Optimum Rebalancing of the 3-Hydroxypropionic Acid Production Pathway from Glycerol in Escherichia coli

ACS Synthetic Biology

Volumn 5, Issue 11, 2016, Pages 1247-1255

  Lim, Hyun Gyu ^a   Noh, Myung Hyun ^a   Jeong, Jun Hong ^a   Park, Sunghoon ^b   Jung, Gyoo Yeol ^a  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

^b Pusan National University   (South Korea)

Author keywords

3 hydroxypropionic acid; balancing enzyme activity; metabolic engineering; synthetic biology

Indexed keywords

ALDEHYDE DEHYDROGENASE; GLYCEROL; HYDRACRYLIC ACID; HYDROLYASE; 3-HYDROXYPROPIONALDEHYDE; BACTERIAL DNA; BACTERIAL PROTEIN; GLYCERALDEHYDE; GLYCEROL DEHYDRATASE; LACTIC ACID; PROPANE;

ARTICLE; BACTERIAL GENE; BIOACCUMULATION; CONTROLLED STUDY; DHAB1 GENE; ENZYME ACTIVITY; ESCHERICHIA COLI; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; ANALOGS AND DERIVATIVES; AZOSPIRILLUM BRASILENSE; BATCH CELL CULTURE; BIOSYNTHESIS; CHEMISTRY; CULTURE MEDIUM; GENETICS; KLEBSIELLA PNEUMONIAE; METABOLISM; MICROBIAL VIABILITY; MICROBIOLOGY; TRANSGENIC MICROORGANISM;

ALDEHYDE DEHYDROGENASE; AZOSPIRILLUM BRASILENSE; BACTERIAL PROTEINS; BATCH CELL CULTURE TECHNIQUES; CULTURE MEDIA; DNA, BACTERIAL; ESCHERICHIA COLI; GLYCERALDEHYDE; GLYCEROL; HYDRO-LYASES; INDUSTRIAL MICROBIOLOGY; KLEBSIELLA PNEUMONIAE; LACTIC ACID; MICROBIAL VIABILITY; MICROORGANISMS, GENETICALLY-MODIFIED; PROPANE;

EID: 85017356007     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00303     Document Type: Article

References (50)

