Chemical logic and enzymatic machinery for biological assembly of peptidyl nucleoside antibiotics

ACS Chemical Biology

Volumn 6, Issue 10, 2011, Pages 1000-1007

  Walsh, Christopher T ^a   Zhang, Wenjun ^b  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; ANTIBIOTIC AGENT; BLASTICIDIN S; CAPRAZAMYCIN; CAPURAMYCIN; CARRIER PROTEIN; CEPHALOSPORIN; DAPTOMYCIN; ERYTHROMYCIN; GLYCOPEPTIDE; LANTIBIOTIC; LIPOPEPTIDE; LIPOSIDOMYCIN; MURAYMYCIN; MUREIDOMYCIN A; NATURAL PRODUCT; NIKKOMYCIN; NUCLEOSIDE DERIVATIVE; PACIDAMYCIN; PENICILLIN DERIVATIVE; PEPTIDOGLYCAN; PEPTIDYL NUCLEOSIDE ANTIBIOTIC; POLYOXIN B; POLYPEPTIDE ANTIBIOTIC AGENT; PROTEIN MRAY; PUROMYCIN; TETRACYCLINE; UNCLASSIFIED DRUG; UNINDEXED DRUG; URIDINE DERIVATIVE; VANCOMYCIN;

BACILLUS SUBTILIS; BACTERIAL CELL WALL; BIOSYNTHESIS; CHEMICAL REACTION; CHEMICAL STRUCTURE; DRUG TARGETING; ENZYME ACTIVITY; ENZYME ANALYSIS; GENE CLUSTER; NONHUMAN; PRIORITY JOURNAL; REVIEW; STREPTOMYCES;

AMINOGLYCOSIDES; ANTI-BACTERIAL AGENTS; BACTERIA; BACTERIAL PROTEINS; NUCLEOSIDES; PEPTIDES; PYRIMIDINE NUCLEOSIDES; TRANSFERASES; URIDINE;

BACTERIA (MICROORGANISMS);

EID: 80055021577     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb200284p     Document Type: Review

References (37)

