishnan Zhuang Kai Sun Jun Risso Carla Bui Olivia Schilling Christophe H Lovley Derek R Methé Barbara A |
| author_facet | Daugherty Sean Kothari Sagar Huot Heather Shrivastava Susmita Ismail Wael DeBoy Robert Mahadevan Radhakrishnan Zhuang Kai Sun Jun Risso Carla Bui Olivia Schilling Christophe H Lovley Derek R Methé Barbara A |
| author_sort | Daugherty Sean |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Rhodoferax ferrireducens </it>is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about <it>R. ferrireducens</it>, the complete genome sequence of this organism was further annotated and then the physiology of <it>R. ferrireducens </it>was investigated with a constraint-based, genome-scale <it>in silico </it>metabolic model and laboratory studies.</p> <p>Results</p> <p>The iterative modeling and experimental approach unveiled exciting, previously unknown physiological features, including an expanded range of substrates that support growth, such as cellobiose and citrate, and provided additional insights into important features such as the stoichiometry of the electron transport chain and the ability to grow via fumarate dismutation. Further analysis explained why <it>R. ferrireducens </it>is unable to grow via photosynthesis or fermentation of sugars like other members of this genus and uncovered novel genes for benzoate metabolism. The genome also revealed that <it>R. ferrireducens </it>is well-adapted for growth in the subsurface because it appears to be capable of dealing with a number of environmental insults, including heavy metals, aromatic compounds, nutrient limitation and oxidative stress.</p> <p>Conclusion</p> <p>This study demonstrates that combining genome-scale modeling with the annotation of a new genome sequence can guide experimental studies and accelerate the understanding of the physiology of under-studied yet environmentally relevant microorganisms.</p> |
| first_indexed | 2024-12-13T16:45:58Z |
| format | Article |
| id | doaj.art-176a70342c494ec19556b9b0f6c28d4e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T16:45:58Z |
| publishDate | 2009-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-176a70342c494ec19556b9b0f6c28d4e2022-12-21T23:38:10ZengBMCBMC Genomics1471-21642009-09-0110144710.1186/1471-2164-10-447Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it>Daugherty SeanKothari SagarHuot HeatherShrivastava SusmitaIsmail WaelDeBoy RobertMahadevan RadhakrishnanZhuang KaiSun JunRisso CarlaBui OliviaSchilling Christophe HLovley Derek RMethé Barbara A<p>Abstract</p> <p>Background</p> <p><it>Rhodoferax ferrireducens </it>is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about <it>R. ferrireducens</it>, the complete genome sequence of this organism was further annotated and then the physiology of <it>R. ferrireducens </it>was investigated with a constraint-based, genome-scale <it>in silico </it>metabolic model and laboratory studies.</p> <p>Results</p> <p>The iterative modeling and experimental approach unveiled exciting, previously unknown physiological features, including an expanded range of substrates that support growth, such as cellobiose and citrate, and provided additional insights into important features such as the stoichiometry of the electron transport chain and the ability to grow via fumarate dismutation. Further analysis explained why <it>R. ferrireducens </it>is unable to grow via photosynthesis or fermentation of sugars like other members of this genus and uncovered novel genes for benzoate metabolism. The genome also revealed that <it>R. ferrireducens </it>is well-adapted for growth in the subsurface because it appears to be capable of dealing with a number of environmental insults, including heavy metals, aromatic compounds, nutrient limitation and oxidative stress.</p> <p>Conclusion</p> <p>This study demonstrates that combining genome-scale modeling with the annotation of a new genome sequence can guide experimental studies and accelerate the understanding of the physiology of under-studied yet environmentally relevant microorganisms.</p>http://www.biomedcentral.com/1471-2164/10/447 |
| spellingShingle | Daugherty Sean Kothari Sagar Huot Heather Shrivastava Susmita Ismail Wael DeBoy Robert Mahadevan Radhakrishnan Zhuang Kai Sun Jun Risso Carla Bui Olivia Schilling Christophe H Lovley Derek R Methé Barbara A Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it> BMC Genomics |
| title | Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it> |
| title_full | Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it> |
| title_fullStr | Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it> |
| title_full_unstemmed | Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it> |
| title_short | Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer <it>Rhodoferax ferrireducens</it> |
| title_sort | genome scale comparison and constraint based metabolic reconstruction of the facultative anaerobic fe iii reducer it rhodoferax ferrireducens it |
| url | http://www.biomedcentral.com/1471-2164/10/447 |
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