ArticlePLoS computational biology2006
Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria.
Article in PLoS computational biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed, 150 citations in OpenAlex.
- The AadR-FixK hierarchy coordinates iron-responsive metabolism via Fur-family regulators inbioRxiv : the preprint server for biology · 2026Article
- A previously uncharacterized Fur-family metalloregulator integrates iron- and manganese-sensing to control virulence gene regulatory networks in Brucella.Scientific reports · 2025Article
- Iron is an important influence of volcanic ash input on the evolution of deep-sea ecosystems.Microbiology spectrum · 2025Article
- Fe-S cluster homeostasis and beyond: The multifaceted roles of IscR.Biochimica et biophysica acta. Molecular cell research · 2024Review
- Stabilisation of the RirA [4Fe-4S] cluster results in loss of iron-sensing function.Chemical science · 2023Article
- Scanning iron response regulator binding sites using Dap-seq in the Brucella genome.PLoS neglected tropical diseases · 2023Article
- Functional Characterization of the CoApplied and environmental microbiology · 2023Article
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- Transcriptomic Response of the Diazotrophic BacteriaInternational journal of molecular sciences · 2022Article
- Repression by the H-NS/YmoA histone-like protein complex enables IscR dependent regulation of the Yersinia T3SS.PLoS genetics · 2022Article
- The FUR-like regulators PerRA and PerRB integrate a complex regulatory network that promotes mammalian host-adaptation and virulence of Leptospira interrogans.PLoS pathogens · 2021Article
- Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean.The ISME journal · 2021Article
- Article
- Bacterial iron detoxification at the molecular level.The Journal of biological chemistry · 2020Review
- Mechanistic insights into heme-mediated transcriptional regulation via a bacterial manganese-binding iron regulator, iron response regulator (Irr).The Journal of biological chemistry · 2020Article
- Genetic Redundancy in Iron and Manganese Transport in the Metabolically Versatile Bacterium Rhodopseudomonas palustris TIE-1.Applied and environmental microbiology · 2020Article
- Iron acquisition system of Sphingobium sp. strain SYK-6, a degrader of lignin-derived aromatic compounds.Scientific reports · 2020Article
- Multiple Sense and Antisense Promoters Contribute to the Regulated Expression of theMicroorganisms · 2019Article
- The Cation Diffusion Facilitator Family Protein EmfA Confers Resistance to Manganese Toxicity in Brucella abortus 2308 and Is an Essential Virulence Determinant in Mice.Journal of bacteriology · 2019Article
32 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
We used comparative genomics to investigate the distribution of conserved DNA-binding motifs in the regulatory regions of genes involved in iron and manganese homeostasis in alpha-proteobacteria. Combined with other computational approaches, this allowed us to reconstruct the metal regulatory network in more than three dozen species with available genome sequences. We identified several classes of cis-acting regulatory DNA motifs (Irr-boxes or ICEs, RirA-boxes, Iron-Rhodo-boxes, Fur-alpha-boxes, Mur-box or MRS, MntR-box, and IscR-boxes) in regulatory regions of various genes involved in iron and manganese uptake, Fe-S and heme biosynthesis, iron storage, and usage. Despite the different nature of the iron regulons in selected lineages of alpha-proteobacteria, the overall regulatory network is consistent with, and confirmed by, many experimental observations. This study expands the range of genes involved in iron homeostasis and demonstrates considerable interconnection between iron-responsive regulatory systems. The detailed comparative and phylogenetic analyses of the regulatory systems allowed us to propose a theory about the possible evolution of Fe and Mn regulons in alpha-proteobacteria. The main evolutionary event likely occurred in the common ancestor of the Rhizobiales and Rhodobacterales, where the Fur protein switched to regulating manganese transporters (and hence Fur had become Mur). In these lineages, the role of global iron homeostasis was taken by RirA and Irr, two transcriptional regulators that act by sensing the physiological consequence of the metal availability rather than its concentration per se, and thus provide for more flexible regulation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.