Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids.
bacteria
conjugation
genomes
horizontal gene transfer
plasmids
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
02 06 2022
02 06 2022
Historique:
pubmed:
1
6
2022
medline:
14
6
2022
entrez:
31
5
2022
Statut:
ppublish
Résumé
Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and extensive loss of other genes. At the microevolutionary scale of plasmid taxonomy, transitions of mobility type sometimes result in the creation of novel taxonomic units. Interestingly, most transitions from conjugative to mobilizable plasmids seem to be lost in the long term. This suggests a source-sink dynamic, where conjugative plasmids generate nonconjugative plasmids that tend to be poorly adapted and are frequently lost. Still, in some cases, these relaxases seem to have evolved to become efficient at plasmid mobilization in trans, possibly by hijacking multiple conjugative systems. This resulted in specialized relaxases of mobilizable plasmids. In conclusion, the evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology of plasmids.
Identifiants
pubmed: 35639760
pii: 6593704
doi: 10.1093/molbev/msac115
pmc: PMC9185392
pii:
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.
Références
Antimicrob Agents Chemother. 2008 Apr;52(4):1472-80
pubmed: 18268088
Environ Microbiol. 2021 Sep;23(9):5131-5146
pubmed: 33728723
Front Microbiol. 2019 Nov 08;10:2557
pubmed: 31781067
Methods Mol Biol. 2014;1079:131-46
pubmed: 24170399
J Bacteriol. 2005 Nov;187(22):7727-37
pubmed: 16267297
Nat Rev Genet. 2015 Aug;16(8):472-82
pubmed: 26184597
Plasmid. 2009 Sep;62(2):57-70
pubmed: 19465049
Mol Biol Evol. 2016 Nov;33(11):2860-2873
pubmed: 27501945
PLoS One. 2014 Oct 17;9(10):e110726
pubmed: 25330359
Mol Biol Evol. 2019 Sep 1;36(9):2069-2085
pubmed: 31127303
ISME J. 2019 Oct;13(10):2437-2446
pubmed: 31147603
Nucleic Acids Res. 2021 May 21;49(9):5177-5188
pubmed: 33939800
EMBO J. 2007 Aug 22;26(16):3847-57
pubmed: 17660746
Front Microbiol. 2017 Mar 20;8:443
pubmed: 28373865
Mob Genet Elements. 2016 Jul 01;6(4):e1208317
pubmed: 27583185
BMC Bioinformatics. 2019 Sep 14;20(1):473
pubmed: 31521110
Int J Med Microbiol. 2013 Aug;303(6-7):298-304
pubmed: 23499304
J Bacteriol. 1998 Nov;180(22):6039-42
pubmed: 9811665
Trends Microbiol. 2000 Mar;8(3):128-33
pubmed: 10707066
BMC Bioinformatics. 2013 Aug 15;14:248
pubmed: 23945046
PLoS Genet. 2011 Aug;7(8):e1002222
pubmed: 21876676
Mol Microbiol. 2016 Mar;99(5):884-96
pubmed: 26560080
Microbiol Mol Biol Rev. 2009 Dec;73(4):750-74
pubmed: 19946140
Curr Opin Microbiol. 2017 Aug;38:1-9
pubmed: 28391142
Nucleic Acids Res. 2014 May;42(9):5715-27
pubmed: 24623814
Front Mol Biosci. 2016 Nov 10;3:71
pubmed: 27891505
Methods Mol Biol. 2020;2075:295-308
pubmed: 31584171
Microbiol Rev. 1987 Dec;51(4):381-95
pubmed: 3325793
Mol Gen Genet. 1997 Apr 28;254(4):400-6
pubmed: 9180693
J Bacteriol. 2006 Nov;188(21):7488-99
pubmed: 16916896
