Determination of the Core of a Minimal Bacterial Gene Set
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SUMMARY: The availability of a large number of complete genome sequences raises the question of how many genes are essential for cellular life. Trying to reconstruct the core of the protein-coding gene set for a hypothetical minimal bacterial cell, we have performed a computational comparative analysis of eight bacterial genomes. Six of the analyzed genomes are very small due to a dramatic genome size reduction process, while the other two, corresponding to free-living relatives, are larger. The available data from several systematic experimental approaches to define all the essential genes in some completely sequenced bacterial genomes were also considered, and a reconstruction of a minimal metabolic machinery necessary to sustain life was carried out. The proposed minimal genome contains 206 protein-coding genes with all the genetic information necessary for self-maintenance and reproduction in the presence of a full complement of essential nutrients and in the absence of environmental stress. The main features of such a minimal gene set, as well as the metabolic functions that must be present in the hypothetical minimal cell, are discussed.
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Estimating genome size of a minimal cell on basis of top-down analysis gives result in order of hundreds of genes.
“What we can do is to estimate the genome size of what is called a “minimal cell,” on the basis of a top-down analysis [124] but the result is still in the order of hundreds of genes.”
From Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems (2017) · cites this paper as [124]
The fpbA gene has been reported in several pathogenic species and in many LAB species.
“The latter gene, which was considered non-essential, has been reported in several pathogenic species and in many LAB species [56, 57].”
From EVALUATION OF ADHESIVE AND AGGREGATION PROPERTIES OF LACTIC ACID BACTERIA ISOLATED FROM DIFFERENT BIOTOPES (2025) · cites this paper as [57]
The Introduction discusses prfB and other genes in reduced bacterial genomes, but it does not address the reported distribution of fpbA. Searches for fpbA, the possible spelling fbpA, and lactic acid bacteria found no passage supporting its presence in pathogenic or LAB species; the copy’s discussion of prfB is about a different gene. (LLM, conf=0.74)
Experimental — accuracy not yet measuredFor the most primitive genome, the length is estimated by Gil et al to be around a value in nucleotides.
“For the most primitive genome, the length is estimated by Gil et al [5] to be around nucleotides”
From Lethal mutants and truncated selection together solve a paradox of the origin of life (2011) · cites this paper as [5]
The big gap between the maximum length maintainable in Eigen's theory and the primitive genome length is the famous error catastrophe paradox.
“The big gap between and is the famous error catastrophe paradox.”
From Lethal mutants and truncated selection together solve a paradox of the origin of life (2011) · cites this paper as [5]
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“The latter gene, which was considered non-essential, has been reported in several pathogenic species and in many LAB species [56, 57].”
Chasapi, A., Michailidis, A., Schriml, L. M., Donati, C., Kyrpides, N. C., & Ouzounis, C. A. (2026) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00403-25
- Authors
- Gil, R., Silva, F. J., Peretó, J., & Moya, A.
- Affiliations
- Universitat de València (ES)
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia
- Venue
- Microbiology and Molecular Biology Reviews
- Publisher
- American Society for Microbiology
- Published
- 2004-09
- Volume
- 68
- Issue
- 3
- Pages
- 518-537
- ISSN
- 1092-2172 (ISSN-L)
- 1098-5557
- PMC
- PMC515251
- OpenAlex
- W2115542536
- Cited by
- 573
- References
- 90
- Citations by year
- 2026: 12 · 2025: 27 · 2024: 8 · 2023: 17 · 2022: 19 · 2021: 31 · 2020: 26 · 2019: 23 · 2018: 21 · 2017: 30 · 2016: 24 · 2015: 31 · 2014: 41 · 2013: 27 · 2012: 45
- FWCI
- 2.03
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Microbiology and Molecular Biology Reviews (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- essential genes, gene essentiality, genome size reduction, comparative genomics, protein-coding genes, minimal cell, bacterial genomes
- MeSH terms
- Bacteria, Bacterial Proteins, Genes, Bacterial, Genome, Bacterial, Computational Biology
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