Establishing a toolkit for precursor-directed polyketide biosynthesis: Exploring substrate promiscuities of acid-CoA ligases

Biochemistry

Volumn 51, Issue 22, 2012, Pages 4568-4579

  Go, Maybelle Kho ^a   Chow, Jeng Yeong ^a   Cheung, Vivian Wing Ngar ^a   Lim, Yan Ping ^a   Yew, Wen Shan ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL-COA; BICYCLIC AROMATICS; COMBINATORIAL BIOSYNTHESIS; ENZYMATIC ROUTE; LIGASES; MALONYL-COA; POLYKETIDE BIOSYNTHESIS; POLYKETIDE SYNTHASES; POLYKETIDES; SYNTHETASES; THIOESTERS;

BIOCHEMISTRY; CARBOXYLIC ACIDS; ENZYMES; KETONES;

BIOSYNTHESIS;

ALIPHATIC COMPOUND; BENZOIC ACID; CARBOXYLIC ACID; CINNAMIC ACID; LONG CHAIN FATTY ACID COENZYME A LIGASE; MALONIC ACID; NAPHTHALENE DERIVATIVE; PHENYLACETIC ACID; POLYKETIDE; PYRIDINE DERIVATIVE; QUINOLINE DERIVATIVE;

ARTICLE; BIOSYNTHESIS; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; RHIZOBIUM TRIFOLII;

ACYL COENZYME A; BACTERIA; BACTERIAL PROTEINS; CARBOXYLIC ACIDS; CLONING, MOLECULAR; COENZYME A LIGASES; ESTERS; MODELS, MOLECULAR; ORYZA SATIVA; PLANTS; POLYKETIDE SYNTHASES; POLYKETIDES; RHIZOBIUM; STREPTOMYCES COELICOLOR; SUBSTRATE SPECIFICITY;

EID: 84861905297     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi300425j     Document Type: Article

References (29)

