Regulatory effects on central carbon metabolism from poly-3-hydroxybutryate synthesis

Metabolic Engineering

Volumn 28, Issue , 2015, Pages 180-189

  Sekar, Karthik ^a   Tyo, Keith E J ^a  

^a Northwestern University   (United States)

Author keywords

Chemostat; Escherichia coli; Flux balance analysis; Metabolic engineering; Poly 3 hydroxybutyrate

Indexed keywords

CHEMOSTATS; ESCHERICHIA COLI; GLUCOSE; METABOLIC ENGINEERING; METABOLISM; METABOLITES; OXIDATION; PHYSIOLOGY; PRODUCTIVITY;

CENTRAL CARBON METABOLISMS; FLUX BALANCE ANALYSIS; INDUSTRIAL PRODUCTION; INTRACELLULAR METABOLITE CONCENTRATION; POLY-3-HYDROXYBUTYRATE; POLY3-HYDROXYBUTYRATE (PHB); REGULATORY MECHANISM; SPECIFIC SUBSTRATES;

SUBSTRATES;

ACETYL COENZYME A; GLUCOSE; OXYGEN; PHOSPHATE; POLY(3 HYDROXYBUTYRIC ACID); REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; SULFATE; CARBON; HYDROXYBUTYRIC ACID; POLY-BETA-HYDROXYBUTYRATE; POLYESTER;

ARTICLE; BACTERIAL STRAIN; CARBON METABOLISM; CARBON SOURCE; CONTROLLED STUDY; ESCHERICHIA COLI; FERMENTATION; GLUCOSE TRANSPORT; IN VITRO STUDY; METABOLIC REGULATION; NITROGEN FIXATION; NONHUMAN; OXIDATION REDUCTION STATE; PRIORITY JOURNAL; REGULATORY MECHANISM; STEADY STATE; SUGAR TRANSPORT; SYNTHESIS; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM;

ESCHERICHIA COLI;

CARBON; ESCHERICHIA COLI; GLUCOSE; HYDROXYBUTYRATES; POLYESTERS;

EID: 84922462319     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2015.01.003     Document Type: Article

References (52)

