Metabolic engineering strategies to bio-adipic acid production

Current Opinion in Biotechnology

Volumn 45, Issue , 2017, Pages 136-143

  Kruyer, Nicholas S ^a,b   Peralta Yahya, Pamela ^a,b,c  

^a Georgia Institute of Technology   (United States)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CARBON; CELLULOSE; CHASSIS; ESCHERICHIA COLI; GREENHOUSE GASES; METABOLISM; MICROORGANISMS; MONOMERS; YEAST;

CARBON SOURCE; CHEMICAL PROCESS; DICARBOXYLIC ACID; GLUCARIC ACID; LIGNIN MONOMER; METABOLIC ROUTES; MICROBIAL SUBSTRATES; NASCENT PROTEIN;

METABOLIC ENGINEERING;

ADIPIC ACID; CARBON; CELLULOSE; HEMICELLULOSE; LIGNIN; LIPID; MUCONIC ACID; SACCHARIC ACID; ADIPIC ACID DERIVATIVE;

CARBON SOURCE; CITRIC ACID CYCLE; DEGRADATION KINETICS; ESCHERICHIA COLI; METABOLIC ENGINEERING; NONHUMAN; PROTEIN ENGINEERING; REVIEW; SACCHAROMYCES CEREVISIAE; ANIMAL FOOD; METABOLISM;

ADIPIC ACID; BACTERIA; CARBOXYLIC ACIDS; MONOMERS; SYNTHESIS;

ADIPATES; ANIMAL FEED; CARBON; CITRIC ACID CYCLE; ESCHERICHIA COLI; METABOLIC ENGINEERING; SACCHAROMYCES CEREVISIAE;

EID: 85016462601     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2017.03.006     Document Type: Review

References (52)

