Characterization of the amicetin biosynthesis gene cluster from Streptomyces vinaceusdrappus NRRL 2363 implicates two alternative strategies for amide bond formation

Applied and Environmental Microbiology

Volumn 78, Issue 7, 2012, Pages 2393-2401

  Zhang, Gaiyun ^a,b   Zhang, Haibo ^a,b   Li, Sumei ^a,b   Xiao, Ji ^a,b   Zhang, Guangtao ^a,b   Zhu, Yiguang ^a,b   Niu, Siwen ^a,b   Ju, Jianhua ^a,b   Zhang, Changsheng ^a,b  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b SOUTH CHINA SEA INSTITUTE OF OCEANOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE BOND; AMIDE BOND FORMATION; ANTIVIRAL AGENTS; BIOSYNTHESIS GENE CLUSTER; CARRIER PROTEINS; COENZYME A; DISACCHARIDE NUCLEOSIDES; GENE CLUSTERS; GLYCOSIDE BOND; HETEROLOGOUS EXPRESSION; IN-SILICO; N-ACETYLTRANSFERASES; P-AMINOBENZOIC ACID; SEQUENCE ANALYSIS; STREPTOMYCES LIVIDANS;

AMIDES; BACTERIA; BIOCHEMISTRY; BIOSYNTHESIS; CLONING; ORGANIC POLYMERS;

GENE EXPRESSION;

AMICETIN; AMIDE; ANTIINFECTIVE AGENT; ANTIVIRUS AGENT; BACTERIAL PROTEIN; NORPLICACETIN; PYRIMIDINE NUCLEOSIDE;

ANTIBIOTICS; BIOACCUMULATION; CLUSTER ANALYSIS; DISACCHARIDE; ENZYME ACTIVITY; FUNGUS; GENE EXPRESSION; MUTATION; ORGANIC ACID; PROTEIN;

ARTICLE; BIOSYNTHESIS; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; ENZYMOLOGY; GENETICS; GLYCOSYLATION; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; STREPTOMYCES; STREPTOMYCES LIVIDANS;

AMIDES; ANTI-BACTERIAL AGENTS; ANTIVIRAL AGENTS; BACTERIAL PROTEINS; CLONING, MOLECULAR; GLYCOSYLATION; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PYRIMIDINE NUCLEOSIDES; SEQUENCE ANALYSIS, DNA; STREPTOMYCES; STREPTOMYCES LIVIDANS;

STREPTOMYCES LIVIDANS; STREPTOMYCES VINACEUSDRAPPUS;

EID: 84861146139     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.07185-11     Document Type: Article

References (61)

