Sequence permutations in the molecular evolution of DNA methyltransferases
Open Access
- 1 January 2002
- journal article
- Published by Springer Nature in BMC Ecology and Evolution
- Vol. 2 (1), 3
- https://doi.org/10.1186/1471-2148-2-3
Abstract
DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the catalytic subdomain, and the target recognition domain (TRD), several classes of permutants have been proposed. The majority of known DNA MTases fall into the α, β, and γ classes. There is only one member of the ζ class known and no members of the δ and ε classes have been identified to date. Two mechanisms of permutation have been proposed: one involving gene duplication and in-frame fusion, and the other involving inter- and intragenic shuffling of gene segments. Two novel cases of sequence permutation in DNA MTases implicated in restriction-modification systems have been identified, which suggest that members of the δ and ζ classes (M.MwoI and M.TvoORF1413P, respectively) evolved from β-class MTases. This is the first identification of the δ-class MTase and the second known ζ-class MTase (the first ζ-class member among DNA:m4C and m6A-MTases). Fragmentation of a DNA MTase gene may result from attack of nucleases, for instance when the RM system invades a new cell. Its reassembly into a functional form, the order of motifs notwithstanding, may be strongly selected for, if the cognate ENase gene remains active and poses a threat to the host's chromosome. The "cut-and-paste" mechanism is proposed for β-δ permutation, which is non-circular and involves relocation of one segment of a gene. The circular β-ζ permutation may be explained both by gene duplication or shuffling of gene fragments. These two mechanisms are not mutually exclusive and probably both played a role in the evolution of permuted DNA MTases.Keywords
This publication has 39 references indexed in Scilit:
- Pcons: A neural‐network–based consensus predictor that improves fold recognitionProtein Science, 2001
- On the Evolution of Protein Folds: Are Similar Motifs in Different Protein Folds the Result of Convergence, Insertion, or Relics of an Ancient Peptide World?Journal of Structural Biology, 2001
- Genetic variation: molecular mechanisms and impact on microbial evolutionFEMS Microbiology Reviews, 2000
- On the Substrate Specificity of DNA MethyltransferasesPublished by Elsevier ,1999
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modelingElectrophoresis, 1997
- Structure-guided Analysis Reveals Nine Sequence Motifs Conserved among DNA Amino-methyl-transferases, and Suggests a Catalytic Mechanism for these EnzymesJournal of Molecular Biology, 1995
- Circular permutation of polypeptide chains: Implications for protein folding and stabilityProgress in Biophysics and Molecular Biology, 1995
- Characterization and cloning of MwoI (GCN7GC), a new type-II restriction-modification system from Methanobacterium wolfeiGene, 1989
- Cytosine-specific type II DNA methyltransferasesJournal of Molecular Biology, 1989