The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?
GC-content
codon usage
environmental selection
evolution of the genetic code
extremophiles
genetic code origin
mutational robustness
origin of life
standard genetic code
Journal
Life (Basel, Switzerland)
ISSN: 2075-1729
Titre abrégé: Life (Basel)
Pays: Switzerland
ID NLM: 101580444
Informations de publication
Date de publication:
30 Jul 2021
30 Jul 2021
Historique:
received:
16
06
2021
revised:
23
07
2021
accepted:
28
07
2021
entrez:
27
8
2021
pubmed:
28
8
2021
medline:
28
8
2021
Statut:
epublish
Résumé
The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
Identifiants
pubmed: 34440517
pii: life11080773
doi: 10.3390/life11080773
pmc: PMC8398314
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : Nemzeti Kutatási Fejlesztési és Innovációs Hivatal
ID : GINOP-2.3.2-15-2016-00057
Organisme : Nemzeti Kutatási Fejlesztési és Innovációs Hivatal
ID : K119347
Organisme : Volkswagen Stiftung initiative "Leben? - Ein neuer Blick der Naturwissenschaften auf die grundlegenden Prinzipien des Lebens"
ID : A unified model of recombination in life
Références
Mol Biol Evol. 2011 Sep;28(9):2661-74
pubmed: 21498602
J Mol Biol. 2003 Mar 21;327(2):347-57
pubmed: 12628242
Nature. 2001 Jan 11;409(6817):175-8
pubmed: 11196637
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
pubmed: 1438297
J Mol Evol. 1980 Dec;16(2):111-20
pubmed: 7463489
Nat Microbiol. 2016 Jul 25;1(9):16116
pubmed: 27562259
BMC Biol. 2020 Oct 20;18(1):146
pubmed: 33081759
PLoS Genet. 2007 Feb 2;3(2):e22
pubmed: 17274688
J Mol Evol. 2018 Dec;86(9):593-597
pubmed: 30361751
BMC Microbiol. 2018 Nov 6;18(1):177
pubmed: 30400856
Cold Spring Harb Symp Quant Biol. 1966;31:723-36
pubmed: 5237212
Gene. 2005 Feb 14;346:7-12
pubmed: 15716095
Genome Biol. 2001;2(11):RESEARCH0049
pubmed: 11737948
Bioinformatics. 2015 Feb 1;31(3):318-23
pubmed: 25297068
J Theor Biol. 2019 Mar 7;464:21-32
pubmed: 30579955
J Mol Biol. 2001 Jun 15;309(4):835-43
pubmed: 11399062
J Theor Biol. 2005 Nov 21;237(2):219-26
pubmed: 15978625
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32761142
Biol Direct. 2014 Dec 12;9:29
pubmed: 25496919
Mol Biol Evol. 2000 Nov;17(11):1581-8
pubmed: 11070046
Biochemistry. 2002 Jun 25;41(25):8152-61
pubmed: 12069608
BMC Evol Biol. 2011 Jul 08;11:199
pubmed: 21740576
J Theor Biol. 2017 Feb 7;414:1-4
pubmed: 27871852
Genome Biol. 2008 Apr 09;9(4):R70
pubmed: 18397532
Nucleic Acids Res. 2018 Mar 16;46(5):2699
pubmed: 29425356
Life (Basel). 2020 Feb 26;10(3):
pubmed: 32110893
PLoS One. 2014 Nov 13;9(11):e112751
pubmed: 25393107
Biol Direct. 2012 Jan 10;7:2
pubmed: 22230424
Nature. 2002 May 16;417(6886):244
pubmed: 12015592
J Mol Evol. 1998 Sep;47(3):238-48
pubmed: 9732450
Proc Natl Acad Sci U S A. 2008 Jul 8;105(27):9272-7
pubmed: 18583475
Genetics. 2004 Jul;167(3):1507-12
pubmed: 15280258
BMC Genomics. 2012 Jun 12;13:236
pubmed: 22691113
Phys Biol. 2011 Jun;8(3):035002
pubmed: 21572170
Gene. 2008 Jan 15;407(1-2):30-41
pubmed: 17977670
Nature. 2008 Feb 7;451(7179):704-7
pubmed: 18256669
Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12742-7
pubmed: 16120678
BMC Evol Biol. 2018 Dec 13;18(1):192
pubmed: 30545289
Genomics. 2010 Jan;95(1):7-15
pubmed: 19747541
IUBMB Life. 2009 Feb;61(2):99-111
pubmed: 19117371
G3 (Bethesda). 2015 Aug 06;5(10):2027-36
pubmed: 26248983
Genome Biol Evol. 2009 Aug 04;1:288-93
pubmed: 20333198
Microbiol Mol Biol Rev. 1999 Dec;63(4):735-50, table of contents
pubmed: 10585964
Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9
pubmed: 2112744
J Mol Biol. 2002 Oct 18;323(2):327-44
pubmed: 12381324
Structure. 2010 Jul 14;18(7):819-28
pubmed: 20637418
J Mol Evol. 2004 Aug;59(2):258-66
pubmed: 15486699
Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2135-9
pubmed: 23341608
Mol Biol Evol. 2010 Mar;27(3):735-41
pubmed: 19910385
Science. 1972 Jul 7;177(4043):52-6
pubmed: 17756316
