ArticleBMC systems biology2008
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis.
Article in BMC systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Advances in genome-scale metabolic modeling of Bacillus subtilis.Biotechnology letters · 2026Review
- Complexity reduction by symmetry: Uncovering the minimal regulatory network for logical computation in bacteria.PLoS computational biology · 2025Article
- Mild Blast Exposure Dysregulates Metabolic Pathways and Correlation Networking as Evident from LC-MS-Based Plasma Profiling.Molecular neurobiology · 2025Article
- Exploring the Genome-wide Expression Level of the Bacterial Strain Belonging to Bacillus safensis (MM19) Against Phomopsis viticola.Current microbiology · 2024Article
- Bioinformatics in Russia: history and present-day landscape.Briefings in bioinformatics · 2024Review
- Efficient, Formal, Material, and Final Causes in Biology and Technology.Entropy (Basel, Switzerland) · 2023Article
- Dynamic Metabolic Control: From the Perspective of Regulation Logic.Synthetic biology and engineering · 2023Article
- Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.PLoS computational biology · 2023Review
- Are microbes and metabolites influencing the parental consumption of nestlings' feces in gray-backed shrikes?Current zoology · 2022Article
- Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria.BMC bioinformatics · 2021Article
- Statistical modelling of bacterial promoter sequences for regulatory motif discovery with the help of transcriptome data: application toJournal of the Royal Society, Interface · 2020Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
- Capacity for instantaneous catabolism of preferred and non-preferred carbon sources in Escherichia coli and Bacillus subtilis.Scientific reports · 2018Article
- Tri11, tri3, and tri4 genes are required for trichodermin biosynthesis of Trichoderma brevicompactum.AMB Express · 2018Article
- Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis.PloS one · 2018Article
- The Dynamical Emergence of Biology From Physics: Branching Causation via Biomolecules.Frontiers in physiology · 2018Article
- The Genome-Scale Integrated Networks in Microorganisms.Frontiers in microbiology · 2018Review
- Optimal resource allocation enables mathematical exploration of microbial metabolic configurations.Journal of mathematical biology · 2017Article
- The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes.Journal of biomedical semantics · 2017Article
- Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli.Molecular systems biology · 2017Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFew genome-scale models of organisms focus on the regulatory networks and none of them integrates all known levels of regulation. In particular, the regulations involving metabolite pools are often neglected. However, metabolite pools link the metabolic to the genetic network through genetic regulations, including those involving effectors of transcription factors or riboswitches. Consequently, they play pivotal roles in the global organization of the genetic and metabolic regulatory networks.
resultsWe report the manually curated reconstruction of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis (transcriptional, translational and post-translational regulations and modulation of enzymatic activities). We provide a systematic graphic representation of regulations of each metabolic pathway based on the central role of metabolites in regulation. We show that the complex regulatory network of B. subtilis can be decomposed as sets of locally regulated modules, which are coordinated by global regulators.
conclusionThis work reveals the strong involvement of metabolite pools in the general regulation of the metabolic network. Breaking the metabolic network down into modules based on the control of metabolite pools reveals the functional organization of the genetic and metabolic regulatory networks of B. subtilis.
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