Reversal of the β-oxidation cycle in saccharomyces cerevisiae for production of fuels and chemicals

ACS Synthetic Biology

Volumn 4, Issue 3, 2015, Pages 332-341

  Lian, Jiazhang ^a   Zhao, Huimin ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

advanced biofuels; fatty acid; synthetic biology; yeast; oxidation

Indexed keywords

BIOFUEL; BUTANOL; FATTY ACID ESTER; MEDIUM CHAIN FATTY ACID; ENZYME; FATTY ACID; RECOMBINANT PROTEIN;

ARTICLE; CELL METABOLISM; CONTROLLED STUDY; CYTOSOL; ENZYME ACTIVITY; ENZYME ASSAY; FATTY ACID OXIDATION; FUNGAL STRAIN; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLIC ENGINEERING; METABOLISM; OXIDATION REDUCTION REACTION; PLASMID; PROCEDURES; SYNTHETIC BIOLOGY;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

1-BUTANOL; BIOFUELS; ENZYMES; FATTY ACIDS; METABOLIC ENGINEERING; OXIDATION-REDUCTION; PLASMIDS; RECOMBINANT PROTEINS; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY;

EID: 84925666935     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb500243c     Document Type: Article

References (60)

1. Du, J., Shao, Z., and Zhao, H. (2011) Engineering microbial factories for synthesis of value-added products J. Ind. Microbiol. Biotechnol. 38, 873-890
2. Hong, K. K. and Nielsen, J. (2012) Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries Cell. Mol. Life Sci. 69, 2671-2690
3. Kung, Y., Runguphan, W., and Keasling, J. D. (2012) From fields to fuels: recent advances in the microbial production of biofuels ACS Synth. Biol. 1, 498-513
4. Lian, J., Chao, R., and Zhao, H. (2014) Metabolic engineering of a Saccharomyces cerevisiae strain capable of simultaneously utilizing glucose and galactose to produce enantiopure (2R, 3R)-butanediol Metab. Eng. 23, 92-99
5. Zhang, F., Rodriguez, S., and Keasling, J. D. (2011) Metabolic engineering of microbial pathways for advanced biofuels production Curr. Opin. Biotechnol. 22, 775-783
6. Handke, P., Lynch, S. A., and Gill, R. T. (2011) Application and engineering of fatty acid biosynthesis in Escherichia coli for advanced fuels and chemicals Metab. Eng. 13, 28-37
7. Harger, M., Zheng, L., Moon, A., Ager, C., An, J. H., Choe, C., Lai, Y. L., Mo, B., Zong, D., Smith, M. D., Egbert, R. G., Mills, J. H., Baker, D., Pultz, I. S., and Siegel, J. B. (2013) Expanding the product profile of a microbial alkane biosynthetic pathway ACS Synth. Biol. 2, 59-62
8. Chan, D. I. and Vogel, H. J. (2010) Current understanding of fatty acid biosynthesis and the acyl carrier protein Biochem. J. 430, 1-19
9. Lennen, R. M. and Pfleger, B. F. (2012) Engineering Escherichia coli to synthesize free fatty acids Trends Biotechnol. 30, 659-667
10. Liu, D., Xiao, Y., Evans, B., and Zhang, F. (2013) Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator ACS Synth. Biol. 10.1021/sb400158w
11. van Roermund, C. W., Waterham, H. R., Ijlst, L., and Wanders, R. J. (2003) Fatty acid metabolism in Saccharomyces cerevisiae Cell. Mol. Life Sci. 60, 1838-1851
12. Trotter, P. J. (2001) The genetics of fatty acid metabolism in Saccharomyces cerevisiae Annu. Rev. Nutr. 21, 97-119
13. Dellomonaco, C., Clomburg, J. M., Miller, E. N., and Gonzalez, R. (2011) Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals Nature 476, 355-359
14. Clomburg, J. M., Vick, J. E., Blankschien, M. D., Rodriguez-Moya, M., and Gonzalez, R. (2012) A synthetic biology approach to engineer a functional reversal of the β-oxidation cycle ACS Synth. Biol. 1, 541-554
15. Fisher, M. A., Boyarskiy, S., Yamada, M. R., Kong, N., Bauer, S., and Tullman-Ercek, D. (2013) Enhancing tolerance to short-chain alcohols by engineering the Escherichia coli AcrB efflux pump to secrete the non-native substrate n -butanol ACS Synth. Biol. 3, 30-40
16. Tsai, S. L., DaSilva, N. A., and Chen, W. (2013) Functional display of complex cellulosomes on the yeast surface via adaptive assembly ACS Synth. Biol. 2, 14-21
17. Yamanishi, M. and Matsuyama, T. (2012) A modified Cre-lox genetic switch to dynamically control metabolic flow in Saccharomyces cerevisiae ACS Synth. Biol. 1, 172-180
