ArticleFrontiers in molecular biosciences2019
Kinetic Modeling of the Genetic Information Processes in a Minimal Cell.
Article in Frontiers in molecular biosciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 22 citations in OpenAlex.
- Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.The journal of physical chemistry. B · 2026Article
- Meeting Proceedings from 4th Minimal Cell Workshop: Exploring JCVI Minimal Cell Fundamental Insights and Integrative Applications.ACS synthetic biology · 2025Article
- Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli.NPJ systems biology and applications · 2024Article
- Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- Cell-Free Expression System Derived from a Near-Minimal Synthetic Bacterium.ACS synthetic biology · 2023Article
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- Integrative illustration of a JCVI-syn3A minimal cell.Journal of integrative bioinformatics · 2022Article
- Article
- Traditional protocols and optimization methods lead to absent expression in a mycoplasma cell-free gene expression platform.Synthetic biology (Oxford, England) · 2022Article
- Integrating experiments, theory and simulations into whole-cell models.Nature methods · 2021Article
- Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps.Frontiers in molecular biosciences · 2021Article
- A Multi-Scale Approach to ModelingEntropy (Basel, Switzerland) · 2020Article
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
JCVI-syn3A is a minimal bacterial cell with a 543 kbp genome consisting of 493 genes. For this slow growing minimal cell with a 105 min doubling time, we recently established the essential metabolism including the transport of required nutrients from the environment, the gene map, and genome-wide proteomics. Of the 452 protein-coding genes, 143 are assigned to metabolism and 212 are assigned to genetic information processing. Using genome-wide proteomics and experimentally measured kinetic parameters from the literature we present here kinetic models for the genetic information processes of DNA replication, replication initiation, transcription, and translation which are solved stochastically and averaged over 1,000 replicates/cells. The model predicts the time required for replication initiation and DNA replication to be 8 and 50 min on average respectively and the number of proteins and ribosomal components to be approximately doubled in a cell cycle. The model of genetic information processing when combined with the essential metabolic and cell growth networks will provide a powerful platform for studying the fundamental principles of life.
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