Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes
Open accessAbstract
Short palindromic sequences (4, 5 and 6 bp palindromes) are avoided at a statistically significant level in the genomes of several bacteria, including the completely sequenced Haemophilus influenzae and Synechocystis sp. genomes and in the complete genome of the archaeon Methanococcus jannaschii. In contrast, there is only moderate avoidance of palindromes in the small genome of the bacterium Mycoplasma genitalium and no detectable avoidance in the genomes of chloroplasts and mitochondria. The sites for type II restriction-modification enzymes detected in the given species tend to be among the most avoided palindromes in a particular genome, indicating a direct connection between the avoidance of short oligonucleotide words and restriction-modification systems with the respective specificity. Palindromes corresponding to sites for restriction enzymes from other species are also avoided, albeit less significantly, suggesting that in the course of evolution bacterial DNA has been exposed to a wide spectrum of restriction enzymes, probably as the result of lateral transfer mediated by mobile genetic elements, such as plasmids and prophages. Palindromic words appear to accumulate in DNA once it becomes isolated from restriction-modification systems, as demonstrated by the case of organellar genomes. By combining these observations with protein sequence analysis, we show that the most avoided 4-palindrome and the most avoided 6-palindrome in the archaeon M.jannaschii are likely to be recognition sites for two novel restriction-modification systems.
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The chromosomal inversion was probably initiated from the symmetrically distributed RERS of the internal region of the LIR and mediated by the restriction enzyme.
“These molecular evidences suggested that the chromosomal inversion was probably initiated from the symmetrically distributed RERS of the internal region of the LIR and mediated by the restriction enzyme as previously proposed.41 , 42”
From Whole genomic DNA sequencing and comparative genomic analysis of<i>Arthrospira platensis</i>: high genome plasticity and genetic diversity (2016) · cites this paper as [42]
The Introduction (p. 1) and Functional and evolutionary interpretations (p. 9) discuss avoidance of palindromic restriction sites and possible DNA cleavage by restriction enzymes. Neither those passages nor searches for chromosomal inversion, RERS, and LIR address the proposed initiation or mediation of this inversion. (LLM, conf=0.78)
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- Authors
- Gelfand, M. S., & Koonin, E. V.
- Affiliations
- Russian Academy of Sciences (RU)
- National Institutes of Health (US)
- Corresponding author
- Gelfand, M. S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1997-06-01
- Volume
- 25
- Issue
- 12
- Pages
- 2430-2439
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1995031
- OpenAlex
- W2099533874
- Cited by
- 134
- References
- 33
- Citations by year
- 2026: 3 · 2025: 1 · 2024: 1 · 2023: 3 · 2022: 3 · 2021: 5 · 2020: 3 · 2019: 2 · 2018: 7 · 2017: 2 · 2016: 4 · 2015: 5 · 2014: 6 · 2013: 8 · 2012: 9
- FWCI
- 2.81
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- U.S. Department of Energy
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- palindromic sequences, restriction-modification systems, type II restriction enzymes, bacterial genomes, archaeal genomes, Methanococcus jannaschii, Haemophilus influenzae, Synechocystis, Mycoplasma genitalium, chloroplast genome, mitochondrial genome, horizontal gene transfer, mobile genetic elements
- MeSH terms
- Cyanobacteria, Archaea, Bacteria, Base Sequence, Chloroplasts, Haemophilus influenzae, Mathematics, Mitochondria, Models, Genetic, Mycoplasma, Organelles, Genome, Bacterial, Methanococcus
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