1. 1 Merchant Research & Consulting: L. Adipic acid 2011 World Market Outlook and Forecast. (2011).
2. 2 Polen, T., Spelberg, M., Bott, M., Toward biotechnological production of adipic acid and precursors from biorenewables. J Biotechnol 167 (2013), 75–84.
3. 2O-decomposition from adipic acid plant. Appl Catal B Environ 70 (2007), 323–329.
4. 4 Peralta-Yahya, P., Zhang, F.Z., del Cardayre, S.B., Keasling, J.D., Microbial engineering for the production of advanced biofuels. Nature 488 (2012), 320–328.
5. 5 Nielsen, J., Keasling, J.D., Engineering cellular metabolism. Cell 164 (2016), 1185–1197.
6. 6 Thompson, B., Machas, M., Nielsen, D.R., Creating pathways towards aromatic building blocks and fine chemicals. Curr Opin Biotechnol 36 (2015), 1–7.
7. 7 Bugg, T.D.H., Rahmanpour, R., Enzymatic conversion of lignin into renewable chemicals. Curr Opin Chem Biol 29 (2015), 10–17.
8. 8 Jung, H.M., Jung, M.Y., Oh, M.K., Metabolic engineering of Klebsiella pneumoniae for the production of muconic acid. Appl Microbiol Biotechnol 99 (2015), 5217–5225.
9. 9 Deng, Y., Ma, L., Mao, Y., Biological production of adipic acid from renewable substrates: current and future methods. Biochem Eng J 105 (2016), 16–26.
10. 10 Xie, N.Z., Liang, H., Huang, R.B., Xu, P., Biotechnological production of muconic acid: current status and future prospects. Biotechnol Adv 32 (2014), 615–622.
11. 11 Draths, K.M., Frost, J.W., Environmentally compatible synthesis of adipic acid from D-glucose. J Am Chem Soc 116 (1994), 399–400.
12. 12 Sprenger, G.A., From scratch to value: engineering Escherichia coli wild type cells to the production of L-phenylalanine and other fine chemicals derived from chorismate. Appl Microbiol Biotechnol 75 (2007), 739–749.
13. 13 Wang, J., Zheng, P., Muconic acid production from glucose using enterobactin precursors in Escherichia coli. J Ind Microbiol Biotechnol 42 (2015), 701–709.
14. 14 Sun, X., Lin, Y., Yuan, Q., Yan, Y., Biological production of muconic acid via a prokaryotic 2,3-dihydroxybenzoic acid decarboxylase. Chemsuschem 7 (2014), 2478–2481.
15. 15 Lin, Y., Sun, X., Yuan, Q., Yan, Y., Extending shikimate pathway for the production of muconic acid and its precursor salicylic acid in Escherichia coli. Metab Eng 23 (2014), 62–69.
16. 16 Noda, S., Shirai, T., Oyama, S., Kondo, A., Metabolic design of a platform Escherichia coli strain producing various chorismate derivatives. Metab Eng 33 (2016), 119–129.
17. 17 Sengupta, S., Jonnalagadda, S., Goonewardena, L., Juturu, V., Metabolic engineering of a novel muconic acid biosynthesis pathway via 4-hydroxybenzoic acid in Escherichia coli. Appl Environ Microbiol 81 (2015), 8037–8043.
18. 18•• Vardon, D.R., Franden, M.A., Johnson, C.W., Karp, E.M., Guarnieri, M.T., Linger, J.G., Salm, M.J., Strathmann, T.J., Beckham, G.T., Adipic acid production from lignin. Energy Environ Sci 8 (2015), 617–628 The authors engineer Pseudomonas putida to produce muconic acid from model lignin monomers as well as from an alkaline pretreated biomass. The purification of muconic acid form the media and chemical hydrogenation of muconic acid to adipic acid is also demonstrated.
19. 19• Moon, T.S., Yoon, S.H., Lanza, A.M., Roy-Mayhew, J.D., Prather, K.L.J., Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl Environ Microbiol, 75, 2009, 4660 Seminal paper describing the engineering of a synthetic pathwya for the production of glucaric acid form glucose.
20. 20 Yu, J.L., Xia, X.X., Zhong, J.J., Qian, Z.G., Direct biosynthesis of adipic acid from a synthetic pathway in recombinant Escherichia coli. Biotechnol Bioeng 111 (2014), 2580–2586.
21. 21 Deng, Y., Mao, Y., Production of adipic acid by the native-occurring pathway in Thermobifida fusca B6. J Appl Microbiol 119 (2015), 1057–1063.
22. 22 Clomburg, J.M., Blankschien, M.D., Vick, J.E., Chou, A., Kim, S., Gonzalez, R., Integrated engineering of beta-oxidation reversal and omega-oxidation pathways for the synthesis of medium chain omega-functionalized carboxylic acids. Metab Eng 28 (2015), 202–212.
23. 23•• Cheong, S., Clomburg, J., Gonzalez, R., Energy- and carbon-efficient synthesis of functionalized small molecules in bacteria using non-decarboxylative Claisen condensation reactions. Nat Biotech 34 (2016), 556–561 The authors engineer a synthetic non-decarboxylative pathway for the production of various value-added chemicals. This route leads to the highest adipic acid titers from simple sugars to date.
24. 24 Rodriguez, A., Martinez, J.A., Flores, N., Escalante, A., Gosset, G., Bolivar, F., Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds. Microb Cell Fact, 13, 2014, 126.
25. 25• Niu, W., Draths, K.M., Frost, J.W., Benzene-free synthesis of adipic acid. Biotechnol Progr 18 (2002), 201–211 This work routes glucose via 3-dehydroshikimic acid to protocatechuic acid, catechol and ultimate muconic acid inE. coli to produce the highest titers of muconic acid to date.
26. 26 Weber, C., Bruckner, C., Weinreb, S., Lehr, C., Essl, C., Boles, E., Biosynthesis of cis,cis-muconic acid and its aromatic precursors, catechol and protocatechuic acid, from renewable feedstocks by Saccharomyces cerevisiae. Appl Environ Microbiol 78 (2012), 8421–8430.