Int J Biol Macromol. 2007 Oct 1;41(4):447-53
pubmed: 17675150
Curr Opin Microbiol. 2015 Jun;25:120-6
pubmed: 26066288
Sci Rep. 2021 May 26;11(1):10963
pubmed: 34040064
Proc Natl Acad Sci U S A. 1975 May;72(5):1909-12
pubmed: 1057181
Biol Lett. 2013 Oct 23;9(5):20130608
pubmed: 24046876
Proc Natl Acad Sci U S A. 2005 Oct 4;102(40):14338-43
pubmed: 16176987
Adv Protein Chem. 1959;14:1-63
pubmed: 14404936
Annu Rev Genet. 2002;36:279-303
pubmed: 12429694
Annu Rev Genet. 2017 Nov 27;51:45-62
pubmed: 28853922
Biol Direct. 2008 Sep 05;3:37
pubmed: 18775066
IEEE/ACM Trans Comput Biol Bioinform. 2011 Jan-Mar;8(1):143-51
pubmed: 21071803
J Mol Biol. 1998 Nov 27;284(2):489-502
pubmed: 9813132
Science. 1999 Jan 8;283(5399):220-1
pubmed: 9880254
Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3578-83
pubmed: 10097079
Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13057-61
pubmed: 16916929
Orig Life Evol Biosph. 2013 Dec;43(6):465-89
pubmed: 24500541
Proc Biol Sci. 2001 Mar 7;268(1466):493-7
pubmed: 11296861
J Mol Evol. 2003 Nov;57(5):533-7
pubmed: 14738311
J Mol Biol. 1999 Jul 9;290(2):595-604
pubmed: 10390356
Life (Basel). 2017 Mar 23;7(2):
pubmed: 28333103
Mol Biol Evol. 2016 Mar;33(3):595-602
pubmed: 26609078
Biochem Biophys Res Commun. 2004 Mar 19;315(4):1097-103
pubmed: 14985126
J Mol Evol. 2008 Nov;67(5):510-6
pubmed: 18855039
Proteins. 2004 Jan 1;54(1):20-40
pubmed: 14705021
PLoS Genet. 2009 Jun;5(6):e1000520
pubmed: 19543367
PLoS Comput Biol. 2007 Mar 23;3(3):e52
pubmed: 17381236
Trends Genet. 2010 Aug;26(8):345-52
pubmed: 20594608
J Chem Inf Model. 2008 Jan;48(1):119-27
pubmed: 18161956
PLoS Genet. 2010 Sep 09;6(9):e1001115
pubmed: 20838599
Trends Genet. 1998 Nov;14(11):442-4
pubmed: 9825671
BMC Genomics. 2006 Dec 05;7:307
pubmed: 17147802
Genome Biol. 2001;2(4):RESEARCH0010
pubmed: 11305938
Gene. 2002 Sep 4;297(1-2):51-60
pubmed: 12384285
J Mol Evol. 1991 Nov;33(5):412-7
pubmed: 1960738
Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12300-5
pubmed: 9770481
Nat Ecol Evol. 2018 Oct;2(10):1556-1562
pubmed: 30127539
Gene. 2000 Dec 30;261(1):189-95
pubmed: 11164050
Nucleic Acids Res. 2001 Apr 1;29(7):1608-15
pubmed: 11266564
PLoS One. 2010 Feb 04;5(2):e9045
pubmed: 20140215
EMBO Rep. 2005 Dec;6(12):1208-13
pubmed: 16200051
Nucleic Acids Res. 2014 Mar;42(5):2879-92
pubmed: 24371267
Bioinformatics. 2007 Sep 1;23(17):2231-8
pubmed: 17599925
Genome Res. 2010 Aug;20(8):1001-9
pubmed: 20530252
Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12462-12466
pubmed: 27791131
Genetics. 2001 Jun;158(2):927-31
pubmed: 11430355
Genome Res. 2001 Oct;11(10):1641-50
pubmed: 11591641
Nature. 2008 Dec 18;456(7224):942-5
pubmed: 19037246
J Theor Biol. 2001 Jan 21;208(2):141-4
pubmed: 11162059
Biophys J. 2010 Feb 17;98(4):667-77
pubmed: 20159163
J Biol Chem. 2000 Oct 20;275(42):32383-6
pubmed: 10940293
Biosystems. 2018 Feb;164:217-225
pubmed: 29031737
Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18147-52
pubmed: 16330755
J Biol Chem. 2003 May 9;278(19):17198-202
pubmed: 12600994
Gene. 2003 Oct 23;317(1-2):39-47
pubmed: 14604790
Nucleic Acids Res. 2019 Jan 8;47(D1):D631-D636
pubmed: 30256983
Extremophiles. 2000 Apr;4(2):91-8
pubmed: 10805563
Life (Basel). 2016 Mar 16;6(1):
pubmed: 26999216
J Theor Biol. 2000 Apr 7;203(3):203-13
pubmed: 10716905
Orig Life Evol Biosph. 2003 Oct;33(4-5):457-77
pubmed: 14604186
J Theor Biol. 2016 Nov 7;408:237-242
pubmed: 27544417
Nat Rev Genet. 2016 Oct 14;17(11):704-714
pubmed: 27739533
Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a002238
pubmed: 20182607
Genetics. 2007 May;176(1):697-702
pubmed: 17194771
Curr Opin Struct Biol. 1998 Dec;8(6):738-48
pubmed: 9914256
BMC Struct Biol. 2007 Mar 29;7:18
pubmed: 17394655
Sci Rep. 2018 Oct 19;8(1):15548
pubmed: 30341344
Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):E4096-102
pubmed: 25225383
Proc Natl Acad Sci U S A. 1980 Feb;77(2):1083-6
pubmed: 6928661