Network analysis of synonymous codon usage.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
08 12 2020
08 12 2020
Historique:
received:
06
07
2019
revised:
05
05
2020
accepted:
22
06
2020
pubmed:
2
7
2020
medline:
4
3
2021
entrez:
2
7
2020
Statut:
ppublish
Résumé
Most amino acids are encoded by multiple synonymous codons, some of which are used more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational protein folding and that positions of some rare codons are evolutionarily conserved. Analyses of their positions in protein 3-dimensional structures, which are richer in biochemical information than sequences alone, might further explain the role of rare codons in protein folding. We model protein structures as networks and use network centrality to measure the structural position of an amino acid. We first validate that amino acids buried within the structural core are network-central, and those on the surface are not. Then, we study potential differences between network centralities and thus structural positions of amino acids encoded by conserved rare, non-conserved rare and commonly used codons. We find that in 84% of proteins, the three codon categories occupy significantly different structural positions. We examine protein groups showing different codon centrality trends, i.e. different relationships between structural positions of the three codon categories. We see several cases of all proteins from our data with some structural or functional property being in the same group. Also, we see a case of all proteins in some group having the same property. Our work shows that codon usage is linked to the final protein structure and thus possibly to co-translational protein folding. https://nd.edu/∼cone/CodonUsage/. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 32609328
pii: 5865853
doi: 10.1093/bioinformatics/btaa603
pmc: PMC7750956
doi:
Substances chimiques
Codon
0
Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
4876-4884Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM120733
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Références
PLoS One. 2009 Jun 26;4(6):e5967
pubmed: 19557139
Bioinformatics. 1998 Jun;14(5):423-9
pubmed: 9682055
Nucleic Acids Res. 2007 Jan;35(Database issue):D291-7
pubmed: 17135200
J Mol Biol. 1998 Aug 7;281(1):31-48
pubmed: 9680473
Proc Natl Acad Sci U S A. 2020 Feb 18;117(7):3528-3534
pubmed: 32015130
PLoS One. 2008;3(10):e3412
pubmed: 18923675
FEBS Lett. 1996 Dec 9;399(1-2):78-82
pubmed: 8980124
Mol Biol Evol. 2009 Jul;26(7):1571-80
pubmed: 19349643
J Mol Biol. 1995 Apr 7;247(4):536-40
pubmed: 7723011
Mol Microbiol. 2015 Sep;97(5):974-87
pubmed: 26032251
PLoS One. 2011;6(8):e23016
pubmed: 21887225
FEBS Lett. 1999 Dec 3;462(3):387-91
pubmed: 10622731
PLoS One. 2020 Apr 30;15(4):e0232003
pubmed: 32352987
Curr Opin Struct Biol. 2016 Jun;38:102-10
pubmed: 27318814
Mol Biol Evol. 1985 Jan;2(1):13-34
pubmed: 3916708
Sci Rep. 2017 Nov 2;7(1):14890
pubmed: 29097661
Biochem Biophys Res Commun. 2000 Mar 24;269(3):692-6
pubmed: 10720478
Nature. 2013 Mar 7;495(7439):111-5
pubmed: 23417067
Annu Rev Biophys. 2015;44:143-66
pubmed: 25747594
Science. 2007 Jan 26;315(5811):525-8
pubmed: 17185560
Sci Signal. 2012 Mar 13;5(215):rs1
pubmed: 22416277
BMC Med Res Methodol. 2002 Jun 17;2:8
pubmed: 12069695
Protein Sci. 1996 Oct;5(10):1973-83
pubmed: 8897597
Mol Cell. 2016 Feb 4;61(3):341-351
pubmed: 26849192
Comput Struct Biotechnol J. 2017 Aug 12;15:412-424
pubmed: 28924459
Trends Biochem Sci. 2009 Jan;34(1):16-24
pubmed: 18996013
Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):11434-11439
pubmed: 29073068
Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
pubmed: 3547335
J Mol Biol. 2004 Dec 3;344(4):1135-46
pubmed: 15544817
Trends Biochem Sci. 2013 Jul;38(7):337-44
pubmed: 23764454
PLoS Comput Biol. 2017 May 5;13(5):e1005531
pubmed: 28475588
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
Proteins. 2009 Nov 15;77(3):499-508
pubmed: 19507241
J Comput Biol. 2010 Jan;17(1):55-72
pubmed: 20078397
J Mol Biol. 1982 May 5;157(1):105-32
pubmed: 7108955
Genome Res. 2003 Sep;13(9):2178-89
pubmed: 12952885
FEBS Lett. 1998 Aug 28;434(1-2):93-6
pubmed: 9738458
Mol Syst Biol. 2010;6:340
pubmed: 20087338
RNA. 2007 Jan;13(1):87-96
pubmed: 17095544
Nat Struct Mol Biol. 2013 Feb;20(2):237-43
pubmed: 23262490
Bioinformation. 2010 Nov 27;5(6):234-9
pubmed: 21364823
R Soc Open Sci. 2020 Jun 3;7(6):191461
pubmed: 32742675
Proteins. 1996 Jun;25(2):237-52
pubmed: 8811739
J Mol Evol. 1986;24(1-2):28-38
pubmed: 3104616
J Mol Biol. 2007 Aug 10;371(2):283-301
pubmed: 17582437
Protein Sci. 2006 Sep;15(9):2120-8
pubmed: 16882992
Bioinformatics. 2014 Jun 15;30(12):1721-9
pubmed: 24554629
Biokhimiia. 1989 Feb;54(2):187-200
pubmed: 2742922
Proc Natl Acad Sci U S A. 1990 Mar;87(6):2264-8
pubmed: 2315319
Curr Protoc Bioinformatics. 2019 Mar;65(1):e66
pubmed: 30489695
J Am Chem Soc. 2014 Jan 22;136(3):858-61
pubmed: 24392935
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Jun;65(6 Pt 1):061910
pubmed: 12188762