Metabolic engineering and directed evolution for the production of pharmaceuticals

Current Opinion in Biotechnology

Volumn 11, Issue 2, 2000, Pages 209-214

  Chartrain, Michel ^a   Salmon, Peter M ^a   Robinson, David K ^a   Buckland, Barry C ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ASTAXANTHIN; DEXTRO PHENYLALANINE; ENZYME; INDINAVIR; LEUCINE; MUTANT PROTEIN; PEPTIDE; POLYKETIDE; PRODRUG; RIBOFLAVIN; STEROID; TRYPTOPHAN; TYROSINE; VITAMIN;

CATALYST; DRUG INDUSTRY; DRUG MANUFACTURE; ENZYME ACTIVITY; ENZYME STABILITY; EVOLUTION; GENETIC ENGINEERING; METABOLISM; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; REVIEW; TECHNIQUE;

EID: 0034026210     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(00)00081-1     Document Type: Review

References (53)

1. Stassi D.L., Kakavas S.J., Reynolds K.A., Gunawardana G., Swanson S., Zeidner D., Jackson M., Liu H., Buko A., Katz L. Ethyl-substituted erythromycin derivatives produced by directed metabolic engineering. Proc Natl Acad Sci USA. 95:1998;7305-7309. A novel erythromycin analog was produced by replacing a methylmalonate-specific acyltransferase (AT) domain in the erythromycin PKS with an ethylmalonate-specific AT domain from the niddamycin PKS. Production of significant amounts of the desired macrolide was obtained only after expression of crotonyl-CoA reductase, a primary metabolic enzyme involved in production of a precursor.
2. Khosla C., Gokhale R.S., Jacobsen J.R., Cane D.E. Tolerance and specificity of polyketide synthases. Annu Rev Biochem. 68:1999;219-253.
3. Stachelhaus T., Mootz H.D., Marahiel M.A. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem Biol. 6:1999;493-505.
4. Pacey M.S., Dirlam J.P., Geldart R.W., Leadlay P.F., McArthur H.A.I., McCormick E.L., Monday R.A., O'Connell T.N., Staunton J., Winchester T.J. Novel erythromycins from a recombinant Saccharopolyspora erythraea strain NRRL 2338 pIG1. I. Fermentation, isolation and biological activity. J Antibiotics. 51:1998;1029-1034.
5. Bao W., Sheldon P.J., Wendt-Pienkowski E., Hutchinson C.R. The Streptomyces peucetius dpsC gene determines the choice of starter unit in biosynthesis of the daunorubicin polyketide. J Bacteriol. 181:1999;4690-4695.
6. Bisang C., Long P.F., Cortés J., Westcott J., Crosby J., Matharu A-L., Cox R.J., Simpson T.J., Staunton J., Leadlay P.F. A chain initiation factor common to both modular and aromatic polyketide synthases. Nature. 401:1999;502-505. A component of aromatic PKSs, previously named chain-length factor (CLF), is a factor required for chain initiation. A specific initiation factor known as KSQ in modular PKSs plays a role similar to CLF. Both KSQ and CLF are similar to ketosynthase domains that catalyze chain extension, but an active-site cysteine residue is replaced by a highly conserved glutamine.
7. Pohl N.L., Gokhale R.S., Cane D.E., Khosla C. Synthesis and incorporation of an N-acetylcysteamine analogue of methylmalonyl-CoA by a modular polyketide synthase. J Am Chem Soc. 120:1998;11206-11207.
8. Jacobsen J.R., Cane D.E., Khosla C. Spontaneous priming of a downstream module in 6-deoxyerythronolide B synthase leads to polyketide biosynthesis. Biochemistry. 37:1998;4928-4934.
9. Gokhale R.S., Tsuji S.Y., Cane D.E., Khosla C. Dissecting and exploiting intermodular communication in polyketide synthases. Science. 284:1999;482-485. Chain transfer between intact modules is permissive provided appropriate linkers are present. These linkers are regions of variable sequence that span the boundaries between the acyl carrier protein domain of an upstream module and the ketosynthase domain of the following module. Efficient chain transfer to an unnatural downstream module can occur if the natural linker is preserved. The results suggest that modules, rather than individual enzymatic domains, may be the appropriate building blocks for combinatorial genetics.
