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For: Rogozin IB, Belinky F, Pavlenko V, Shabalina SA, Kristensen DM, Koonin EV. Evolutionary switches between two serine codon sets are driven by selection. Proc Natl Acad Sci U S A 2016;113:13109-13. [PMID: 27799560 DOI: 10.1073/pnas.1615832113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Stojanovski BM, Di Cera E. Codon switching of conserved Ser residues in coagulation and fibrinolytic proteases. J Thromb Haemost 2024;22:2495-2501. [PMID: 38821294 PMCID: PMC11343676 DOI: 10.1016/j.jtha.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/02/2024]
2
Tapia SM, Pérez‐Torrado R, Adam AC, Macías LG, Barrio E, Querol A. Adaptive evolution in the Saccharomyces kudriavzevii Aro4p promoted a reduced production of higher alcohols. Microb Biotechnol 2022;15:2958-2969. [PMID: 36307988 PMCID: PMC9733642 DOI: 10.1111/1751-7915.14154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/30/2022]  Open
3
Belinky F, Bykova A, Yurchenko V, Rogozin IB. No evidence for widespread positive selection on double substitutions within codons in primates and yeasts. Front Genet 2022;13:991249. [PMID: 36159983 PMCID: PMC9500374 DOI: 10.3389/fgene.2022.991249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022]  Open
4
Ho AT, Hurst LD. Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection. PLoS Biol 2022;20:e3001588. [PMID: 35550630 PMCID: PMC9129041 DOI: 10.1371/journal.pbio.3001588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/24/2022] [Accepted: 04/20/2022] [Indexed: 11/18/2022]  Open
5
Ma X, Øvrebø JI, Thompson EM. Evolution of CDK1 Paralog Specializations in a Lineage With Fast Developing Planktonic Embryos. Front Cell Dev Biol 2022;9:770939. [PMID: 35155443 PMCID: PMC8832800 DOI: 10.3389/fcell.2021.770939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/27/2021] [Indexed: 12/03/2022]  Open
6
Trigila AP, Pisciottano F, Franchini LF. Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals. BMC Biol 2021;19:244. [PMID: 34784928 PMCID: PMC8594068 DOI: 10.1186/s12915-021-01170-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/21/2021] [Indexed: 11/26/2022]  Open
7
Moreira A, Croze M, Delehelle F, Cussat-Blanc S, Luga H, Mollereau C, Balaresque P. Hearing Sensitivity of Primates: Recurrent and Episodic Positive Selection in Hair Cells and Stereocilia Protein-Coding Genes. Genome Biol Evol 2021;13:6302699. [PMID: 34137817 PMCID: PMC8358225 DOI: 10.1093/gbe/evab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2021] [Indexed: 12/29/2022]  Open
8
Ho AT, Hurst LD. Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors. Mol Biol Evol 2021;38:244-262. [PMID: 32797190 PMCID: PMC7783166 DOI: 10.1093/molbev/msaa210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
9
Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes. PLoS One 2021;16:e0248337. [PMID: 33711070 PMCID: PMC7954308 DOI: 10.1371/journal.pone.0248337] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/24/2021] [Indexed: 01/03/2023]  Open
10
Belinky F, Ganguly I, Poliakov E, Yurchenko V, Rogozin IB. Analysis of Stop Codons within Prokaryotic Protein-Coding Genes Suggests Frequent Readthrough Events. Int J Mol Sci 2021;22:ijms22041876. [PMID: 33672790 PMCID: PMC7918605 DOI: 10.3390/ijms22041876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023]  Open
11
Evolution of the genetic code; Evidence from serine codon use disparity in Escherichia coli. Proc Natl Acad Sci U S A 2020;117:28572-28575. [PMID: 33168748 DOI: 10.1073/pnas.2014567117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
12
Lichman BR, Godden GT, Hamilton JP, Palmer L, Kamileen MO, Zhao D, Vaillancourt B, Wood JC, Sun M, Kinser TJ, Henry LK, Rodriguez-Lopez C, Dudareva N, Soltis DE, Soltis PS, Buell CR, O’Connor SE. The evolutionary origins of the cat attractant nepetalactone in catnip. SCIENCE ADVANCES 2020;6:eaba0721. [PMID: 32426505 PMCID: PMC7220310 DOI: 10.1126/sciadv.aba0721] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/02/2020] [Indexed: 05/07/2023]
13
Weber M, Burgos R, Yus E, Yang J, Lluch‐Senar M, Serrano L. Impact of C-terminal amino acid composition on protein expression in bacteria. Mol Syst Biol 2020;16:e9208. [PMID: 32449593 PMCID: PMC7246954 DOI: 10.15252/msb.20199208] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 11/30/2022]  Open
14
Belinky F, Sela I, Rogozin IB, Koonin EV. Crossing fitness valleys via double substitutions within codons. BMC Biol 2019;17:105. [PMID: 31842858 PMCID: PMC6916188 DOI: 10.1186/s12915-019-0727-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]  Open
15
Schwartz GW, Shauli T, Linial M, Hershberg U. Serine substitutions are linked to codon usage and differ for variable and conserved protein regions. Sci Rep 2019;9:17238. [PMID: 31754132 PMCID: PMC6872785 DOI: 10.1038/s41598-019-53452-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/01/2019] [Indexed: 11/11/2022]  Open
16
Ho AT, Hurst LD. In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3' additional stop codons. PLoS Genet 2019;15:e1008386. [PMID: 31527909 PMCID: PMC6764699 DOI: 10.1371/journal.pgen.1008386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/27/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022]  Open
17
Kleinnijenhuis AJ. Visualization of Genetic Drift Processes Using the Conserved Collagen 1α1 GXY Domain. J Mol Evol 2019;87:106-130. [PMID: 30863881 DOI: 10.1007/s00239-019-09890-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/06/2019] [Indexed: 11/30/2022]
18
Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nat Ecol Evol 2018;2:1280-1288. [PMID: 29967485 PMCID: PMC6093625 DOI: 10.1038/s41559-018-0584-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 05/18/2018] [Indexed: 11/08/2022]
19
Purifying and positive selection in the evolution of stop codons. Sci Rep 2018;8:9260. [PMID: 29915293 PMCID: PMC6006363 DOI: 10.1038/s41598-018-27570-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022]  Open
20
Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions. Sci Rep 2017;7:12422. [PMID: 28963504 PMCID: PMC5622118 DOI: 10.1038/s41598-017-12619-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/06/2017] [Indexed: 11/29/2022]  Open
21
Self-Referential Encoding on Modules of Anticodon Pairs-Roots of the Biological Flow System. Life (Basel) 2017;7:life7020016. [PMID: 28383509 PMCID: PMC5492138 DOI: 10.3390/life7020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 12/22/2022]  Open
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