Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work.
amino acid preferences
contingency
entrenchment
epistasis
protein evolution
site-specific fitness landscapes
Journal
Protein science : a publication of the Protein Society
ISSN: 1469-896X
Titre abrégé: Protein Sci
Pays: United States
ID NLM: 9211750
Informations de publication
Date de publication:
10 2021
10 2021
Historique:
revised:
19
07
2021
received:
13
05
2021
accepted:
26
07
2021
pubmed:
30
7
2021
medline:
25
12
2021
entrez:
29
7
2021
Statut:
ppublish
Résumé
Amino acid preferences vary across sites and time. While variation across sites is widely accepted, the extent and frequency of temporal shifts are contentious. Our understanding of the drivers of amino acid preference change is incomplete: To what extent are temporal shifts driven by adaptive versus nonadaptive evolutionary processes? We review phenomena that cause preferences to vary (e.g., evolutionary Stokes shift, contingency, and entrenchment) and clarify how they differ. To determine the extent and prevalence of shifted preferences, we review experimental and theoretical studies. Analyses of natural sequence alignments often detect decreases in homoplasy (convergence and reversions) rates, and variation in replacement rates with time-signals that are consistent with temporally changing preferences. While approaches inferring shifts in preferences from patterns in natural alignments are valuable, they are indirect since multiple mechanisms (both adaptive and nonadaptive) could lead to the observed signal. Alternatively, site-directed mutagenesis experiments allow for a more direct assessment of shifted preferences. They corroborate evidence from multiple sequence alignments, revealing that the preference for an amino acid at a site varies depending on the background sequence. However, shifts in preferences are usually minor in magnitude and sites with significantly shifted preferences are low in frequency. The small yet consistent perturbations in preferences could, nevertheless, jeopardize the accuracy of inference procedures, which assume constant preferences. We conclude by discussing if and how such shifts in preferences might influence widely used time-homogenous inference procedures and potential ways to mitigate such effects.
Identifiants
pubmed: 34322924
doi: 10.1002/pro.4161
pmc: PMC8442975
doi:
Substances chimiques
Amino Acids
0
Proteins
0
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
2009-2028Informations de copyright
© 2021 The Protein Society.
Références
Mol Biol Evol. 2008 Sep;25(9):1943-53
pubmed: 18583353
Nat Ecol Evol. 2017 Dec;1(12):1923-1930
pubmed: 29062121
Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4003-11
pubmed: 18852102
Mol Biol Evol. 2005 Dec;22(12):2472-9
pubmed: 16107592
Mol Biol Evol. 2021 May 27;:
pubmed: 34043795
Nature. 2013 Oct 10;502(7470):228-31
pubmed: 24005325
Biol Lett. 2012 Oct 23;8(5):825-8
pubmed: 22628094
Mol Biol Evol. 2001 May;18(5):866-73
pubmed: 11319270
Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12957-62
pubmed: 15326304
Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):21071-6
pubmed: 24324165
Mol Biol Evol. 2014 Feb;31(2):484-95
pubmed: 24132121
Genetics. 2016 Jul;203(3):1335-51
pubmed: 27194749
Mol Biol Evol. 2018 Jun 1;35(6):1473-1488
pubmed: 29596684
Nature. 2014 Aug 14;512(7513):203-7
pubmed: 24930765
Mol Biol Evol. 2015 May;32(5):1232-6
pubmed: 25631926
Elife. 2013 May 14;2:e00631
pubmed: 23682315
BMC Bioinformatics. 2015 May 20;16:168
pubmed: 25990960
Mol Biol Evol. 2017 Jan;34(1):204-214
pubmed: 27744408
Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14878-83
pubmed: 12403824
Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):E3226-35
pubmed: 26056312
Mol Biol Evol. 2015 Jun;32(6):1373-81
pubmed: 25737491
Genome Biol Evol. 2019 Jan 1;11(1):121-135
pubmed: 30496400
Syst Biol. 2011 Jan;60(1):60-73
pubmed: 21081481
Mol Biol Evol. 2002 Jun;19(6):908-17
pubmed: 12032247
Mol Biol Evol. 2009 Jul;26(7):1663-76
pubmed: 19383983
Proteins. 2011 May;79(5):1396-407
pubmed: 21337623
Mol Biol Evol. 2015 May;32(5):1237-41
pubmed: 25631925
BMC Evol Biol. 2008 Dec 16;8:331
pubmed: 19087270
Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4453-4458
pubmed: 29626131
Mol Biol Evol. 2003 Oct;20(10):1692-704
pubmed: 12885968
Mol Biol Evol. 2010 Jul;27(7):1546-60
pubmed: 20159780
PLoS Comput Biol. 2008 Feb 29;4(2):e1000002
pubmed: 18463696
Mol Syst Biol. 2020 Jul;16(7):e9380
pubmed: 32627955
Genes (Basel). 2018 Aug 13;9(8):
pubmed: 30104502
Virus Evol. 2018 Nov 06;4(2):vey033
pubmed: 30425841
Mol Biol Evol. 2015 Feb;32(2):542-54
pubmed: 25415964
Nat Methods. 2018 Oct;15(10):816-822
pubmed: 30250057
Elife. 2018 Mar 28;7:
pubmed: 29590010
Protein Sci. 2021 Oct;30(10):2009-2028
pubmed: 34322924
Biol Lett. 2015 Oct;11(10):
pubmed: 26445980
Mol Biol Evol. 2015 Feb;32(2):440-55
pubmed: 25392342
Viruses. 2020 Nov 16;12(11):
pubmed: 33207801
Evolution. 2013 Apr;67(4):1204-8
pubmed: 23550768
Mol Biol Evol. 2017 Feb 1;34(2):391-407
pubmed: 28110273
Nat Commun. 2020 Sep 14;11(1):4603
pubmed: 32929079
Syst Biol. 2020 Jul 1;69(4):722-738
pubmed: 31730199
Genome Biol Evol. 2013;5(9):1584-93
pubmed: 23884461
Mol Biol Evol. 2005 Apr;22(4):1107-18
pubmed: 15689528
Viruses. 2016 Jun 03;8(6):
pubmed: 27271655
Mol Biol Evol. 2001 May;18(5):691-9
pubmed: 11319253
Nature. 2012 Oct 25;490(7421):535-8
pubmed: 23064225
Nat Commun. 2017 Mar 06;8:14614
pubmed: 28262665
Mol Biol Evol. 2015 Nov;32(11):2944-60
pubmed: 26226986
Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):E1450
pubmed: 24706894
Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8276-E8285
pubmed: 30104379
Mol Biol Evol. 2014 Mar;31(3):736-49
pubmed: 24307688
Mol Biol Evol. 2014 Oct;31(10):2753-69
pubmed: 25063439
Biol Lett. 2015 Apr;11(4):20141031
pubmed: 25854546
Genetics. 1918 Sep;3(5):422-99
pubmed: 17245914
Mol Biol Evol. 2020 Nov 1;37(11):3131-3148
pubmed: 32897316
Mol Biol Evol. 2015 Aug;32(8):2085-96
pubmed: 25862140
Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21104-21112
pubmed: 31578251
Mol Biol Evol. 2007 Aug;24(8):1769-82
pubmed: 17522088
Mol Biol Evol. 2015 Apr;32(4):1097-108
pubmed: 25576365
Curr Opin Struct Biol. 2017 Feb;42:59-66
pubmed: 27865208
Nat Methods. 2014 Aug;11(8):801-7
pubmed: 25075907
Mol Biol Evol. 2014 Aug;31(8):1956-78
pubmed: 24859245
Mol Biol Evol. 2016 Dec;33(12):3299-3307
pubmed: 27634870
Mol Biol Evol. 2008 Jun;25(6):1054-66
pubmed: 18319244
Syst Biol. 2013 Mar;62(2):330-8
pubmed: 22949482
ACS Chem Neurosci. 2020 Sep 16;11(18):2861-2868
pubmed: 32786311
Genetics. 1998 Oct;150(2):911-9
pubmed: 9755219
PLoS One. 2009 Dec 09;4(12):e7891
pubmed: 20011052
Nat Rev Genet. 2016 Feb;17(2):109-21
pubmed: 26781812
Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1352-9
pubmed: 22547823
Proc Natl Acad Sci U S A. 2011 May 10;108(19):7896-901
pubmed: 21464309
Nature. 2020 Dec;588(7838):503-508
pubmed: 33299178
Nat Rev Genet. 2013 Nov;14(11):751-64
pubmed: 24105273
PLoS Comput Biol. 2006 Jun 23;2(6):e69
pubmed: 16789817
Nature. 1970 Feb 7;225(5232):563-4
pubmed: 5411867
PLoS Comput Biol. 2017 May 15;13(5):e1005541
pubmed: 28505183
Mol Biol Evol. 1998 Jul;15(7):910-7
pubmed: 9656490
Nucleic Acids Res. 2017 Jul 3;45(W1):W201-W206
pubmed: 28498993
Trends Ecol Evol. 2020 Jan;35(1):43-55
pubmed: 31606140
PLoS Genet. 2010 Oct 21;6(10):e1001162
pubmed: 20975933