Synonymous mutations in consultant yeast genes are largely strongly non-neutral
Kimura, M. Genetic variability maintained in a finite inhabitants on account of mutational manufacturing of impartial and almost impartial isoalleles. Genet Res 11, 247–269 (1968).
Google Scholar
King, J. L. & Jukes, T. H. Non-Darwinian evolution. Science 164, 788–798 (1969).
Google Scholar
Nei, M. & Kumar, S. Molecular Evolution and Phylogenetics (Oxford Univ. Press, 2000).
Li, W.-H. Molecular Evolution (Sinauer, 1997).
Graur, D., Sater, A. Okay. & Cooper, T. F. Molecular and Genome Evolution (Sinauer, 2016).
Hershberg, R. & Petrov, D. A. Choice on codon bias. Annu. Rev. Genet. 42, 287–299 (2008).
Google Scholar
Chamary, J. V., Parmley, J. L. & Hurst, L. D. Listening to silence: non-neutral evolution at synonymous websites in mammals. Nat. Rev. Genet. 7, 98–108 (2006).
Google Scholar
Plotkin, J. B. & Kudla, G. Synonymous however not the identical: the causes and penalties of codon bias. Nat. Rev. Genet. 12, 32–42 (2011).
Google Scholar
Stergachis, A. B. et al. Exonic transcription issue binding directs codon alternative and impacts protein evolution. Science 342, 1367–1372 (2013).
Google Scholar
Zhou, Z. et al. Codon utilization is a vital determinant of gene expression ranges largely by its results on transcription. Proc. Natl Acad. Sci. USA 113, E6117–E6125 (2016).
Google Scholar
Park, C., Chen, X., Yang, J. R. & Zhang, J. Differential necessities for mRNA folding partially clarify why extremely expressed proteins evolve slowly. Proc. Natl Acad. Sci. USA 110, E678–E686 (2013).
Google Scholar
Presnyak, V. et al. Codon optimality is a serious determinant of mRNA stability. Cell 160, 1111–1124 (2015).
Google Scholar
Chen, S. et al. Codon-resolution evaluation reveals a direct and context-dependent impression of particular person synonymous mutations on mRNA degree. Mol. Biol. Evol. 34, 2944–2958 (2017).
Google Scholar
Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255–258 (2009).
Google Scholar
Qian, W., Yang, J. R., Pearson, N. M., Maclean, C. & Zhang, J. Balanced codon utilization optimizes eukaryotic translational effectivity. PLoS Genet. 8, e1002603 (2012).
Google Scholar
Frumkin, I. et al. Codon utilization of extremely expressed genes impacts proteome-wide translation effectivity. Proc. Natl Acad. Sci. USA 115, E4940–E4949 (2018).
Google Scholar
Akashi, H. Synonymous codon utilization in Drosophila melanogaster: pure choice and translational accuracy. Genetics 136, 927–935 (1994).
Google Scholar
Solar, M. & Zhang, J. Most well-liked synonymous codons are translated extra precisely: proteomic proof, among-species variation, and mechanistic foundation. Sci. Adv. (within the press).
Buhr, F. et al. Synonymous codons direct cotranslational folding towards completely different protein conformations. Mol. Cell. 61, 341–351 (2016).
Google Scholar
Walsh, I. M., Bowman, M. A., Soto Santarriaga, I. F., Rodriguez, A. & Clark, P. L. Synonymous codon substitutions perturb cotranslational protein folding in vivo and impair cell health. Proc. Natl Acad. Sci. USA 117, 3528–3534 (2020).
Google Scholar
Gilissen, C., Hoischen, A., Brunner, H. G. & Veltman, J. A. Illness gene identification methods for exome sequencing. Eur. J. Hum. Genet. 20, 490–497 (2012).
Google Scholar
Agashe, D., Martinez-Gomez, N. C., Drummond, D. A. & Marx, C. J. Good codons, dangerous transcript: massive reductions in gene expression and health arising from synonymous mutations in a key enzyme. Mol. Biol. Evol. 30, 549–560 (2013).
Google Scholar
Kristofich, J. et al. Synonymous mutations make dramatic contributions to health when development is proscribed by a weak-link enzyme. PLoS Genet. 14, e1007615 (2018).
Google Scholar
Lebeuf-Taylor, E., McCloskey, N., Bailey, S. F., Hinz, A. & Kassen, R. The distribution of health results amongst synonymous mutations in a gene beneath directional choice. eLife 8, e45952 (2019).
Google Scholar
Lind, P. A., Berg, O. G. & Andersson, D. I. Mutational robustness of ribosomal protein genes. Science 330, 825–827 (2010).
Google Scholar
Sharon, E. et al. Useful genetic variants revealed by massively parallel exact genome modifying. Cell 175, 544–557 (2018).
Google Scholar
She, R. & Jarosz, D. F. Mapping causal variants with single-nucleotide decision reveals biochemical drivers of phenotypic change. Cell 172, 478–490 (2018).
Google Scholar
Qian, W., Ma, D., Xiao, C., Wang, Z. & Zhang, J. The genomic panorama and evolutionary decision of antagonistic pleiotropy in yeast. Cell Rep. 2, 1399–1410 (2012).
Google Scholar
Li, C., Qian, W., Maclean, M. & Zhang, J. The health panorama of a tRNA gene. Science 352, 837–840 (2016).
Google Scholar
Chen, P. & Zhang, J. Asexual experimental evolution of yeast doesn’t curtail transposable components. Mol. Biol. Evol. 38, 2831–2842 (2021).
