Redesigning Enzymes Based on Adaptive Evolution for Optimal Function in Synthetic Metabolic Pathways

Chemistry and Biology

Volumn 15, Issue 6, 2008, Pages 607-618

  Yoshikuni, Yasuo ^a,c   Dietrich, Jeffrey A ^a,c   Nowroozi, Farnaz F ^a,c   Babbitt, Patricia C ^a,b,d   Keasling, Jay D ^a,b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

CHEMBIO

Indexed keywords

AMINO ACID; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE; PRIMER DNA; TERPENE SYNTHASE; TRANSFERASE;

ARTICLE; CHEMISTRY; EVOLUTION; GENETICS; MASS FRAGMENTOGRAPHY; METABOLISM; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SITE DIRECTED MUTAGENESIS;

ALKYL AND ARYL TRANSFERASES; AMINO ACIDS; BASE SEQUENCE; DNA PRIMERS; EVOLUTION; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HYDROXYMETHYLGLUTARYL COA REDUCTASES; MUTAGENESIS, SITE-DIRECTED; POLYMERASE CHAIN REACTION;

ESCHERICHIA COLI;

EID: 44949201614     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2008.05.006     Document Type: Article

References (22)

1. Amin N., Liu A.D., Ramer S., Aehle W., Meijer D., Metin M., Wong S., Gualfetti P., and Schellenberger V. Construction of stabilized proteins by combinatorial consensus mutagenesis. Protein Eng. Des. Sel. 17 (2004) 787-793
2. Daujotyte D., Vilkaitis G., Manelyte L., Skalicky J., Szyperski T., and Klimasauskas S. Solubility engineering of the HhaI methyltransferase. Protein Eng. 16 (2003) 295-301
3. Donald K.A., Hampton R.Y., and Fritz I.B. Effects of overproduction of the catalytic domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase on squalene synthesis in Saccharomyces cerevisiae. Appl. Environ. Microbiol. 63 (1997) 3341-3344
4. Endo T., Fedorov A., de Souza S.J., and Gilbert W. Do introns favor or avoid regions of amino acid conservation?. Mol. Biol. Evol. 19 (2002) 521-522
5. Graur D. Amino acid composition and the evolutionary rates of protein-coding genes. J. Mol. Evol. 22 (1985) 53-62
6. Kraut D.A., Carroll K.S., and Herschlag D. Challenges in enzyme mechanism and energetics. Annu. Rev. Biochem. 72 (2003) 517-571
7. Lehmann M., Loch C., Middendorf A., Studer D., Lassen S.F., Pasamontes L., van Loon A.P., and Wyss M. The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Eng. 15 (2002) 403-411
8. Little D.B., and Croteau R.B. Alteration of product formation by directed mutagenesis and truncation of the multiple-product sesquiterpene synthases delta-selinene synthase and gamma-humulene synthase. Arch. Biochem. Biophys. 402 (2002) 120-135
9. Martin V.J., Yoshikuni Y., and Keasling J.D. The in vivo synthesis of plant sesquiterpenes by Escherichia coli. Biotechnol. Bioeng. 75 (2001) 497-503
10. Martin V.J., Pitera D.J., Withers S.T., Newman J.D., and Keasling J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21 (2003) 796-802
11. Nasreen A., Vogt M., Kim H.J., Eichinger A., and Skerra A. Solubility engineering and crystallization of human apolipoprotein D. Protein Sci. 15 (2006) 190-199
12. Pal C., Papp B., and Lercher M.J. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37 (2005) 1372-1375
13. Pal C., Papp B., and Lercher M.J. An integrated view of protein evolution. Nat. Rev. Genet. 7 (2006) 337-348
14. Pitera D.J., Paddon C.J., Newman J.D., and Keasling J.D. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab. Eng. 9 (2007) 193-207
15. Reiling K.K., Yoshikuni Y., Martin V.J., Newman J., Bohlmann J., and Keasling J.D. Mono and diterpene production in Escherichia coli. Biotechnol. Bioeng. 87 (2004) 200-212
16. Roodveldt C., Aharoni A., and Tawfik D.S. Directed evolution of proteins for heterologous expression and stability. Curr. Opin. Struct. Biol. 15 (2005) 50-56
17. Schmidt S., Sunyaev S., Bork P., and Dandekar T. Metabolites: a helping hand for pathway evolution?. Trends Biochem. Sci. 28 (2003) 336-341
18. Steele C.L., Crock J., Bohlmann J., and Croteau R. Sesquiterpene synthases from grand fir (Abies grandis): comparison of constitutive and wound-induced activities, and cDNA isolation, characterization, and bacterial expression of delta-selinene synthase and gamma-humulene synthase. J. Biol. Chem. 273 (1998) 2078-2089
19. Steipe B., Schiller B., Pluckthun A., and Steinbacher S. Sequence statistics reliably predict stabilizing mutations in a protein domain. J. Mol. Biol. 240 (1994) 188-192
20. Yoshikuni Y., and Keasling J.D. Pathway engineering by designed divergent evolution. Curr. Opin. Chem. Biol. 11 (2007) 233-239
21. Yoshikuni Y., Ferrin T.E., and Keasling J.D. Designed divergent evolution of enzyme function. Nature 440 (2006) 1078-1082
22. Yoshikuni Y., Martin V.J., Ferrin T.E., and Keasling J.D. Engineering cotton (+)-delta-cadinene synthase to an altered function: germacrene D-4-ol synthase. Chem. Biol. 13 (2006) 91-98