Evolution of primate interferon-induced transmembrane proteins (IFITMs): a story of gain and loss with a differentiation into a canonical cluster and IFITM retrogenes.
antiviral proteins
evolution
innate immunity
interferon-induced transmembrane proteins
primates
retrogene
transposable elements
Journal
Frontiers in microbiology
ISSN: 1664-302X
Titre abrégé: Front Microbiol
Pays: Switzerland
ID NLM: 101548977
Informations de publication
Date de publication:
2023
2023
Historique:
received:
03
05
2023
accepted:
06
07
2023
medline:
14
8
2023
pubmed:
14
8
2023
entrez:
14
8
2023
Statut:
epublish
Résumé
Interferon-inducible transmembrane proteins (IFITMs) are a family of transmembrane proteins. The subgroup of immunity-related (IR-)IFITMs is involved in adaptive and innate immune responses, being especially active against viruses. Here, we suggest that IFITMs should be classified as (1) a canonical IFITM gene cluster, which is located on the same chromosome, and (2) IFITM retrogenes, with a random and unique location at different positions within the genome. Phylogenetic analyses of the canonical cluster revealed the existence of three novel groups of primate IFITMs (pIFITM) in the IR-IFITM clade: the prosimian pIFITMs(pro), the new world monkey pIFITMs(nwm) and the old world monkey pIFITMs(owm). Therefore, we propose a new nomenclature: IR-pIFITM1, IR-pIFITM2, IR-pIFITM3, IR-pIFITMnwm, IR-pIFITMowm, and IR-pIFITMpro. We observed divergent evolution for pIFITM5 and pIFITM10, and evidence for concerted evolution and a mechanism of birth-and-death evolution model for the IR-pIFITMs. In contrast, the IFITMs scattered throughout the genomes possessed features of retrogenes retrotransposed by class 1 transposable elements. The origin of the IFITM retrogenes correspond to more recent events. We hypothesize that the transcript of a canonical IFITM3 has been constantly retrotransposed using class 1 transposable elements resulting in the IFITM retro(pseudo)genes. The unique pattern of each species has most likely been caused by constant pseudogenization and loss of the retro(pseudo)genes. This suggests a third mechanism of evolution for the IR-IFITMs in primates, similar to the birth-and-death model of evolution, but via a transposable element mechanism, which resulted in retro(pseudo)genes.
Identifiants
pubmed: 37577422
doi: 10.3389/fmicb.2023.1213685
pmc: PMC10415907
doi:
Types de publication
Journal Article
Langues
eng
Pagination
1213685Informations de copyright
Copyright © 2023 Schelle, Abrantes, Baldauf and Esteves.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Références
Front Microbiol. 2019 May 16;10:1097
pubmed: 31156602
Cell. 1993 Feb 26;72(4):595-605
pubmed: 7679954
J Virol. 2021 Oct 13;95(21):e0027721
pubmed: 34287042
Bioessays. 2021 Nov;43(11):e2100186
pubmed: 34569081
PLoS One. 2016 Jun 03;11(6):e0156739
pubmed: 27257969
BMC Genomics. 2012 Apr 26;13:155
pubmed: 22537233
Mol Biol Evol. 2021 Jun 25;38(7):3022-3027
pubmed: 33892491
Mol Immunol. 2021 Apr;132:79-81
pubmed: 33550067
Life Sci Alliance. 2019 Dec 11;3(1):
pubmed: 31826928
Nat Rev Immunol. 2013 Jan;13(1):46-57
pubmed: 23237964
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Immunology. 2020 Apr;159(4):365-372
pubmed: 31792954
EMBO Rep. 2016 Nov;17(11):1657-1671
pubmed: 27601221
Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7799-806
pubmed: 9223266
Genome Res. 2003 Dec;13(12):2541-58
pubmed: 14656962
Bone. 2022 Sep;162:116451
pubmed: 35654352
J Virol. 2021 Oct 13;95(21):e0068021
pubmed: 34319781
Mol Cell. 2015 Dec 3;60(5):728-741
pubmed: 26585388
Annu Rev Virol. 2014 Nov 1;1:261-283
pubmed: 25599080
Trends Genet. 2004 Feb;20(2):62-7
pubmed: 14746985
J Bone Miner Metab. 2011 May;29(3):279-90
pubmed: 20838829
Mol Biol Evol. 2022 Aug 06;:
pubmed: 35932227
Front Microbiol. 2019 Jan 08;9:3228
pubmed: 30687247
PLoS One. 2012;7(11):e49265
pubmed: 23166625
J Biol Chem. 2013 Nov 8;288(45):32184-32193
pubmed: 24067232
Hum Mol Genet. 2013 Sep 15;22(18):3730-48
pubmed: 23696454
Annu Rev Genet. 2005;39:121-52
pubmed: 16285855
Genome Res. 2004 Jun;14(6):1188-90
pubmed: 15173120
Nat Struct Mol Biol. 2006 Jul;13(7):655-60
pubmed: 16783376
Nat Genet. 2000 Apr;24(4):363-7
pubmed: 10742098
Cell. 1984 Oct;38(3):745-55
pubmed: 6548414
Mech Dev. 2002 Dec;119 Suppl 1:S261-7
pubmed: 14516695
Intractable Rare Dis Res. 2021 Aug;10(3):165-172
pubmed: 34466338
J Interferon Cytokine Res. 2011 Jan;31(1):183-97
pubmed: 21166591
Comput Appl Biosci. 1992 Jun;8(3):275-82
pubmed: 1633570
Nat Rev Genet. 2009 Jan;10(1):19-31
pubmed: 19030023