1. Staunton, J., and Weissman, K. J. (2001) Polyketide biosynthesis: A millennium review. Nat. Prod. Rep. 18, 380-416. (Pubitemid 32773840)
2. Walsh, C. T. (2004) Polyketide and nonribosomal peptide antibiotics: Modularity and versatility. Science 303, 1805-1810.
3. Shen, B. (2003) Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms. Curr. Opin. Chem. Biol. 7, 285-295.
4. Horinouchi, S. (2008) Combinatorial Biosynthesis of Non-bacterial and Unnatural Flavonoids, Stilbenoids and Curcuminoids by Microorganisms. J. Antibiot. 61, 709-728.
5. Wong, F. T., and Khosla, C. (2012) Combinatorial biosynthesis of polyketides: A perspective. Curr. Opin. Chem. Biol. 16, 1-7.
6. Fisch, K. M., Bakeer, W., Yakasai, A. A., Song, Z., Pedrick, J., Wasil, Z., Bailey, A. M., Lazarus, C. M., Simpson, T. J., and Cox, R. J. (2011) Rational Domain Swaps Decipher Programming in Fungal Highly Reducing Polyketide Synthases and Resurrect an Extinct Metabolite. J. Am. Chem. Soc. 133, 16635-16641.
7. Ridley, C. P., Lee, H. Y., and Khosla, C. (2008) Evolution of polyketide synthases in bacteria. Proc. Natl. Acad. Sci. U.S.A. 105, 4595-4600. (Pubitemid 351753793)
8. Zhang, F., He, H.-Y., Tang, M.-C., Tang, Y.-M., Zhou, Q., and Tang, G.-L. (2011) Cloning and Elucidation of the FR901464 Gene Cluster Revealing a Complex Acyltransferase-less Polyketide Synthase Using Glycerate as Starter Units. J. Am. Chem. Soc. 133, 2452-2462.
9. Babbitt, P. C., Kenyon, G. L., Martin, B. M., Charest, H., Slyvestre, M., Scholten, J. D., Chang, K. H., Liang, P. H., and Dunaway-Mariano, D. (1992) Ancestry of the 4-chlorobenzoate dehalogenase: Analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/ isomerases, and acyl-CoA thioesterases. Biochemistry 31, 5594-5604.
10. Gulick, A. M., Lu, X., and Dunaway-Mariano, D. (2004) Crystal structure of 4-chlorobenzoate:CoA ligase/synthetase in the unliganded and aryl substrate-bound states. Biochemistry 43, 8670-8679. (Pubitemid 38880037)
11. Horswill, A. R., and Escalante-Semerena, J. C. (2002) Characterization of the propionyl-CoA synthetase (PrpE) enzyme of Salmonella enterica: Residue Lys592 is required for propionyl-AMP synthesis. Biochemistry 41, 2379-2387. (Pubitemid 34160900)
12. Kaneko, M., Ohnishi, Y., and Horinouchi, S. (2003) Cinnamate:coenzyme A ligase from the filamentous bacterium Streptomyces coelicolor A3(2). J. Bacteriol. 185, 20-27. (Pubitemid 36008817)
13. Lindermayr, C., Fliegmann, J., and Ebel, J. (2003) Deletion of a single amino acid residue from different 4-coumarate:CoA ligases from soybean results in the generation of new substrate specificities. J. Biol. Chem. 278, 2781-2786. (Pubitemid 36801179)
14. Pohl, N. L., Hans, M., Lee, H. Y., Kim, Y. S., Cane, D. E., and Khosla, C. (2001) Remarkably Broad Substrate Tolerance of Malonyl- CoA Synthetase, an Enzyme Capable of Intracellular Synthesis of Polyketide Precursors. J. Am. Chem. Soc. 123, 5822-5823. (Pubitemid 32904726)
15. Schneider, K., Hovel, K., Witzel, K., Hamberger, B., Schomburg, D., Kombrink, E., and Stuible, H. P. (2003) The substrate specificity-determining amino acid code of 4-coumarate:CoA ligase. Proc. Natl. Acad. Sci. U.S.A. 100, 8601-8606. (Pubitemid 36842590)
16. Wu, R., Reger, A. S., Cao, J., Gulick, A. M., and Dunaway-Mariano, D. (2007) Rational redesign of the 4-chlorobenzoate binding site of 4-chlorobenzoate:coenzyme A ligase for expanded substrate range. Biochemistry 46, 14487-14499. (Pubitemid 350276355)
17. Koetsier, M. J., Jekel, P. A., van den Berg, M. A., Bovenberg, R. A., and Janssen, D. B. (2009) Characterization of a phenylacetate-CoA ligase from Penicillium chrysogenum. Biochem. J. 417, 467-476.
18. Hughes, A. J., and Keatinge-Clay, A. (2011) Enzymatic Extender Unit Generation for In Vitro Polyketide Synthase Reactions: Structural and Func-tional Showcasing of Streptomyces coelicolor MatB. Chem. Biol. 18, 165-176.
19. Beuerle, T., and Pichersky, E. (2002) Enzymatic Synthesis and Purification of Aromatic Coenzyme A Esters. Anal. Biochem. 302, 305-312. (Pubitemid 34229738)
20. Yew, W. S., and Gerlt, J. A. (2002) Utilization of L-ascorbate by Escherichia coli K-12: Assignments of functions to products of the yjfsga and yia-sgb operons. J. Bacteriol. 184, 302-306.
21. Kim, Y. S., and Bang, S. K. (1988) Assays for malonyl-coenzyme A synthase. Anal. Biochem. 170, 45-49.
22. Reger, A. S., Wu, R., Dunaway-Mariano, D., and Gulick, A. M. (2008) Structural characterization of a 140°domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry 47, 8016-8025.
23. Kim, M. I., Kwon, S. J., and Dordick, J. S. (2009) In vitro precursor-directed synthesis of polyketide analogues with coenzyme A regeneration for the development of antiangiogenic agents. Org. Lett. 11, 3806-3809.
24. McDaniel, R., Ebert-Khosla, S., Hopwood, D. A., and Khosla, C. (1995) Rational design of aromatic polyketide natural products by recombinant assembly of enzymatic subunits. Nature 375, 549-554.
25. Horinouchi, S. (2009) Combinatorial biosynthesis of plant medicinal polyketides by microorganisms. Curr. Opin. Chem. Biol. 13, 197-204.
26. Weeks, A. M., and Chang, M. C. Y. (2011) Constructing de Novo Biosynthetic Pathways for Chemical Synthesis inside Living Cells. Biochemistry 50, 5404-5418.
27. Gerlt, J. A., and Babbitt, P. C. (2009) Enzyme (re)design: Lessons from natural evolution and computation. Curr. Opin. Chem. Biol. 13, 10-18.
28. Tawfik, D. S. (2006) Biochemistry. Loop grafting and the origins of enzyme species. Science 311, 475-476.
29. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF Chimera: A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612.