1. Kumar, V., Ashok, S., and Park, S. (2013) Recent advances in biological production of 3-hydroxypropionic acid Biotechnol. Adv. 31, 945-961 10.1016/j.biotechadv.2013.02.008
2. Pina, D. C., Falletta, E., and Rossi, M. (2011) A green approach to chemical building blocks. The case of 3-hydroxypropanoic acid Green Chem. 13, 1624-1632 10.1039/c1gc15052a
3. Werpy, T., Petersen, G., Aden, A., Bozell, J., Holladay, J., White, J., Manheim, A., Elliot, D., Lasure, L., Jones, S., Gerber, M., Ibsen, K., Lumberg, L., and Kelley, S. (2004) Top Value Added Chemicals From Biomass, Vol. 1-Results of Screening for Potential Candidates from Sugars and Synthesis Gas, U.S. Department of Energy.
4. Jiang, X. L., Meng, X., and Xian, M. (2009) Biosynthetic pathways for 3-hydroxypropionic acid production Appl. Microbiol. Biotechnol. 82, 995-1003 10.1007/s00253-009-1898-7
5. Ko, Y., Ashok, S., Seol, E., Ainala, S., and Park, S. (2015) Deletion of putative oxidoreductases from Klebsiella pneumoniae J2B could reduce 1,3-propanediol during the production of 3-hydroxypropionic acid from glycerol Biotechnol. Bioprocess Eng. 20, 834-843 10.1007/s12257-015-0166-1
6. Raj, S. M., Rathnasingh, C., Jo, J.-E., and Park, S. (2008) Production of 3-hydroxypropionic acid from glycerol by a novel recombinant Escherichia coli BL21 strain Process Biochem. 43, 1440-1446 10.1016/j.procbio.2008.04.027
7. Rathnasingh, C., Raj, S. M., Lee, Y., Catherine, C., Ashoka, S., and Park, S. (2012) Production of 3-hydroxypropionic acid via malonyl-CoA pathway using recombinant Escherichia coli strains J. Biotechnol. 157, 633-640 10.1016/j.jbiotec.2011.06.008
8. Liao, H. H., Gokarn, R. R., Gort, S. J., Jessen, H. J., and Selifonova, O. V. (2012) Production of 3-hydroxypropionic acid using beta-alanine/pyruvate aminotransferase, US 8,124,388 B2.
9. Borodina, I., Kildegaard, K. R., Jensen, N. B., Blicher, T. H., Maury, J., Sherstyk, S., Schneider, K., Lamosa, P., Herrgard, M. J., Rosenstand, I., Oberg, F., Forster, J., and Nielsen, J. (2015) Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via beta-alanine Metab. Eng. 27, 57-64 10.1016/j.ymben.2014.10.003
10. Sankaranarayanan, M., Ashok, S., and Park, S. (2014) Production of 3-hydroxypropionic acid from glycerol by acid tolerant Escherichia coli J. Ind. Microbiol. Biotechnol. 41, 1039-1050 10.1007/s10295-014-1451-2
11. Kim, K., Kim, S. K., Park, Y. C., and Seo, J. H. (2014) Enhanced production of 3-hydroxypropionic acid from glycerol by modulation of glycerol metabolism in recombinant Escherichia coli Bioresour. Technol. 156, 170-175 10.1016/j.biortech.2014.01.009
12. Chu, H. S., Kim, Y. S., Lee, C. M., Lee, J. H., Jung, W. S., Ahn, J. H., Song, S. H., Choi, I. S., and Cho, K. M. (2015) Metabolic Engineering of 3-Hydroxypropionic Acid Biosynthesis in Escherichia coli Biotechnol. Bioeng. 112, 356-364 10.1002/bit.25444
13. Jung, W. S., Kang, J. H., Chu, H. S., Choi, I. S., and Cho, K. M. (2014) Elevated production of 3-hydroxypropionic acid by metabolic engineering of the glycerol metabolism in Escherichia coli Metab. Eng. 23, 116-122 10.1016/j.ymben.2014.03.001
14. Barbirato, F., Grivet, J. P., Soucaille, P., and Bories, A. (1996) 3-hydroxypropionaldehyde, an inhibitory metabolite of glycerol fermentation to 1,3-propanediol by enterobacterial species Appl. Environ. Microbiol. 62, 1448-1451
15. Celińska, E. (2010) Debottlenecking the 1,3-propanediol pathway by metabolic engineering Biotechnol. Adv. 28, 519-530 10.1016/j.biotechadv.2010.03.003
16. Barbirato, F., Soucaille, P., and Bories, A. (1996) Physiologic Mechanisms Involved in Accumulation of 3-Hydroxypropionaldehyde during Fermentation of Glycerol by Enterobacter agglomerans Appl. Environ. Microbiol. 62, 4405-9
