Phylogenetic analysis of antibiotic glycosyltransferases

Journal of Molecular Evolution

Volumn 64, Issue 3, 2007, Pages 342-353

  Liang, Dongmei ^a   Qiao, Jianjun ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

Antibiotic glycosyltransferase; Glycopeptide antibiotic; Horizontal gene transfer; Molecular phylogeny; Polyene macrolide antibiotic

Indexed keywords

AGLYCONE; ANTIBIOTIC AGENT; AVILAMYCIN; BALHIMYCIN; BUTIROSIN; CHLOREREMOMYCIN; DAUNORUBICIN; ERYTHROMYCIN DERIVATIVE; GENTAMICIN; GLYCOPEPTIDE; GLYCOSYLTRANSFERASE; GRANATICIN; HYGROMYCIN; HYGROMYCIN B; ISTAMYCIN; KANAMYCIN; MACROLIDE; MEGALOMICIN; MYTHRAMYCIN; NEOMYCIN; POLYENE ANTIBIOTIC AGENT; POLYKETIDE; RIBOSTAMYCIN; SISOMICIN; SPECTINOMYCIN; TEICOPLANIN; TOBRAMYCIN; UNCLASSIFIED DRUG; UNINDEXED DRUG; VANCOMYCIN; VICENISTATIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL CELL WALL; BAYES THEOREM; EUKARYOTE; GENE CLUSTER; GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY;

AMINO ACID SEQUENCE; ANTI-BACTERIAL AGENTS; BACILLUS; BAYES THEOREM; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GLUCOSYLTRANSFERASES; GLYCOPEPTIDES; GLYCOSYLTRANSFERASES; GRAM-POSITIVE BACTERIA; MACROLIDES; MICROMONOSPORA; MOLECULAR SEQUENCE DATA; PHYLOGENY; STREPTOMYCES;

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 33847680014     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-006-0110-2     Document Type: Article

References (52)

