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Gene essentiality determines chromosome organisation in bacteria
Open accessAbstract
In Escherichia coli and Bacillus subtilis, essentiality, not expressivity, drives the distribution of genes between the two replicating strands. Although essential genes tend to be coded in the leading replicating strand, the underlying selective constraints and the evolutionary extent of these findings have still not been subject to comparative studies. Here, we extend our previous analysis to the genomes of low G + C firmicutes and gamma-proteobacteria, and in a second step to all sequenced bacterial genomes. The inference of essentiality by homology allows us to show that essential genes are much more frequent in the leading strand than other genes, even when compared with non- essential highly expressed genes. Smaller biases were found in the genomes of obligatory intracellular bacteria, for which the assignment of essentiality by homology from fast growing free-living bacteria is most problematic. Cross-comparisons used to assess potential errors in the assignment of essentiality by homology revealed that, in most cases, variations in the assignment criteria have little influence on the overall results. Essential genes tend to be more conserved in the leading strand than average genes, which is consistent with selection for this positioning and may impose a strong constraint on chromosomal rearrangements. These results indicate that essentiality plays a fundamental role in the distribution of genes in most bacterial genomes.
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“even a single-nucleotide mutation in an essential gene can be incompatible with life if it disrupts that gene’s expression or function (72).”
From Sequence modeling and design from molecular to genome scale with Evo (2024) · cites this paper as [72]
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Metadata
- Authors
- Rocha, E. P. C.
- Affiliations
- Institut Pasteur (FR)
- Corresponding author
- Rocha, E. P. C.
- ORCID
- Rocha, E. P. C.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-11-15
- Volume
- 31
- Issue
- 22
- Pages
- 6570-6577
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC275555
- OpenAlex
- W2160736206
- Cited by
- 166
- References
- 46
- Citations by year
- 2026: 3 · 2025: 2 · 2024: 6 · 2023: 4 · 2022: 6 · 2021: 4 · 2020: 11 · 2019: 3 · 2018: 14 · 2017: 10 · 2016: 6 · 2015: 7 · 2014: 10 · 2013: 8 · 2012: 12
- FWCI
- 3.35
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- gene essentiality, chromosome organization, Escherichia coli, Bacillus subtilis, gene expression, chromosomal rearrangements, obligate intracellular bacteria, low G+C Gram-positive bacteria, Gammaproteobacteria, comparative genomics
- MeSH terms
- Bacillus subtilis, Bacteria, Base Composition, Chromosomes, Bacterial, DNA Replication, DNA, Bacterial, Escherichia coli, Genes, Bacterial, Haemophilus influenzae, Genome, Bacterial, Genes, Essential, Mycoplasma genitalium
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