17. Vollenweider, S., Evers, S., Zurbriggen, K., and Lacroix, C. (2010) Unraveling the Hydroxypropionaldehyde (HPA) System: An Active Antimicrobial Agent against Human Pathogens J. Agric. Food Chem. 58, 10315-10322 10.1021/jf1010897
18. Jones, J. A., Toparlak, Ö. D., and Koffas, M. A. G. (2015) Metabolic pathway balancing and its role in the production of biofuels and chemicals Curr. Opin. Biotechnol. 33, 52-59 10.1016/j.copbio.2014.11.013
19. Seo, S., Kim, S., and Jung, G. (2012) Synthetic regulatory tools for microbial engineering Biotechnol. Bioprocess Eng. 17, 1-7 10.1007/s12257-011-0563-z
20. Martin, V. J. J., Pitera, D. J., Withers, S. T., Newman, J. D., and Keasling, J. D. (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids Nat. Biotechnol. 21, 796-802 10.1038/nbt833
21. Ajikumar, P. K., Xiao, W.-H., Tyo, K. E. J., Wang, Y., Simeon, F., Leonard, E., Mucha, O., Phon, T. H., Pfeifer, B., and Stephanopoulos, G. (2010) Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli Science 330, 70-74 10.1126/science.1191652
22. Pitera, D. J., Paddon, C. J., Newman, J. D., and Keasling, J. D. (2007) Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli Metab. Eng. 9, 193-207 10.1016/j.ymben.2006.11.002
23. Xu, P., Gu, Q., Wang, W., Wong, L., Bower, A. G. W., Collins, C. H., and Koffas, M. A. G. (2013) Modular optimization of multi-gene pathways for fatty acids production in E. coli Nat. Commun. 4, 1409 10.1038/ncomms2425
24. Seo, S. W., Yang, J.-S., Cho, H.-S., Yang, J., Kim, S. C., Park, J. M., Kim, S., and Jung, G. Y. (2014) Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels Sci. Rep. 4, 4515 10.1038/srep04515
25. Seo, S. W., Yang, J.-S., Kim, I., Yang, J., Min, B. E., Kim, S., and Jung, G. Y. (2013) Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency Metab. Eng. 15, 67-74 10.1016/j.ymben.2012.10.006
26. Lim, H. G., Seo, S. W., and Jung, G. Y. (2013) Engineered Escherichia coli for simultaneous utilization of galactose and glucose Bioresour. Technol. 135, 564-567 10.1016/j.biortech.2012.10.124
27. Lim, J. H., Seo, S. W., Kim, S. Y., and Jung, G. Y. (2013) Refactoring redox cofactor regeneration for high-yield biocatalysis of glucose to butyric acid in Escherichia coli Bioresour. Technol. 135, 568-573 10.1016/j.biortech.2012.09.091
28. Bui, L. M., Lee, J. Y., Geraldi, A., Rahman, Z., Lee, J. H., and Kim, S. C. (2015) Improved n-butanol tolerance in Escherichia coli by controlling membrane related functions J. Biotechnol. 204, 33-44 10.1016/j.jbiotec.2015.03.025
29. Li, X.-R., Tian, G.-Q., Shen, H.-J., and Liu, J.-Z. (2015) Metabolic engineering of Escherichia coli to produce zeaxanthin J. Ind. Microbiol. Biotechnol. 42, 627-636 10.1007/s10295-014-1565-6
30. Lim, J. H., Seo, S. W., Kim, S. Y., and Jung, G. Y. (2013) Model-driven rebalancing of the intracellular redox state for optimization of a heterologous n-butanol pathway in Escherichia coli Metab. Eng. 20, 56-62 10.1016/j.ymben.2013.09.003
31. Lim, H., Lim, J., and Jung, G. (2015) Modular design of metabolic network for robust production of n-butanol from galactose-glucose mixtures Biotechnol. Biofuels 8, 137 10.1186/s13068-015-0327-7
32. Baek, A. H., Jeon, E.-Y., Lee, S.-M., and Park, J.-B. (2015) Expression levels of chaperones influence biotransformation activity of recombinant Escherichia coli expressing Micrococcus luteus alcohol dehydrogenase and Pseudomonas putida Baeyer-Villiger monooxygenase Biotechnol. Bioeng. 112, 889-895 10.1002/bit.25521
33. Kim, S. C., Min, B. E., Hwang, H. G., Seo, S. W., and Jung, G. Y. (2015) Pathway optimization by re-design of untranslated regions for L-tyrosine production in Escherichia coli Sci. Rep. 5, 13853 10.1038/srep13853