Google Scholar
Keren, L. et al. Massively parallel interrogation of the results of gene expression ranges on health. Cell 166, 1282–1294 (2016).
Google Scholar
Chang, Y. F., Imam, J. S. & Wilkinson, M. F. The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 76, 51–74 (2007).
Google Scholar
Monteiro, P. T. et al. YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. Nucleic Acids Res. 48, D642–D649 (2020).
Google Scholar
Sharp, P. M. & Li, W. H. The codon adaptation index—a measure of directional synonymous codon utilization bias, and its potential functions. Nucleic Acids Res. 15, 1281–1295 (1987).
Google Scholar
Radhakrishnan, A. et al. The DEAD-Field protein Dhh1p {couples} mRNA decay and translation by monitoring codon optimality. Cell 167, 122–132 (2016).
Google Scholar
Yang, J. R., Chen, X. & Zhang, J. Codon-by-codon modulation of translational velocity and accuracy through mRNA folding. PLoS Biol. 12, e1001910 (2014).
Google Scholar
Faure, G., Ogurtsov, A. Y., Shabalina, S. A. & Koonin, E. V. Function of mRNA construction within the management of protein folding. Nucleic Acids Res. 44, 10898–10911 (2016).
Google Scholar
Goncalves, P., Valerio, E., Correia, C., de Almeida, J. M. & Sampaio, J. P. Proof for divergent evolution of development temperature desire in sympatric Saccharomyces species. PLoS ONE 6, e20739 (2011).
Google Scholar
Kimura, M. The Impartial Principle of Molecular Evolution (Cambridge Univ. Press, 1983).
Lewontin, R. C. & Cohen, D. On inhabitants development in a randomly various surroundings. Proc. Natl Acad. Sci. USA 62, 1056–1060 (1969).
Google Scholar
Gillespie, J. H. Pure choice for within-generation variance in offspring quantity II. Discrite haploid fashions. Genetics 81, 403–413 (1975).
Google Scholar
Kimura, M. & Ohta, T. The typical variety of generations till fixation of a mutant gene in a finite inhabitants. Genetics 61, 763–771 (1969).
Google Scholar
Flynn, J. M. et al. Complete health maps of Hsp90 present widespread environmental dependence. eLife 9, e53810 (2020).
Google Scholar
Dandage, R. et al. Differential strengths of molecular determinants information surroundings particular mutational fates. PLoS Genet. 14, e1007419 (2018).
Google Scholar
Chen, P. & Zhang, J. Antagonistic pleiotropy conceals molecular variations in altering environments. Nat. Ecol. Evol. 4, 461–469 (2020).
Google Scholar
Azizoglu, A., Brent, R. & Rudolf, F. A exactly adjustable, variation-suppressed eukaryotic transcriptional controller to allow genetic discovery. eLife 10, e69549 (2021).
Google Scholar
Natsume, T. & Kanemaki, M. T. Conditional degrons for controlling protein expression on the protein degree. Annu. Rev. Genet. 51, 83–102 (2017).
Google Scholar
Zhang, J. & Yang, J. R. Determinants of the speed of protein sequence evolution. Nat. Rev. Genet. 16, 409–420 (2015).
Google Scholar
Wu, Z. et al. Expression degree is a serious modifier of the health panorama of a protein coding gene. Nat. Ecol. Evol. 6, 103–115 (2022).
Google Scholar
Sauna, Z. E. & Kimchi-Sarfaty, C. Understanding the contribution of synonymous mutations to human illness. Nat. Rev. Genet. 12, 683–691 (2011).
Google Scholar
Lee, T. I. & Younger, R. A. Transcriptional regulation and its misregulation in illness. Cell 152, 1237–1251 (2013).
Google Scholar
Chou, H. J., Donnard, E., Gustafsson, H. T., Garber, M. & Rando, O. J. Transcriptome-wide evaluation of roles for tRNA modifications in translational regulation. Mol. Cell. 68, 978–992 (2017).
Google Scholar
Laughery, M. F. et al. New vectors for easy and streamlined CRISPR–Cas9 genome modifying in Saccharomyces cerevisiae. Yeast 32, 711–720 (2015).
Google Scholar
Warringer, J., Ericson, E., Fernandez, L., Nerman, O. & Blomberg, A. Excessive-resolution yeast phenomics resolves completely different physiological options within the saline response. Proc. Natl Acad. Sci. USA 100, 15724–15729 (2003).
Google Scholar
Honlinger, A. et al. Tom7 modulates the dynamics of the mitochondrial outer membrane translocase and performs a pathway-related function in protein import. EMBO J. 15, 2125–2137 (1996).
Google Scholar
Potapov, V. & Ong, J. L. Inspecting sources of error in PCR by single-molecule sequencing. PLoS ONE 12, e0169774 (2017).
Google Scholar
Stanke, M. & Morgenstern, B. AUGUSTUS: an online server for gene prediction in eukaryotes that permits user-defined constraints. Nucleic Acids Res. 33, W465–W467 (2005).
Google Scholar
Ranwez, V., Douzery, E. J. P., Cambon, C., Chantret, N. & Delsuc, F. MACSE v2: toolkit for the alignment of coding sequences accounting for frameshifts and cease codons. Mol. Biol. Evol. 35, 2582–2584 (2018).
Google Scholar
Hofacker, I. L. et al. Quick folding and comparability of RNA secondary constructions. Monatsh. Chem. 125, 167–188 (1994).
Google Scholar
Zhang, J. & He, X. Vital impression of protein dispensability on the instantaneous fee of protein evolution. Mol. Biol. Evol. 22, 1147–1155 (2005).
Google Scholar
