ArticleBMC genomics2009
Snapshot of iron response in Shewanella oneidensis by gene network reconstruction.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 54 citations in OpenAlex.
- Multifaceted regulation of siderophore synthesis by multiple regulatory systems in Shewanella oneidensis.Communications biology · 2024Article
- Rapid Single-Shot Synthesis of the 214 Amino Acid-Long N-Terminal Domain of Pyocin S2.ACS chemical biology · 2023Article
- Transcriptomic Response of the Diazotrophic BacteriaInternational journal of molecular sciences · 2022Article
- Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.Microbiome · 2022Article
- Genome-wide characterization of Salmonella Typhimurium genes required for the fitness under iron restriction.BMC genomic data · 2022Article
- Recent Advances in the Siderophore Biology ofFrontiers in microbiology · 2022Review
- Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community.Microbiome · 2020Article
- Progressive Microbial Community Networks with Incremental Organic Loading Rates Underlie Higher Anaerobic Digestion Performance.mSystems · 2020Article
- Structure and reactivity of a siderophore-interacting protein from the marine bacteriumThe Journal of biological chemistry · 2019Article
- Article
- The Small RNA RyhB Is a Regulator of Cytochrome Expression inFrontiers in microbiology · 2018Article
- Cationic Peptides Facilitate Iron-induced Mutagenesis in Bacteria.PLoS genetics · 2015Article
- Unraveling the Mechanism for the Viability Deficiency of Shewanella oneidensis oxyR Null Mutant.Journal of bacteriology · 2015Article
- Catabolic and regulatory systems in Shewanella oneidensis MR-1 involved in electricity generation in microbial fuel cells.Frontiers in microbiology · 2015Review
- The microbial gene diversity along an elevation gradient of the Tibetan grassland.The ISME journal · 2014Article
- Roles of UndA and MtrC of Shewanella putrefaciens W3-18-1 in iron reduction.BMC microbiology · 2013Article
- Article
- The regulatory role of ferric uptake regulator (Fur) during anaerobic respiration of Shewanella piezotolerans WP3.PloS one · 2013Article
- Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.Nucleic acids research · 2012Article
- Molecular ecological network analyses.BMC bioinformatics · 2012Article
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Authors and funding
12 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIron homeostasis of Shewanella oneidensis, a gamma-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.
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