1. Abe T, Hashimoto Y, Hosaka H, Tomita-Yokotani K, Kobayashi M. 2008. Discovery of amide (peptide) bond synthetic activity in acyl-CoA synthetase. J. Biol. Chem. 283:11312-11321.
2. Basnet DB, et al. 2006. Angucyclines Sch 47554 and Sch 47555 from Streptomyces sp. SCC-2136: cloning, sequencing, and characterization. Mol. Cells 22:154-162.
3. Brown MP, Aidoo KA, Vining LC. 1996. A role for pabAB, a paminobenzoate synthase gene of Streptomyces venezuelae ISP5230, in chloramphenicol biosynthesis. Microbiology 142(Pt. 6):1345-1355.
4. Bruntner C, Lauer B, Schwarz W, Mohrle V, Bormann C. 1999. Molecular characterization of co-transcribed genes from Streptomyces tendae Tu901 involved in the biosynthesis of the peptidyl moiety of the peptidyl nucleoside antibiotic nikkomycin. Mol. Gen. Genet. 262:102-114.
5. Carrasco L, Vazquez D. 1984. Molecular bases for the action and selectivity of nucleoside antibiotics. Med. Res. Rev. 4:471-512.
6. Chang Z, Sun Y, He J, Vining LC. 2001. p-Aminobenzoic acid and chloramphenicol biosynthesis in Streptomyces venezuelae: gene sets for a key enzyme, 4-amino-4-deoxychorismate synthase. Microbiology 147: 2113-2126.
7. Chen S, et al. 2003. Organizational and mutational analysis of a complete FR-008/candicidin gene cluster encoding a structurally related polyene complex. Chem. Biol. 10:1065-1076.
8. Chen W, et al. 2009. Characterization of the polyoxin biosynthetic gene cluster from Streptomyces cacaoi and engineered production of polyoxin H. J. Biol. Chem. 284:10627-10638.
9. Chen W, et al. 2010. Characterization of the tunicamycin gene cluster unveiling unique steps involved in its biosynthesis. Protein Cell 1:1093-1105
10. Chen Y, et al. 2010. Characterization of FdmV as an amide synthetase for fredericamycin A biosynthesis in Streptomyces griseus ATCC 43944. J. Biol. Chem. 285:38853-38860.
11. Chen Y, Zeeck A, Chen Z, Zahner H. 1985. Studies on metabolites produced by Streptomyces ramuloses Tue-34. II. The structural elucidation of oxyplicacetin, a new member of amicetin group. Kangshengsu 10:285-295.
12. Cheng L, et al. 2011. Identification of the gene cluster involved in muraymycin biosynthesis from Streptomyces sp. NRRL 30471. Mol. Biosyst. 7:920-927.
13. Cone MC, Yin X, Grochowski LL, Parker MR, Zabriskie TM. 2003. The blasticidin S biosynthesis gene cluster from Streptomyces griseochromogenes: sequence analysis, organization, and initial characterization. Chembiochem 4:821-828.
14. Coutinho PM, Deleury E, Davies GJ, Henrissat B. 2003. An evolving hierarchical family classification for glycosyltransferases. J. Mol. Biol. 328: 307-317.
15. Daum M, et al. 2009. Organisation of the biosynthetic gene cluster and tailoring enzymes in the biosynthesis of the tetracyclic quinone glycoside antibiotic polyketomycin. Chembiochem 10:1073-1083.
16. DeBoer C, Caron EL, Hinman JW. 1953. Amicetin, a new streptomyces antibiotic. J. Am. Chem. Soc. 75:499-500.
17. Decker H, et al. 1996. A general approach for cloning and characterizing dNDP-glucose dehydratase genes from actinomycetes. FEMS Microbiol. Lett. 141:195-201.
18. Donarski J, Shammas C, Banks R, Ramesh V. 2006. NMR and molecular modelling studies of the binding of amicetin antibiotic to conserved secondary structural motifs of 23S ribosomal RNAs. J. Antibiot. 59:177-183.
19. Dyda F, Klein DC, Hickman AB. 2000. GCN5-related N-acetyltransferases: a structural overview. Annu. Rev. Biophys. Biomol. Struct. 29:81-103.
20. Ettwig KF, et al. 2010. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature 464:543-548.
21. Evans JR, Weare G. 1977. Norplicacetin, a new antibiotic from Streptomyces plicatus. J. Antibiot. 30:604-606.
22. Flynn EH, Hinman JW, Caron EL, Woolf DO. 1953. The chemistry of amicetin, a new antibiotic. J. Am. Chem. Soc. 75:5867-5871.
23. Fortin PD, Walsh CT, Magarvey NA. 2007. A transglutaminase homologue as a condensation catalyst in antibiotic assembly lines. Nature 448: 824-827.
24. Funabashi M, et al. 2010. The biosynthesis of liposidomycin-like A-90289 antibiotics featuring a new type of sulfotransferase. Chembiochem 11: 184-190.
25. Funabashi M, et al. 2009. Identification of the biosynthetic gene cluster of A-500359s in Streptomyces griseus SANK60196. J. Antibiot. 62:325-332.
26. Funabashi M, et al. 2010. An ATP-independent strategy for amide bond formation in antibiotic biosynthesis. Nat. Chem. Biol. 6:581-586.
27. Gaudet R, Wiley DC. 2001. Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing. EMBO J. 20:4964-4972.
28. Grochowski LL, Zabriskie TM. 2006. Characterization of BlsM, a nucleotide hydrolase involved in cytosine production for the biosynthesis of blasticidin S. Chembiochem 7:957-964.
29. Gust B, Challis GL, Fowler K, Kieser T, Chater KF. 2003. PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin. Proc. Natl. Acad. Sci. U. S. A. 100:1541-1546.
30. Haneda K, et al. 1994. Cytosaminomycins, new anticoccidial agents produced by Streptomyces sp. KO-8119. I. Taxonomy, production, isolation and physico-chemical and biological properties. J. Antibiot. 47:774-781.
