ArticlePLoS computational biology2014
A model for sigma factor competition in bacterial cells.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed, 101 citations in OpenAlex.
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- The latent cis-regulatory potential of mobile DNA in Escherichia coli.Nature communications · 2025Article
- Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses.PLoS computational biology · 2025Article
- Competition effects regulating the composition of the microRNA pool.Journal of the Royal Society, Interface · 2025Article
- Transcription activation inEcoSal Plus · 2024Review
- Engineering Sequestration-Based Biomolecular Classifiers with Shared Resources.ACS synthetic biology · 2024Article
- Deletions of conserved extracytoplasmic function sigma factors-encoding genes in Streptomyces have a major impact on secondary metabolism.Microbial cell factories · 2024Article
- Context-dependent redesign of robust synthetic gene circuits.Trends in biotechnology · 2024Review
- (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner.Nature microbiology · 2024Article
- σCommunications biology · 2024Article
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- Strain-Specific Gifsy-1 Prophage Genes Are Determinants for Expression of the RNA Repair Operon during the SOS Response in Salmonella enterica Serovar Typhimurium.Journal of bacteriology · 2023Article
- Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete.Nature communications · 2023Article
- Transcriptional organization and regulation of theMicrobiology (Reading, England) · 2023Article
- Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria.Science (New York, N.Y.) · 2022Article
- Review
- Genome-wide promoter assembly inGenome research · 2022Article
- Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response.BMC bioinformatics · 2021Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sigma factors control global switches of the genetic expression program in bacteria. Different sigma factors compete for binding to a limited pool of RNA polymerase (RNAP) core enzymes, providing a mechanism for cross-talk between genes or gene classes via the sharing of expression machinery. To analyze the contribution of sigma factor competition to global changes in gene expression, we develop a theoretical model that describes binding between sigma factors and core RNAP, transcription, non-specific binding to DNA and the modulation of the availability of the molecular components. The model is validated by comparison with in vitro competition experiments, with which excellent agreement is found. Transcription is affected via the modulation of the concentrations of the different types of holoenzymes, so saturated promoters are only weakly affected by sigma factor competition. However, in case of overlapping promoters or promoters recognized by two types of sigma factors, we find that even saturated promoters are strongly affected. Active transcription effectively lowers the affinity between the sigma factor driving it and the core RNAP, resulting in complex cross-talk effects. Sigma factor competition is not strongly affected by non-specific binding of core RNAPs, sigma factors and holoenzymes to DNA. Finally, we analyze the role of increased core RNAP availability upon the shut-down of ribosomal RNA transcription during the stringent response. We find that passive up-regulation of alternative sigma-dependent transcription is not only possible, but also displays hypersensitivity based on the sigma factor competition. Our theoretical analysis thus provides support for a significant role of passive control during that global switch of the gene expression program.
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