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Adaptive evolution of a minimal organism with a synthetic genome
Open accessAbstract
The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with a minimized synthetic genome, derived from the Mycoplasma mycoides genome and chemically synthesized in vitro. Here we report the experimental evolution of a syn3.0-derived strain. Ten independent replicates were evolved for several hundred generations, leading to growth rate improvements of >15%. Endpoint strains possessed an average of 8 mutations composed of indels and SNPs, with a pronounced C/G->A/T transversion bias. Multiple genes were repeated mutational targets across the independent lineages, including phase variable lipoprotein activation, 5 distinct nonsynonymous substitutions in the same membrane transporter protein, and inactivation of an uncharacterized gene. Transcriptomic analysis revealed an overall tradeoff reflected in upregulated ribosomal proteins and downregulated DNA and RNA related proteins during adaptation. This work establishes the suitability of synthetic, minimal strains for laboratory evolution, providing a means to optimize strain growth characteristics and elucidate gene functionality.
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Analysis of DNA sequencing coverage data from a recent evolution study found ori:ter values ranging from 1.0 to 1.2.
“As additional validation for the ori:ter ratio of 1.21, we analyzed DNA sequencing coverage data from a recent study that tracked the evolution of Syn3A over 400 generations and found values ranging from 1.0 to 1.2.20”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [20]
A similar observation was made in the evolutionary study, where mutations frequently arose in tetM.
“A similar observation was made in the evolutionary study mentioned above, where mutations frequently arose in tetM.20”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [20]
Many genes are transcribed cooperatively into polycistronic RNA.
“It is known that many genes are transcribed cooperatively into polycistronic RNA,20”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [20]
The Results discuss RNA-seq expression patterns, and the Transcriptomics methods describe RNA sequencing, but neither addresses whether multiple genes are transcribed into polycistronic RNA. Searches for polycistronic transcripts and operons found no passage supporting the claim. (LLM, conf=0.72)
Experimental — accuracy not yet measuredFor 10 evolutionary endpoints, the ori:ter ratios were 1.06, 1.10, 1.05, 1.13, 1.12, 1.07, 1.02, 1.12, 1.19, and 1.16.
“The ratios were 1.06 (endpoint a1: 365/345), 1.10 (endpoint a2: 217/197), 1.05 (endpoint a3: 281/267), 1.13 (endpoint a4: 268/237), 1.12 (endpoint a5: 200/178), 1.07 (endpoint a6: 158/148), 1.02 (endpoint a7: 246/242), 1.12 (endpoint a8: 195/174), 1.19 (endpoint a9: 238/200), and 1.16 (endpoint a10: 243/210).”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [20]
The Results describe ten evolved lineages and endpoint clones, but do not report ori:ter ratios for them. Searches of our copy for the ratio values, the listed numerators and denominators, and origin-to-terminus replication coverage found no passage supporting those measurements. The Methods discuss genome sequencing without giving the claimed ratios. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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Metadata
- Authors
- Sandberg, T. E., Wise, K. S., Dalldorf, C., Szubin, R., Feist, A. M., Glass, J. I., & Palsson, B. O.
- Affiliations
- University of California San Diego (US)
- J. Craig Venter Institute (US)
- Novo Nordisk Foundation (DK)
- Venue
- iScience
- Publisher
- Elsevier BV
- Published
- 2023-09
- Volume
- 26
- Issue
- 9
- Pages
- 107500
- ISSN
- 2589-0042 (ISSN-L)
- PMC
- PMC10448532
- OpenAlex
- W4385323819
- Cited by
- 23
- References
- 27
- Citations by year
- 2026: 6 · 2025: 4 · 2024: 11 · 2023: 2
- FWCI
- 2.56
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- iScience (publishedVersion, cc-by-nc-nd)
- SSRN Electronic Journal (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Foundation (MCB 2221237, MCB 1840301, MCB 1840320, MCB 1818344)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- experimental evolution, adaptive evolution, Mycoplasma mycoides, growth rate optimization, membrane transporters, gene function
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