Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering

Biotechnology Journal

Volumn 9, Issue 11, 2014, Pages 1446-1457

  Fehér, Tamás ^a   Planson, Anne Gaëlle ^a,c   Carbonell, Pablo ^a   Fernández Castané, Alfred ^a   Grigoras, Ioana ^a   Dariy, Ekaterina ^b   Perret, Alain ^b   Faulon, Jean Loup ^a  

^a UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^c UMR1319 MICALIS   (France)

Author keywords

Computer aided design; Flavonoid production; Pathway prediction; Rational pathway engineering; Synthetic biology

Indexed keywords

BIOCHEMISTRY; BIOSYNTHESIS; CELL ENGINEERING; COMPUTER CONTROL; ENZYMES; METABOLIC ENGINEERING; METABOLISM; METABOLITES; SYNTHETIC BIOLOGY;

BIOCHEMICAL REACTIONS; COMPUTER AIDED DESIGN TOOLS; ENDOGENOUS METABOLITES; FLAVONOID; INTERMEDIATE METABOLITES; METABOLIC PATHWAY ENGINEERING; PATHWAY ENGINEERINGS; RELATIVE PERFORMANCE;

COMPUTER AIDED DESIGN;

ACETYL COENZYME A CARBOXYLASE; ADENOSINE TRIPHOSPHATE; COENZYME A; FLAVONOID; MALONATE COENZYME TRANSFERASE; MALONYL COENZYME A; PINOCEMBRINE; UNCLASSIFIED DRUG; FLAVANONE DERIVATIVE;

ALGORITHM; ANALYTIC METHOD; ARTICLE; BACTERIUM CULTURE; BIOLOGICAL ACTIVITY; BIOSYNTHESIS; COMPUTER AIDED DESIGN; DATA BASE; DRUG SYNTHESIS; ENZYME ACTIVITY; ESCHERICHIA COLI; METABOLIC ENGINEERING; METABOLIC FLUX ANALYSIS; NONHUMAN; RETROPATH; SIGNAL TRANSDUCTION; SYNTHESIS; SYNTHETIC BIOLOGY; TARGET CELL; TOXICITY TESTING; VALIDATION PROCESS; VALIDATION STUDY; BIOTECHNOLOGY; COMPUTER PROGRAM; FACTUAL DATABASE; METABOLISM; PHYSIOLOGY; PROCEDURES; REPRODUCIBILITY;

BIOTECHNOLOGY; COMPUTER-AIDED DESIGN; DATABASES, FACTUAL; ESCHERICHIA COLI; FLAVANONES; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; REPRODUCIBILITY OF RESULTS; SOFTWARE; SYNTHETIC BIOLOGY;

EID: 84910130469     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201400055     Document Type: Article

References (47)