18. Crook, N. C., Schmitz, A. C., and Alper, H. S. (2014) Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering ACS Synth. Biol. 3, 307-313
19. Yamanishi, M., Ito, Y., Kintaka, R., Imamura, C., Katahira, S., Ikeuchi, A., Moriya, H., and Matsuyama, T. (2013) A genome-wide activity assessment of terminator regions in Saccharomyces cerevisiae provides a "terminatome" toolbox ACS Synth. Biol. 2, 337-347
20. Kunau, W. H., Dommes, V., and Schulz, H. (1995) β-Oxidation of fatty acids in mitochondria, peroxisomes, and bacteria: a century of continued progress Prog. Lipid Res. 34, 267-342
21. Campbell, J. W., Morgan-Kiss, R. M., and Cronan, J. E. (2003) A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic β-oxidation pathway Mol. Microbiol. 47, 793-805
22. Hiltunen, J. K., Mursula, A. M., Rottensteiner, H., Wierenga, R. K., Kastaniotis, A. J., and Gurvitz, A. (2003) The biochemistry of peroxisomal β-oxidation in the yeast Saccharomyces cerevisiae FEMS Microbiol. Rev. 27, 35-64
23. Shao, Z., Zhao, H., and Zhao, H. (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Nucleic Acids Res. 37, e16
24. Poirier, Y., Antonenkov, V. D., Glumoff, T., and Hiltunen, J. K. (2006) Peroxisomal β-oxidation - a metabolic pathway with multiple functions Biochim. Biophys. Acta 1763, 1413-1426
25. Claros, M. G. and Vincens, P. (1996) Computational method to predict mitochondrially imported proteins and their targeting sequences Eur. J. Biochem. 241, 779-786
26. Schluter, A., Real-Chicharro, A., Gabaldon, T., Sanchez-Jimenez, F., and Pujol, A. (2010) PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome Nucleic Acids Res. 38, D800-D805
27. Lutke-Eversloh, T. and Bahl, H. (2011) Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production Curr. Opin. Biotechnol. 22, 634-647
28. Hiser, L., Basson, M. E., and Rine, J. (1994) ERG10 from Saccharomyces cerevisiae encodes acetoacetyl-CoA thiolase J. Biol. Chem. 269, 31383-31389
29. Steen, E. J., Chan, R., Prasad, N., Myers, S., Petzold, C. J., Redding, A., Ouellet, M., and Keasling, J. D. (2008) Metabolic engineering of Saccharomyces cerevisiae for the production of n -butanol Microb. Cell Fact. 7, 36
30. Vorapreeda, T., Thammarongtham, C., Cheevadhanarak, S., and Laoteng, K. (2012) Alternative routes of acetyl-CoA synthesis identified by comparative genomic analysis: involvement in the lipid production of oleaginous yeast and fungi Microbiology 158, 217-228
31. Lee, S. Y., Park, J. H., Jang, S. H., Nielsen, L. K., Kim, J., and Jung, K. S. (2008) Fermentative butanol production by Clostridia Biotechnol. Bioeng. 101, 209-228
32. Tucci, S. and Martin, W. (2007) A novel prokaryotic trans-2-enoyl-CoA reductase from the spirochete Treponema denticola FEBS Lett. 581, 1561-1566
33. Bond-Watts, B. B., Weeks, A. M., and Chang, M. C. (2012) Biochemical and structural characterization of the trans-enoyl-CoA reductase from Treponema denticola Biochemistry 51, 6827-6837
34. Hoffmeister, M., Piotrowski, M., Nowitzki, U., and Martin, W. (2005) Mitochondrial trans -2-enoyl-CoA reductase of wax ester fermentation from Euglena gracilis defines a new family of enzymes involved in lipid synthesis J. Biol. Chem. 280, 4329-4338
35. Bond-Watts, B. B., Bellerose, R. J., and Chang, M. C. Y. (2011) Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways Nat. Chem. Biol. 7, 222-227
36. Shen, C. R., Lan, E. I., Dekishima, Y., Baez, A., Cho, K. M., and Liao, J. C. (2011) Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli Appl. Environ. Microb 77, 2905-2915
37. Shao, Z., Rao, G., Li, C., Abil, Z., Luo, Y., and Zhao, H. (2013) Refactoring the silent spectinabilin gene cluster using a plug-and-play scaffold ACS Synth. Biol. 2, 662-669
38. Roof, D. M. and Roth, J. R. (1988) Ethanolamine utilization in Salmonella typhimurium J. Bacteriol. 170, 3855-3863
