Reconstruction of Gene Networks of Iron Response in Shewanella oneidensis

Journal Article · Thu Jan 01 04:00:00 EST 2009 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-10-131· OSTI ID:953652

Yang, Yunfeng ^[1]; Harris, Daniel P ^[1]; Luo, Feng ^[2]; Joachimiak, Marcin ^[2]; Wu, Liyou ^[3]; Dehal, Paramvir ^[4]; Jacobsen, Janet ^[4]; Yang, Zamin Koo ^[1]; Gao, Haichun ^[3]; Arkin, Adam ^[4]; Palumbo, Anthony Vito ^[1]; Zhou, Jizhong ^[3]

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1. ORNL
2. Clemson University
3. University of Oklahoma
4. Lawrence Berkeley National Laboratory (LBNL)

It is of great interest to study the iron response of the -proteobacterium Shewanella oneidensis since it possesses a high content of iron and is capable of utilizing iron for anaerobic respiration. We report here that the iron response in S. oneidensis is a rapid process. To gain more insights into the bacterial response to iron, temporal gene expression profiles were examined for iron depletion and repletion, resulting in identification of iron-responsive biological pathways in a gene co-expression network. Iron acquisition systems, including genes unique to S. oneidensis, were rapidly and strongly induced by iron depletion, and repressed by iron repletion. Some were required for iron depletion, as exemplified by the mutational analysis of the putative siderophore biosynthesis protein SO3032. Unexpectedly, a number of genes related to anaerobic energy metabolism were repressed by iron depletion and induced by repletion, which might be due to the iron storage potential of their protein products. Other iron-responsive biological pathways include protein degradation, aerobic energy metabolism and protein synthesis. Furthermore, sequence motifs enriched in gene clusters as well as their corresponding DNA-binding proteins (Fur, CRP and RpoH) were identified, resulting in a regulatory network of iron response in S. oneidensis. Together, this work provides an overview of iron response and reveals novel features in S. oneidensis, including Shewanella-specific iron acquisition systems, and suggests the intimate relationship between anaerobic energy metabolism and iron response.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 953652
• Journal Information: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 131 Vol. 10; ISSN 1471-2164
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
BIOLOGICAL PATHWAYS
BIOSYNTHESIS
ENERGY
GAIN
GENES
IRON
METABOLISM
POTENTIALS
PROTEINS
RESPIRATION
STORAGE
SYNTHESIS
Shewanella
iron response
microarray