Evidence for selection on SARS-CoV-2 RNA translation revealed by the evolutionary dynamics of mutations in UTRs and CDSs

References

• Crick F. Central dogma of molecular biology. Nature. 1970;227(5258):561–563.
   PubMed Web of Science ®Google Scholar
• Wang Y, Gai Y, Li Y, et al. SARS-CoV-2 has the advantage of competing the iMet-tRNAs with human hosts to allow efficient translation. Mol Genet Genomics. 2021;296(1):113–118.
   PubMed Web of Science ®Google Scholar
• Li Y, Yang X, Wang N, et al. GC usage of SARS-CoV-2 genes might adapt to the environment of human lung expressed genes. Mol Genet Genomics. 2020;295(6):1537–1546.
   PubMed Web of Science ®Google Scholar
• Chu D, Wei L. Direct in vivo observation of the effect of codon usage bias on gene expression in Arabidopsis hybrids. J Plant Physiol. 2021;265:153490.
   PubMed Web of Science ®Google Scholar
• Yu YY, Li Y, Dong Y, et al. Natural selection on synonymous mutations in SARS-CoV-2 and the impact on estimating divergence time. Future Virol. 2021;16(7):447–450.
   Web of Science ®Google Scholar
• Quax TEF, Claassens NJ, Soll D, et al. Codon bias as a means to fine-tune gene expression. Mol Cell. 2015;59(2):149–161.
   PubMed Web of Science ®Google Scholar
• Zhao S, Song S, Qi Q, et al. Cost-efficiency tradeoff is optimized in various cancer types revealed by genome-wide analysis. Mol Genet Genomics. 2021;296(2):369–378.
   PubMed Web of Science ®Google Scholar
• Chu D, Wei L. Characterizing the heat response of Arabidopsis thaliana from the perspective of codon usage bias and translational regulation. J Plant Physiol. 2019;240:153012.
   PubMed Web of Science ®Google Scholar
• Akirtava C, McManus CJ. Control of translation by eukaryotic mRNA transcript leaders-Insights from high-throughput assays and computational modeling. Wiley Interdiscip Rev RNA. 2021;12(3):e1623.
   PubMed Web of Science ®Google Scholar
• Hata T, Satoh S, Takada N, et al. Kozak sequence acts as a negative regulator for de novo transcription initiation of newborn coding sequences in the plant genome. Mol Biol Evol. 2021;38(7):2791–2803.
   PubMed Web of Science ®Google Scholar
• Wang Y, Wang F, Xu S, et al. Optimization of a 2A self-cleaving peptide-based multigene expression system for efficient expression of upstream and downstream genes in silkworm. Mol Genet Genomics. 2019;294(4):849–859.
   PubMed Web of Science ®Google Scholar
• Xu G, Yuan M, Ai C, et al. uORF-mediated translation allows engineered plant disease resistance without fitness costs. Nature. 2017;545(7655):491–494.
   PubMed Web of Science ®Google Scholar
• Leppek K, Das R, Barna M. Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol. 2018;19(3):158–174.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Jin X, Wang H, et al. SARS-CoV-2 competes with host mRNAs for efficient translation by maintaining the mutations favorable for translation initiation. J Appl Genet. 2022;63(1):159–167.
   PubMed Web of Science ®Google Scholar
• Hall MN, Gabay J, Debarbouille M, et al. A role for mRNA secondary structure in the control of translation initiation. Nature. 1982;295(5850):616–618.
   PubMed Web of Science ®Google Scholar
• Yu CH, Dang Y, Zhou Z, et al. Codon usage influences the local rate of translation elongation to regulate co-translational protein folding. Mol Cell. 2015;59(5):744–754.
   PubMed Web of Science ®Google Scholar
• Li Q, Li J, Yu C-P, et al. Synonymous mutations that regulate translation speed might play a non-negligible role in liver cancer development. BMC Cancer. 2021;21(1):388.
   PubMed Web of Science ®Google Scholar
• Wei L. Selection on synonymous mutations revealed by 1135 genomes of Arabidopsis thaliana. Evol Bioinform Online. 2020;16:1176934320916794.
   Web of Science ®Google Scholar
• Eyre-Walker A. The genomic rate of adaptive evolution. Trends Ecol Evol. 2006;21(10):569–575.
