Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation

Davies, Bryan W.; Bogard, Ryan W.; Mekalanos, John J.

doi:10.1073/pnas.1107894108

Cited by 69Bacterial Genetics and BiotechnologyVibrio bacteria research studiesGenomics and Chromatin Dynamics

Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation

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Davies, Bryan W., Bogard, Ryan W., Mekalanos, John J.·2011·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.1107894108PMC PMC3145737

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Abstract

ChIP coupled with next-generation sequencing (ChIP-seq) has revolutionized whole-genome mapping of DNA-binding protein sites. Although ChIP-seq rapidly gained support in eukaryotic systems, it remains underused in the mapping of bacterial transcriptional regulator-binding sites. Using the virulence-required iron-responsive ferric uptake regulator (Fur), we report a simple, broadly applicable ChIP-seq method in the pathogen Vibrio cholerae . Combining our ChIP-seq results with available microarray data, we clarify direct and indirect Fur regulation of known iron-responsive genes. We validate a subset of Fur-binding sites in vivo and show a common motif present in all Fur ChIP-seq peaks that has enhanced binding affinity for purified V. cholerae Fur. Further analysis shows that V. cholerae Fur directly regulates several additional genes associated with Fur-binding sites, expanding the role of this transcription factor into the regulation of ribosome formation, additional transport functions, and unique sRNAs.

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The findings explain why Fur recognizes >90 diverse genes and degenerate sequences in the pathogens V. cholerae and Campylobacter jejuni.
“Our findings explain why Fur recognizes >90 diverse genes and degenerate sequences in the pathogens V. cholerae and Campylobacter jejuni 17 , 30 .”
From Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator (2015) · cites this paper as [30]
Consensus sequences bound by Fur in E. coli, P. aeruginosa, V. cholerae and C. jejuni are also AT rich.
“Consensus sequences bound by Fur in E. coli , P. aeruginosa , V. cholerae and C. jejuni are also AT rich 10 , 17 , 30 , 32 .”
From Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator (2015) · cites this paper as [30]

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Authors: Davies, B. W., Bogard, R. W., & Mekalanos, J. J.
Affiliations: Harvard University (US)
ORCID: Davies, Bryan W.
Mekalanos, John J.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2011-07-12
Volume: 108
Issue: 30
Pages: 12467-12472
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.1107894108
PMC: PMC3145737
OpenAlex: W2140829667
Cited by: 69
References: 52
Citations by year: 2025: 1 · 2024: 3 · 2023: 5 · 2022: 4 · 2021: 3 · 2020: 8 · 2019: 1 · 2018: 4 · 2017: 5 · 2016: 3 · 2015: 10 · 2014: 4 · 2013: 8 · 2012: 8
FWCI: 4.38
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Jane Coffin Childs Memorial Fund for Medical Research
National Institutes of Health
National Institute of Allergy and Infectious Diseases (R01AI018045, AI-018045, R37AI018045)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Vibrio bacteria research studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: Vibrio cholerae, ferric uptake regulator, regulon, ChIP-seq, DNA binding sites, iron-responsive genes, gene expression regulation, ribosome biogenesis, sRNA, transcriptional regulation
MeSH terms: Bacterial Proteins, Base Sequence, Binding Sites, Chromosome Mapping, DNA, Bacterial, Genes, Bacterial, Iron, Repressor Proteins, RNA, Bacterial, Vibrio cholerae, Gene Expression Regulation, Bacterial, Regulon, Chromatin Immunoprecipitation

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Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation

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