Divergence among genes encoding the elongation factor Tu of Yersinia Species.
Elongation factor Tu (EF-Tu), encoded by tuf genes, carries aminoacyl-tRNA to the ribosome during protein synthesis. Duplicated tuf genes (tufA and tufB), which are commonly found in enterobacterial species, usually coevolve via gene conversion and are very similar to one another. However, sequence analysis of tuf genes in our laboratory has revealed highly divergent copies in 72 strains spanning the genus Yersinia (representing 12 Yersinia species). The levels of intragenomic divergence between tufA and tufB sequences ranged from 8.3 to 16.2% for the genus Yersinia, which is significantly greater than the 0.0 to 3.6% divergence observed for other enterobacterial genera. We further explored tuf gene evolution in Yersinia and other Enterobacteriaceae by performing directed sequencing and phylogenetic analyses. Phylogenetic trees constructed using concatenated tufA and tufB sequences revealed a monophyletic genus Yersinia in the family Enterobacteriaceae. Moreover, Yersinia strains form clades within the genus that mostly correlate with their phenotypic and genetic classifications. These genetic analyses revealed an unusual divergence between Yersinia tufA and tufB sequences, a feature unique among sequenced Enterobacteriaceae and indicative of a genus-wide loss of gene conversion. Furthermore, they provided valuable phylogenetic information for possible reclassification and identification of Yersinia species.
Isabel
Sandra
S
Centre de recherche en infectiologie de l'Université Laval, Centre hospitalier universitaire de Québec, Québec, Canada G1V 4G2.
Leblanc
Eric
E
Boissinot
Maurice
M
Boudreau
Dominique K
DK
Grondin
Myrian
M
Picard
François J
FJ
Martel
Eric A
EA
Parham
Nicholas J
NJ
Chain
Patrick S G
PS
Bader
Douglas E
DE
Mulvey
Michael R
MR
Bryden
Louis
L
Roy
Paul H
PH
Ouellette
Marc
M
Bergeron
Michel G
MG
D001426:Bacterial Proteins / Q000235:genetics*; D004755:Enterobacteriaceae / Q000145:classification / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010444:Peptide Elongation Factor Tu / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D015007:Yersinia / Q000145:classification / Q000235:genetics*
D001426:Bacterial Proteins; D010444:Peptide Elongation Factor Tu
J Mol Biol. 2004 Apr 30;338(3):463-7
15081805
Science. 2000 Nov 10;290(5494):1151-5
11073452
Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):831-835
15774670
BMC Evol Biol. 2008 Jan 24;8:22
18218099
FEMS Microbiol Lett. 2003 Nov 7;228(1):45-9
14612235
J Bacteriol. 2000 Dec;182(24):6913-20
11092850
FEMS Microbiol Lett. 2004 Sep 15;238(2):423-8
15358429
J Bacteriol. 2006 Jun;188(12):4453-63
16740952
Nature. 1993 Sep 9;365(6442):126-32
8371755
Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11030-5
15258291
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
1438297
Nature. 2001 Oct 25;413(6858):852-6
11677609
Contrib Microbiol Immunol. 1995;13:112-6
8833810
Lancet. 2007 Apr 7;369(9568):1196-207
17416264
Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13826-31
15358858
Int J Syst Evol Microbiol. 2000 Jul;50 Pt 4:1415-1417
10939643
J Mol Biol. 1996 Jul 26;260(4):506-22
8759317
Mol Biol Evol. 2002 Oct;19(10):1727-36
12270899
Int J Syst Bacteriol. 1992 Jan;42(1):191-2
1736967
J Bacteriol. 1996 Apr;178(8):2272-8
8636028
Eur J Biochem. 1987 Dec 30;170(1-2):93-8
2826164
Mol Biol Evol. 1996 Mar;13(3):451-61
8742634
Trends Genet. 2007 May;23(5):215-8
17383049
Mol Biol Evol. 2006 Feb;23(2):254-67
16221896
BMC Microbiol. 2007 Oct 29;7:96
17963531
Int J Syst Evol Microbiol. 2008 Apr;58(Pt 4):779-84
18398169
Microbes Infect. 2000 Apr;2(5):497-513
10865195
J Bacteriol. 2003 Feb;185(3):966-72
12533472
FEBS Lett. 2001 Aug 3;502(3):113-6
11583110
Nucleic Acids Res. 2003 Jul 1;31(13):3497-500
12824352
Contrib Microbiol Immunol. 1995;13:140-4
8833818
Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):2013-2025
16166704
Mol Biol Evol. 2004 Feb;21(2):255-65
14660700
J Bacteriol. 2002 Aug;184(16):4601-11
12142430
J Biol Chem. 1998 May 8;273(19):11478-82
9565560
PLoS Genet. 2006 Dec 15;2(12):e206
17173484
Biotechniques. 1994 Jun;16(6):1134-7
8074881
Electrophoresis. 2003 Aug;24(16):2864-82
12929182
J Clin Microbiol. 2005 Jun;43(6):2674-84
15956383
Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11105-10
15263089
Nature. 2001 Oct 4;413(6855):523-7
11586360
Mol Biol Evol. 2007 Aug;24(8):1596-9
17488738
Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):14043-8
10570195
Nature. 2000 Aug 3;406(6795):477-83
10952301
FEMS Microbiol Lett. 1993 Dec 1;114(2):173-7
7506685
J Bacteriol. 2004 Aug;186(15):5147-52
15262951
Appl Environ Microbiol. 1993 Feb;59(2):442-50
8434911
Evolution. 1985 Jul;39(4):783-791
28561359
J Mol Biol. 2000 Mar 24;297(2):355-64
10715206
J Bacteriol. 2006 May;188(10):3645-53
16672618
Genetics. 1987 Nov;117(3):543-57
3692140
Int J Med Microbiol. 2000 Mar;290(1):61-4
11043982
Int J Syst Evol Microbiol. 2008 Apr;58(Pt 4):952-8
18398201
Nat Biotechnol. 2003 Nov;21(11):1307-13
14528314
Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
7984417
J Clin Microbiol. 2001 Jul;39(7):2541-7
11427566
Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17020-4
12471157