Enhancing muconic acid production from glucose and lignin-derived aromatic compounds via increased protocatechuate decarboxylase activity

Metabolic Engineering Communications

Volumn 3, Issue , 2016, Pages 111-119

  Johnson, Christopher W ^a   Salvachúa, Davinia ^a   Khanna, Payal ^a   Smith, Holly ^a   Peterson, Darren J ^a   Beckham, Gregg T ^a  

^a NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

Author keywords

Cis,cis Muconate; Lignin valorization; Muconic acid; Protocatechuate decarboxylase; Pseudomonas Putida KT2440

Indexed keywords

AROMATIC COMPOUND; CARBOXYLYASE; CATECHOL; DISSOLVED OXYGEN; GLUCOSE; LIGNIN; MUCONIC ACID; PROTOCATECHUIC ACID;

ARTICLE; BACILLUS CEREUS; BACTERIAL STRAIN; BIOMASS PRODUCTION; BIOREACTOR; CATA GENE; ELECTROPORATION; ENTEROBACTER CLOACAE; GENE; GENE EXPRESSION; GENOTYPE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PRODUCTIVITY; PSEUDOMONAS PUTIDA;

EID: 84964949918     PISSN: None     EISSN: 22140301     Source Type: Journal    
DOI: 10.1016/j.meteno.2016.04.002     Document Type: Article

References (46)

