The DOI matches its Crossref record; 45 of the 46 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Sharp, P. M., & Li, W.-H. (1987) · Nucleic Acids Research · doi:10.1093/nar/15.3.1281 · Cited by 3,992
A genomic perspective on protein families.
Tatusov, R., Koonin, E., & Lipman, D. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,777
Essential Bacillus subtilis genes
Kobayashi, K., Ehrlich, S., Albertini, A., Amati, G., Andersen, K. K., Arnaud, M., Asai, K., Ashikaga, S., Aymerich, S., Bessières, P., et al. (2003) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0730515100 · Cited by 1,451
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., & Ishikawa, H. (2000) · Nature · doi:10.1038/35024074 · Cited by 1,338
Genome sequence of Yersinia pestis, the causative agent of plague
Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T. G., Prentice, M. B., Sebaihia, M., James, K., Churcher, C. M., Mungall, K. L., et al. (2001) · Nature · doi:10.1038/35097083 · Cited by 1,244
An evolutionary perspective on synonymous codon usage in unicellular organisms
Sharp, P. M., & Li, W. (1986) · Journal of Molecular Evolution · doi:10.1007/bf02099948 · Cited by 1,015
Global Transposon Mutagenesis and a Minimal Mycoplasma Genome
Hutchison, C. A., Peterson, S. N., Gill, S. R., Cline, R. T., White, O. R., Fraser, C. M., Smith, H. O., & Venter, J. C. (1999) · Science · doi:10.1126/science.286.5447.2165 · Cited by 925
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
Mushegian, A. R., & Koonin, E. V. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.19.10268 · Cited by 916
Nanodevice motion at microwave frequencies
Huang, X. M. H., Zorman, C. A., Mehregany, M., & Roukes, M. L. (2003) · Nature · doi:10.1038/421496a · Cited by 588
Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis
Ochman, H., & Moran, N. A. (2001) · Science · doi:10.1126/science.1058543 · Cited by 566
Research works printed but not linked: 1
- Rocha,E.P.C. and Danchin,A. (2003) An analysis of determinants of protein substitution rates in bacteria. Mol. Biol. Evol., in press.
Cited by
Sorted by citations
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
Koonin, E. V., & Wolf, Y. I. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn668 · Cited by 817
Sequence modeling and design from molecular to genome scale with Evo
Nguyen, E., Poli, M., Durrant, M. G., Kang, B., Katrekar, D., Li, D. B., Bartie, L. J., Thomas, A. W., King, S. H., Brixi, G., et al. (2024) · Science · doi:10.1126/science.ado9336 · Cited by 580
Dynamics of Pseudomonas aeruginosa genome evolution
Mathee, K., Narasimhan, G., Valdes, C., Qiu, X., Matewish, J. M., Koehrsen, M., Rokas, A., Yandava, C., Engels, R., Zeng, E., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0711982105 · Cited by 495
Biodegradation and Rhodococcus – masters of catabolic versatility
Larkin, M. J., Kulakov, L. A., & Allen, C. C. R. (2005) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2005.04.007 · Cited by 460
Rocha, E. P. C. (2004) · Genome Research · doi:10.1101/gr.2896904 · Cited by 416
Self-citation
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
