Leucine zipper-mediated targeting of multi-enzyme cascade reactions to inclusion bodies in Escherichia coli for enhanced production of 1-butanol

Metabolic Engineering

Volumn 40, Issue , 2017, Pages 41-49

  Han, Gui Hwan ^a   Seong, Wonjae ^a,b   Fu, Yaoyao ^a   Yoon, Paul K ^a,c   Kim, Seong Keun ^a,b   Yeom, Soo Jin ^a   Lee, Dae Hee ^a,b   Lee, Seung Goo ^a,b  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b University of Science and Technology (UST)   (South Korea)

^c Korea University   (South Korea)

Author keywords

1 Butanol; Cellulose binding domain; Enzyme cascade; Inclusion body; Leucine zipper; Metabolon

Indexed keywords

AMINO ACIDS; BINS; CELLULOSE; ESCHERICHIA COLI; GENES; METABOLIC ENGINEERING; PEPTIDES; PRODUCTIVITY; TRANSCRIPTION FACTORS;

1-BUTANOL; CELLULOSE BINDING DOMAINS; ENZYME CASCADES; INCLUSION BODIES; LEUCINE ZIPPERS; METABOLON;

ENZYMES;

3 HYDROXYBUTYRYL COA DEHYDRATASE; 3 HYDROXYBUTYRYL COA DEHYDROGENASE; ACETYL COENZYME A ACETYLTRANSFERASE; ALDEHYDE ALCOHOL DEHYDROGENASE; AMPICILLIN; BUTANOL; CELLULOSE; CHLORAMPHENICOL; GENOMIC DNA; GLUCOSE; LEUCINE ZIPPER PROTEIN; MULTIENZYME COMPLEX; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; UNCLASSIFIED DRUG; ESCHERICHIA COLI PROTEIN;

ARTICLE; CELL INCLUSION; CELLULOMONAS; CELLULOMONAS FIMI; CLINICAL ASSESSMENT; ENZYME ACTIVITY; ENZYME MECHANISM; ESCHERICHIA COLI; GENE OVEREXPRESSION; IN VITRO STUDY; IN VIVO STUDY; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS; BIOSYNTHESIS; GENE TARGETING; GENETIC ENHANCEMENT; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; PHYSIOLOGY; PROCEDURES;

BACTERIA; BUTANOLS; CATALYSTS; CHEMICAL REACTIONS; GENES; PEPTIDES; SYNTHESIS;

1-BUTANOL; BIOSYNTHETIC PATHWAYS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE TARGETING; GENETIC ENHANCEMENT; INCLUSION BODIES; LEUCINE ZIPPERS; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; MULTIENZYME COMPLEXES;

EID: 85008466182     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2016.12.012     Document Type: Article

References (31)