1. Aparicio JF, Caffrey P, Gil JA, Zotchev SB (2003) Polyene antibiotic biosynthesis gene clusters. Appl Microbiol Biotechnol 61(3):179-188
2. Blanco G, Patallo EP, Brana AF, Trefzer A, Bechthold A, Rohr J, Mendez C, Salas JA (2001) Identification of a sugar flexible glycosyltransferase from Streptomyces olivaceus, the producer of the antitumor polyketide elloramycin. Chem Biol 8(3):253-263
3. Bolard J (1986) How do the polyene macrolide antibiotics affect the cellular membrane properties? Biochim Biophys Acta 864(3/4):257-304
4. Borisova SA, Zhao L, Melancon CE III, Kao CL, Liu HW (2004) Characterization of the glycosyltransferase activity of des VII: analysis of and implications for the biosynthesis of macrolide antibiotics. J Am Chem Soc 126(21):6534-6535
5. Campbell JA, Davies GJ, Bulone V, Henrisat B (1997) A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem J 326:929-942
6. Cane DE, Walsh CT (1999) The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases. Chem Biol 6(12):R319-R325
7. Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823-826
8. Doolittle RF (2002) Biodiversity: microbial genome multiply. Nature 416(6882):697-700
9. Du L, Sanchez C, Chen M, Edwards DJ, Shen B (2000) The biosynthetic gene cluster for the antitumor drug bleomycin from Streptomyces verticillus ATCC15003 supporting functional interactions between nonribosomal peptide synthetases and a polyketide synthase. Chem Biol 7(8):623-642
10. Faust B, Hoffmeister D, Weitnauer G, Westrich L, Haag S, Schneider P, Decker H, Kunzel E, Rohr J, Bechthold A (2000) Two new tailoring enzymes, a glycosyltransferase and an oxygenase, involved in biosynthesis of the angucycline antibiotic urdamycin A in Streptomyces fradiae Tu2717. Microbiology 146(P t1):147-154
11. Felsenstein J (2002) PHYLIP (phylogeny inference package). Version 3.6. Distributed by the author. University of Seattle, WA
12. Fischer C, Lipata F, Rohr J (2003) The complete gene cluster of the antitumor agent gilvocarcin V and its implication for the biosynthesis of the gilvocarcins. J Am Chem Soc 125(26):7818-7819
13. Frankel BA, McCafferty DG (2004) Profiling natural product biosynthesis. Chem Biol 11(3):290-291
14. Fu X, Albermann C, Jiang J, Liao J, Zhang C, Thorson JS (2003) Antibiotic optimization via in vitro glycorandomization. Nat Biotechnol 21(12):1467-1469
15. Fu X, Jiao W, Chang Z (2006) Phylogenetic and biochemical studies reveal a potential evolutionary origin of small heat shock proteins of animals from bacterial class A. J Mol Evol 62(3):257-266
16. Gachon CM, Langlois-Meurinne M, Saindrenan P (2005) Plant secondary metabolism glycosyltransferases: the emerging functional analysis. Trends Plant Sci 10(11):542-549
17. Ginolhac A, Jarrin C, Robe P, Perriere G, Vogel TM, Simonet P, Nalin R (2005) Type I polyketide synthases may have evolved through horizontal gene transfer. J Mol Evol 60(6):716-725
18. Hans J, Brandt W, Vogt T (2004) Site-directed mutagenesis and protein 3D-homology modeling suggest a catalytic mechanism for UDP-glucose-dependent betanidin 5-O-glucosyltransferase from Dorotheanthus bellidiformis. Plant J 39(3):319-333
19. Hofmann C, Boll R, Heitmann B, Hauser G, Durr C, Frerich A, Weitnauer G, Glaser SJ, Bechthold A (2005) Genes encoding enzymes responsible for biosynthesis of L-lyxose and attachment of eurekanate during avilamycin biosynthesis. Chem Biol 12(10):1137-1143
20. Hosted TJ, Wang TX, Alexander DC, Horan AC (2001) Characterization of the biosynthetic gene cluster for the oligosaccharide antibiotic, Evernimicin, in Micromanospora carbonacea var. africana ATCC39149. J Ind Microbiol Biotechnol 27(6):386-392
21. Hu Y, Chen L, Ha S, Gross B, Falcone B, Walker D, Mokhtarzadeh M, Walker S (2003) Crystal structure of the MurG:UDP-GlcNAc complex reveals common structural principles of a superfamily of glycosyltransferases. Proc Natl Acad Sci USA 100(3):845-849
22. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754-755
23. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8(3):275-282
24. Kahne D, Leimkuhler C, Lu W, Walsh C (2005) Glycopeptide and lipoglycopeptide antibiotics. Chem Rev 105(2):425-448
25. Kamra P, Gokhale RS, Mohanty D (2005) SEARCHGTr:a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. Nucleic Acids Res 33:W220-W225
26. Karolewiez A, Geisen R (2005) Cloning a part of the ochratoxin A biosynthetic gene cluster of Penicillium nordicum and characterization of the ochratoxin polyketide synthase. Syst Appl Microbiol 28(7):588-595
27. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5(2):150-163
28. Lemke A, Kiderlen AF, Kayser O (2005) Amphotericin B. Appl Microbiol Biotechnol 68(2):151-162
