ArticleMolecular systems biology2014
A system-level model for the microbial regulatory genome.
Article in Molecular systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 73 citations in OpenAlex.
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- TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii.Nucleic acids research · 2024Article
- MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance.Cell reports · 2023Article
- Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli.mSystems · 2023Article
- The transcription factor network of E. coli steers global responses to shifts in RNAP concentration.Nucleic acids research · 2022Article
- Mathematical models to study the biology of pathogens and the infectious diseases they cause.iScience · 2022Review
- Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME.NPJ systems biology and applications · 2021Article
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- Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile.Cell host & microbe · 2021Article
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- Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma.NPJ precision oncology · 2021Article
- A systems-level gene regulatory network model for Plasmodium falciparum.Nucleic acids research · 2021Article
- Identifying Components of aFrontiers in microbiology · 2021Article
- A Bayesian non-parametric mixed-effects model of microbial growth curves.PLoS computational biology · 2020Article
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- Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum.mSystems · 2020Article
- Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.Journal of molecular biology · 2019Review
- The Primary Antisense Transcriptome ofGenes · 2019Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 3 countries.
Funding
Abstract
Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of the environment and genome-encoded regulatory programs of two types of prokaryotes: Escherichia coli (a bacterium) and Halobacterium salinarum (an archaeon). The models reveal how the genome-wide distributions of cis-acting gene regulatory elements and the conditional influences of transcription factors at each of those elements encode programs for eliciting a wide array of environment-specific responses. We demonstrate how these programs partition transcriptional regulation of genes within regulons and operons to re-organize gene-gene functional associations in each environment. The models capture fitness-relevant co-regulation by different transcriptional control mechanisms acting across the entire genome, to define a generalized, system-level organizing principle for prokaryotic gene regulatory networks that goes well beyond existing paradigms of gene regulation. An online resource (http://egrin2.systemsbiology.net) has been developed to facilitate multiscale exploration of conditional gene regulation in the two prokaryotes.
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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.