Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions

Biotechnology Journal

Volumn 5, Issue 7, 2010, Pages 716-725

  Ranganathan, Sridhar ^a   Maranas, Costas D ^b  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b The Pennsylvania State University   (United States)

Author keywords

Biofuels; Butanol; Metabolic engineering; Metabolic pathways; Strain optimization

Indexed keywords

ALCOHOLS; ENGINEERING; ESCHERICHIA COLI; GENETIC ENGINEERING; METABOLISM; OPTIMIZATION; SYNTHESIS (CHEMICAL);

1-BUTANOL; GRAPH-BASED; IN-SILICO; METABOLIC ENGINEERING; METABOLIC MODELS; METABOLIC PATHWAYS; NON-NATIVE; PRODUCT YIELDS; PRODUCTION ROUTE; SEARCH METHOD; STRAIN OPTIMIZATION;

BIOFUELS;

2 OXOISOVALERIC ACID; BUTANOL; BIOFUEL;

ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; BIOENGINEERING; BIOFUEL PRODUCTION; ESCHERICHIA COLI; METABOLITE; NONHUMAN; PRIORITY JOURNAL; BIOLOGICAL MODEL; BIOSYNTHESIS; GENETIC ENGINEERING; GENETICS; METABOLISM; PROCEDURES;

ESCHERICHIA COLI;

1-BUTANOL; BIOENGINEERING; BIOFUELS; BIOSYNTHETIC PATHWAYS; ESCHERICHIA COLI; GENETIC ENGINEERING; MODELS, BIOLOGICAL;

EID: 77954732846     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201000171     Document Type: Article

References (50)