34. Yamanishi, M., Yunoki, M., Tobimatsu, T., Sato, H., Matsui, J., Dokiya, A., Iuchi, Y., Oe, K., Suto, K., Shibata, N., Morimoto, Y., Yasuoka, N., and Toraya, T. (2002) The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol Eur. J. Biochem. 269, 4484-4494 10.1046/j.1432-1033.2002.03151.x
35. Chun, A., Yunxiao, L., Ashok, S., Seol, E., and Park, S. (2014) Elucidation of toxicity of organic acids inhibiting growth of Escherichia coli W Biotechnol. Bioprocess Eng. 19, 858-865 10.1007/s12257-014-0420-y
36. Pfleger, B. F., Fawzi, N. J., and Keasling, J. D. (2005) Optimization of DsRed production in Escherichia coli: Effect of ribosome binding site sequestration on translation efficiency Biotechnol. Bioeng. 92, 553-558 10.1002/bit.20630
37. Joyce, S. A. and Dreyfus, M. (1998) In the absence of translation, RNase E can bypass 5′ mRNA stabilizers in Escherichia coli J. Mol. Biol. 282, 241-254 10.1006/jmbi.1998.2027
38. Blazeck, J. and Alper, H. S. (2013) Promoter engineering: Recent advances in controlling transcription at the most fundamental level Biotechnol. J. 8, 46-58 10.1002/biot.201200120
39. Ahn, J.-H., Keum, J.-W., and Kim, D.-M. (2008) High-Throughput, Combinatorial Engineering of Initial Codons for Tunable Expression of Recombinant Proteins J. Proteome Res. 7, 2107-2113 10.1021/pr700856s
40. Tao, L., Wilczek, J., Odom, J. M., and Cheng, Q. (2006) Engineering a β-carotene ketolase for astaxanthin production Metab. Eng. 8, 523-531 10.1016/j.ymben.2006.06.001
41. Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., and Salis, H. M. (2014) Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria Mol. Syst. Biol. 10, 731 10.15252/msb.20134955
42. Dietrich, J. A., McKee, A. E., and Keasling, J. D. (2010) High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection Annu. Rev. Biochem. 79, 563-590 10.1146/annurev-biochem-062608-095938
43. Yang, J., Seo, S. W., Jang, S., Shin, S.-I., Lim, C. H., Roh, T.-Y., and Jung, G. Y. (2013) Synthetic RNA devices to expedite the evolution of metabolite-producing microbes Nat. Commun. 4, 1413 10.1038/ncomms2404
44. Lim, S. I., Min, B. E., and Jung, G. Y. (2008) Lagging Strand-Biased Initiation of Red Recombination by Linear Double-Stranded DNAS J. Mol. Biol. 384, 1098-1105 10.1016/j.jmb.2008.10.047
45. Datsenko, K. A. and Wanner, B. L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Proc. Natl. Acad. Sci. U. S. A. 97, 6640-6645 10.1073/pnas.120163297
46. Toraya, T. and Mori, K. (1999) A Reactivating Factor for Coenzyme B12-dependent Diol Dehydratase J. Biol. Chem. 274, 3372-3377 10.1074/jbc.274.6.3372
47. Schmittgen, T. D. and Livak, K. J. (2008) Analyzing real-time PCR data by the comparative CT method Nat. Protoc. 3, 1101-1108 10.1038/nprot.2008.73
48. Riesenberg, D., Schulz, V., Knorre, W. A., Pohl, H. D., Korz, D., Sanders, E. A., Roß, A., and Deckwer, W. D. (1991) High cell density cultivation of Escherichia coli at controlled specific growth rate J. Biotechnol. 20, 17-27 10.1016/0168-1656(91)90032-Q
49. Ashok, S., Sankaranarayanan, M., Ko, Y., Jae, K.-E., Ainala, S. K., Kumar, V., and Park, S. (2013) Production of 3-hydroxypropionic acid from glycerol by recombinant Klebsiella pneumoniae ΔdhaTΔyqhD which can produce vitamin B12 naturally Biotechnol. Bioeng. 110, 511-524 10.1002/bit.24726
50. Ko, Y., Ashok, S., Zhou, S., Kumar, V., and Park, S. (2012) Aldehyde dehydrogenase activity is important to the production of 3-hydroxypropionic acid from glycerol by recombinant Klebsiella pneumoniae Process Biochem. 47, 1135-1143 10.1016/j.procbio.2012.04.007