10. Hunziker D., Yu T-W., Hutchinson C.R., Floss H.G., Khosla C. Primer unit specificity in rifamycin biosynthesis principally resides in the later stages of the biosynthetic pathway. J Am Chem Soc. 120:1998;1092-1093.
11. Weissman K.J., Bycroft M., Cutter A.L., Hanefeld U., Frost E.J., Timoney M.C., Harris R., Handa S., Roddis M., Staunton J., Leadlay P.F. Evaluating precursor-directed biosynthesis towards novel erythromycins through in vitro studies on bimodular polyketide synthase. Chem Biol. 5:1998;743-754.
12. Lau J., Fu H., Cane D.E., Khosla C. Dissecting the role of acyltransferase domains of modular polyketide synthases in the choice and stereochemical fate of extender units. Biochemistry. 38:1999;643-1651. A 25-35 amino acid segment present in all modular PKS acyltransferase domains seems to be important for substrate specificity. This segment is highly variable, and may be a good target for genetic manipulation to alter specificity.
13. Cane D.E., Walsh C.T., Khosla C. Harnessing the biosynthetic code: combinations, permutations, and mutations. Science. 282:1998;63-68.
14. Gokhale R.S., Hunziker D., Cane D.E., Khosla C. Mechanism and specificity of the terminal thioesterase domain from the erythromycin polyketide synthase. Chem Biol. 6:1999;117-125.
15. Shen Y.M., Yoon P., Yu T-W., Floss H.G., Hopwood D., Moore B.S. Ectopic expression of the minimal whiE polyketide synthase generates a library of aromatic polyketides of diverse sizes and shapes. Proc Natl Acad Sci USA. 96:1999;3622-3627.
16. Lomovskaya N., Doi-Katayama Y., Filippini S., Nastro C., Fonstein L., Gallo M., Colombo A.L., Hutchinson C.R. The Streptomyces peucetius dpsY and dnrX genes govern early and late steps of daunorubicin and doxorubicin biosynthesis. J Bacteriol. 180:1998;2379-2386.
17. Lomovskaya N., Otten S.L., Doi-Katayama Y., Fonstein L., Liu X-C., Takatsu T., Inventi-Solari A., Filippini S., Torti F., Colombo A.L., Hutchinson C.R. Doxorubicin overproduction in Streptomyces peucetius: cloning and characterization of the dnrU ketoreductase and dnrV genes and the doxA cytochrome P-450 hydroxylase gene. J Bacteriol. 181:1999;305-318. Doxorubicin production can be increased by an order of magnitude through overexpression of key post-PKS biosynthetic genes and through disruption of genes for enzymes that catalyze conversion of products or intermediates to unwanted or unstable species.
18. Olano C., Lomovskaya N., Fonstein L., Roll J.T., Hutchinson C.R. A two-plasmid system for the glycosylation of polyketide antibiotics: bioconversion of ε-rhodomycinone to rhodomycin D. Chem Biol. 6:1999;645-655.
19. Madduri K., Kennedy J., Rivola G., Inventi-Solari A., Filippini S., Zanuso G., Colombo A.L., Gewain K.M., Occi J.L., MacNeil D.J., Hutchinson C.R. Production of the antitumor drug epirubicin (4′-epidoxorubicin) and its precursor by a genetically engineered strain of Streptomyces peucetius. Nat Biotechnol. 16:1998;69-74.
20. Duport C., Spagnoli R., Degryse E., Pompon D. Self-sufficient biosynthesis of pregnenolone and progesterone in engineered yeast. Nat Biotechnol. 16:1998;186-189. This paper describes the construction of a S. cerevisiae strain capable of producing pregnenolone and progesterone directly from a simple carbon source.