Annu Rev Genet. 2015;49:577-601
pubmed: 26473380
Bioinformatics. 2019 Feb 1;35(3):526-528
pubmed: 30016406
Q Rev Biol. 1990 Mar;65(1):3-22
pubmed: 2186429
Bioinformatics. 2010 Sep 15;26(18):2334-5
pubmed: 20624783
Nat Commun. 2021 Oct 6;12(1):5845
pubmed: 34615859
Heredity (Edinb). 2011 Jan;106(1):1-10
pubmed: 20332804
Microbiol Spectr. 2017 Sep;5(5):
pubmed: 28944751
FEMS Microbiol Lett. 2013 Nov;348(2):87-96
pubmed: 23980652
FEMS Microbiol Rev. 2009 May;33(3):657-87
pubmed: 19396961
Nucleic Acids Res. 2015 Sep 18;43(16):7971-83
pubmed: 26243776
Nat Commun. 2022 Feb 3;13(1):683
pubmed: 35115531
Bacteriol Rev. 1965 Jun;29:161-72
pubmed: 14310189
Mol Biol Evol. 2018 Sep 1;35(9):2230-2239
pubmed: 29905872
Antimicrob Agents Chemother. 2018 Apr 26;62(5):
pubmed: 29507063
BMC Bioinformatics. 2021 Jul 31;22(1):390
pubmed: 34332528
PLoS Comput Biol. 2019 Apr 25;15(4):e1006946
pubmed: 31022176
J Bacteriol. 2018 Apr 9;200(9):
pubmed: 29463604
Trends Genet. 2001 Oct;17(10):589-96
pubmed: 11585665
Mol Biol Evol. 2013 Feb;30(2):315-31
pubmed: 22977114
Clin Microbiol Rev. 2018 Aug 1;31(4):
pubmed: 30068738
J Evol Biol. 2011 Jul;24(7):1462-76
pubmed: 21545421
PLoS Biol. 2020 Dec 2;18(12):e3001007
pubmed: 33264284
Curr Top Microbiol Immunol. 2018;418:443-462
pubmed: 29500561
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
J Bacteriol. 1994 Jul;176(14):4455-8
pubmed: 8021231
Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):
pubmed: 33526659
Nucleic Acids Res. 2021 Jan 25;49(2):832-846
pubmed: 33406256
Antimicrob Agents Chemother. 2014 Jul;58(7):3895-903
pubmed: 24777092
Front Microbiol. 2014 Dec 22;5:730
pubmed: 25566238
PLoS Biol. 2019 Jul 19;17(7):e3000390
pubmed: 31323028
Nat Rev Microbiol. 2006 Jul;4(7):548-55
pubmed: 16778839
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Microbiol Mol Biol Rev. 2010 Sep;74(3):434-52
pubmed: 20805406
ISME J. 2014 Mar;8(3):601-612
pubmed: 24152711
Proc Natl Acad Sci U S A. 1989 Mar;86(6):1771-5
pubmed: 2538813
Mol Microbiol. 2007 Sep;65(6):1405-14
pubmed: 17714446
Nat Commun. 2020 Jul 17;11(1):3602
pubmed: 32681114
Nucleic Acids Res. 2017 Sep 6;45(15):8943-8956
pubmed: 28911112
J Bacteriol. 2010 Dec;192(23):6309-12
pubmed: 20889746
Plasmid. 2014 Jul;74:15-31
pubmed: 24942190
mSphere. 2020 Aug 19;5(4):
pubmed: 32817379
Mob DNA. 2019 May 03;10:18
pubmed: 31073337
PLoS Genet. 2017 Feb 16;13(2):e1006586
pubmed: 28207825
Bioinformatics. 2017 Jan 15;33(2):283-285
pubmed: 27663497
Bioinformatics. 2016 May 1;32(9):1323-30
pubmed: 26743509
Genome Res. 2006 Dec;16(12):1537-47
pubmed: 17068325
Philos Trans R Soc Lond B Biol Sci. 2017 Dec 5;372(1735):
pubmed: 29061896
PLoS Genet. 2017 Mar 10;13(3):e1006669
pubmed: 28282376
Front Microbiol. 2017 Aug 04;8:1479
pubmed: 28824602
Trends Microbiol. 2010 Apr;18(4):141-8
pubmed: 20080407
Plasmid. 1980 Nov;4(3):332-9
pubmed: 7012869
FEMS Microbiol Rev. 2010 Jan;34(1):18-40
pubmed: 19919603
Plasmid. 2013 Jul;70(1):42-51
pubmed: 23415796