Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites

Metabolic Engineering

Volumn 28, Issue , 2015, Pages 104-113

  Brockman, Irene M ^a   Prather, Kristala L J ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Dynamic metabolic control; Metabolic flux redirection; Primary metabolism; Protein degradation; Synthetic biology

Indexed keywords

ALCOHOLS; ENZYMES; ESCHERICHIA COLI; GLUCOSE; PHYSIOLOGY; POLYOLS; PROTEINS; SUGARS;

CENTRAL METABOLISMS; CONTROLLED DEGRADATION; GLUCOSE 6 PHOSPHATES; METABOLIC CONTROL; METABOLIC FLUX; PROTEIN DEGRADATION; PROTEIN EXPRESSIONS; SYNTHETIC BIOLOGY;

METABOLISM;

6 PHOSPHOFRUCTOKINASE; GLUCOSE 6 PHOSPHATE; INOSITOL; SACCHARIC ACID; 1-PHOSPHOFRUCTOKINASE; ESCHERICHIA COLI PROTEIN;

ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; ENZYME DEGRADATION; ESCHERICHIA COLI; GENE SILENCING; GLUCOSE TRANSPORT; GLYCOLYSIS; GROWTH RATE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; STEADY STATE; THERMODYNAMICS; GENETICS; METABOLISM;

ESCHERICHIA COLI;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE KNOCKDOWN TECHNIQUES; GLUCOSE-6-PHOSPHATE; INOSITOL; PHOSPHOFRUCTOKINASE-1;

EID: 84920747663     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2014.12.005     Document Type: Article

References (44)

