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Skewed oligomers and origins of replication
Open accessAbstract
The putative origin of replication in prokaryotic genomes can be located by a new method that finds short oligomers whose orientation is preferentially skewed around the origin. The skewed oligomer method is shown to work for all bacterial genomes and one of three archaeal genomes sequences to date, confirming known or predicted origins in most cases and in three cases (H. pylori, M. thermoautotrophicum, and Synechocystis sp.), suggesting origins that were previously unknown. In many cases, the presence of conserved genes and nucleotide motifs confirms the predictions. An algorithm for finding these skewed seven-base and eight-base sequences is described, along with a method for combining evidence from multiple skewed oligomers to accurately locate the replication origin. Possible explanations for the phenomenon of skewed oligomers are discussed. Explanations are presented for why some bacterial genomes contain hundreds of highly skewed oligomers, whereas others contain only a handful.
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Cites
The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessières, P., Bolotin, A., Borchert, S., et al. (1997) · Nature · doi:10.1038/36786 · Cited by 3,679
Cited by
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
Salzberg, S. L., Sommer, D. D., Schatz, M. C., Phillippy, A. M., Rabinowicz, P. D., Tsuge, S., Furutani, A., Ochiai, H., Delcher, A. L., Kelley, D., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-204 · Cited by 371
Self-citationEvolution of prokaryotic gene order: genome rearrangements in closely related species
Suyama, M., & Bork, P. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(00)02159-4 · Cited by 169
Chromosomal constraints in Gram‐positive bacteria revealed by artificial inversions
Campo, N., Dias, M. J., Daveran‐Mingot, M. ‐., Ritzenthaler, P., & Le Bourgeois, P. (2004) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03847.x · Cited by 68
Metadata
- Authors
- Salzberg, S. L., Salzberg, A. J., Kerlavage, A. R., & Tomb, J.-F.
- Venue
- Gene
- Publisher
- Elsevier BV
- Published
- 1998-09
- Volume
- 217
- Issue
- 1-2
- Pages
- 57-67
- ISSN
- 0378-1119 (ISSN-L)
- OpenAlex
- W1988035696
- Cited by
- 179
- References
- 1
- FWCI
- 5.18
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Salzberg, S. L., Salzberg, A. J., Kerlavage, A. R., & Tomb, J.-F. (1998). Skewed oligomers and origins of replication. Gene. https://doi.org/10.1016/s0378-1119(98)00374-6
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