1. Curran, K. A., Alper, H. S., Expanding the chemical palate of cells by combining systems biology and metabolic engineering. Metab. Eng. 2012, 14, 289-297.
2. Shin, J. H., Kim, H. U., Kim, D. I., Lee, S. Y., Production of bulk chemicals via novel metabolic pathways in microorganisms. Biotechnol. Adv. 2012, 31, 925-935.
3. Copeland, W. B., Bartley, B. A., Chandran, D., Galdzicki, M. et al., Computational tools for metabolic engineering. Metab. Eng. 2012, 14, 270-280.
4. Leonard, E., Yan, Y., Fowler, Z. L., Li, Z. et al., Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Mol. Pharm. 2008, 5, 257-265.
5. Miyahisa, I., Kaneko, M., Funa, N., Kawasaki, H. et al., Efficient production of (2S)-flavanones by Escherichia coli containing an artificial biosynthetic gene cluster. Appl. Microbiol. Biotechnol. 2005, 68, 498-504.
6. Santos, C. N., Koffas, M., Stephanopoulos, G., Optimization of a heterologous pathway for the production of flavonoids from glucose. Metab. Eng. 2011, 13, 392-400.
7. Carbonell, P., Planson, A. G., Fichera, D., Faulon, J. L., A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst. Biol. 2011, 5, 122.
8. Carbonell, P., Planson, A. G., Faulon, J. L., Retrosynthetic design of heterologous pathways. Methods Mol. Biol. 2013, 985, 149-173.
9. Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M., KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012, 40, D109-D114.
10. Caspi, R., Altman, T., Dreher, K., Fulcher, C. A. et al., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2012, 40, D742-D753.
11. Curran, K. A., Crook, N. C., Alper, H. S., Using flux balance analysis to guide microbial metabolic engineering. Methods Mol. Biol. 2012, 834, 197-216.
12. Planson, A. G., Carbonell, P., Grigoras, I., Faulon, J. L., A retrosynthetic biology approach to therapeutics: From conception to delivery. Curr. Opin. Biotechnol. 2012, 23, 948-956.
13. Chin, Y. W., Balunas, M. J., Chai, H. B., Kinghorn, A. D., Drug discovery from natural sources. AAPS J. 2006, 8, E239-E253.
14. Cragg, G. M., Newman, D. J., Natural products: A continuing source of novel drug leads. Biochim. Biophys. Acta 2013, 1830, 3670-3695.
15. Dixon, R. A., Lamb, C. J., Masoud, S., Sewalt, V. J., Paiva, N. L., Metabolic engineering: Prospects for crop improvement through the genetic manipulation of phenylpropanoid biosynthesis and defense responses - a review. Gene 1996, 179, 61-71.
16. Leonard, E., Lim, K. H., Saw, P. N., Koffas, M. A., Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli. Appl. Environ. Microbiol. 2007, 73, 3877-3886.
17. Miyahisa, I., Funa, N., Ohnishi, Y., Martens, S. et al., Combinatorial biosynthesis of flavones and flavonols in Escherichia coli. Appl. Microbiol. Biotechnol. 2006, 71, 53-58.
18. Hwang, E. I., Kaneko, M., Ohnishi, Y., Horinouchi, S., Production of plant-specific flavanones by Escherichia coli containing an artificial gene cluster. Appl. Environ. Microbiol. 2003, 69, 2699-2706.
19. Kaneko, M., Hwang, E. I., Ohnishi, Y., Horinouchi, S., Heterologous production of flavanones in Escherichia coli: Potential for combinatorial biosynthesis of flavonoids in bacteria. J. Ind. Microbiol. Biotechnol. 2003, 30, 456-461.
20. Watts, K. T., Lee, P. C., Schmidt-Dannert, C., Exploring recombinant flavonoid biosynthesis in metabolically engineered Escherichia coli. ChemBioChem 2004, 5, 500-507.
21. Liu, R., Wu, C. X., Zhou, D., Yang, F. et al., Pinocembrin protects against beta-amyloid-induced toxicity in neurons through inhibiting receptor for advanced glycation end products (RAGE)-independent signaling pathways and regulating mitochondrion-mediated apoptosis. BMC Med. 2012, 10, 105.
22. Soromou, L. W., Zhang, Y., Cui, Y., Wei, M. et al., Subinhibitory concentrations of pinocembrin exert anti-Staphylococcus aureus activity by reducing alpha-toxin expression. J. Appl. Microbiol. 2013, 115, 41-49.
