Cited by 166Bacterial Genetics and BiotechnologyGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

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Gene essentiality determines chromosome organisation in bacteria

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Rocha, E. P. C.·2003·Nucleic Acids Research

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Abstract

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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Rocha,E.P.C. and Danchin,A. (2003) An analysis of determinants of protein substitution rates in bacteria. Mol. Biol. Evol., in press.

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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
DOI: 10.1093/nar/gkg859
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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Gene essentiality determines chromosome organisation in bacteria

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