Reconstruction and Analysis of the Gene Regulatory Networks of <em>Shewanella onedensis</em> MR-1

doi:10.13523/j.cb.20141106

China Biotechnology

2014, Vol. 34

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

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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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

Received: 20 September 2014 Published: 25 November 2014

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Cite this article:

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.

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

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