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Molecular evolution of Protein Sequences and Codon Usage in Monkeypox Viruses

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 89-97页

作者： Ke-Jia Shan Changcheng Wu Xiaolu Tang Roujian Lu Yaling Hu Wenjie Tan Jian Lu State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China Sinovac Biotech Ltd. Beijing 100085China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 100052China

The monkeypox virus(mpox virus,MPXV)epidemic in 2022 has posed a significant public health ***,the evolutionary principles of MPXV remain largely ***,we examined the evolutionary patterns of protein sequences and codon usage in *** first demonstrated the signal of positive selection in OPG027,specifically in the CladeⅠlineage of ***,we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 ***,we showed strong epistasis between amino acid substitutions located in different *** codon adaptation index(CAI)analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes,and the CAI decreased over time and diverged between clades,with CladeⅠ>Ⅱa andⅡb-A>Ⅱ*** the decrease in fatality rate among the three groups aligned with the CAI pattern,it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality *** study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.

关键词： Mpox virus Positive selection OPG027 accelerated evolution Codon usage bias

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Molecular evolution of scorpion α-toxins——accelerated substitutions and functional divergence

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Progress in Natural Science:Materials International 2002年第2期 30-36+84页

作者： ZHU Shunyi and LI Wenxin(Department of Biotechnology, College of Life Sciences, Wuhan University, Wuhan 430072, China)

Scorpion a-toxins are a family of toxic proteins with similar scaffold, but possess divergent pharmacological properties. Analysis of cDNA sequences reveals that the numbers of nucleotide substitutions per site (K) for 5’ and 3’ UTRs are smaller than those per synonymous site (Ks) for the mature peptide-coding sequences, whereas the numbers of nucleotide substitutions per nonsynonymous site (Ka) are close to or larger than Ks values for relevant pairs of cDNAs. These results, together with phylogenetic analysis, indicate that scorpion α-toxins have evolved by accelerated substitutions in the mature toxin regions. In addition, the 15 amino acids, absolutely conserved in all the scorpion α-toxins described so far, are mostly located in molecular interior, which may be involved in structural constraints for stabilizing the CSαβ fold in evolution of these molecules- Four hot spot mutation sites in the molecular surface are found to distribute in the putative functional regions of a-toxins, suggesting th

关键词： scorpion α-toxins cDNA accelerated evolution functional divergence.

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