Evolutionary Origins and Functional Diversification of 2′-O-Methyltransferases: Insights from Phylogenetic and Structural Analysis
Abstract
1. Introduction
2. Results
2.1. Literature-Based Collection of 2′-O-MTases Reveals 11 Distinct MTase Domains for Nm Catalyzation
2.2. Phylogenetic Distribution of the 11 MTase Domain-Containing Proteins Suggests Ancient and Life Kingdom-Specific Origins of 2′-O-MTases
2.3. Diverse Domain Architectures of 2′-O-MTases
2.4. Evolutionary Features of Sequence and Structure of 2′-O-MTases
2.5. Ancient Divergence and Substrate-Adaptive Evolution of the FtsJ Protein Family
3. Discussion
4. Materials and Methods
4.1. Identification of 2′-O-MTase-Conserved, Methyltransferase-Associated Domains
4.2. Identification of 2′-O-MTases Across the Tree of Life
4.3. Domain Architecture Pattern Analysis
4.4. Multiple-Sequence Alignment and Phylogenetic Analysis
4.5. Ka/Ks Analysis
4.6. Structural Similarity Analysis and Clustering
4.7. Polyphony Analysis
4.8. Motif Identification
4.9. Tetrahedron KDKE Volume Calculation and Pairwise Distance Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
Nm | 2′-O-methylation |
2′-O-MTase | 2′-O-methyltransferase |
MTase | Methyltransferase |
LUCA | Last Universal Common Ancestor |
Ka | Nonsynonymous substitution rate |
Ks | Synonymous substitution rate |
m6A | N6-methyladenosine |
m5C | 5-methylcytosine |
m1A | N1-methyladenosine |
m7G | N7-methylguanosine |
ac4C | N4-acetylcytosine |
Ψ | pseudouridine |
SAM | S-adenosylmethionine |
piRNA | Piwi-interacting RNA |
miRNA | MicroRNA |
snoRNP | Small nucleolar ribonucleoprotein |
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Wang, S.-N.; Liu, X.-X.; Lei, L.-J.; Wang, Q.; Shao, Z.-Q.; Liu, Y. Evolutionary Origins and Functional Diversification of 2′-O-Methyltransferases: Insights from Phylogenetic and Structural Analysis. Int. J. Mol. Sci. 2025, 26, 5260. https://doi.org/10.3390/ijms26115260
Wang S-N, Liu X-X, Lei L-J, Wang Q, Shao Z-Q, Liu Y. Evolutionary Origins and Functional Diversification of 2′-O-Methyltransferases: Insights from Phylogenetic and Structural Analysis. International Journal of Molecular Sciences. 2025; 26(11):5260. https://doi.org/10.3390/ijms26115260
Chicago/Turabian StyleWang, Sai-Nan, Xiao-Xia Liu, Ling-Jie Lei, Qiang Wang, Zhu-Qing Shao, and Yang Liu. 2025. "Evolutionary Origins and Functional Diversification of 2′-O-Methyltransferases: Insights from Phylogenetic and Structural Analysis" International Journal of Molecular Sciences 26, no. 11: 5260. https://doi.org/10.3390/ijms26115260
APA StyleWang, S.-N., Liu, X.-X., Lei, L.-J., Wang, Q., Shao, Z.-Q., & Liu, Y. (2025). Evolutionary Origins and Functional Diversification of 2′-O-Methyltransferases: Insights from Phylogenetic and Structural Analysis. International Journal of Molecular Sciences, 26(11), 5260. https://doi.org/10.3390/ijms26115260