1. Andersen J.B., Sternberg C., Poulsen L.K., Bjorn S.P., Givskov M., Molin S. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 1998, 64:2240-2246.
2. Anesiadis N., Cluett W.R., Mahadevan R. Dynamic metabolic engineering for increasing bioprocess productivity. Metab. Eng. 2008, 10:255-266.
3. Anesiadis N., Kobayashi H., Cluett W.R., Mahadevan R. Analysis and design of a genetic circuit for dynamic metabolic engineering. ACS Synth. Biol 2013, 2:442-452.
4. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K.A., Tomita M., Wanner B.L., Mori H. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2006, 2. 2006.0008.
5. Bar-Even A., Noor E., Savir Y., Liebermeister W., Davidi D., Tawfik D.S., Milo R. The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 2011, 50:4402-4410.
6. Bennett B.D., Kimball E.H., Gao M., Osterhout R., Van Dien S.J., Rabinowitz J.D. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol. 2009, 5:593-599.
7. Bergmeyer H.U., Bergmeyer J., Grassl M. Methods of Enzymatic Analysis 1983, (editor-in-chief, Hans Ulrich Bergmeyer), Verlag Chemie, Weinheim; Deerfield Beach, Florida. 3rd ed. J. Bergmeyer, M. Grassl (Eds.).
8. Callura J.M., Cantor C.R., Collins J.J. Genetic switchboard for synthetic biology applications. Proc. Nat. Acad. Sci. USA 2012, 109:5850-5855.
9. Cardinale S., Arkin A.P. Contextualizing context for synthetic biology-identifying causes of failure of synthetic biological systems. Biotechnol. J. 2012, 7:856-866.
10. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Nat. Acad. Sci. USA 2000, 97:6640-6645.
11. Davis J.H., Baker T.A., Sauer R.T. Small-molecule control of protein degradation using split adaptors. ACS Chem. Biol 2011, 6:1205-1213.
12. De Anda R., Lara A.R., Hernández V., Hernández-Montalvo V., Gosset G., Bolívar F., Ramírez O.T. Replacement of the glucose phosphotransferase transport system by galactose permease reduces acetate accumulation and improves process performance of Escherichia coli for recombinant protein production without impairment of growth rate. Metab. Eng. 2006, 8:281-290.
13. Delgado J., Meruane J., Liao J.C. Experimental determination of flux control distribution in biochemical systems: in vitro model to analyze transient metabolite concentrations. Biotechnol. Bioeng. 1993, 41:1121-1128.
14. Farmer W.R., Liao J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 2000, 18:533-537.
15. Gadkar K.G., Doyle Iii F.J., Edwards J.S., Mahadevan R. Estimating optimal profiles of genetic alterations using constraint-based models. Biotechnol. Bioeng. 2005, 89:243-251.
16. Gonzalez B., François J., Renaud M. A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol. Yeast 1997, 13:1347-1355.
17. Hansen C.A., Dean A.B., Draths K.M., Frost J.W. Synthesis of 1,2,3,4-tetrahydroxybenzene from d-Glucose: exploiting myo-inositol as a precursor to aromatic chemicals. J. Am. Chem.l Soc. 1999, 121:3799-3800.
18. Hiller J., Franco-Lara E., Weuster-Botz D. Metabolic profiling of Escherichia coli cultivations: evaluation of extraction and metabolite analysis procedures. Biotechnol. Lett. 2007, 29:1169-1178.
19. Holtz W.J., Keasling J.D. Engineering static and dynamic control of synthetic pathways. Cell 2010, 140:19-23.
20. Kamionka A., Bogdanska-Urbaniak J., Scholz O., Hillen W. Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor. Nucleic Acids Res. 2004, 32:842-847.
21. Keseler I.M., Collado-Vides J., Santos-Zavaleta A., Peralta-Gil M., Gama-Castro S., Muñiz-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.
22. Kotlarz D., Buc H. Methods Enzymology 1982, 90:60-70. Academic Press, NewYork.
23. Kotlarz D., Garreau H., Buc H. Regulation of the amount and of the activity of phosphofructokinases and pyruvate kinases in Escherichia coli. Biochim. Biophys. Acta 1975, 381:257-268.
24. Kuhlman T.E., Cox E.C. Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res 2010, 38:e92.
25. Lee J.W., Na D., Park J.M., Lee J., Choi S., Lee S.Y. Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat. Chem. Biol. 2012, 8:536-546.
26. Lutz R., Bujard H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997, 25:1203-1210.
27. Majumder A.L., Johnson M.D., Henry S.A. 1-myo-Inositol-1-phosphate synthase. Biochim. Biophys. Acta 1997, 1348:245-256.
28. McGinness K.E., Baker T.A., Sauer R.T. Engineering controllable protein degradation. Mol. Cell 2006, 22:701-707.
29. Moon T.S., Yoon S.H., Lanza A.M., Roy-Mayhew J.D., Prather K.L. Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl. Environ. Microbiol. 2009, 75:589-595.
30. Mutalik V.K., Guimaraes J.C., Cambray G., Lam C., Christoffersen M.J., Mai Q.-A., Tran A.B., Paull M., Keasling J.D., Arkin A.P., Endy D. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat. Methods 2013, 10:354-360.
31. Quan J., Tian J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 2009, 4:e6441.
32. Shiue E., Brockman I.M., Prather K.L.J Improving product yields on D-glucose in Escherichia coli via knockout of pgi and zwf and feeding of supplemental carbon sources. Biotechnol. Bioeng. 2014, 10.1002/bit.25470.
33. Solomon K.V., Moon T.S., Ma B., Sanders T.M., Prather K.L.J. Tuning primary metabolism for heterologous pathway productivity. ACS Synth. Biol 2012.
34. Solomon K.V., Sanders T.M., Prather K.L. A dynamic metabolite valve for the control of central carbon metabolism. Metab. Eng. 2012, 14:661-671.
35. Soma Y., Tsuruno K., Wada M., Yokota A., Hanai T. Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metab. Eng. 2014, 23:175-184.
36. St-Pierre F., Cui L., Priest D.G., Endy D., Dodd I.B., Shearwin K.E. One-step cloning and chromosomal integration of DNA. ACS Synth. Biol 2013, 2:537-541.
37. Stephanopoulos G., Aristidou A.A., Nielsen J.H. Metabolic Engineering: Principles and Methodologies 1998, Academic Press, San Diego.
38. Torella J.P., Ford T.J., Kim S.N., Chen A.M., Way J.C., Silver P.A. Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc. Nat. Acad. Sci. USA 2013, 110:11290-11295.
39. Tseng H.-C., Martin C.H., Nielsen D.R., Prather K.L.J. Metabolic engineering of Escherichia coli for enhanced production of (R)- and (S)-3-hydroxybutyrate. Appl. Environ. Microbiol. 2009, 75:3137-3145.
40. Tyo K.E.J., Kocharin K., Nielsen J. Toward design-based engineering of industrial microbes. Curr. Opin. Microbiol. 2010, 13:255-262.
41. Werpy T., Petersen G. Top Value Added Chemical From Biomass, Volume 1-Results of Screening for Potential Candidates from Sugars and Synthetic Gas 2004, U.S. Department of Energy, Washington, D.C.
42. Woolston B.M., Edgar S., Stephanopoulos G. Metabolic engineering: past and future. Annu. Rev. Chem. Biomol. Eng. 2013, 4:259-288.
43. Yamaoka M., Osawa S., Morinaga T., Takenaka S., Yoshida K.-i. A cell factory of Bacillus subtilis engineered for the simple bioconversion of myo-inositol to scyllo-inositol, a potential therapeutic agent for Alzheimer[U+05F3]s disease. Microb. Cell Factories 2011, 10:1-6.
44. Zor T., Selinger Z. Linearization of the bradford protein assay increases its sensitivity: theoretical and experimental studies. Anal. Biochem. 1996, 236:302-308.