Production of bulk chemicals via novel metabolic pathways in microorganisms

Biotechnology Advances

Volumn 31, Issue 6, 2013, Pages 925-935

  Shin, Jae Ho ^a   Kim, Hyun Uk ^a   Kim, Dong In ^a   Lee, Sang Yup ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

Bulk chemicals; De novo pathway design; Enzyme modification; Genome mining; Metabolic engineering; Pathway prediction; Promiscuous enzyme; Strain optimization; Synthetic biology

Indexed keywords

BULK CHEMICALS; DE NOVO PATHWAY; ENZYME MODIFICATION; GENOME MINING; STRAIN OPTIMIZATION; SYNTHETIC BIOLOGY;

BIODEGRADATION; CHEMICAL ANALYSIS; CHEMICALS; DESIGN; ENZYMES; METABOLIC ENGINEERING; MICROORGANISMS; OPTIMIZATION;

METABOLISM;

BIOMASS; DATA SET; ENZYME; GENOME; METABOLISM; MICROORGANISM; OPTIMIZATION;

1,4-BUTANEDIOL; ALCOHOL DEHYDROGENASE; GOLD; PHYTOHEMAGGLUTININ; POLYHYDROXYALKANOIC ACID; VASOPRESSIN;

1,4-BDO; 2-KETO-ACID DECARBOXYLASE; 3-HYDROXYPROPIONIC ACID; 3HP; 4-HYDROXYBUTYRYL-COA; 4HB-COA; BACTERIUM; BEM; BIOCHEMICAL NETWORK INTEGRATED COMPUTATIONAL EXPLORER; BIOLOGY; BIOTECHNOLOGY; BNICE; BOND AND ELECTRON MATRIX; BULK CHEMICALS; DE NOVO PATHWAY DESIGN; EC; ENZYME COMMISSION; ENZYME MODIFICATION; ENZYMOLOGY; GENETICS; GENOME MINING; GENOMES ONLINE DATABASE; HUMAN; KDC; KEGG; KYOTO ENCYCLOPEDIA OF GENES AND GENOMES; METABOLIC ENGINEERING; METABOLISM; PATHWAY PREDICTION; PROMISCUOUS ENZYME; REVIEW; SIMPLIFIED MOLECULAR-INPUT LINE-ENTRY SYSTEMS; SMILES; STRAIN OPTIMIZATION; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY; UM-BBD; UNIVERSITY OF MINNESOTA BIOCATALYSIS/BIODEGRADATION DATABASE;

1,4-BDO; 1,4-BUTANEDIOL; 2-KETO-ACID DECARBOXYLASE; 3-HYDROXYPROPIONIC ACID; 3HP; 4-HYDROXYBUTYRYL-COA; 4HB-COA; ADH; ALCOHOL DEHYDROGENASE; BEM; BIOCHEMICAL NETWORK INTEGRATED COMPUTATIONAL EXPLORER; BNICE; BOND AND ELECTRON MATRIX; BULK CHEMICALS; DE NOVO PATHWAY DESIGN; EC; ENZYME COMMISSION; ENZYME MODIFICATION; GENOME MINING; GENOMES ONLINE DATABASE; GOLD; KDC; KEGG; KYOTO ENCYCLOPEDIA OF GENES AND GENOMES; METABOLIC ENGINEERING; PATHWAY PREDICTION; PHA; POLYHYDROXYALKANOATE; PROMISCUOUS ENZYME; SIMPLIFIED MOLECULAR-INPUT LINE-ENTRY SYSTEMS; SMILES; STRAIN OPTIMIZATION; SYNTHETIC BIOLOGY; UM-BBD; UNIVERSITY OF MINNESOTA BIOCATALYSIS/BIODEGRADATION DATABASE;

BACTERIA; BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; HUMANS; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

EID: 84883001788     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2012.12.008     Document Type: Review

References (94)

