产电微生物基因调控网络的构建和特异性通路分析

doi:10.13523/j.cb.20141106

中国生物工程杂志

2014, Vol. 34

Issue (11): 42-46 DOI: 10.13523/j.cb.20141106

计算生物学与生物信息学专辑

产电微生物基因调控网络的构建和特异性通路分析

徐军, 刘翠翠, 丁德武, 孙啸, 谢建明

东南大学生物电子学国家重点实验室生物科学与医学工程学院南京 210096

Reconstruction and Analysis of the Gene Regulatory Networks of Shewanella onedensis MR-1

XU Jun, LIU Cui-cui, DING De-wu, SUN Xiao, XIE Jian-ming

State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Nanjing 210096, China

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摘要：

研究产电微生物胞外电子传递过程和机制,发现与产电效率相关的关键基因、通路和代谢物,是微生物燃料电池研究中的关键技术。为了发现在胞外电子传递过程中起到关键作用的基因以及通路,首先利用比较基因组学的方法,以模式微生物大肠杆菌和同属希瓦氏菌的其他菌株为参考,构建了Shewanella.onedensis MR-1的全基因组基因转录调控网络,大大扩展了目前已知的基因调控关系。然后以此网络为基础,结合基于蛋白质相互作用分析得到的胞外电子传递通路,构建了与胞外电子传递直接传递密切相关的细胞色素C编码基因及其相关调控基因构成的子网络,结合全基因组基因表达数据,研究了特异性条件下胞外电子传递的可能通路和基因调控过程。

关键词： 产电微生物; 胞外电子传递; 基因转录调控网络; 基因表达数据分析

Abstract:

To improve the efficiency of electricity production of MFC, it is necessary to understand the principles of extracellular electron transfer(EET) of Shewanella oneidensis MR-1,for example, the EET pathways under specific conditions(different grow conditions or different terminal electron acceptor and so on).41 c-type cytochromes of Shewanella oneidensis MR-1 were obtained from literatures and 50 related proteins were downloaded in STRING, then the coding genes of these proteins in NCBI. As the GRN of Shewanella oneidensis MR-1 had been reconstructed before, and 3367 transcription relationships were discovered, in which the transcription relationships between c-type cytochromes related genes were identified.Using R platform, we built the gene regulatory networks and explored the possible pathways to clarify the principles of EET, the bacterial growth conditions were controlled by using different gene expression datasets. At last, three specific EET pathways were proposed while analyzing GSE7973,GSE15334 and GSE25821.

Key words: Extracellular electron transfer c-type cytochromes Gene expression data Generegulatory networks

收稿日期: 2014-09-20 出版日期: 2014-11-25

ZTFLH:

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通讯作者: 谢建明,xiejm@seu.edu.cn E-mail: xiejm@seu.edu.cn

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引用本文:

徐军, 刘翠翠, 丁德武, 孙啸, 谢建明. 产电微生物基因调控网络的构建和特异性通路分析[J]. 中国生物工程杂志, 2014, 34(11): 42-46.

XU Jun, LIU Cui-cui, DING De-wu, SUN Xiao, XIE Jian-ming. Reconstruction and Analysis of the Gene Regulatory Networks of Shewanella onedensis MR-1. China Biotechnology, 2014, 34(11): 42-46.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20141106 或 https://manu60.magtech.com.cn/biotech/CN/Y2014/V34/I11/42

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