21. Taylor P., Pantaleone D., Senkpeil R., Fotheringham I. Novel biosynthetic approaches to the production of unnatural amino acids using transaminases. Trends Biotechnol. 16:1998;412-418. This article presents the strategy that led to the construction of an E. coli strain capable to produce D-amino acids from a simple inexpensive L-amino acid source.
22. Ager D., Fotheringham I., Laneman S., Pantaleone D., Taylor P. The large scale synthesis of unnatural amino acids. Chim Oggi. 15:1997;11-15.
23. Miura Y., Kondo K., Saito T., Shimada H., Fraser P., Misawa N. Production of the carotenoids lycopene, beta-carotene, and astaxnathin in the food yeast Candida utilis. Appl Environ Microbiol. 64:1998;1226-1229. This paper presents the construction of a Candida strain that produces several carotenoids. The authors combined the utilization of a pre-existing pathway and added exogenous genes to reach their goal.
24. Miura Y., Kondo K., Shimada H., Saito T., Nakamura K., Misawa N. Production of lycopene by the food yeast, Candida utilis that does not naturally synthesize carotenoid. Biotechnol Bioeng. 58:1998;306-308.
25. Shimada H., Kondo K., Fraser P., Miura Y., Saito T., Misawa N. Increased carotenoid production by the food yeast Candida utilis through metabolic engineering of the isoprenoid pathway. Appl Environ Microbiol. 64:1998;2676-2680.
26. Albrech M., Misawa N., Sandmann G. Metabolic engineering of the terpenoid biosynthetic pathway of Escherichia coli for production of the carotenoid beta-carotene and zeaxanthin. Biotechnol Lett. 21:1999;791-795.
27. Wang C.W., Oh M.K., Liao J. Engineered isoprenoid pathway enhances astaxanthin production in Escherichia coli. Biotechnol Bioeng. 62:1999;235-241.
28. Perkins J., Sloma A., Hermanm T., Thieriault K., Zachgo E., Erdenberger T., Hannet N., Chatterjee N., Williams V., Rufo G., Hatch R., Pero J. Genetic engineering of Bacillus subtilis for the commercial production of riboflavin. J Indus Microbiol Biotechnol. 22:1999;8-12. The authors describe the construction of a B. subtilis strain that produces riboflavin at industrially acceptable levels.
29. Chartrain M., Jackey B., Taylor C., Sandford V., Gbewonyo K., Lister L., DiMichele L., Hirsch C., Heimbuch B., Maxwell C.et al. Bioconversion of indene to cis (1S,2R) indandiol and trans (1R,2R) indandiol by Rhodococcus species. J Ferment Bioeng. 86:1998;550-558.
30. Buckland B., Robinson D., Chartrain M. Biocatalysis for pharmaceuticals. Status and prospects for a key technology. Metab Eng. 2:2000;1-7. This paper highlights the potential impact of metabolic engineering in the field of bioconversion.
31. Treadway S., Yanagimachi K., Lankenau E., Lessard P., Stephanopoulos G., Sinskey A. Isolation, characterization of indene metabolism genes from Rhodococcus strain I 24. Appl Microbiol Biotechnol. 51:1999;786-793.
32. Treadway S., Yanagimachi K., Lessard P., Stephanopoulos G., Sinskey A. Characterization of the nidC diol dehydrogenase from Rhodococcus strain I 24. Appl Environ Microbiol. 1999;. in press.
33. Yanagimachi R., Rijhwani S., Drew S., Buckland B., Sinskey A., Stephanopoulos G. Metabolic engineering of indene bioconversion in Rhodococcus sp. Proceedings of the Second Metabolic Engineering Conference; 1998: Germany. 1998;United Engineering Foundation, New York, NY.
34. Marrs B., Delagrave S., Murphy D. Novel approaches for discovering industrial enzymes. Curr Opin Microbiol. 2:1999;241-245.
35. Hough D.W., Danson M.J. Extremozymes. Curr Opin Chem Biology. 3:1999;39-46.
36. May S.W. Applications of oxidoreductases. Curr Opin Biotechnol. 10:1999;370-375.
37. Swanson P.E. Dehalogenases applied to industrial-scale biocatalysis. Curr Opin Biotechnol. 10:1999;365-369.