1. Abubucker S., Segata N., Goll J., Schubert A.M., Izard J., Cantarel B.L., et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 2012, 8:e1002358.
2. Althoff E.A., Wang L., Jiang L., Giger L., Lassila J.K., Wang Z., et al. Robust design and optimization of retroaldol enzymes. Protein Sci 2012, 21:717-726.
3. Atsumi S., Hanai T., Liao J.C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-89.
4. Barker J.L., Frost J.W. Microbial synthesis of p-hydroxybenzoic acid from glucose. Biotechnol Bioeng 2001, 76:376-390.
5. Beare P.A., Chen C., Bouman T., Pablo J., Unal B., Cockrell D.C., et al. Candidate antigens for Q fever serodiagnosis revealed by immunoscreening of a Coxiella burnetii protein microarray. Clin Vaccine Immunol 2008, 15:1771-1779.
6. Brunk E., Neri M., Tavernelli I., Hatzimanikatis V., Rothlisberger U. Integrating computational methods to retrofit enzymes to synthetic pathways. Biotechnol Bioeng 2012, 109:572-582.
7. 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.
8. Cann A.F., Liao J.C. Production of 2-methyl-1-butanol in engineered Escherichia coli. Appl Microbiol Biotechnol 2008, 81:89-98.
9. Car R., Parrinello M. Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 1985, 55:2471-2474.
10. Carbonell P., Faulon J.L. Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics 2010, 26:2012-2019.
11. 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.
12. Chatsurachai S., Furusawa C., Shimizu H. An in silico platform for the design of heterologous pathways in nonnative metabolite production. BMC Bioinformatics 2012, 13:93.
13. Cho A., Yun H., Park J.H., Lee S.Y., Park S. Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst Biol 2010, 4:35.
14. Choi H.S., Lee S.Y., Kim T.Y., Woo H.M. In silico identification of gene amplification targets for improvement of lycopene production. Appl Environ Microbiol 2010, 76:3097-3105.
15. Colmer J.A., Fralick J.A., Hamood A.N. Isolation and characterization of a putative multidrug resistance pump from Vibrio cholerae. Mol Microbiol 1998, 27:63-72.
16. Connor M.R., Liao J.C. Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol. Appl Environ Microbiol 2008, 74:5769-5775.
17. Dellomonaco C., Clomburg J.M., Miller E.N., Gonzalez R. Engineered reversal of the beta-oxidation cycle for the synthesis of fuels and chemicals. Nature 2011, 476:355-359.
18. Draths K.M., Frost J.W. Environmentally compatible synthesis of adipic acid from d-glucose. J Am Chem Soc 1994, 116:399-400.
19. Draths K.M., Frost J.W. Environmentally compatible synthesis of catechol from d-glucose. J Am Chem Soc 1995, 117:2395-2400.
20. Faulon J.L., Collins M.J., Carr R.D. The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences. J Chem Inf Comput Sci 2004, 44:427-436.
21. Felnagle E.A., Chaubey A., Noey E.L., Houk K.N., Liao J.C. Engineering synthetic recursive pathways to generate non-natural small molecules. Nat Chem Biol 2012, 8:518-526.
22. Finley S.D., Broadbelt L.J., Hatzimanikatis V. Computational framework for predictive biodegradation. Biotechnol Bioeng 2009, 104:1086-1097.
23. Gao J.F., Ellis L.B.M., Wackett L.P. The University of Minnesota Pathway Prediction System: multi-level prediction and visualization. Nucleic Acids Res 2011, 39:W406-W411.
24. Gengenbacher M., Xu T., Niyomrattanakit P., Spraggon G., Dick T. Biochemical and structural characterization of the putative dihydropteroate synthase ortholog Rv1207 of Mycobacterium tuberculosis. FEMS Microbiol Lett 2008, 287:128-135.
25. Gibrat J.F., Madej T., Bryant S.H. Surprising similarities in structure comparison. Curr Opin Struct Biol 1996, 6:377-385.
26. Hatzimanikatis V., Li C., Ionita J.A., Henry C.S., Jankowski M.D., Broadbelt L.J. Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21:1603-1609.
27. Henry C.S., Broadbelt L.J., Hatzimanikatis V. Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol Bioeng 2010, 106:462-473.
28. Hermann J.C., Marti-Arbona R., Fedorov A.A., Fedorov E., Almo S.C., Shoichet B.K., et al. Structure-based activity prediction for an enzyme of unknown function. Nature 2007, 448:775-779.
29. Holm L., Rosenstrom P. Dali server: conservation mapping in 3D. Nucleic Acids Res 2010, 38:W545-W549.
30. Jankowski M.D., Henry C.S., Broadbelt L.J., Hatzimanikatis V. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 2008, 95:1487-1499.
31. Jewell J.B., Coutinho J.B., Kropinski A.M. Bioconversion of propionic, valeric, and 4-hydroxybutyric acids into the corresponding alcohols by Clostridium acetobutylicum NRRL 527. Curr Microbiol 1986, 13:215-219.
