Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents.
GTA
Sphingomonadales
addAB
codon usage bias
head completion protein
homologous recombination
nutrient depletion
tonB
Journal
mSystems
ISSN: 2379-5077
Titre abrégé: mSystems
Pays: United States
ID NLM: 101680636
Informations de publication
Date de publication:
20 12 2022
20 12 2022
Historique:
pubmed:
15
11
2022
medline:
23
12
2022
entrez:
14
11
2022
Statut:
ppublish
Résumé
Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by carbon depletion and results in host lysis and the release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for GTA-mediated DNA acquisition. Here, we detected a codon usage bias toward codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in
Identifiants
pubmed: 36374047
doi: 10.1128/msystems.00892-22
pmc: PMC9765227
doi:
Substances chimiques
DNA
9007-49-2
Banques de données
figshare
['10.6084/m9.figshare.20082749']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0089222Références
Nat Rev Genet. 2015 Aug;16(8):472-82
pubmed: 26184597
Nat Commun. 2020 Jun 15;11(1):3034
pubmed: 32541663
Appl Environ Microbiol. 2007 Feb;73(4):1355-61
pubmed: 17194842
PLoS One. 2007 Feb 21;2(2):e224
pubmed: 17311090
Nat Commun. 2019 Feb 5;10(1):595
pubmed: 30723210
Mol Microbiol. 1993 Mar;7(6):915-23
pubmed: 8387145
J Bacteriol. 2008 Aug;190(15):5230-8
pubmed: 18539735
Microbiology (Reading). 2017 Sep;163(9):1355-1363
pubmed: 28869409
Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9033-8
pubmed: 15175431
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
PLoS One. 2012;7(8):e43772
pubmed: 22916305
Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10626-31
pubmed: 21670266
Nat Rev Microbiol. 2012 Jun 11;10(7):472-82
pubmed: 22683880
PLoS Biol. 2021 Apr 19;19(4):e3001185
pubmed: 33872297
Mol Microbiol. 2014 Jun;92(6):1260-78
pubmed: 24784901
mBio. 2020 Jul 14;11(4):
pubmed: 32665274
PLoS Genet. 2019 Jul 31;15(7):e1008304
pubmed: 31365533
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Mol Biol Evol. 2021 Dec 9;38(12):5825-5829
pubmed: 34597405
Trends Microbiol. 2017 Apr;25(4):280-292
pubmed: 28038926
Mol Biol Evol. 2016 Oct;33(10):2530-43
pubmed: 27343288
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
PLoS Genet. 2010 Jun 24;6(6):e1001004
pubmed: 20585573
Virus Evol. 2017 Dec 07;3(2):vex036
pubmed: 29250433
J Microbiol. 2015 Dec;53(12):820-8
pubmed: 26626352
Annu Rev Virol. 2017 Sep 29;4(1):87-104
pubmed: 28784044
PLoS One. 2012;7(7):e41204
pubmed: 22829928
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296
pubmed: 33885785
Nucleic Acids Res. 2021 Jan 8;49(D1):D545-D551
pubmed: 33125081
Nucleic Acids Res. 2004 Sep 24;32(17):5036-44
pubmed: 15448185
Mol Microbiol. 2012 Jul;85(2):314-25
pubmed: 22640804
Bioinformatics. 2012 Apr 1;28(7):1033-4
pubmed: 22332237
Nucleic Acids Res. 2003 Dec 1;31(23):6976-85
pubmed: 14627830
Sci Rep. 2016 Jul 27;6:30372
pubmed: 27460944
Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):859-64
pubmed: 10639170
Gene. 1990 Mar 1;87(1):23-9
pubmed: 2110097
Trends Genet. 2000 Jul;16(7):287-9
pubmed: 10858656
Trends Microbiol. 2007 Feb;15(2):54-62
pubmed: 17184993
J Bacteriol. 2015 Aug;197(16):2653-63
pubmed: 26031909
Sci Rep. 2019 Aug 26;9(1):12374
pubmed: 31451723
Genome Biol. 2019 Nov 14;20(1):238
pubmed: 31727128
Nucleic Acids Res. 2021 Jan 8;49(D1):D605-D612
pubmed: 33237311
Genome Res. 2004 Nov;14(11):2279-86
pubmed: 15479947
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Mol Cell. 2015 Jul 16;59(2):149-61
pubmed: 26186290
Nucleic Acids Res. 2013 Oct;41(19):8842-52
pubmed: 23921637
Mol Biol Evol. 2018 Feb 1;35(2):518-522
pubmed: 29077904
FEMS Microbiol Lett. 2010 Oct;311(1):44-50
pubmed: 20722738
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Genome Biol Evol. 2019 Oct 1;11(10):2941-2953
pubmed: 31560374
Cell Syst. 2017 Jun 28;4(6):611-621.e6
pubmed: 28624614
Nucleic Acids Res. 2021 Jan 8;49(D1):D480-D489
pubmed: 33237286
Nat Rev Genet. 2011 Jan;12(1):32-42
pubmed: 21102527
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096
pubmed: 34417604
Sci Rep. 2015 Feb 09;5:8331
pubmed: 25660389
J Biol Chem. 2019 Feb 8;294(6):2109-2120
pubmed: 30401745
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):E6117-E6125
pubmed: 27671647
Bioinformatics. 2017 Feb 15;33(4):589-591
pubmed: 27797757
Proc Natl Acad Sci U S A. 1974 Mar;71(3):971-3
pubmed: 4522805
BMC Bioinformatics. 2018 May 8;19(Suppl 6):153
pubmed: 29745866
Science. 2010 Oct 1;330(6000):50
pubmed: 20929803
Bioinformatics. 2013 Nov 15;29(22):2933-5
pubmed: 24008419
J Bacteriol. 1998 Feb;180(4):846-54
pubmed: 9473038
Nat Chem Biol. 2007 Jul;3(7):408-14
pubmed: 17576428
Virus Evol. 2022 Oct 15;8(2):veac100
pubmed: 36381234