38. Roberts G.C.K. The power of evolution: accessing the synthetic potential of P450s. Chem Biol. 6:1999;R269-R272.
39. DeSantis G., Jones J.B. Chemical modification of enzymes for enhanced functionality. Curr Opin Biotechnol. 10:1999;324-330.
40. Bull A.T., Bunch A.W., Robinson G.K. Biocatalysts for clean industrial products and processes. Curr Opin Microbiol. 2:1999;246-251.
41. Crameri A., Whitehorn E.A., Tate E., Stemmer W.P.C. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol. 14:1996;315-319.
42. Moore J., Arnold F.H. Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents. Nat Biotechnol. 14:1996;458-467.
43. Arnold F.H., Volkov A.A. Directed evolution of biocatalysts. Curr Opin Chem Biol. 3:1999;54-59.
44. Hart E.A., Hua L., Darr L.B., Wilson W.K., Pang J., Matsuda S.P.T. Directed evolution to investigate steric control of enzymatic oxidosqualene cyclization: an isoleucine-to-valine mutation in cylcoartenol synthase allows lanosterol and parkeol biosynthesis. J Am Chem Soc. 121:1999;9887-9888. This paper illustrates the use of spontaneous mutations and selection of mutants by complementation to isolate enzymes with altered product specificity.
45. Bornscheuer U.T., Altenbuchner J., Meyer H.H. Directed evolution of an esterase for the stereoselective resolution of a key intermediate in the synthesis of epothilones. Biotechnol Bioeng. 58:1998;554-556. This paper highlights the use of an indirect measure of activity, monitoring the pH change caused by a hydrolytic reaction, to screen for mutant enzymes with esterase activity. It also illustrates the use of random mutagenesis in a mutator strain to generate variants.
46. Zhao H., Giver L., Shao Z., Affholter J.A., Arnold F.H. Molecular evolution by staggered extension proess (StEP) in vitro recombination. Nat Biotechnol. 391:1998;258-261.
47. Joo H., Lin Z., Arnold F.H. Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation. Nature. 399:1999;670-673. The authors describe the directed evolution of a cytochrome P450 to cofactor independence, using hydrogen peroxide as the oxygen donor. Horseradish peroxidase was co-expressed with the cytochrome P450 to allow the hydroxylated napthalene to form a fluorescent product detectable by a high-throughput imaging system.
48. Joo H., Arisawa A., Lin Z., Arnold F.H. A high-throughput digital imaging screen for discovery and directed evolution of oxygenases. Chem Biol. 6:1999;699-706.
49. Chen R. A general strategy for enzyme engineering. Trends Biotechnol. 17:1999;344-345.
50. Zhao H., Arnold F.H. Directed evolution converts subtilisin E into a functional equivalent of thermitase. Protein Eng. 12:1999;47-53.
51. Giver L., Gershonen A., Freskgard P.O., Arnold F.H. Directed evolution of a thermostable esterase. Proc Natl Acad Sci USA. 95:1998;12809-12813.
52. Spiller B., Gershenson A., Arnold F.H., Stevens R.C. A structural view of evolutionary divergence. Proc Natl Acad Sci USA. 96:1999;12305-12310. The authors describe the genetic and structural differences observed in a p-nitrobenzyl esterase and its organophilic and thermophilic variants selected after multiple rounds of directed evolution in appropriate environments. The study clearly indicates that the mutations selected by directed evolution would not have been predicted from a structure-based site-directed mutagenic approach.
53. Lin Z., Thorsen T., Arnold F.H. Functional expression of horseradish peroxidase in E. coli via directed evolution. Biotechnol Progr. 15:1999;467-471. Directed evolution applied to the expression of horseradish perioxidase in E. coli demonstrates the ability to improve protein expression/folding in heterologous hosts.