32. Jiang L., Althoff E.A., Clemente F.R., Doyle L., Rothlisberger D., Zanghellini A., et al. De novo computational design of retro-aldol enzymes. Science 2008, 319:1387-1391.
33. Jung Y.K., Kim T.Y., Park S.J., Lee S.Y. Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers. Biotechnol Bioeng 2010, 105:161-171.
34. Kanehisa M., Goto S., Furumichi M., Tanabe M., Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360.
35. Khersonsky O., Kiss G., Rothlisberger D., Dym O., Albeck S., Houk K.N., et al. Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. Proc Natl Acad Sci U S A 2012, 109:10358-10363.
36. Kim H.U., Kim T.Y., Lee S.Y. Metabolic flux analysis and metabolic engineering of microorganisms. Mol Biosyst 2008, 4:113-120.
37. Kimelman A., Levy A., Sberro H., Kidron S., Leavitt A., Amitai G., et al. A vast collection of microbial genes that are toxic to bacteria. Genome Res 2012, 22:802-809.
38. Korbel J.O., Doerks T., Jensen L.J., Perez-Iratxeta C., Kaczanowski S., Hooper S.D., et al. Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol 2005, 3:e134.
39. Krissinel E., Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 2004, 60:2256-2268.
40. Kuhlman B., Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A 2000, 97:10383-10388.
41. Kuhn M., Szklarczyk D., Franceschini A., Campillos M., von Mering C., Jensen L.J., et al. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res 2010, 38:D552-D556.
42. Lee S.Y. Bacterial polyhydroxyalkanoates. Biotechnol Bioeng 1996, 49:1-14.
43. Lee J.W., Kim T.Y., Jang Y.S., Choi S., Lee S.Y. Systems metabolic engineering for chemicals and materials. Trends Biotechnol 2011, 29:370-378.
44. 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.
45. Li C.H., Henry C.S., Jankowski M.D., Ionita J.A., Hatzimanikatis V., Broadbelt L.J. Computational discovery of biochemical routes to specialty chemicals. Chem Eng Sci 2004, 59:5051-5060.
46. Liolios K., Chen I.M., Mavromatis K., Tavernarakis N., Hugenholtz P., Markowitz V.M., et al. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010, 38:D346-D354.
47. Lo W.C., Lee C.Y., Lee C.C., Lyu P.C. iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res 2009, 37:W545-W551.
48. Machado H.B., Dekishima Y., Luo H., Lan E.I., Liao J.C. A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols. Metab Eng 2012, 14:504-511.
49. Marcheschi R.J., Li H., Zhang K., Noey E.L., Kim S., Chaubey A., et al. A synthetic recursive "+1" pathway for carbon chain elongation. ACS Chem Biol 2012, 7:689-697.
50. Markowitz V.M., Chen I.M., Palaniappan K., Chu K., Szeto E., Grechkin Y., et al. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res 2010, 38:D382-D390.
51. Martin C.H., Nielsen D.R., Solomon K.V., Prather K.L. Synthetic metabolism: engineering biology at the protein and pathway scales. Chem Biol 2009, 16:277-286.
52. Matte A., Jia Z., Sunita S., Sivaraman J., Cygler M. Insights into the biology of Escherichia coli through structural proteomics. J Struct Funct Genomics 2007, 8:45-55.
53. Mavrovouniotis M.L. Estimation of standard Gibbs energy changes of biotransformations. J Biol Chem 1991, 266:14440-14445.
54. McKenna R., Nielsen D.R. Styrene biosynthesis from glucose by engineered E. coli. Metab Eng 2011, 13:544-554.
55. Medema M.H., van Raaphorst R., Takano E., Breitling R. Computational tools for the synthetic design of biochemical pathways. Nat Rev Microbiol 2012, 10:191-202.
56. 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.
57. Moon T.S., Dueber J.E., Shiue E., Prather K.L. Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab Eng 2010, 12:298-305.
58. Na D., Lee D. RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics 2010, 26:2633-2634.
59. Niu W., Draths K.M., Frost J.W. Benzene-free synthesis of adipic acid. Biotechnol Prog 2002, 18:201-211.
60. Parekh S., Vinci V.A., Strobel R.J. Improvement of microbial strains and fermentation processes. Appl Microbiol Biotechnol 2000, 54:287-301.
61. Park H.S., Nam S.H., Lee J.K., Yoon C.N., Mannervik B., Benkovic S.J., et al. Design and evolution of new catalytic activity with an existing protein scaffold. Science 2006, 311:535-538.
62. Park J.H., Lee K.H., Kim T.Y., Lee S.Y. Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci U S A 2007, 104:7797-7802.
63. Park J.H., Lee S.Y., Kim T.Y., Kim H.U. Application of systems biology for bioprocess development. Trends Biotechnol 2008, 26:404-412.
64. Park J.M., Kim T.Y., Lee S.Y. Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnol Adv 2009, 27:979-988.