1. Anderson A.J., Dawes E.A. Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol. Rev. 1990, 54:450-472.
2. Bekker M., Alexeeva S., Laan W., Sawers G., Teixeira de Mattos J., Hellingwerf K. The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool. J. Bacteriol. 2010, 192:746-754.
3. Bernofsky C., Swan M. An improved cycling assay for nicotinamide adenine dinucleotide. Anal. Biochem. 1973, 53:452-458.
4. Bogorad I.W., Lin T.S., Liao J.C. Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 2013, 502:693-697.
5. Campos-Bermudez V.A., Bologna F.P., Andreo C.S., Drincovich M.F. Functional dissection of Escherichia coli phosphotransacetylase structural domains and analysis of key compounds involved in activity regulation. FEBS J. 2010, 277:1957-1966.
6. Carlson R., Wlaschin A., Srienc F. Kinetic studies and biochemical pathway analysis of anaerobic poly-(R)-3-hydroxybutyric acid synthesis in Escherichia coli. Appl. Environ. Microbiol. 2005, 71:713-720.
7. Chen G.Q. A microbial polyhydroxyalkanoates (PHA) based bio- and materials industry. Chem. Soc. Rev. 2009, 38:2434-2446.
8. Chubukov V., Gerosa L., Kochanowski K., Sauer U. Coordination of microbial metabolism. Nat. Rev. Microbiol. 2014, 12:327-340.
9. Clark D.P. The fermentation pathways of Escherichia coli. FEMS Microbiol. Rev. 1989, 5:223-234.
10. Dawes E.A., Senior P.J. The role and regulation of energy reserve polymers in micro-organisms. Adv. Microb. Physiol. 1973, 10:135-266.
11. Doucette C.D., Schwab D.J., Wingreen N.S., Rabinowitz J.D. Alpha-Ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition. Nat. Chem. Biol. 2011, 7:894-901.
12. Escalante A., Salinas Cervantes A., Gosset G., Bolivar F. Current knowledge of the Escherichia coli phosphoenolpyruvate-carbohydrate phosphotransferase system: peculiarities of regulation and impact on growth and product formation. Appl. Microbiol. Biotechnol. 2012, 94:1483-1494.
13. Haywood G.W., Anderson A.J., Chu L., Dawes E.A. Characterization of two 3-ketothiolases possessing differing substrate specificities in the polyhydroxyalkanoate synthesizing organism Alcaligenes eutrophus. FEMS Microbiol. Lett. 1988, 52:91-96.
14. Jeong J.Y., Kim Y.J., Cho N., Shin D., Nam T.W., Ryu S., Seok Y.J. Expression of ptsG encoding the major glucose transporter is regulated by ArcA in Escherichia coli. J. Biol. Chem. 2004, 279:38513-38518.
15. Jiang G.R., Nikolova S., Clark D.P. Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology 2001, 147:2437-2446.
16. Keasling J.D. Gene-expression tools for the metabolic engineering of bacteria. Trends Biotechnol. 1999, 17:452-460.
17. Keseler I.M., Collado-Vides J., Santos-Zavaleta A., Peralta-Gil M., Gama-Castro S., Muniz-Rascado L., Bonavides-Martinez C., Paley S., Krummenacker M., Altman T., Kaipa P., Spaulding A., Pacheco J., Latendresse M., Fulcher C., Sarker M., Shearer A.G., Mackie A., Paulsen I., Gunsalus R.P., Karp P.D. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011, 39:D583-D590.
18. Kidwell J., Valentin H.E., Dennis D. Regulated expression of the Alcaligenes eutrophus pha biosynthesis genes in Escherichia coli. Appl. Environ. Microbiol. 1995, 61:1391-1398.
19. Kim H.J., Hou B.K., Lee S.G., Kim J.S., Lee D.W., Lee S.J. Genome-wide analysis of redox reactions reveals metabolic engineering targets for d-lactate overproduction in Escherichia coli. Metab. Eng. 2013, 18:44-52.
20. Klumpp S., Zhang Z., Hwa T. Growth rate-dependent global effects on gene expression in bacteria. Cell 2009, 139:1366-1375.
21. Leaf T.A., Srienc F. Metabolic modeling of polyhydroxybutyrate biosynthesis. Biotechnol. Bioeng. 1998, 57:557-570.
22. Lee I.Y., Kim M.K., Park Y.H., Lee S.Y. Regulatory effects of cellular nicotinamide nucleotides and enzyme activities on poly(3-hydroxybutyrate) synthesis in recombinant Escherichia coli. Biotechnol. Bioeng. 1996, 52:707-712.
23. Lesley J.A., Waldburger C.D. Repression of Escherichia coli PhoP-PhoQ signaling by acetate reveals a regulatory role for acetyl coenzyme A. J. Bacteriol. 2003, 185:2563-2570.
24. Maaløe O. Regulation of the protein-synthesizing machinery-ribosomes, tRNA, factors, and so on. Biological Regulation and Development 1979, vol. 1:487-542. Springer, USA.
25. Madison L.L., Huisman G.W. Metabolic engineering of poly(3-hydroxyalkanoates): from DNA to plastic. Microbiol. Mol. Biol. Rev. 1999, 63:21-53.
26. Malpica R., Sandoval G.R., Rodriguez C., Franco B., Georgellis D. Signaling by the arc two-component system provides a link between the redox state of the quinone pool and gene expression. Antioxid. Redox Signal. 2006, 8:781-795.
