ArticleNucleic acids research2013
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Surfactin-Like Lipopeptides FromFrontiers in bioengineering and biotechnology · 2021Pooled it
- Advances in genome-scale metabolic modeling of Bacillus subtilis.Biotechnology letters · 2026Review
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Longitudinal big biological data in the AI era.Molecular systems biology · 2025Review
- The DnaJK chaperone ofmBio · 2025Article
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- Standards, dissemination, and best practices in systems biology.Current opinion in biotechnology · 2023Review
- New Insights on Metabolic Features ofInternational journal of molecular sciences · 2023Article
- Greedy reduction of Bacillus subtilis genome yields emergent phenotypes of high resistance to a DNA damaging agent and low evolvability.Nucleic acids research · 2023Article
- The media composition as a crucial element in high-throughput metabolic network reconstruction.Interface focus · 2023Article
- ecBSU1: A Genome-Scale Enzyme-Constrained Model ofMicroorganisms · 2023Article
- In silico-guided metabolic engineering of Bacillus subtilis for efficient biosynthesis of purine nucleosides by blocking the key backflow nodes.Biotechnology for biofuels and bioproducts · 2022Article
- Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening ofInternational journal of molecular sciences · 2022Article
- Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis.Nucleic acids research · 2021Article
- Advances on systems metabolic engineering ofSynthetic and systems biotechnology · 2020Article
- Screening of a genome-reduced Corynebacterium glutamicum strain library for improved heterologous cutinase secretion.Microbial biotechnology · 2020Article
- A bacterial cell factory converting glucose into scyllo-inositol, a therapeutic agent for Alzheimer's disease.Communications biology · 2020Article
- High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities.Environmental microbiology · 2020Article
- Multiple integration of the gene ganA into the Bacillus subtilis chromosome for enhanced β-galactosidase production using the CRISPR/Cas9 system.AMB Express · 2019Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
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10 authors.
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Abstract
The nonessential regions in bacterial chromosomes are ill-defined due to incomplete functional information. Here, we establish a comprehensive repertoire of the genome regions that are dispensable for growth of Bacillus subtilis in a variety of media conditions. In complex medium, we attempted deletion of 157 individual regions ranging in size from 2 to 159 kb. A total of 146 deletions were successful in complex medium, whereas the remaining regions were subdivided to identify new essential genes (4) and coessential gene sets (7). Overall, our repertoire covers ~76% of the genome. We screened for viability of mutant strains in rich defined medium and glucose minimal media. Experimental observations were compared with predictions by the iBsu1103 model, revealing discrepancies that led to numerous model changes, including the large-scale application of model reconciliation techniques. We ultimately produced the iBsu1103V2 model and generated predictions of metabolites that could restore the growth of unviable strains. These predictions were experimentally tested and demonstrated to be correct for 27 strains, validating the refinements made to the model. The iBsu1103V2 model has improved considerably at predicting loss of viability, and many insights gained from the model revisions have been integrated into the Model SEED to improve reconstruction of other microbial models.
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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.