ArticleNucleic acids research2018
Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 104 citations in OpenAlex.
- Strategies and applications for alleviating carbon catabolite repression.Synthetic and systems biotechnology · 2027Review
- Transposon insertion sequencing identifies novel genes involved in product synthesis in gas-fermentingSynthetic and systems biotechnology · 2026Article
- A tripartite RpoS-CRP-cAMP-Cra circuit orchestrates metabolic reprogramming during stress adaptation.Nucleic acids research · 2026Article
- Regulating microbial cell factories to resist ROS stress in chemical production.Archives of microbiology · 2026Review
- The adaptive landscapes of three globaleLife · 2026Article
- A systems-level atlas of carbon-response transcriptional states inProceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Cytoplasmic MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens.Nucleic acids research · 2025Article
- OpDetect: A convolutional and recurrent neural network classifier for precise and sensitive operon detection from RNA-seq data.PloS one · 2025Article
- An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets.Journal of microbiology (Seoul, Korea) · 2024Article
- Insights into the regulatory mechanisms and application prospects of the transcription factor Cra.Applied and environmental microbiology · 2024Review
- Unveiling the novel regulatory roles of RpoD-family sigma factors in Salmonella Typhimurium heat shock response through systems biology approaches.PLoS genetics · 2024Article
- Synthetic redesign of Escherichia coli W for faster metabolism of sugarcane molasses.Microbial cell factories · 2024Article
- Transcriptome data are insufficient to control false discoveries in regulatory network inference.Cell systems · 2024Article
- Proteome partitioning constraints in long-term laboratory evolution.Nature communications · 2024Article
- Effect of adaptive laboratory evolution of engineered Escherichia coli in acetate on the biosynthesis of succinic acid from glucose in two-stage cultivation.Bioresources and bioprocessing · 2024Article
- Flexible gold standards for transcription factor regulatory interactions inFrontiers in genetics · 2024Article
Corrections and comments
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Authors and funding
7 authors at 5 institutions in 3 countries.
Funding
Abstract
Two major transcriptional regulators of carbon metabolism in bacteria are Cra and CRP. CRP is considered to be the main mediator of catabolite repression. Unlike for CRP, in vivo DNA binding information of Cra is scarce. Here we generate and integrate ChIP-exo and RNA-seq data to identify 39 binding sites for Cra and 97 regulon genes that are regulated by Cra in Escherichia coli. An integrated metabolic-regulatory network was formed by including experimentally-derived regulatory information and a genome-scale metabolic network reconstruction. Applying analysis methods of systems biology to this integrated network showed that Cra enables optimal bacterial growth on poor carbon sources by redirecting and repressing glycolysis flux, by activating the glyoxylate shunt pathway, and by activating the respiratory pathway. In these regulatory mechanisms, the overriding regulatory activity of Cra over CRP is fundamental. Thus, elucidation of interacting transcriptional regulation of core carbon metabolism in bacteria by two key transcription factors was possible by combining genome-wide experimental measurement and simulation with a genome-scale metabolic model.
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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.