   PubMed Web of Science ®Google Scholar
• Kimura M. The neutral theory of molecular evolution. Sci Am. 1979;241(5):98–100.
   PubMed Web of Science ®Google Scholar
• Chang S, Li J, and Li Q, et al. Retrieving the deleterious mutations before extinction: genome-wide comparison of shared derived mutations in liver cancer and normal population. Postgrad Med J. 2021. http://dx.doi.org/10.1136/postgradmedj-2021-139993
   Web of Science ®Google Scholar
• Zhang YP, Jiang W, Li Y, et al. Fast evolution of SARS-CoV-2 driven by deamination systems in hosts. Future Virol. 2021;16(9):587–590.
   PubMed Web of Science ®Google Scholar
• Shu Y, and McCauley J. GISAID: global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017;22(13). https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494
   Google Scholar
• Plante JA, Liu Y, Liu J, et al. Spike mutation D614G alters SARS-CoV-2 fitness. Nature. 2021;592(7852):116–121.
   PubMed Web of Science ®Google Scholar
• Volz E, Hill V, McCrone JT, et al. Evaluating the effects of sars-cov-2 spike mutation d614g on transmissibility and pathogenicity. Cell. 2021;184(1):64–75 e11.
   PubMed Web of Science ®Google Scholar
• Lu L, Chu AW, Zhang RR, et al. The impact of spike N501Y mutation on neutralizing activity and RBD binding of SARS-CoV-2 convalescent serum. EBioMedicine. 2021;71:103544.
   PubMed Web of Science ®Google Scholar
• Tian F, Tong B, and Sun L, et al. N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2. Elife. 2021;10. https://doi.org/10.7554/eLife.69091
   Web of Science ®Google Scholar
• Li Y, Yang XN, Wang N, et al. The divergence between SARS-CoV-2 and RaTG13 might be overestimated due to the extensive RNA modification. Future Virol. 2020;15(6):341–347.
   Web of Science ®Google Scholar
• Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31(13):3429–3431.
   PubMed Web of Science ®Google Scholar
• Sun L, Li P, Ju X, et al. In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs. Cell. 2021;184(7):1865–1883. e1820.
   PubMed Web of Science ®Google Scholar
• Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673–4680.
   PubMed Web of Science ®Google Scholar
• Miller JB, Brase LR, Ridge PG. ExtRamp: a novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness. NAR. 2019;47(3):1123–1131.
   PubMed Web of Science ®Google Scholar
• Martignano F, Di Giorgio S, Mattiuz G, et al. Commentary on “poor evidence for host-dependent regular RNA editing in the transcriptome of SARS-CoV-2”. J Appl Genet. 2022;63(2):423–428.
   PubMed Web of Science ®Google Scholar
• Zong J, Zhang Y, Guo F, et al. Poor evidence for host-dependent regular RNA editing in the transcriptome of SARS-CoV-2. J Appl Genet. 2022;63(2):413–421.
   PubMed Web of Science ®Google Scholar
• Li Y, Yang XN, Wang N, et al. Pros and cons of the application of evolutionary theories to the evolution of SARS-CoV-2. Future Virol. 2020;15(6):369–372.
   Web of Science ®Google Scholar
• Liu X, Liu X, Zhou J, et al. Rampant C-to-U deamination accounts for the intrinsically high mutation rate in SARS-CoV-2 spike gene. RNA. 2022. DOI:10.1261/rna.079160.122
   Web of Science ®Google Scholar
• Di Giorgio S, Martignano F, Torcia MG, et al. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2. Sci Adv. 2020;6(25):eabb5813.
   PubMed Web of Science ®Google Scholar
• Li Y, Yang X, Wang N, et al. Mutation profile of over 4500 SARS-CoV-2 isolations reveals prevalent cytosine-to-uridine deamination on viral RNAs. Future Microbiol. 2020;15:1343–1352.
   PubMed Web of Science ®Google Scholar
• Cai H, Liu X, Zheng X. RNA editing detection in SARS-CoV-2 transcriptome should be different from traditional SNV identification. J Appl Genet. 2022. DOI:10.1007/s13353-022-00706-y
   PubMed Web of Science ®Google Scholar
• Wei L. Reconciling the debate on deamination on viral RNA. J Appl Genet. 2022. DOI:10.1007/s13353-022-00698-9
   Web of Science ®Google Scholar