1. Beckham G.T., Johnson C.W., Karp E.M., Salvachúa D., Vardon D.R. Opportunities and challenges in biological lignin valorization. Curr. Opin. Biotechnol. 2016, 42:40-53. 10.1016/j.copbio.2016.02.030.
2. Belda E., van Heck R.G.A., Lopez-Sanchez M.J., Cruveiller S., Barbe V., Fraser C., Klenk H.-P., Petersen J., Morgat A., Nikel P.I., Vallenet D., Rouy Z., Sekowska A., Martins dos Santos V.A.P., de Lorenzo V., Danchin A., Médigue C. The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis. Environ. Microbiol. 2016, 10.1111/1462-2920.13230.
3. Borujeni A.E., Channarasappa A.S., Salis H.M. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids 2013, 10.1093/nar/gkt1139/-/DC1.
4. Chavarría M., Nikel P.I., Pérez-Pantoja D., de Lorenzo V. The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ. Microbiol. 2013, 15:1772-1785. 10.1111/1462-2920.12069.
5. Choi K.-H., Kumar A., Schweizer H.P. A 10-min method for preparation of highly electrocompetent Pseudomonas aeruginosa cells: Application for DNA fragment transfer between chromosomes and plasmid transformation. J. Microbiol. Methods 2006, 64:391-397. 10.1016/j.mimet.2005.06.001.
6. Chow K.T., Pope M.K., Davies J. Characterization of a vanillic acid non-oxidative decarboxylation gene cluster from Streptomyces sp. D7. Microbiology 1999, 145:2393-2403.
7. Curran K.A., Leavitt J.M., Karim A.S., Alper H.S. Metabolic engineering of muconic acid production in Saccharomyces cerevisiae. Metab. Eng. 2013, 15:55-66. 10.1016/j.ymben.2012.10.003.
8. del Castillo T., Ramos J.L., Rodriguez-Herva J.J., Fuhrer T., Sauer U., Duque E. Convergent peripheral pathways catalyze initial glucose catabolism in pseudomonas putida: genomic and flux analysis. J. Bacteriol. 2007, 189:5142-5152. 10.1128/JB.00203-07.
9. Deng Y., Ma L., Mao Y. Biological production of adipic acid from renewable substrates: Current and future methods. Biochem. Eng. J. 2016, 105:16-26. 10.1016/j.bej.2015.08.015.
10. Draths K.M., Frost J.W. Environmentally compatible synthesis of adipic acid from D-glucose. J. Am. Chem. Soc. 1994, 116:399-400.
11. Fox, D.T., Hotta, K., Kim, C.-Y., Koppisch, A.T., 2008. The Missing Link in Petrobactin Biosynthesis: asbF Encodes a (-)-3-Dehydroshikimate Dehydratase. Biochemistry 47, 12251-12253. http://dx.doi.org/:10.1021/bi801876q.
12. Harwood C.S., Parales R.E. The beta-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 1996, 50:553-590. 10.1146/annurev.micro.50.1.553.
13. He Z., Wiegel J. Purification and characterization of an oxygen-sensitive, reversible 3,4-dihydroxybenzoate decarboxylase from Clostridium hydroxybenzoicum. J. Bacteriol. 1996, 178:3539-3543.
14. Jiménez, J.I., Nogales, J., García, J.L., Díaz, E., 2010. A Genomic View of the Catabolism of Aromatic Compounds in Pseudomonas, in: Handbook of Hydrocarbon and Lipid Microbiology. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 1297-1325. doi:10.1007/978-3-540-77587-4_91.
15. Jiménez J.I., Miñambres B., García J.L., Díaz E. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol. 2002, 4:824-841.
16. Johnson C.W., Beckham G.T. Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin. Metab. Eng. 2015, 28:240-247. 10.1016/j.ymben.2015.01.005.
17. Jung H.-M., Jung M.-Y., Oh M.-K. Metabolic engineering of Klebsiella pneumoniae for the production of cis,cis-muconic acid. Appl. Microbiol. Biotechnol. 2015, 10.1007/s00253-015-6442-3.
18. Karp E.M., Donohoe B.S., O'Brien M.H., Ciesielski P.N., Mittal A., Biddy M.J., Beckham G.T. Alkaline Pretreatment of Corn Stover: Bench-Scale Fractionation and Stream Characterization. ACS Sustain. Chem. Eng. 2014, 2:1481-1491. 10.1021/sc500126u.
19. Karp E.M., Resch M.G., Donohoe B.S., Ciesielski P.N., O'Brien M.H., Nill J.E., Mittal A., Biddy M.J., Beckham G.T. Alkaline pretreatment of switchgrass. ACS Sustain. Chem. Eng. 2015, 3:1479-1491. 10.1021/acssuschemeng.5b00201.
20. Katahira R., Mittal A., McKinney K., Chen X. Base-catalyzed depolymerization of biorefinery lignins. ACS Sustain Chem. Eng. 2016, 5:b01451. 10.1021/acssuschemeng.5b01451.
21. Kruger J.S., Cleveland N.S., Zhang S., Katahira R., Black B.A., Chupka G.M., Lammens T., Hamilton P.G., Biddy M.J., Beckham G.T. Lignin Depolymerization with Nitrate-Intercalated Hydrotalcite. Catal. ACS Catal. 2016, 1316-1328. 10.1021/acscatal.5b02062.
22. Lin, F., Ferguson, K.L., Boyer, D.R., Lin, X.N., Marsh, E.N.G., 2015. Isofunctional Enzymes PAD1 and UbiX Catalyze Formation of a Novel Cofactor Required by Ferulic Acid Decarboxylase and 4-Hydroxy-3-polyprenylbenzoic Acid Decarboxylase. ACS Chem. Biol. 10, 1137-1144. doi:10.1021/cb5008103.