1. Xie, L. and van der Donk, W. A. (2004) Post-translational modifications during lantibiotic biosynthesis Curr. Opin. Chem. Biol. 8, 498-507 (Pubitemid 39278346)
2. Walsh, C. T., Acker, M. G., and Bowers, A. A. (2010) Thiazolyl peptide antibiotic biosynthesis: a cascade of post-translational modifications on ribosomal nascent proteins J. Biol. Chem. 285, 27525-27531
3. Martin, J. F. (2000) Alpha-aminoadipyl-cysteinyl-valine synthetases in beta-lactam producing organisms. From Abraham's discoveries to novel concepts of non-ribosomal peptide synthesis J. Antibiot. (Tokyo) 53, 1008-1021
4. Baltz, R. H. (2008) Biosynthesis and genetic engineering of lipopeptide antibiotics related to daptomycin Curr. Top. Med. Chem. 8, 618-638 (Pubitemid 351982571)
5. Hubbard, B. K. and Walsh, C. T. (2003) Vancomycin assembly: nature's way Angew. Chem., Int. Ed. 42, 730-765 (Pubitemid 36288220)
6. Cone, M. C., Petrich, A. K., Gould, S. J., and Zabriskie, T. M. (1998) Cloning and heterologous expression of blasticidin S biosynthetic genes from Streptomyces griseochromogenes J. Antibiot. (Tokyo) 51, 570-578 (Pubitemid 28336293)
7. Tercero, J. A., Espinosa, J. C., Lacalle, R. A., and Jimenez, A. (1996) The biosynthetic pathway of the aminonucleoside antibiotic puromycin, as deduced from the molecular analysis of the pur cluster of Streptomyces alboniger J. Biol. Chem. 271, 1579-1590 (Pubitemid 26028648)
8. Hansen, J. L., Moore, P. B., and Steitz, T. A. (2003) Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit J. Mol. Biol. 330, 1061-1075 (Pubitemid 36818903)
9. Endo, A., Kakiki, K., and Misato, T. (1970) Mechanism of action of the antifugal agent polyoxin D J. Bacteriol. 104, 189-196
10. Dahn, U., Hagenmaier, H., Hohne, H., Konig, W. A., Wolf, G., and Zahner, H. (1976) Metabolic products of microorganisms. 154. Nikkomycin, a new inhibitor of fungal chitin synthesis Arch. Microbiol. 107, 143-160
11. Winn, M., Goss, R. J., Kimura, K., and Bugg, T. D. (2010) Antimicrobial nucleoside antibiotics targeting cell wall assembly: recent advances in structure-function studies and nucleoside biosynthesis Nat. Prod. Rep. 27, 279-304
12. Bouhss, A., Mengin-Lecreulx, D., Le Beller, D., and Van Heijenoort, J. (1999) Topological analysis of the MraY protein catalysing the first membrane step of peptidoglycan synthesis Mol. Microbiol. 34, 576-585 (Pubitemid 29507317)
13. Bouhss, A., Crouvoisier, M., Blanot, D., and Mengin-Lecreulx, D. (2004) Purification and characterization of the bacterial MraY translocase catalyzing the first membrane step of peptidoglycan biosynthesis J. Biol. Chem. 279, 29974-29980 (Pubitemid 38937917)
14. Bryskier, A. (2005) Antimicrobial Agents: Antibacterials and Antifungals, ASM Press, Washington.
15. Funabashi, M., Nonaka, K., Yada, C., Hosobuchi, M., Masuda, N., Shibata, T., and Van Lanen, S. G. (2009) Identification of the biosynthetic gene cluster of A-500359s in Streptomyces griseus SANK60196 J. Antibiot. (Tokyo) 62, 325-332
16. Kaysser, L., Lutsch, L., Siebenberg, S., Wemakor, E., Kammerer, B., and Gust, B. (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
17. Funabashi, M., Baba, S., Nonaka, K., Hosobuchi, M., Fujita, Y., Shibata, T., and Van Lanen, S. G. (2010) The biosynthesis of liposidomycin-like A-90289 antibiotics featuring a new type of sulfotransferase ChemBioChem 11, 184-190
18. Kaysser, L., Siebenberg, S., Kammerer, B., and Gust, B. (2010) Analysis of the liposidomycin gene cluster leads to the identification of new caprazamycin derivatives ChemBioChem 11, 191-196
19. Rackham, E. J., Gruschow, S., Ragab, A. E., Dickens, S., and Goss, R. J. (2010) Pacidamycin biosynthesis: identification and heterologous expression of the first uridyl peptide antibiotic gene cluster ChembBioChem 11, 1700-1709
20. Zhang, W., Ostash, B., and Walsh, C. T. (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
