Asymmetric evolution in viral overlapping genes is a source of selective protein adaptation.
Ancestral frame
De novo frame
Homologs
Non-synonymous nucleotide substitution
Selection pressure
Synonymous nucleotide substitution
Virus adaptation
Journal
Virology
ISSN: 1096-0341
Titre abrégé: Virology
Pays: United States
ID NLM: 0110674
Informations de publication
Date de publication:
06 2019
06 2019
Historique:
received:
03
01
2019
revised:
25
03
2019
accepted:
26
03
2019
pubmed:
21
4
2019
medline:
8
7
2020
entrez:
21
4
2019
Statut:
ppublish
Résumé
Overlapping genes represent an intriguing puzzle, as they encode two proteins whose ability to evolve is constrained by each other. Overlapping genes can undergo "symmetric evolution" (similar selection pressures on the two proteins) or "asymmetric evolution" (significantly different selection pressures on the two proteins). By sequence analysis of 75 pairs of homologous viral overlapping genes, I evaluated their accordance with one or the other model. Analysis of nucleotide and amino acid sequences revealed that half of overlaps undergo asymmetric evolution, as the protein from one frame shows a number of substitutions significantly higher than that of the protein from the other frame. Interestingly, the most variable protein (often known to interact with the host proteins) appeared to be encoded by the de novo frame in all cases examined. These findings suggest that overlapping genes, besides to increase the coding ability of viruses, are also a source of selective protein adaptation.
Identifiants
pubmed: 31004987
pii: S0042-6822(19)30088-1
doi: 10.1016/j.virol.2019.03.017
pmc: PMC7125799
pii:
doi:
Substances chimiques
Viral Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
39-47Informations de copyright
Copyright © 2019 Elsevier Inc. All rights reserved.
Références
PLoS One. 2014 Oct 01;9(10):e108768
pubmed: 25271416
Biol Direct. 2016 May 21;11:26
pubmed: 27209091
Cell. 1979 Oct;18(2):247-56
pubmed: 498271
J Virol. 1994 Jan;68(1):346-51
pubmed: 8254747
Virus Genes. 2001 Jan;22(1):47-52
pubmed: 11210938
Virology. 2008 Dec 20;382(2):199-206
pubmed: 18954886
Virus Res. 2015 Jan 22;196:113-21
pubmed: 25445351
Trends Biochem Sci. 2004 Jun;29(6):279-81
pubmed: 15276178
Sci Rep. 2016 Oct 24;6:35759
pubmed: 27775080
Virology. 2016 Jan;487:129-40
pubmed: 26519899
Plant Cell. 2004 May;16(5):1302-13
pubmed: 15100397
Infect Genet Evol. 2010 Jan;10(1):84-8
pubmed: 19879378
Nat Med. 2001 Dec;7(12):1306-12
pubmed: 11726970
PLoS One. 2008;3(12):e3996
pubmed: 19098983
BMC Bioinformatics. 2008 Jul 10;9:304
pubmed: 18616801
Mol Biol Evol. 2001 May;18(5):763-76
pubmed: 11319261
PLoS Pathog. 2013;9(6):e1003474
pubmed: 23825954
Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12807-12
pubmed: 17652172
J Biol Chem. 2013 Jul 26;288(30):21824-35
pubmed: 23760502
PLoS One. 2016 Feb 12;11(2):e0147619
pubmed: 26871901
Nat Rev Microbiol. 2006 May;4(5):405-11
pubmed: 16518419
Cell. 2016 Dec 15;167(7):1762-1773.e12
pubmed: 27984726
Evolution. 2000 Jun;54(3):731-9
pubmed: 10937248
Nat Commun. 2014 Aug 20;5:4713
pubmed: 25140902
Vet Microbiol. 2010 Aug 26;144(3-4):257-63
pubmed: 20079581
J Mol Evol. 1997 Jun;44(6):625-31
pubmed: 9169554
BMC Evol Biol. 2013 Nov 13;13:249
pubmed: 24225158
Virus Res. 2008 May;133(2):228-38
pubmed: 18304672
Genome Biol Evol. 2014 Dec 31;7(1):381-90
pubmed: 25552532
J Med Virol. 2007 Oct;79(10):1527-36
pubmed: 17705180
PLoS Pathog. 2011 Jun;7(6):e1002067
pubmed: 21695240
PLoS One. 2018 Oct 19;13(10):e0202513
pubmed: 30339683
PLoS Comput Biol. 2013;9(8):e1003162
pubmed: 23966842
Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9489-93
pubmed: 1329098
BMC Evol Biol. 2015 Dec 18;15:283
pubmed: 26677845
PLoS Pathog. 2011 Dec;7(12):e1002413
pubmed: 22174679
Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10381-6
pubmed: 16006510
J Gen Virol. 2002 Jul;83(Pt 7):1799-1807
pubmed: 12075102
J Gen Virol. 2007 Aug;88(Pt 8):2137-2143
pubmed: 17622615
J Virol. 2009 Oct;83(20):10719-36
pubmed: 19640978
J Virol. 2017 Apr 13;91(9):
pubmed: 28202767
BMC Evol Biol. 2008 Jan 28;8:31
pubmed: 18226237
J Mol Evol. 1979 Oct;13(3):245-52
pubmed: 228047
Cell Host Microbe. 2017 Sep 13;22(3):387-399.e6
pubmed: 28867387
PLoS One. 2013 Aug 12;8(8):e70698
pubmed: 23950983
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
EMBO J. 2002 Jun 17;21(12):3070-80
pubmed: 12065420
Mol Biol Evol. 2012 Dec;29(12):3767-80
pubmed: 22821011
Virus Genes. 2015 Feb;50(1):29-38
pubmed: 25410051
Nature. 1978 Apr 6;272(5653):532-5
pubmed: 692657
J Mol Evol. 2004 Oct;59(4):520-7
pubmed: 15638463
J Virol. 2001 Sep;75(17):7966-72
pubmed: 11483741
Proc Biol Sci. 2010 Dec 22;277(1701):3809-17
pubmed: 20610432
Methods Mol Biol. 2014;1079:105-16
pubmed: 24170397
Genetics. 2018 Sep;210(1):303-313
pubmed: 30026186
Mol Biol Evol. 2013 Aug;30(8):1916-28
pubmed: 23686658
Trends Genet. 1991 Aug;7(8):261-6
pubmed: 1771674
PLoS One. 2016 Jul 12;11(7):e0158419
pubmed: 27404108
J Mol Evol. 1997;44 Suppl 1:S83-90
pubmed: 9071016
PLoS Pathog. 2016 Feb 05;12(2):e1005427
pubmed: 26849127
J Gen Virol. 2015 Dec;96(12):3577-3586
pubmed: 26446206
J Gen Virol. 2013 Feb;94(Pt 2):263-269
pubmed: 23100370
Cell. 2003 Dec 26;115(7):799-811
pubmed: 14697199
Arch Virol. 2018 Sep;163(9):2601-2631
pubmed: 29754305