31. Haskell TH, et al. 1958. The isolation and characterization of three crystalline antibiotics from Streptomyces plicatus. J. Am. Chem. Soc. 80:743-747.
32. He J, Hertweck C. 2003. Iteration as programmed event during polyketide assembly; molecular analysis of the aureothin biosynthesis gene cluster. Chem. Biol. 10:1225-1232.
33. Hinman JW, Caron EL, DeBoer C. 1953. The isolation and purification of amicetin. J. Am. Chem. Soc. 75:5864-5866.
34. Hong L, Zhao Z, Liu HW. 2006. Characterization of SpnQ from the spinosyn biosynthetic pathway of Saccharopolyspora spinosa: mechanistic and evolutionary implications for C-3 deoxygenation in deoxysugar biosynthesis. J. Am. Chem. Soc. 128:14262-14263.
35. Hong L, Zhao Z, Melancon CE III, Zhang H, Liu HW. 2008. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130:4954-4967.
36. Isono K. 1988. Nucleoside antibiotics: structure, biological activity, and biosynthesis. J. Antibiot. 41:1711-1739.
37. Itoh J, Miyadoh S. 1992. SF2457, a new antibiotic related to amicetin. J. Antibiot. 45:846-853.
38. Kaysser L, et al. 2009. Identification and manipulation of the caprazamycin gene cluster lead to new simplified liponucleoside antibiotics and give insights into the biosynthetic pathway. J. Biol. Chem. 284:14987-14996.
39. Kaysser L, Siebenberg S, Kammerer B, Gust B. 2010. Analysis of the liposidomycin gene cluster leads to the identification of new caprazamycin derivatives. Chembiochem 11:191-196.
40. Kieser T, Bibb M, Butter M, Chater KF, Hopwood DA. 2000. Practical Streptomyces genetics. The John Innes Foundation, Norwich, United Kingdom.
41. Kirillov S, Porse BT, Vester B, Woolley P, Garrett RA. 1997. Movement of the 3′-end of tRNA through the peptidyl transferase centre and its inhibition by antibiotics. FEBS Lett. 406:223-233.
42. Konishi M, Naruishi M, Tsuno T, Tsukiura H, Kawaguchi H. 1973. Oxamicetin, a new antibiotic of bacterial origin. II. Structure of oxamicetin. J. Antibiot. 26:757-764.
43. Law CJ, Maloney PC, Wang DN. 2008. Ins and outs of major facilitator superfamily antiporters. Annu. Rev. Microbiol. 62:289-305.
44. Leviev IG, et al. 1994. A conserved secondary structural motif in 23S rRNA defines the site of interaction of amicetin, a universal inhibitor of peptide bond formation. EMBO J. 13:1682-1686.
45. Li L, et al. 2008. The mildiomycin biosynthesis: initial steps for sequential generation of 5-hydroxymethylcytidine 5′-monophosphate and 5-hydroxymethylcytosine in Streptoverticillium rimofaciens ZJU5119. Chembiochem 9:1286-1294.
46. Liu G, Tian Y, Yang H, Tan H. 2005. A pathway-specific transcriptional regulatory gene for nikkomycin biosynthesis in Streptomyces ansochromogenes that also influences colony development. Mol. Microbiol. 55: 1855-1866.
47. Luft T, Li SM, Scheible H, Kammerer B, Heide L. 2005. Overexpression, purification and characterization of SimL, an amide synthetase involved in simocyclinone biosynthesis. Arch. Microbiol. 183:277-285.
48. Ogasawara Y, et al. 2004. Cloning, sequencing, and functional analysis of the biosynthetic gene cluster of macrolactam antibiotic vicenistatin in Streptomyces halstedii. Chem. Biol. 11:79-86.
49. Pompeo F, Mushtaq A, Sim E. 2002. Expression and purification of the rifamycin amide synthase, RifF, an enzyme homologous to the prokaryotic arylamine N-acetyltransferases. Protein Expr. Purif. 24:138-151.
50. Rackham EJ, Gruschow S, Ragab AE, Dickens S, Goss RJ. 2010. Pacidamycin biosynthesis: identification and heterologous expression of the first uridyl peptide antibiotic gene cluster. Chembiochem 11:1700-1709.
51. Ramos JL, et al. 2005. The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69:326-356.
52. Riley LK, Caffrey CJ. 1990. Identification of enterotoxigenic Escherichia coli by colony hybridization with nonradioactive digoxigenin-labeled DNA probes. J. Clin. Microbiol. 28:1465-1468.
53. Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
54. Schirch L, Jenkins WT. 1964. Serine transhydroxymethylase. Transamination of D-alanine. J. Biol. Chem. 239:3797-3800.
55. Smith JL, Sundaralingam M. 1981. The structure of the antibiotic amicetin consisting of nucleobase, disaccharide and amino acid moieties. Acta Crystallogr. B 37:1095-1101.
56. Stevens CL, Nagarajan K, Haskell TH. 1962. The structure of amicetin. J. Org. Chem. 2:2991-3005.
57. Thibodeaux CJ, Melancon CE III, Liu HW. 2008. Natural-product sugar biosynthesis and enzymatic glycodiversification. Angew. Chem. Int. Ed. Engl. 47:9814-9859.
58. Williams GJ, Thorson JS. 2009. Natural product glycosyltransferases: properties and applications. Adv. Enzymol. Relat. Areas Mol. Biol. 76:55-119.
59. Zhang W, Ntai I, Kelleher NL, Walsh CT. 11 July 2011, posting date. tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics. Proc. Natl. Acad. Sci. U. S. A. doi:10.1073/pnas.1109539108.
60. Zhang W, Ostash B, Walsh CT. 2010. Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics. Proc. Natl. Acad. Sci. U. S. A. 107:16828-16833.
61. Zhang Y, Bai L, Deng Z. 2009. Functional characterization of the first two actinomycete 4-amino-4-deoxychorismate lyase genes. Microbiology 155: 2450-2459.