Engineering Escherichia coli for poly-(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis

Enzyme and Microbial Technology

Volumn 106, Issue , 2017, Pages 60-66

  Zheng, Yangyang ^a,b   Yuan, Qianqian ^a,c   Yang, Xiaoyan ^a,c   Ma, Hongwu ^a  

^a Chinese Academy of Sciences   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c TIANJIN UNIVERSITY   (China)

Author keywords

Escherichia coli; Genome scale metabolic network analysis; Non oxidative glycolysis pathway; Poly (3 hydroxybutyrate)

Indexed keywords

BIODEGRADABLE POLYMERS; BOTTLES; ESCHERICHIA COLI; GENES; METABOLISM; PATHOLOGY;

BIODEGRADABLE PLASTICS; CARBON CONSERVATIONS; FLUX BALANCE ANALYSIS; GENOME-SCALE METABOLIC NETWORK; NADPH AVAILABILITY; NON-OXIDATIVE; POLY-3-HYDROXYBUTYRATE; SHAKE-FLASK CULTURES;

GLUCOSE;

ACETYL COENZYME A; CARBON; ENZYME; GLUCOSE; PHOSPHOKETOLASE; POLY(3 HYDROXYBUTYRIC ACID); REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; UNCLASSIFIED DRUG; BIODEGRADABLE PLASTIC; HYDROXYBUTYRIC ACID; POLY-BETA-HYDROXYBUTYRATE; POLYESTER;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIUM CULTURE; BIOAVAILABILITY; CITRIC ACID CYCLE; CONTROLLED STUDY; DOWN REGULATION; ESCHERICHIA COLI; GENE OVEREXPRESSION; GLYCOLYSIS; METABOLIC ENGINEERING; MOLECULAR WEIGHT; PNTAB GENE; CHEMISTRY; GENE KNOCKOUT; GENETICS; METABOLISM; PROCEDURES; UPREGULATION;

BIODEGRADABLE PLASTICS; CITRIC ACID CYCLE; ESCHERICHIA COLI; GENE KNOCKOUT TECHNIQUES; GENOME, BACTERIAL; GLUCOSE; HYDROXYBUTYRATES; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; POLYESTERS; UP-REGULATION;

EID: 85023647760     PISSN: 01410229     EISSN: 18790909     Source Type: Journal    
DOI: 10.1016/j.enzmictec.2017.07.003     Document Type: Article

References (37)