27. 27• Curran, K.A., Leavitt, J.M., Karim, A.S., Alper, H.S., Metabolic engineering of muconic acid production in Saccharomyces cerevisiae. Metab Eng 15 (2013), 55–66 Latests engineering ofS. cerevisiae for the production of muconic acid. This work shows that extensive regulation of aromatic amino acid biosynthesis in this organism significantly hingers high muconic acid titers.
28. 28 Suastegui, M., Matthiesen, J.E., Carraher, J.M., Hernandez, N., Quiroz, N.R., Okerlund, A., Cochran, E.W., Shao, Z.Y., Tessonnier, J.P., Combining metabolic engineering and electrocatalysis: application to the production of polyamides from sugar. Angew Chem Int Ed 55 (2016), 2368–2373.
29. 29 Sun, X., Lin, Y., Qin, H., Qipeng, Y., Yan, Y., A novel muconic acid biosynthesis approach by shunting tryptophan biosynthesis via anthranilate. Appl Environ Microbiol 79 (2013), 4024–4030.
30. 30 Tepper, N., Shlomi, T., Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 26 (2010), 536–543.
31. 31 Lin, Y.H., Shen, X.L., Yuan, Q.P., Yan, Y.J., Microbial biosynthesis of the anticoagulant precursor 4-hydroxycoumarin. Nat Commun, 4, 2013, 2603.
32. 32 Linger, J.G., Vardon, D.R., Guarnieri, M.T., Karp, E.M., Hunsinger, G.B., Franden, M.A., Johnson, C.W., Chupka, G., Strathmann, T.J., Pienkos, P.T., et al. Lignin valorization through integrated biological funneling and chemical catalysis. Proc Natl Acad Sci U S A 111 (2014), 12013–12018.
33. 33 van Duuren, J.B.J.H., Wijte, D., Karge, B., Martins dos Santos, V.A.P., Yang, Y., Mars, A.E., Eggink, G., pH-stat fed-batch process to enhance the production of cis,cis-muconate from benzoate by Pseudomonas putida KT2440-JD1. Biotechnol Progr 28 (2012), 85–92.
34. 34 Johnson, C.W., Salvachúa, D., Khanna, P., Smith, H., Peterson, D.J., Beckham, G.T., Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity. Metab Eng Commun 3 (2016), 111–119.
35. 35 Han, L., Liu, P., Sun, J.X., Wu, Y.Q., Zhang, Y.Y., Chen, W.J., Lin, J.P., Wang, Q.H., Ma, Y.H., Engineering catechol 1,2-dioxygenase by design for improving the performance of the cis,cis-muconic acid synthetic pathway in Escherichia coli. Sci Rep, 5, 2015, 11.
36. 36 Lanza, A.M., Curran, K.A., Rey, L.G., Alper, H.S., A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae. BMC Syst Biol, 8, 2014, Artn 33.
37. 37 Sonoki, T., Morooka, M., Sakamoto, K., Otsuka, Y., Nakamura, M., Jellison, J., Goodell, B., Enhancement of protocatechuate decarboxylase activity for the effective production of muconate from lignin-related aromatic compounds. J Biotechnol 192 (2014), 71–77.
38. 38 Werpy T, Peterse G: In: N.R.E.L. and P.N.N.L. Top Value added chemicals from biomass, vol I: Results of screenign for potential cadidates from sugars and syntehsis gas, 2004.
39. 39 Moon, T.S., Dueber, J.E., Shiue, E., Prather, K.L.J., Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab Eng 12 (2010), 298–305.
40. 40 Shiue, E., Prather, K.L.J., Improving D-glucaric acid production from myo-inositol in E. coli by increasing MIOX stability and myo-inositol transport. Metab Eng 22 (2014), 22–31.
41. 41 Gupta, A., Reizman, I.M., Reisch, C.R., Prather, K.L., Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nat Biotechnol 35 (2017), 273–279.
42. 42 Schrewe, M., Julsing, M.K., Lange, K., Czarnotta, E., Schmid, A., Buhler, B., Reaction and catalyst engineering to exploit kinetically controlled whole-cell multistep biocatalysis for terminal FAME oxyfunctionalization. Biotechnol Bioeng 111 (2014), 1820–1830.
43. 43 Cheng, Q., Thomas, S.M., Kostichka, K., Valentine, J.R., Nagarajan, V., Genetic analysis of a gene cluster for cyclohexanol oxidation in Acinetobacter sp. strain SE19 by in vitro transposition. J Bacteriol 182 (2000), 4744–4751.
44. 44 Yu, J.L., Xia, X.X., Zhong, J.J., Qian, Z.G., Direct biosynthesis of adipic acid from a synthetic pathway in recombinant Escherichia coli. Biotechnol Bioeng 111 (2014), 2580–2586.
45. 45 Dekishima, Y., Lan, E.I., Shen, C.R., Cho, K.M., Liao, J.C., Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli. J Am Chem Soc 133 (2011), 11399–11401.
46. 46 Shen, C.R., Lan, E.I., Dekishima, Y., Baez, A., Cho, K.M., Liao, J.C., Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microb 77 (2011), 2905–2915.
47. 47 Zhang, H., Li, Z., Pereira, B., Stephanopoulos, G., Engineering E. coli-E. coli cocultures for production of muconic acid from glycerol. Microb Cell Fact, 14, 2015, 134.
48. 48•• Zhang, H.R., Pereira, B., Li, Z.J., Stephanopoulos, G., Engineering Escherichia coli coculture systems for the production of biochemical products. Proc Natl Acad Sci U S A 112 (2015), 8266–8271 The authors use an E. coli co-culture strategy to split the muconic acid pathway to achieve not only high muconic acid titers, but also to enable the production of muconic acid form glucose and xylose simmultanously.
49. 49 Schellenberger, J., Que, R., Fleming, R.M.T., Thiele, I., Orth, J.D., Feist, A.M., Zielinski, D.C., Bordbar, A., Lewis, N.E., Rahmanian, S., Kang, J., Hyduke, D.R., Palsson, B.O., Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6 (2011), 1290–1307.
50. 50 Feist, A.M., Zielinski, D.C., Orth, J.D., Schellenberger, J., Herrgard, M.J., Palsson, B.O., Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 12 (2010), 173–186.
51. 51 Nogales, J., Palsson, B.O., Thiele, I., A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol, 2, 2008, Artn 79.
52. 52 Mo, M.L., Palsson, B.O., Herrgard, M.J., Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol, 3, 2009, Artn 37.