23. 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., Beckham, G.T., 2014. Lignin valorization through integrated biological funneling and chemical catalysis. Proceedings of the National Academy of Sciences 111, 12013-12018. doi:10.1073/pnas.1410657111.
24. Lu R., Lu F., Chen J., Yu W., Huang Q., Zhang J., Xu J. Production of diethyl terephthalate from biomass-derived muconic acid. Angew. Chem. Int. Ed. 2015, 55:249-253. 10.1002/anie.201509149.
25. Lupa B., Lyon D., Gibbs M.D., Reeves R.A., Wiegel J. Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases. Genomics 2005, 86:342-351. 10.1016/j.ygeno.2005.05.002.
26. Lupa B., Lyon D., Shaw L.N., Sieprawska-Lupa M., Wiegel J. Properties of the reversible nonoxidative vanillate /4-hydroxybenzoate decarboxylase from Bacillus subtilis. Can. J. Microbiol. 2008, 54:75-81. 10.1139/W07-113.
27. Marx C.J. Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Res. Notes 2008, 1:1. 10.1186/1756-0500-1-1.
28. Matsui T., Yoshida T., Hayashi T., Nagasawa T. Purification, characterization, and gene cloning of 4-hydroxybenzoate decarboxylase of Enterobacter cloacae P240. Arch. Microbiol. 2006, 186:21-29. 10.1007/s00203-006-0117-5.
29. Nicolaou S.A., Gaida S.M., Papoutsakis E.T. A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing From biofuels and chemicals, to biocatalysis and bioremediation. Metab. Eng. 2010, 12:307-331. 10.1016/j.ymben.2010.03.004.
30. Nikel P.I., Chavarría M., Fuhrer T., Sauer U., de Lorenzo V. Pseudomonas putida KT2440 strain metabolizes glucose through a cycle formed by enzymes of the entner-doudoroff, embden-meyerhof-parnas, and pentose phosphate pathways. J. Biol. Chem. 2015, 290:25920-25932. 10.1074/jbc.M115.687749.
31. Nikel P.I., Martínez-García E., de Lorenzo V. Biotechnological domestication of pseudomonads using synthetic biology. Nat. Rev. Microbiol. 2014, 12:368-379. 10.1038/nrmicro3253.
32. Niu W., Draths K.M., Frost J.W. Benzene-free synthesis of adipic acid. Biotechnol. Prog. 2002, 18:201-211. 10.1021/bp010179x.
33. Ornston L.N., Stanier R.Y. The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida. J. Biol. Chem. 1966, 241:3776-3786.
34. Payne K.A.P., White M.D., Fisher K., Khara B., Bailey S.S., Parker D., Rattray N.J.W., Trivedi D.K., Goodacre R., Beveridge R., Barran P., Rigby S.E.J., Scrutton N.S., Hay S., Leys D. New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature 2015, 522:497-501. 10.1038/nature14560.
35. Polen T., Spelberg M., Bott M. Toward biotechnological production of adipic acid and precursors from biorenewables. J. Biotechnol. 2013, 167:75-84. 10.1016/j.jbiotec.2012.07.008.
36. Rojo F. Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol. Rev. 2010, 1-27. 10.1111/j.1574-6976.2010.00218.x.
37. Salis H.M., Mirsky E.A., Voigt C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Publ. Group 2009, 27:946-950. 10.1038/nbt.1568.
38. Salvachúa D., Karp E.M., Nimlos C.T., Vardon D.R., Beckham G.T. Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria. Green Chem. 2015, 17:4951-4967. 10.1039/C5GC01165E.
39. 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. 2014, 192:71-77. 10.1016/j.jbiotec.2014.10.027.
40. Van de Vyver S., Román-Leshkov Y. Emerging catalytic processes for the production of adipic acid. Catal. Sci. Technol. 2013, 3:1465-1479. 10.1039/C3CY20728E.
41. 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. 2015, 8:617-628. 10.1039/C4EE03230F.
42. Vardon D.R., Rorrer N.A., Salvachúa D., Settle A.E., Johnson C.W., Menart M.J., Cleveland N.S., Ciesielski P.N., Steirer K.X., Dorgan J.R., Beckham G.T. cis,cis-Muconic acid: separation and catalysis to bio-adipic acid for nylon-6,6 polymerization. Green. Chem. 2016, 1-17. 10.1039/C5GC02844B.
43. Weber C., Brückner 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. 2012, 78:8421-8430. 10.1128/AEM.01983-12.
44. White M.D., Payne K.A.P., Fisher K., Marshall S.A., Parker D., Rattray N.J.W., Trivedi D.K., Goodacre R., Rigby S.E.J., Scrutton N.S., Hay S., Leys D. UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis. Nature 2015, 522:502-506. 10.1038/nature14559.
45. Xie N.-Z., Liang H., Huang R.-B., Xu P. Biotechnological production of muconic acid: current status and future prospects. Biotechnol. Adv. 2014, 32:615-622. 10.1016/j.biotechadv.2014.04.001.
46. Yoshida T., Inami Y., Matsui T., Nagasawa T. Regioselective carboxylation of catechol by 3,4-dihydroxybenzoate decarboxylase of Enterobacter cloacae P. Biotechnol. Lett. 2010, 32:701-705. 10.1007/s10529-010-0210-3.