1. Baek, J.M., Mazumdar, S., Lee, S.W., Jung, M.Y., Lim, J.H., Seo, S.W., Jung, G.Y., Oh, M.K., Butyrate production in engineered Escherichia coli with synthetic scaffolds. Biotechnol. Bioeng. 110 (2013), 2790–2794.
2. Bradford, M.M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976), 248–254.
3. Choi, S.-L., Lee, S.J., Ha, J.-S., Song, J.J., Rhee, Y.H., Lee, S.-G., Generation of catalytic protein particles in Escherichia coli cells using the cellulose-binding domain from Cellulomonas fimi as a fusion partner. Biotechnol. Biopro. Eng. 16 (2011), 1173–1179.
4. Choi, S.-L., Lee, S.J., Yeom, S.-J., Kim, H.J., Rhee, Y.H., Jung, H.-C., Lee, S.-G., Controlled localization of functionally active proteins to inclusion bodies using leucine zippers. PLoS One, 9, 2014, e97093.
5. Conrado, R.J., Wu, G.C., Boock, J.T., Xu, H., Chen, S.Y., Lebar, T., Turnšek, J., Tomšič, N., Avbelj, M., Gaber, R., Koprivnjak, T., Mori, J., Glavnik, V., Vovk, I., Benčina, M., Hodnik, V., Anderluh, G., Dueber, J.E., Jerala, R., DeLisa, M.P., DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res. 40 (2012), 1879–1889.
6. Dueber, J.E., Wu, G.C., Malmirchegini, G.R., Moon, T.S., Petzold, C.J., Ullal, A.V., Prather, K.L., Keasling, J.D., Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 27 (2009), 753–759.
7. Hartmanis, M.G.N., Gatenbeck, S., Intermediary metabolism in Clostridium acetobutylicum: levels of enzymes involved in the formation of acetate and butyrate. Appl. Environ. Microbiol. 47 (1984), 1277–1283.
8. Ishikawa, M., Tsuchiya, D., Oyama, T., Tsunaka, Y., Morikawa, K., Structural basis for channelling mechanism of a fatty acid β‐oxidation multienzyme complex. EMBO J. 23 (2004), 2745–2754.
9. Jørgensen, K., Rasmussen, A.V., Morant, M., Nielsen, A.H., Bjarnholt, N., Zagrobelny, M., Bak, S., Møller, B.L., Metabolon formation and metabolic channeling in the biosynthesis of plant natural products. Curr. Opin. Plant Biol. 8 (2005), 280–291.
10. Kerfeld, C.A., Heinhorst, S., Cannon, G.C., Bacterial microcompartments. Annu. Rev. Microbiol. 64 (2010), 391–408.
11. Kerfeld, C.A., Sawaya, M.R., Tanaka, S., Nguyen, C.V., Phillips, M., Beeby, M., Yeates, T.O., Protein structures forming the shell of primitive bacterial organelles. Science 309 (2005), 936–938.
12. Lee, H., DeLoache, W.C., Dueber, J.E., Spatial organization of enzymes for metabolic engineering. Metab. Eng. 14 (2012), 242–251.
13. Lee, M.J., Brown, I.R., Juodeikis, R., Frank, S., Warren, M.J., Employing bacterial microcompartment technology to engineer a shell-free enzyme-aggregate for enhanced 1,2-propanediol production in Escherichia coli. Metab. Eng. 36 (2016), 48–56.
14. Magliery, T.J., Wilson, C.G., Pan, W., Mishler, D., Ghosh, I., Hamilton, A.D., Regan, L., Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism. J. Am. Chem. Soc. 127 (2005), 146–157.
15. Martin, V.J.J., Pitera, D.J., Withers, S.T., Newman, J.D., Keasling, J.D., Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21 (2003), 796–802.
16. McLean, B.W., Bray, M.R., Boraston, A.B., Gilkes, N.R., Haynes, C.A., Kilburn, D.G., Analysis of binding of the family 2a carbohydrate-binding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues. Protein Eng. 13 (2000), 801–809.
17. Menard, L., Maughan, D., Vigoreaux, J., The structural and functional coordination of glycolytic enzymes in muscle: evidence of a metabolon?. Biology 3 (2014), 623–644.
18. Moon, T.S., Dueber, J.E., Shiue, E., Prather, K.L.J., Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab. Eng. 12 (2010), 298–305.
19. Moon, T.S., Yoon, S.-H., Lanza, A.M., Roy-Mayhew, J.D., Prather, K.L.J., Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl. Environ. Microbiol. 75 (2009), 589–595.
20. Pfeifer, B.A., Khosla, C., Biosynthesis of polyketides in heterologous hosts. Microbiol. Mol. Biol. Rev. 65 (2001), 106–118.
21. Pröschel, M., Detsch, R., Boccaccini, A.R., Sonnewald, U., Engineering of metabolic pathways by artificial enzyme channels. Front. Bioeng. Biotechnol., 3, 2015.
22. Sachdeva, G., Garg, A., Godding, D., Way, J.C., Silver, P.A., In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner. Nucleic Acids Res. 42 (2014), 9493–9503.
23. Scheu, K., Gill, R., Saberi, S., Meyer, P., Emberly, E., Localization of aggregating proteins in bacteria depends on the rate of addition. Front. Microbiol., 5, 2014.
24. Shen, C.R., Lan, E.I., Dekishima, Y., Baez, A., Cho, K.M., Liao, J.C., Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl. Environ. Microbiol. 77 (2011), 2905–2915.
25. Sun, Q., Madan, B., Tsai, S.-L., DeLisa, M.P., Chen, W., Creation of artificial cellulosomes on DNA scaffolds by zinc finger protein-guided assembly for efficient cellulose hydrolysis. Chem. Commun. 50 (2014), 1423–1425.
26. Vick, J.E., Johnson, E.T., Choudhary, S., Bloch, S.E., Lopez-Gallego, F., Srivastava, P., Tikh, I.B., Wawrzyn, G.T., Schmidt-Dannert, C., Optimized compatible set of BioBrick vectors for metabolic pathway engineering. Appl. Microbiol. Biotechnol. 92 (2011), 1275–1286.
27. Wang, Y., Yu, O., Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. J. Biotechnol. 157 (2012), 258–260.
28. Welch, G.R., Gaertner, F.H., Enzyme organization in the polyaromatic—biosynthetic pathway: The arom conjugate and other multienzyme systems. Bernard, L.H., Earl, R.S., (eds.) Current Topics in Cellular Regulation, 16, 1980, Academic Press, New York, 113–162.
29. You, C., Zhang, Y.H.P., Self-assembly of synthetic metabolons through synthetic protein scaffolds: one-step purification, co-immobilization, and substrate channeling. ACS Synth. Biol. 2 (2013), 102–110.
30. Zhao, S., Jones, J.A., Lachance, D.M., Bhan, N., Khalidi, O., Venkataraman, S., Wang, Z., Koffas, M.A., Improvement of catechin production in Escherichia coli through combinatorial metabolic engineering. Metab. Eng. 28 (2015), 43–53.
31. + availability for Escherichia coli whole-cell biocatalysis: a case study for dihydroxyacetone production. Microb. Cell Fact. 12 (2013), 1–12.