29. Li TL, Huang F, Haydock SF, Mironenko T, Leadlay PF, Spencer JB (2004) Biosynthetic gene cluster of the glycopeptide antibiotic teicoplanin: characterization of two glycosyltransferases and the key acyltransferase. Chem Biol 11(1):107-119
30. Mulichak AM, Losey HC, Walsh CT, Garavito RM (2001) Structure of UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics. Structure 9(7):547-557
31. Mulichak AM, Losey HC, Lu W, Wawizak Z, Walsh CT, Garavito RM (2003) Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway. Proc Natl Acad Sci USA 100(16):9238-9243
32. Muller R (2004) Don't classify polyketide synthases. Chem Biol 11(1):4-6
33. Nembaware V, Seoiqhe C, Sayed M, Gehring C (2004) A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry. BMC Evol Biol 4(10):1-7
34. Ogasawara Y, Katayama K, Minami A, Otsuka M, Eguchi T, Kakinuma K (2004) Cloning, sequencing, and functional analysis of the biosynthetic gene cluster of macrolactam antibiotic vicenistatin in Streptomyces halstedii. Chem Biol 11(1):79-86
35. Parker CT, Kloser AW, Schnaitman CA, Stein MA, Gottesman S, Gibson BW (1992) Role of the rfaG and rfaP genes in determining the lipopolysaccharide core structure and cell surface properties of Escherichia coli K-12. J Bacteriol 174(8):2525-2538
36. Pelzer S, Sussmuth R, Heckmann D, Recktenwald J, Huber P, Jung G, Wohlleben W (1999) Identification and analysis of the balhimycin biosynthetic gene cluster and its use for manipulating glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908. Antimicrob Agents Chemother 43(7):1565-1573
37. Pereto J, Lopez-Garcia P, Moreira D (2005) Phylogenetic analysis of eukaryotic thiolases suggests multiple proteobacterial origins. J Mol Evol 61(1):65-74
38. Reeves P (1993) Evolution of Salmonella O antigen variation by interspecific gene transfer on a large scale. Trends Genet 9(1):17-22
39. Royer M, Costet L, Vivien E, Bes M, Cousin A, Damain A, Pieretti I, Savin A, Megessier S, Viard M, Frutos R, Gabriel DW, Rott PC (2004) Albicidin pathotoxin produced by Xanthomonas albilineans is encoded by three large PKS and NRPS genes present in a gene cluster also containing several putative modifying, regulatory, and resistance genes. Mol Plant Microbe Interact 17(4):414-427
40. Schlunzen F, Zarivach R, Harms J, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F (2001) Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413(6858):814-821
41. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18(3):502-504
42. Seco EM, Perez-Zuniga FJ, Rolon MS, Malpartida F (2004) Starter unit choice determines the production of two tetraene macrolides, rimocidin and CE-108, in Streptomyces diastaticus var. 108. Chem Biol 11(3):357-366
43. Shen B (2003) Polyketide biosynthesis beyond the type I, II, and III polyketide synthase paradigms. Curr Opin Chem Biol 7(2):285-295
44. Sosio M, Stinchi S, Beltrametti F, Lazzarini A, Donadio S (2003) The gene cluster for the biosynthesis of the glycopeptide antibiotic A40926 by nonomuraea species. Chem Biol 10(6):541-549
45. Sun Y, Zhou X, Dong H, Tu G, Wang M, Wang B, Deng Z (2003) A complete gene cluster from Streptomyces nanchangensis NS3226 encoding biosynthesis of the polyether ionophore Nanchangmycin. Chem Biol 10(5):431-441
46. Suzuki N, Nakano Y, Yoshida Y, Nezu T, Terada Y, Yamashita Y, Koga T (2002) Guanosine diphosphate-4-keto-6-deoxy-d-mannose reductase in the pathway for the synthesis of GDP-6-deoxy-d-talose in Actinobacillus actinomycetemcomitans. Eur J Biochem 269(23):5963-5971
47. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876-4882
48. Torson JS, Hosted TJ Jr, Jiang JQ, Biggins JB, Ahlert J (2001) Nature's carbohydrate chemists :the enzymatic glycosylation of bioactive bacterial metabolites. Curr Org Chem 5:139-167
49. Volchegursky Y, Hu Z, Katz L, McDaniel R (2000) Biosynthesis of the anti-parasitic agent megalomicin: transformation of erythromycin to megalomicin in Saccharopolyspora erythraea. Mol Microbiol 37(4):752-762
50. Walsh CT, Losey HC, Freel Meyers CL (2003) Antibiotic glycosyltransferases. Biochem Soc Trans 31(Pt 3):487-492
51. Wang L, White RL, Vining LC (2002) Biosynthesis of the dideoxysugar component of jadomycin B:genes in the jad cluster of Streptomyces venezuelae ISP5230 for L-digitoxose assembly and transfer to the angucycline aglycone. Microbiology 148(Pt 4):1091-1103
52. Weitnauer G, Muhlenweg A, Trefzer A, Hoffmeister D, Sussmuth RD, Jung G, Welzel K, Vente A, Girreser U, Bechthold A (2001) Biosynthesis of the orthosomycin antibiotic avilamycin A: deductions from the molecular analysis of the avi biosynthetic gene cluster of Streptomyces viridochromogenes Tu57 and production of new antibiotics. Chem Biol 8(6):569-581