1. Stephanopoulos, G., Challenges in engineering microbes for biofuels production. Science 2007, 315, 801-804.
2. Atsumi, S., Liao, J. C., Metabolic engineering for advanced biofuels production from Escherichia coli. Curr. Opin. Biotechnol. 2008, 19, 414-419.
3. Janssen, P. H., Propanol as an end product of threonine fermentation. Arch. Microbiol. 2004, 182, 482-486.
4. Jones, D. T., Woods, D. R., Acetone-butanol fermentation revisited. Microbiol. Rev. 1986, 50, 484-524.
5. Nair, R. V., Papoutsakis, E. T., Expression of plasmid-encoded aad in Clostridium acetobutylicum M5 restores vigorous butanol production. J. Bacteriol. 1994, 176, 5843-5846.
6. Formanek, J., Mackie, R., Blaschek, H. P., Enhanced butanol production by Clostridium beijerinckii BA101 grown in semidefined P2 medium containing 6 percent maltodextrin or glucose. Appl. Environ. Microbiol. 1997, 63, 2306-2310. (Pubitemid 27232930)
7. Lin,Y. L., Blaschek, H. P., Butanol production by a butanol-tolerant strain of Clostridium acetobutylicum in extruded corn broth. Appl. Environ. Microbiol. 1983, 45, 966-973.
8. Lee, J. Y., Jang, Y. S., Lee, J., Papoutsakis, E. T., Lee, S. Y., Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol. J. 2009, 4, 1432-1440.
9. Sillers, R., Chow, A., Tracy, B., Papoutsakis, E. T., Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance. Metab. Eng. 2008, 10, 321-332.
10. Hanai, T., Atsumi, S., Liao, J. C., Engineered synthetic pathway for isopropanol production in Escherichia coli. Appl. Environ. Microbiol. 2007, 73, 7814-7818.
11. Yan, Y., Liao, J. C., Engineering metabolic systems for production of advanced fuels. J. Ind. Microbiol. Biotechnol. 2009, 36, 471-479.
12. Boynton, Z. L., Bennett, G. N., Rudolph, F. B., Cloning, sequencing, and expression of genes encoding phosphotransacetylase and acetate kinase from Clostridium acetobutylicum ATCC 824. Appl. Environ. Microbiol. 1996, 62, 2758-2766. (Pubitemid 126752181)
13. Fontaine, L., Meynial-Salles, I., Girbal, L., Yang, X. et al., Molecular characterization and transcriptional analysis of adhE2, the gene encoding the NADH-dependent aldehyde/alcohol dehydrogenase responsible for butanol production in alcohologenic cultures of Clostridium acetobutylicum ATCC 824. J. Bacteriol. 2002, 184, 821-830.
14. Wiesenborn, D. P., Rudolph, F. B., Papoutsakis, E. T., Thiolase from Clostridium acetobutylicum ATCC 824 and its role in the synthesis of acids and solvents. Appl. Environ. Microbiol. 1988, 54, 2717-2722.
15. Becker, D. F., Fuchs, J. A., Banfield, D. K., Funk, W. D. et al., Characterization of wild-type and an active-site mutant in Escherichia coli of short-chain acyl-CoA dehydrogenase from Megasphaera elsdenii. Biochemistry 1993, 32, 10736-10742.
16. O'Neill, H., Mayhew, S. G., Butler, G., Cloning and analysis of the genes for a novel electron-transferring flavoprotein from Megasphaera elsdenii. Expression and characterization of the recombinant protein. J. Biol. Chem. 1998, 273, 21015-21024.
17. Wallace, K. K., Bao, Z. Y., Dai, H., Digate, R. et al., Purification of crotonyl-CoA reductase from Streptomyces collinus and cloning, sequencing and expression of the corresponding gene in Escherichia coli. Eur. J. Biochem. 1995, 233, 954-962.
18. Sentheshanuganathan, S., The mechanism of the formation of higher alcohols from amino acids by Saccharomyces cerevisiae. Biochem. J. 1960, 74, 568-576.
19. Atsumi, S., Hanai, T., Liao, J. C., Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451, 86-89.
20. Shen, C. R., Liao, J. C., Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the ketoacid pathways. Metab. Eng. 2008, 10, 312-320.
21. Atsumi, S., Cann, A. F., Connor, M. R., Shen, C. R. et al., Metabolic engineering of Escherichia coli for 1-butanol production. Metab. Eng. 2008, 10, 305-311.
22. Steen, E. J., Chan, R., Prasad, N., Myers, S. et al., Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb. Cell Fact. 2008, 7, 36.
23. Bode, H. B., Muller, R., The impact of bacterial genomics on natural product research. Angew. Chem. Int. Ed. Engl. 2005, 44, 6828-6846.
24. Wenzel, S. C., Muller, R., Recent developments towards the heterologous expression of complex bacterial natural product biosynthetic pathways. Curr. Opin. Biotechnol. 2005, 16, 594-606. (Pubitemid 41654637)
25. Kanehisa, M., Araki, M., Goto, S., Hattori, M. et al., KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36, D480-484.
26. Chang, A., Scheer, M., Grote, A., Schomburg, I., Schomburg, D., BRENDA, AMENDA and FRENDA the enzyme information system: New content and tools in 2009. Nucleic Acids Res. 2009, 37, D588-592.
27. Bader, G. D., Cary, M. P., Sander, C., Pathguide: A pathway resource list. Nucleic Acids Res. 2006, 34, D504-506.
28. Pharkya, P., Burgard, A. P., Maranas, C. D., OptStrain: A computational framework for redesign of microbial production systems. Genome Res. 2004, 14, 2367-2376.
29. Ma, H., Zeng, A. P., Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19, 270-277.
30. Hatzimanikatis, V., Li, C., Ionita, J. A., Henry, C. S. et al., Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21, 1603-1609.
31. 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.
32. 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.
33. McShan, D. C., Rao, S., Shah, I., PathMiner: Predicting metabolic pathways by heuristic search. Bioinformatics 2003, 19, 1692-1698.
34. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F. et al., From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res. 2006, 34, D354-357.
35. Karp, P. D., Paley, S., Romero, P., The Pathway Tools software. Bioinformatics 2002, 18 Suppl 1, S225-232.
36. Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M. et al., Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology. Brief Bioinform. 2009.
37. Blum, T., Kohlbacher, O., MetaRoute: Fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics 2008, 24, 2108-2109.
38. Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J., Giegerich, R., PathFinder: Reconstruction and dynamic visualization of metabolic pathways. Bioinformatics 2002, 18, 124-129.
39. Ellis, L. B., Roe, D., Wackett, L. P., The University of Minnesota Biocatalysis/Biodegradation Database: The first decade. Nucleic Acids Res. 2006, 34, D517-521.
40. Yen, J. Y., Finding K shortest loopless paths in a network. Management Science 1971, 17, 712-716.
41. 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.
42. Ranganathan, S., Suthers, P. F., Maranas, C. D., OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput. Biol. 2010, 6, e1000744.
43. Wang, Y., Xiao, J., Suzek, T. O., Zhang, J. et al., PubChem: A public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 2009, 37, W623-633.
44. Clomburg, J. M., Gonzalez, R., Biofuel production in Escherichia coli: The role of metabolic engineering and synthetic biology. Appl. Microbiol. Biotechnol. 86, 419-434.
45. Kagamiyama, H., Hayashi, H., Branched-chain amino-acid aminotransferase of Escherichia coli. Methods Enzymol. 2000, 324, 103-113.
46. Smit, B. A., van Hylckama Vlieg, J. E., Engels, W. J., Meijer, L. et al., Identification, cloning, and characterization of a Lactococcus lactis branched-chain alpha-keto acid decarboxylase involved in flavor formation. Appl. Environ. Microbiol. 2005, 71, 303-311.
47. Perpete, P., Collin, S., Contribution of 3-methylthiopropionaldehyde to the worty flavor of alcohol-free beers. J. Agric. Food Chem. 1999, 47, 2374-2378.
48. 13C-labeling experiments and integration of the information with gene and protein expression patterns. Adv. Biochem. Eng. Biotechnol. 2004, 91, 1-49.
49. Nielsen, D. R., Leonard, E., Yoon, S. H., Tseng, H. C. et al., Engineering alternative butanol production platforms in heterologous bacteria. Metab. Eng. 2009, 11, 262-273.
50. Kanehisa, M., The KEGG database. Novartis Found. Symp. 2002, 247, 91-101; discussion 101-103, 119-128, 244-152.