Integrative modeling of JCVI-Syn3A nucleoids with a modular approach
Open accessAbstract
A lattice-based method is presented for creating 3D models of entire bacterial nucleoids integrating ultrastructural information cryoelectron tomography, genomic and proteomic data, and experimental atomic structures of biomolecules and assemblies. The method is used to generate models of the minimal genome bacterium JCVI-Syn3A, producing a series of models that test hypotheses about transcription, condensation, and overall distribution of the genome. Lattice models are also used to generate atomic models of an entire JCVI-Syn3A cell.
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Structural models of Mycoplasma genitalium and JCVI-syn3A have also been created.
“Structural models of Mycoplasma genitalium and JCVI-syn3A have also been created.”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [9]
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Cites
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“The SMC loop and POL loop models represent two extremes that result from random insertion of SMC, which is likely found in many bacteria, and the single SMC insertion model is an alternate arrangement that has been observed in specific organisms, such as Bacillus subtilis (Wang et al. , 2017) .”
BackgroundEssential metabolism for a minimal cell
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“…cell JCVI-Syn3A was created with a synthetic genome containing essential genes from Mycoplasma mycoides , reducing the number of genes from 901 to 493, making it the organism with the smallest genome that can be grown in laboratory culture (Breuer et al., 2019; Hutchison et al., 2016).”
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Cited by
Sorted by citations
Bringing the genetically minimal cell to life on a computer in 4D
Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44 · see citing works
- Authors
- Goodsell, D. S., & Autin, L.
- Affiliations
- Rutgers, The State University of New Jersey (US)
- Scripps Research Institute (US)
- Corresponding author
- Goodsell, David S.
- Venue
- Current Research in Structural Biology
- Publisher
- Elsevier BV
- Published
- 2024
- Volume
- 7
- Pages
- 100121
- ISSN
- 2665-928X (ISSN-L)
- PMC
- PMC10784680
- OpenAlex
- W4390108568
- Cited by
- 6
- References
- 8
- Citations by year
- 2026: 4 · 2024: 2
- FWCI
- 0.53
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Current Research in Structural Biology (publishedVersion, cc-by)
- SSRN Electronic Journal (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (GM120604)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- bacterial nucleoid, 3D genome organization, cryo-electron tomography, transcription, genome distribution, modular modeling
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