39. Toth, J., Ismaiel, A. A., and Chen, J. S. (1999) The ald gene, encoding a coenzyme A-acylating aldehyde dehydrogenase, distinguishes Clostridium beijerinckii and two other solvent-producing clostridia from Clostridium acetobutylicum Appl. Environ. Microbiol. 65, 4973-4980
40. Krivoruchko, A., Serrano-Amatriain, C., Chen, Y., Siewers, V., and Nielsen, J. (2013) Improving biobutanol production in engineered Saccharomyces cerevisiae by manipulation of acetyl-CoA metabolism J. Ind. Microbiol. Biotechnol. 40, 1051-1056
41. Lian, J., Si, T., Nair, N. U., and Zhao, H. (2014) Design and construction of acetyl-CoA overproducing Saccharomyces cerevisiae strains Metab. Eng. 24, 139-149
42. Jing, F., Cantu, D. C., Tvaruzkova, J., Chipman, J. P., Nikolau, B. J., Yandeau-Nelson, M. D., and Reilly, P. J. (2011) Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity BMC Biochem. 12, 44
43. Leber, C. and Da Silva, N. A. (2013) Engineering of Saccharomyces cerevisiae for the synthesis of short chain fatty acids Biotechnol. Bioeng. 111, 347-358
44. Pronk, J. T., van der Linden-Beuman, A., Verduyn, C., Scheffers, W. A., and van Dijken, J. P. (1994) Propionate metabolism in Saccharomyces cerevisiae: implications for the metabolon hypothesis Microbiology 140, 717-722
45. Saerens, S. M., Delvaux, F., Verstrepen, K. J., Van Dijck, P., Thevelein, J. M., and Delvaux, F. R. (2008) Parameters affecting ethyl ester production by Saccharomyces cerevisiae during fermentation Appl. Environ. Microbiol. 74, 454-461
46. Saerens, S. M., Verstrepen, K. J., Van Laere, S. D., Voet, A. R., Van Dijck, P., Delvaux, F. R., and Thevelein, J. M. (2006) The Saccharomyces cerevisiae EHT1 and EEB1 genes encode novel enzymes with medium-chain fatty acid ethyl ester synthesis and hydrolysis capacity J. Biol. Chem. 281, 4446-4456
47. Eriksen, D. T., Lian, J., and Zhao, H. (2014) Protein design for pathway engineering J. Struct. Biol. 185, 234-242
48. Lian, J., Li, Y., Hamedirad, M., and Zhao, H. (2014) Directed evolution of a cellodextrin transporter for improved biofuel production under anaerobic conditions in Saccharomyces cerevisiae Biotechnol. Bioeng. 111, 1521-1531
49. Guest, J. R., Angier, S. J., and Russell, G. C. (1989) Structure, expression, and protein engineering of the pyruvate dehydrogenase complex of Escherichia coli Ann. N.Y. Acad. Sci. 573, 76-99
50. Knappe, J. and Sawers, G. (1990) A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli FEMS Microbiol. Rev. 6, 383-398
51. Strijbis, K. and Distel, B. (2010) Intracellular acetyl unit transport in fungal carbon metabolism Eukaryot. Cell 9, 1809-1815
52. Starai, V. J. and Escalante-Semerena, J. C. (2004) Acetyl-coenzyme A synthetase (AMP forming) Cell. Mol. Life Sci. 61, 2020-2030
53. Shiba, Y., Paradise, E. M., Kirby, J., Ro, D. K., and Keasling, J. D. (2007) Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids Metab. Eng. 9, 160-168
54. Chen, Y., Daviet, L., Schalk, M., Siewers, V., and Nielsen, J. (2013) Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism Metab. Eng. 15, 48-54
55. Kocharin, K., Chen, Y., Siewers, V., and Nielsen, J. (2012) Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae AMB Express 2, 52
56. Kocharin, K., Siewers, V., and Nielsen, J. (2013) Improved polyhydroxybutyrate production by Saccharomyces cerevisiae through the use of the phosphoketolase pathway Biotechnol. Bioeng. 110, 2216-2224
57. Tang, X., Feng, H., and Chen, W. N. (2013) Metabolic engineering for enhanced fatty acids synthesis in Saccharomyces cerevisiae Metab. Eng. 16, 95-102
58. Avalos, J. L., Fink, G. R., and Stephanopoulos, G. (2013) Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols Nat. Biotechnol. 31, 335-341
59. Farhi, M., Marhevka, E., Masci, T., Marcos, E., Eyal, Y., Ovadis, M., Abeliovich, H., and Vainstein, A. (2011) Harnessing yeast subcellular compartments for the production of plant terpenoids Metab. Eng. 13, 474-481
60. Gietz, R. D. and Schiestl, R. H. (2007) High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method Nat. Protoc. 2, 31-34