21. Kaysser, L., Tang, X., Wemakor, E., Sedding, K., Hennig, S., Siebenberg, S., and Gust, B. (2011) Identification of a napsamycin biosynthesis gene cluster by genome mining ChemBioChem 12, 477-487
22. Yang, Z., Chi, X., Funabashi, M., Baba, S., Nonaka, K., Pahari, P., Unrine, J., Jacobsen, J. M., Elliott, G. I., Rohr, J., and Van Lanen, S. G. (2011) Characterization of LipL as a non-heme, Fe(II)-dependent alpha-ketoglutarate:UMP dioxygenase that generates uridine-5′-aldehyde during A-90289 biosynthesis J. Biol. Chem. 286, 7885-7892
23. Isono, K., Sato, T., Hirasawa, K., Funayama, S., and Suzuki, S. (1978) Biosynthesis of the nucleoside skeleton of polyoxins J. Am. Chem. Soc. 100, 3937-3939 (Pubitemid 8353688)
24. Ginj, C., Ruegger, H., Amrhein, N., and Macheroux, P. (2005) 3′-Enolpyruvyl-UMP, a novel and unexpected metabolite in nikkomycin biosynthesis ChembBioChem 6, 1974-1976 (Pubitemid 41598169)
25. Chen, W., Huang, T., He, X., Meng, Q., You, D., Bai, L., Li, J., Wu, M., Li, R., Xie, Z., Zhou, H., Zhou, X., Tan, H., and Deng, Z. (2009) Characterization of the polyoxin biosynthetic gene cluster from Streptomyces cacaoi and engineered production of polyoxin H J. Biol. Chem. 284, 10627-10638
26. Chen, R. H., Buko, A. M., Whittern, D. N., and McAlpine, J. B. (1989) Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. II. Isolation and structural elucidation J. Antibiot. (Tokyo) 42, 512-520 (Pubitemid 19119087)
27. Fronko, R. M., Lee, J. C., Galazzo, J. G., Chamberland, S., Malouin, F., and Lee, M. D. (2000) New pacidamycins produced by Streptomyces coeruleorubidus, NRRL 18370 J. Antibiot. (Tokyo) 53, 1405-1410 (Pubitemid 32042470)
28. Chatterjee, S., Nadkarni, S. R., Vijayakumar, E. K., Patel, M. V., Ganguli, B. N., Fehlhaber, H. W., and Vertesy, L. (1994) Napsamycins, new Pseudomonas active antibiotics of the mureidomycin family from Streptomyces sp. HIL Y-82,11372 J. Antibiot. (Tokyo) 47, 595-598 (Pubitemid 24166635)
29. Zhang, W., Ames, B. D., and Walsh, C. T. (2011) Identification of phenylalanine 3-hydroxylase for meta-tyrosine biosynthesis Biochemistry 50, 5401-5403
30. Zhang, W., Heemstra, J. R., Jr., Walsh, C. T., and Imker, H. J. (2010) Activation of the pacidamycin PacL adenylation domain by MbtH-like proteins Biochemistry 49, 9946-9947
31. Zhang, W., Ntai, I., Bolla, M. L., Malcolmson, S. J., Kahne, D., Kelleher, N. L., and Walsh, C. T. (2011) Nine enzymes are required for assembly of the pacidamycin group of peptidyl nucleoside antibiotics J. Am. Chem. Soc. 133, 5240-5243
32. Hirschma, R, Strachan, R. G., Schwam, H., choenew, Ef, Joshua, H., Barkemey., B, Veber, D. F., Paleveda, W. J., Jacob, T. A., Beesley, T. E., and Denkewal, Rg. (1967) Controlled synthesis of peptides in aqueous medium. 3. Use of leuchs anhydrides in synthesis of dipeptides. Mechanism and control of side reactions J. Org. Chem. 32, 3415
33. Itou, Y., Suzuki, S., Ishida, K., and Murakami, M. (1999) Anabaenopeptins G and H, potent carboxypeptidase A inhibitors from the cyanobacterium Oscillatoria agardhii (NIES-595) Bioorg. Med. Chem. Lett. 9, 1243-1246 (Pubitemid 29207440)
34. Imker, H. J., Walsh, C. T., and Wuest, W. M. (2009) SylC catalyzes ureido-bond formation during biosynthesis of the proteasome inhibitor syringolin A J. Am. Chem. Soc. 131, 18263-18265
35. Walther, T., Renner, S., Waldmann, H., and Arndt, H. D. (2009) Synthesis and structure-activity correlation of a brunsvicamide-inspired cyclopeptide collection ChemBioChem 10, 1153-1162
36. Zhang, W., Ntai, I., Kelleher, N. L., and Walsh, C. T. (2011) 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. 108, 12249-12253
37. Gruschow, S., Rackham, E. J., Elkins, B., Newill, P. L., Hill, L. M., and Goss, R. J. (2009) New pacidamycin antibiotics through precursor-directed biosynthesis ChemBioChem 10, 355-360