Snapshot of iron response in Shewanella oneidensis by gene network reconstructionReport as inadecuate




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BMC Genomics

, 10:131

First Online: 25 March 2009Received: 09 October 2008Accepted: 25 March 2009

Abstract

BackgroundIron homeostasis of Shewanella oneidensis, a γ-proteobacterium possessing high iron content, is regulated by a global transcription factor Fur. However, knowledge is incomplete about other biological pathways that respond to changes in iron concentration, as well as details of the responses. In this work, we integrate physiological, transcriptomics and genetic approaches to delineate the iron response of S. oneidensis.

ResultsWe show that the iron response in S. oneidensis is a rapid process. Temporal gene expression profiles were examined for iron depletion and repletion, and a gene co-expression network was reconstructed. Modules of iron acquisition systems, anaerobic energy metabolism and protein degradation were the most noteworthy in the gene network. Bioinformatics analyses suggested that genes in each of the modules might be regulated by DNA-binding proteins Fur, CRP and RpoH, respectively. Closer inspection of these modules revealed a transcriptional regulator SO2426 involved in iron acquisition and ten transcriptional factors involved in anaerobic energy metabolism. Selected genes in the network were analyzed by genetic studies. Disruption of genes encoding a putative alcaligin biosynthesis protein SO3032 and a gene previously implicated in protein degradation SO2017 led to severe growth deficiency under iron depletion conditions. Disruption of a novel transcriptional factor SO1415 caused deficiency in both anaerobic iron reduction and growth with thiosulfate or TMAO as an electronic acceptor, suggesting that SO1415 is required for specific branches of anaerobic energy metabolism pathways.

ConclusionUsing a reconstructed gene network, we identified major biological pathways that were differentially expressed during iron depletion and repletion. Genetic studies not only demonstrated the importance of iron acquisition and protein degradation for iron depletion, but also characterized a novel transcriptional factor SO1415 with a role in anaerobic energy metabolism.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-10-131 contains supplementary material, which is available to authorized users.

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Author: Yunfeng Yang - Daniel P Harris - Feng Luo - Wenlu Xiong - Marcin Joachimiak - Liyou Wu - Paramvir Dehal - Janet Jacobsen

Source: https://link.springer.com/article/10.1186/1471-2164-10-131







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