1. Lee, S.Y., Bacterial polyhydroxyalkanoates. Biotechnol. Bioeng. 49 (1996), 1–14.
2. Gao, X., Chen, J.C., Wu, Q., Chen, G.Q., Polyhydroxyalkanoates as a source of chemicals, polymers, and biofuels. Curr. Opin. Biotechnol. 22 (2011), 768–774.
3. Chen, G.Q., Wang, Y., Medical applications of biopolyesters polyhydroxyalkanoates. Chin. J. Polym. Sci. 31 (2013), 719–736.
4. Tavares, L.Z., da Silva, E.S., Pradella, J.G.D., Production of poly (3-hydroxybutyrate) in an airlift bioreactor by Ralstonia eutropha. Biochem. Eng. J. 18 (2004), 21–31.
5. Fernandez-Castillo, R., Rodriguez-Valera, F., Gonzalez-Ramos, J., Ruiz-Berraquero, F., Accumulation of poly (beta-hydroxybutyrate) by halobacteria. Appl. Environ. Microbiol. 51 (1986), 214–216.
6. Lopez, N.I., Pettinari, M.J., Stackebrandt, E., Tribelli, P.M., Potter, M., Steinbuchel, A., Mendez, B.S., Pseudomonas extremaustralis sp. nov., a Poly(3-hydroxybutyrate) producer isolated from an antarctic environment. Curr. Microbiol. 59 (2009), 514–519.
7. Ramachandran, H., Iqbal, N.M., Sipaut, C.S., Abdullah, A.A., Biosynthesis and characterization of poly (3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) terpolymer with various monomer compositions by Cupriavidus sp. USMAA2-4. Appl. Biochem. Biotechnol. 164 (2011), 867–877.
8. Cho, C., Choi, S.Y., Luo, Z.W., Lee, S.Y., Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering. Biotechnol. Adv. 33 (2015), 1455–1466.
9. Spiekermann, P., Rehm, B.H.A., Kalscheuer, R., Baumeister, D., Steinbuchel, A., A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch. Microbiol. 171 (1999), 73–80.
10. Sanchez, A.M., Andrews, J., Hussein, I., Bennett, G.N., San, K.Y., Effect of overexpression of a soluble pyridine nucleotide transhydrogenase (UdhA) on the production of poly(3-hydroxybutyrate) in Escherichia coli. Biotechnol. Progr. 22 (2006), 420–425.
11. Centeno-Leija, S., Huerta-Beristain, G., Giles-Gomez, M., Bolivar, F., Gosset, G., Martinez, A., Improving poly-3-hydroxybutyrate production in Escherichia coli by combining the increase in the NADPH pool and acetyl-CoA availability. Antonie Van Leeuwenhoek 105 (2014), 687–696.
12. Li, Z.J., Cai, L., Wu, Q., Chen, G.Q., Overexpression of NAD kinase in recombinant Escherichia coli harboring the phbCAB operon improves poly(3-hydroxybutyrate) production. Appl. Microbiol. Biotechnol. 83 (2009), 939–947.
13. Lee, S.H., Kang, K.H., Kim, E.Y., Chae, T.U., Oh, Y.H., Hong, S.H., Song, B.K., Jegals, J., Park, S.J., Lee, S.Y., Metabolic engineering of Escherichia coli for enhanced biosynthesis of poly(3-hydroxybutyrate) based on proteome analysis. Biotechnol. Lett. 35 (2013), 1631–1637.
14. Jiang, X.R., Wang, H., Shen, R., Chen, G.Q., Engineering the bacterial shapes for enhanced inclusion bodies accumulation. Metab. Eng. 29 (2015), 227–237.
15. Fu, X.Z., Tan, D., Aibaidula, G., Wu, Q., Chen, J.C., Chen, G.Q., Development of Halomonas TD01 as a host for open production of chemicals. Metab. Eng. 23 (2014), 78–91.
16. Tan, D., Wu, Q., Chen, J.C., Chen, G.Q., Engineering Halomonas TD01 for the low-cost production of polyhydroxyalkanoates. Metab. Eng. 26 (2014), 34–47.
17. Jian, J., Zhang, S.Q., Shi, Z.Y., Wang, W., Chen, G.Q., Wu, Q., Production of polyhydroxyalkanoates by Escherichia coli mutants with defected mixed acid fermentation pathways. Appl. Microbiol. Biotechnol. 87 (2010), 2247–2256.
18. Lin, Z., Zhang, Y., Yuan, Q., Liu, Q., Li, Y., Wang, Z., Ma, H., Chen, T., Zhao, X., Metabolic engineering of Escherichia coli for poly(3-hydroxybutyrate) production via threonine bypass. Microb. Cell Fact., 14, 2015, 185.
19. Bogorad, I.W., Lin, T.S., Liao, J.C., Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 502 (2013), 693–697.
20. Meadows, A.L., Hawkins, K.M., Tsegaye, Y., Antipov, E., Kim, Y., Raetz, L., Dahl, R.H., Tai, A., Mahatdejkul-Meadows, T., Xu, L., Zhao, L., Dasika, M.S., Murarka, A., Lenihan, J., Eng, D., Leng, J.S., Liu, C.L., Wenger, J.W., Jiang, H., Chao, L., Westfall, P., Lai, J., Ganesan, S., Jackson, P., Mans, R., Platt, D., Reeves, C.D., Saija, P.R., Wichmann, G., Holmes, V.F., Benjamin, K., Hill, P.W., Gardner, T.S., Tsong, A.E., Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature 537 (2016), 694–697.
21. Orth, J.D., Thiele, I., Palsson, B.O., What is flux balance analysis?. Nat. Biotechnol. 28 (2010), 245–248.
22. Orth, J.D., Conrad, T.M., Na, J., Lerman, J.A., Nam, H., Feist, A.M., Palsson, B.O., A comprehensive genome-scale reconstruction of Escherichia coli metabolism–2011. Mol. Syst. Biol., 7, 2011, 535.
23. Schellenberger, J., Que, R., Fleming, R.M., Thiele, I., Orth, J.D., Feist, A.M., Zielinski, D.C., Bordbar, A., Lewis, N.E., Rahmanian, S., Kang, J., Hyduke, D.R., Palsson, B.O., Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 6 (2011), 1290–1307.
24. Canton, B., Labno, A., Endy, D., Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 26 (2008), 787–793.
25. Lin, Z., Xu, Z., Li, Y., Wang, Z., Chen, T., Zhao, X., Metabolic engineering of Escherichia coli for the production of riboflavin. Microb. Cell Fact., 13, 2014, 104.
26. Livak, K.J., Schmittgen, T.D., Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25 (2001), 402–408.
27. Boynton, Z.L., Bennett, G.N., Rudolph, F.B., Intracellular concentrations of coenzyme a and its derivatives from clostridium acetobutylicum ATCC 824 and their roles in enzyme regulation. Appl. Environ. Microbiol. 60 (1994), 39–44.
28. Fuhrer, T., Fischer, E., Sauer, U., Experimental identification and quantification of glucose metabolism in seven bacterial species. J. Bacteriol. 187 (2005), 1581–1590.
29. Zhu, X., Tan, Z., Xu, H., Chen, J., Tang, J., Zhang, X., Metabolic evolution of two reducing equivalent-conserving pathways for high-yield succinate production in Escherichia coli. Metab. Eng. 24 (2014), 87–96.
30. Canonaco, F., Hess, T.A., Heri, S., Wang, T., Szyperski, T., Sauer, U., Metabolic flux response to phosphoglucose isomerase knock-out in Escherichia coli and impact of overexpression of the soluble transhydrogenase UdhA. FEMS Microbiol. Lett. 204 (2001), 247–252.
31. Sauer, U., Canonaco, F., Heri, S., Perrenoud, A., Fischer, E., The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli. J. Biol. Chem. 279 (2004), 6613–6619.
32. Wolfe, A.J., The acetate switch. Microbiol. Mol. Biol. Rev.: MMBR 69 (2005), 12–50.
33. Dittrich, C.R., Vadali, R.V., Bennett, G.N., San, K.Y., Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate. Biotechnol. Progr. 21 (2005), 627–631.
34. Lin, H., Castro, N.M., Bennett, G.N., San, K.Y., Acetyl-CoA synthetase overexpression in Escherichia coli demonstrates more efficient acetate assimilation and lower acetate accumulation: a potential tool in metabolic engineering. Appl. Microbiol. Biotechnol. 71 (2006), 870–874.
35. Castano-Cerezo, S., Bernal, V., Rohrig, T., Termeer, S., Canovas, M., Regulation of acetate metabolism in Escherichia coli BL21 by protein N(epsilon)-lysine acetylation. Appl. Microbiol. Biotechnol. 99 (2015), 3533–3545.
36. Xu, P., Ranganathan, S., Fowler, Z.L., Maranas, C.D., Koffas, M.A., Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. Metab. Eng. 13 (2011), 578–587.
37. Salis, H.M., The ribosome binding site calculator. Methods Enzymol. 498 (2011), 19–42.