27. Marzan L.W., Shimizu K. Metabolic regulation of Escherichia coli and its phoB and phoR genes knockout mutants under phosphate and nitrogen limitations as well as at acidic condition. Microb. Cell factories 2011, 10:39.
28. Matsumoto Y., Murakami Y., Tsuru S., Ying B.W., Yomo T. Growth rate-coordinated transcriptome reorganization in bacteria. BMC Genomics 2013, 14:808.
29. Matsuoka Y., Shimizu K. Metabolic regulation in Escherichia coli in response to culture environments via global regulators. Biotechnol. J. 2011, 6:1330-1341.
30. Natarajan A., Srienc F. Glucose uptake rates of single E. coli cells grown in glucose-limited chemostat cultures. J. Microbiol. Methods 2000, 42:87-96.
31. Peekhaus N., Conway T. Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex. J. Bacteriol. 1998, 180:1777-1785.
32. Peoples O.P., Sinskey A.J. Poly-beta-hydroxybutyrate biosynthesis in Alcaligenes eutrophus H16. Characterization of the genes encoding beta-ketothiolase and acetoacetyl-CoA reductase. J. Biol. Chem. 1989, 264:15293-15297.
33. Reed J.L., Vo T.D., Schilling C.H., Palsson B.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 2003, 4:R54.
34. San K.Y., Bennett G.N., Berrios-Rivera S.J., Vadali R.V., Yang Y.T., Horton E., Rudolph F.B., Sariyar B., Blackwood K. Metabolic engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli. Metab. Eng. 2002, 4:182-192.
35. 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. Prog. 2006, 22:420-425.
36. 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. 2011, 6:1290-1307.
37. Schubert P., Steinbuchel A., Schlegel H.G. Cloning of the Alcaligenes eutrophus genes for synthesis of poly-beta-hydroxybutyric acid (PHB) and synthesis of PHB in Escherichia coli. J. Bacteriol. 1988, 170:5837-5847.
38. Song B.G., Kim T.K., Jung Y.M., Lee Y.H. Modulation of talA gene in pentose phosphate pathway for overproduction of poly-beta-hydroxybutyrate in transformant Escherichia coli harboring phbCAB operon. J. Biosci. Bioeng. 2006, 102:237-240.
39. Stover P., Zamora M., Shostak K., Gautam-Basak M., Schirch V. Escherichia coli serine hydroxymethyltransferase. The role of histidine 228 in determining reaction specificity. J. Biol. Chem. 1992, 267:17679-17687.
40. Sun Z., Do P.M., Rhee M.S., Govindasamy L., Wang Q., Ingram L.O., Shanmugam K.T. Amino acid substitutions at glutamate-354 in dihydrolipoamide dehydrogenase of Escherichia coli lower the sensitivity of pyruvate dehydrogenase to NADH. Microbiology 2012, 158:1350-1358.
41. Suzuki T. Phosphotransacetylase of Escherichia coli B, activation by pyruvate and inhibition by NADH and certain nucleotides. Biochim. Biophys. Acta 1969, 191:559-569.
42. Takamura Y., Nomura G. Changes in the intracellular concentration of acetyl-CoA and malonyl-CoA in relation to the carbon and energy metabolism of Escherichia coli K12. J. Gen. Microbiol. 1988, 134:2249-2253.
43. Tarmy E.M., Kaplan N.O. Kinetics of Escherichia coli B d-lactate dehydrogenase and evidence for pyruvate-controlled change in conformation. J. Biol. Chem. 1968, 243:2587-2596.
44. Tyo K.E., Ajikumar P.K., Stephanopoulos G. Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat. Biotechnol. 2009, 27:760-765.
45. Tyo K.E., Fischer C.R., Simeon F., Stephanopoulos G. Analysis of polyhydroxybutyrate flux limitations by systematic genetic and metabolic perturbations. Metab. Eng. 2010, 12:187-195.
46. Tyo K.E., Zhou H., Stephanopoulos G.N. High-throughput screen for poly-3-hydroxybutyrate in Escherichia coli and Synechocystis sp. strain PCC6803. Appl. Environ. Microbiol. 2006, 72:3412-3417.
47. van Wegen R.J., Lee S.Y., Middelberg A.P. Metabolic and kinetic analysis of poly(3-hydroxybutyrate) production by recombinant Escherichia coli. Biotechnol. Bioeng. 2001, 74:70-80.
48. Vemuri G.N., Eiteman M.A., McEwen J.E., Olsson L., Nielsen J. Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 2007, 104:2402-2407.
49. Wang B., Sharma-Shivappa R.R., Olson J.W., Khan S.A. Upstream process optimization of polyhydroxybutyrate (PHB) by Alcaligenes latus using two-stage batch and fed-batch fermentation strategies. Bioprocess Biosyst. Eng. 2012, 35:1591-1602.
50. Wang F., Lee S.Y. Production of poly(3-hydroxybutyrate) by fed-batch culture of filamentation-suppressed recombinant Escherichia coli. Appl. Environ. Microbiol. 1997, 63:4765-4769.
51. You C., Okano H., Hui S., Zhang Z., Kim M., Gunderson C.W., Wang Y.P., Lenz P., Yan D., Hwa T. Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature 2013, 500:301-306.
52. Youngquist J.T., Rose J.P., Pfleger B.F. Free fatty acid production in Escherichia coli under phosphate-limited conditions. Appl. Microbiol. Biotechnol. 2013, 97:5149-5159.