ArticleProceedings of the National Academy of Sciences of the United States of America2013
Genome-wide identification of Bacillus subtilis CodY-binding sites at single-nucleotide resolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
70 citing papers in PubMed.
- Naturally Occurring CodY Variants Alter Ligand Binding, DNA Target Affinity, and Virulence in Clostridioides difficile.Molecular microbiology · 2026Article
- Metabolic engineering of Bacillus subtilis for high-yield surfactin production.Biotechnology for biofuels and bioproducts · 2026Article
- Article
- Article
- Novel archaeal ribosome dimerization factor facilitating unique 30S-30S dimerization.Nucleic acids research · 2025Article
- Citrate serves as a signal molecule to modulate carbon metabolism and iron homeostasis in Staphylococcus aureus.PLoS pathogens · 2024Article
- Two Distinct Regulatory Systems Control Pulcherrimin Biosynthesis inbioRxiv : the preprint server for biology · 2024Article
- Elucidating the CodY regulon inmSystems · 2023Article
- CodY: An Essential Transcriptional Regulator Involved in Environmental Stress Tolerance in FoodborneFoods (Basel, Switzerland) · 2023Article
- Structural insights into CodY activation and DNA recognition.Nucleic acids research · 2023Article
- Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective.Journal of advanced research · 2023Review
- Article
- Microbial synthesis of bacitracin: Recent progress, challenges, and prospects.Synthetic and systems biotechnology · 2023Review
- Genome-wide mapping of thebioRxiv : the preprint server for biology · 2023Article
- Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase.PLoS genetics · 2023Article
- (p)ppGpp - an important player during heat shock response.microLife · 2023Review
- Identification of a Putative CodY Regulon in the Gram-Negative Phylum Synergistetes.International journal of molecular sciences · 2022Article
- Article
- Systems-Level Analysis of the Global Regulatory Mechanism of CodY in Lactococcus lactis Metabolism and Nisin Immunity Modulation.Applied and environmental microbiology · 2022Article
- The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus.Nucleic acids research · 2022Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The CodY protein is a global transcriptional regulator that controls, directly or indirectly, expression of more than 100 genes and operons in Bacillus subtilis. We used in vitro DNA affinity purification combined with massively parallel sequencing, to identify B. subtilis chromosomal DNA fragments that bind CodY in vitro. A nonstandard strand-specific analysis of the data allowed us to pinpoint CodY-binding sites at single-nucleotide resolution. By comparing the extent of binding at decreasing CodY concentrations, we were able to classify binding regions according to their relative strengths and construct a subset of the 323 strongest CodY-binding regions that included sites associated with nearly all genes reported to be direct CodY targets. Many of the identified sites were located within coding regions. At such sites within the ispA, rapA, and rapE genes CodY-dependent repression was demonstrated using lacZ fusions and mutational analysis.
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Registered trials
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.