title: Evolution of threonine aldolases, a diverse family involved in the second pathway of glycine biosynthesis.
abstract: Threonine aldolases (TAs) catalyze the interconversion of threonine and glycine plus acetaldehyde in a pyridoxal phosphate-dependent manner. This class of enzymes complements the primary glycine biosynthetic pathway catalyzed by serine hydroxymethyltransferase (SHMT), and was shown to be necessary for yeast glycine auxotrophy. Because the reverse reaction of TA involves carbon-carbon bond formation, resulting in a β-hydroxyl-α-amino acid with two adjacent chiral centers, TAs are of high interests in synthetic chemistry and bioengineering studies. Here, we report systematic phylogenetic analysis of TAs. Our results demonstrated that L-TAs and D-TAs that are specific for L- and D-threonine, respectively, are two phylogenetically unique families, and both enzymes are different from their closely related enzymes SHMTs and bacterial alanine racemases (ARs). Interestingly, L-TAs can be further grouped into two evolutionarily distinct families, which share low sequence similarity with each other but likely possess the same structural fold, suggesting a convergent evolution of these enzymes. The first L-TA family contains enzymes of both prokaryotic and eukaryotic origins, and is related to fungal ARs, whereas the second contains only prokaryotic L-TAs. Furthermore, we show that horizontal gene transfer may occur frequently during the evolution of both L-TA families. Our results indicate the complex, dynamic, and convergent evolution process of TAs and suggest an updated classification scheme for L-TAs.
authors: Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China.
authors: Guangxiu
authors: G
authors: Liu
authors: Manxiao
authors: M
authors: Zhang
authors: Ximing
authors: X
authors: Chen
authors: Wei
authors: W
authors: Zhang
authors: Wei
authors: W
authors: Ding
authors: Qi
authors: Q
authors: Zhang
mesh_terms: D001105:Archaea / Q000201:enzymology / Q000235:genetics; D001419:Bacteria / Q000201:enzymology / Q000235:genetics; D056890:Eukaryota / Q000201:enzymology / Q000235:genetics; D019143:Evolution, Molecular; D005998:Glycine / Q000096:biosynthesis / Q000235:genetics; D012696:Glycine Hydroxymethyltransferase / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D010802:Phylogeny
chemical_list: D012696:Glycine Hydroxymethyltransferase; D005998:Glycine
references: Nat Protoc. 2007;2(10):2366-82
references: 17947979
references: Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1695-703
references: 24914980
references: Biochemistry. 2002 Oct 1;41(39):11711-20
references: 12269813
references: Nat Genet. 1993 Mar;3(3):266-72
references: 8485583
references: J Biochem. 1995 Sep;118(3):463-73
references: 8690703
references: Syst Biol. 2012 May;61(3):539-42
references: 22357727
references: Mol Biol Evol. 2001 May;18(5):691-9
references: 11319253
references: Appl Microbiol Biotechnol. 2000 Jul;54(1):44-51
references: 10952004
references: PLoS One. 2009;4(2):e4345
references: 19190775
references: Eur J Biochem. 1998 Jul 1;255(1):220-6
references: 9692922
references: FEBS J. 2014 Jan;281(1):129-45
references: 24165453
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: J Biol Chem. 1998 Jul 3;273(27):16678-85
references: 9642221
references: Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7
references: 22392983
references: BMC Genomics. 2005 Mar 09;6:32
references: 15757516
references: Appl Microbiol Biotechnol. 2010 Sep;88(2):409-24
references: 20683718
references: Adv Appl Microbiol. 2014;88:57-101
references: 24767426
references: Eur J Biochem. 1997 Apr 15;245(2):289-93
references: 9151955
references: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references: 9396791
references: Eur J Biochem. 2001 Dec;268(24):6508-25
references: 11737206
references: Annu Rev Biochem. 2004;73:383-415
references: 15189147
references: Elife. 2014 Jun 30;3:null
references: 24980702
references: Appl Environ Microbiol. 1998 Feb;64(2):549-54
references: 9464392
references: Syst Biol. 2003 Oct;52(5):696-704
references: 14530136
references: Syst Biol. 2006 Aug;55(4):539-52
references: 16785212
references: Biochim Biophys Acta. 2003 Apr 11;1647(1-2):214-9
references: 12686135
references: Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
references: 17130148
references: Biometrics. 1999 Mar;55(1):1-12
references: 11318142
references: J Biol Chem. 1994 Mar 25;269(12):9155-65
references: 8132653
references: Eur J Biochem. 1997 Sep 1;248(2):385-93
references: 9346293
references: FEMS Microbiol Lett. 1997 Jun 15;151(2):245-8
references: 9228760
references: J Bacteriol. 1997 Jun;179(11):3555-60
references: 9171400
references: Plant J. 2004 Aug;39(3):465-75
references: 15255874