65. Park J.H., Kim T.Y., Lee K.H., Lee S.Y. Fed-batch culture of Escherichia coli for l-valine production based on in silico flux response analysis. Biotechnol Bioeng 2011, 108:934-946.
66. 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.
67. Reyes-Duarte D., Ferrer M., Garcia-Arellano H. Functional-based screening methods for lipases, esterases, and phospholipases in metagenomic libraries. Methods Mol Biol 2012, 861:101-113.
68. Rodrigo G., Carrera J., Prather K.J., Jaramillo A. DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics 2008, 24:2554-2556.
69. Rothlisberger D., Khersonsky O., Wollacott A.M., Jiang L., DeChancie J., Betker J., et al. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453:190-195.
70. Sacan A., Toroslu I.H., Ferhatosmanoglu H. Integrated search and alignment of protein structures. Bioinformatics 2008, 24:2872-2879.
71. Salis H.M., Mirsky E.A., Voigt C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 2009, 27:946-950.
72. Savile C.K., Janey J.M., Mundorff E.C., Moore J.C., Tam S., Jarvis W.R., et al. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 2010, 329:305-309.
73. Shin D.H., Hou J., Chandonia J.M., Das D., Choi I.G., Kim R., et al. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics 2007, 8:99-105.
74. Siegel J.B., Zanghellini A., Lovick H.M., Kiss G., Lambert A.R., St Clair J.L., et al. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010, 329:309-313.
75. Soh K.C., Hatzimanikatis V. DREAMS of metabolism. Trends Biotechnol 2010, 28:501-508.
76. Solomon K.V., Prather K.L. The zero-sum game of pathway optimization: emerging paradigms for tuning gene expression. Biotechnol J 2011, 6:1064-1070.
77. Song H., Kim T.Y., Choi B.K., Choi S.J., Nielsen L.K., Chang H.N., et al. Development of chemically defined medium for Mannheimia succiniciproducens based on its genome sequence. Appl Microbiol Biotechnol 2008, 79:263-272.
78. Szklarczyk D., Franceschini A., Kuhn M., Simonovic M., Roth A., Minguez P., et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011, 39:D561-D568.
79. Tantillo D.J., Chen J., Houk K.N. Theozymes and compuzymes: theoretical models for biological catalysis. Curr Opin Chem Biol 1998, 2:743-750.
80. Ugi I., Bauer J., Brandt J., Friedrich J., Gasteiger J., Jochum C., et al. New applications of computers in chemistry. Angew Chem Int Ed 1979, 18:111-123.
81. Verhoef S., Ruijssenaars H.J., de Bont J.A.M., Wery J. Bioproduction of p-hydroxybenzoate from renewable feedstock by solvent-tolerant Pseudomonas putida S12. J Biotechnol 2007, 132:49-56.
82. Villalobos A., Ness J.E., Gustafsson C., Minshull J., Govindarajan S. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 2006, 7:285.
83. Weininger D. SMILES, a chemical language and information-system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 1988, 28:31-36.
84. Wierckx N.J.P., Ballerstedt H., de Bont J.A.M., Wery J. Engineering of solvent-tolerant Pseudomonas putida S12 for bioproduction of phenol from glucose. Appl Environ Microbiol 2005, 71:8221-8227.
85. Wittmann C., Lee S.Y. Systems metabolic engineering 2012, Springer, Dordrecht.
86. Yang T.H., Kim T.W., Kang H.O., Lee S.H., Lee E.J., Lim S.C., et al. Biosynthesis of polylactic acid and its copolymers using evolved propionate CoA transferase and PHA synthase. Biotechnol Bioeng 2010, 105:150-160.
87. Ye Y., Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003, 19(Suppl. 2):ii246-ii255.
88. Yim H., Haselbeck R., Niu W., Pujol-Baxley C., Burgard A., Boldt J., et al. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 2011, 7:445-452.
89. Yoon S.H., Han M.J., Jeong H., Lee C.H., Xia X.X., Lee D.H., et al. Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol 2012, 13:R37.
90. Zanghellini A., Jiang L., Wollacott A.M., Cheng G., Meiler J., Althoff E.A., et al. New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 2006, 15:2785-2794.
91. Zhang K., Sawaya M.R., Eisenberg D.S., Liao J.C. Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci U S A 2008, 105:20653-20658.
92. Zhang Y., Thiele I., Weekes D., Li Z., Jaroszewski L., Ginalski K., et al. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 2009, 325:1544-1549.
93. Zhang K., Li H., Cho K.M., Liao J.C. Expanding metabolism for total biosynthesis of the nonnatural amino acid l-homoalanine. Proc Natl Acad Sci U S A 2010, 107:6234-6239.
94. Zhang Z.H., Bharatham K., Sherman W.A., Mihalek I. deconSTRUCT: general purpose protein database search on the substructure level. Nucleic Acids Res 2010, 38:W590-W594.