一种新型 Paracoccus denitrificans 菌株的基因组，该菌株能够降解 N,N-二甲基甲酰胺。
Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide.
机构信息
Department of Animal Sciences, School of Life Sciences, University of Hyderabad, Professor CR Rao Road, Gachibowli, Hyderabad 500 046, India.
出版信息
J Bacteriol. 2011 Oct;193(19):5598-9. doi: 10.1128/JB.05667-11.
Abstract
The bacterial genus Paracoccus is comprised of metabolically versatile organisms having diverse degradative capabilities and potential industrial and environmental applications for bioremediation in particular. We report a de novo-assembled sequence and annotation of the genome of a novel isolate of Paracoccus denitrificans originally sourced from coal mine tailings in India. The isolate was capable of utilizing N,N-dimethylformamide (DMF) as a source of carbon and nitrogen and therefore holds potential for bioremediation and mineralization of industrial pollutants. The genome sequence and biological circuitry revealed thereupon will be invaluable in understanding the metabolic capabilities, functioning, and evolution of this important bacterial organism.
摘要
副球菌属是一个代谢多样的细菌属，具有多种降解能力，在生物修复，特别是在工业和环境应用方面具有潜在的应用价值。我们报告了一种新型副球菌（Paracoccus denitrificans）的从头组装序列和基因组注释，该菌最初来源于印度的煤矿尾矿。该菌能够利用 N,N-二甲基甲酰胺（DMF）作为碳源和氮源，因此具有生物修复和工业污染物矿化的潜力。由此揭示的基因组序列和生物电路将对理解这种重要细菌的代谢能力、功能和进化具有不可估量的价值。
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2
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3
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4
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7
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8
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Genome Biol. 2004;5(2):R12. doi: 10.1186/gb-2004-5-2-r12. Epub 2004 Jan 30.
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