23. Fowler, Z. L., Koffas, M. A., Biosynthesis and biotechnological production of flavanones: Current state and perspectives. Appl. Microbiol. Biotechnol. 2009, 83, 799-808.
24. Scheich, C., Kummel, D., Soumailakakis, D., Heinemann, U., Bussow, K., Vectors for co-expression of an unrestricted number of proteins. Nucleic Acids Res. 2007, 35, e43.
25. Grigoras, I., Timchenko, T., Gronenborn, B., Transcripts encoding the nanovirus master replication initiator proteins are terminally redundant. J. Gen. Virol. 2008, 89, 583-593.
26. Wu, J., Du, G., Zhou, J., Chen, J., Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy. Metab. Eng. 2013, 16, 48-55.
27. Xu, P., Vansiri, A., Bhan, N., Koffas, M. A., ePathBrick: A synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synth. Biol. 2014, 1, 256-266.
28. Sambrook, J., Fritch, E. F., Maniatis, T., Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY 1987.
29. Blackwell, J. R., Horgan, R., A novel strategy for production of a highly expressed recombinant protein in an active form. FEBS Lett. 1991, 295, 10-12.
30. Carbonell, P., Fichera, D., Pandit, S. B., Faulon, J. L., Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst. Biol. 2012, 6, 10.
31. Faulon, J. L., Misra, M., Martin, S., Sale, K., Sapra, R., Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. Bioinformatics 2008, 24, 225-233.
32. Carbonell, P., Faulon, J. L., Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics 2010, 26, 2012-2019.
33. Planson, A. G., Carbonell, P., Paillard, E., Pollet, N., Faulon, J. L., Compound toxicity screening and structure-activity relationship modeling in Escherichia coli. Biotechnol. Bioeng. 2012, 109, 846-850.
34. Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M. et al., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 2007, 3, 121.
35. Li, C., Donizelli, M., Rodriguez, N., Dharuri, H. et al., BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol. 2010, 4, 92.
36. Ebrahim, A., Lerman, J. A., Palsson, B. O., Hyduke, D. R., COBRApy: COnstraints-Based Reconstruction and Analysis for python. BMC Syst. Biol. 2013, 7, 74.
37. Conrad, T. M., Frazier, M., Joyce, A. R., Cho, B. K. et al., RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc. Natl. Acad. Sci. USA 2010, 107, 20500-20505.
38. Kaneko, M., Ohnishi, Y., Horinouchi, S., Cinnamate: Coenzyme A ligase from the filamentous bacterium Streptomyces coelicolor A3(2). J. Bacteriol. 2003, 185, 20-27.
39. An, J. H., Lee, G. Y., Jung, J. W., Lee, W., Kim, Y. S., Identification of residues essential for a two-step reaction by malonyl-CoA synthetase from Rhizobium trifolii. Biochem. J. 1999, 344, 159-166.
40. Davis, M. S., Solbiati, J., Cronan, J. E. Jr., Overproduction of acetyl-CoA carboxylase activity increases the rate of fatty acid biosynthesis in Escherichia coli. J. Biol. Chem. 2000, 275, 28593-28598.
41. Heath, R. J., Rock, C. O., Regulation of malonyl-CoA metabolism by acyl-acyl carrier protein and beta-ketoacyl-acyl carrier protein synthases in Escherichia coli. J. Biol. Chem. 1995, 270, 15531-15538.
42. Shen, H. B., Chou, K. C., EzyPred: A top-down approach for predicting enzyme functional classes and subclasses. Biochem. Biophys. Res. Commun. 2007, 364, 53-59.
43. Matsuta, Y., Ito, M., Tohsato, Y., ECOH: An enzyme commission number predictor using mutual information and a support vector machine. Bioinformatics 2013, 29, 365-372.
44. Burgard, A. P., Pharkya, P., Maranas, C. D., Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 2003, 84, 647-657.
45. Rockwell, G., Guido, N. J., Church, G. M., Redirector: Designing cell factories by reconstructing the metabolic objective. PLoS Comput. Biol. 2013, 9, e1002882.
46. Carbonell, P., Parutto, P., Baudier, C., Junot, C., Faulon, J. L., RetroPath: Automated pipeline for embedded metabolic circuits. ACS Synth. Biol. 2014, 3, 565-577.
47. Carbonell, P., Parutto, P., Herisson, J., Pandit, S. B., Faulon, J. L., XTMS: Pathway design in an eXTended metabolic space. Nucleic Acids Res. 2014, DOI:10.1093/nar/gku362.