Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin

Metabolic Engineering

Volumn 28, Issue , 2015, Pages 240-247

  Johnson, Christopher W ^a   Beckham, Gregg T ^a  

^a NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

Author keywords

Aromatic degradation; Lignin valorization; Pseudomonas putida KT2440; Sphingobium sp. strain SYK 6; ketoadipate pathway

Indexed keywords

AROMATIC COMPOUNDS; AROMATIZATION; BACTERIA; BIODEGRADATION; CARBON; MOLECULES; PHENOLS; STRAIN;

DEGRADATION PATHWAYS; DIOXYGENASE ENZYMES; META-CLEAVAGE PATHWAY; OPTIMAL PRODUCTION; PSEUDOMONAS PUTIDA; PYRUVATE PRODUCTION; SPHINGOBIUM; TECHNICAL DEVELOPMENT;

LIGNIN;

PSEUDOMONAS PUTIDA; SPHINGOBIUM;

LACTIC ACID; LIGNIN; PYRUVIC ACID;

BIOSYNTHESIS; GENETICS; METABOLIC ENGINEERING; METABOLISM; PSEUDOMONAS PUTIDA;

LACTIC ACID; LIGNIN; METABOLIC ENGINEERING; PSEUDOMONAS PUTIDA; PYRUVIC ACID;

EID: 84930198715     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2015.01.005     Document Type: Article

References (64)

1. Bagdasarian M.M., Amann E., Lurz R., Rückert B., Bagdasarian M. Activity of the hybrid trp-lac (tac) promoter of Escherichia coli in Pseudomonas putida. Construction of broad-host-range, controlled-expression vectors. Gene 1983, 26:273-282.
2. Berríos-Rivera S. Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD+-dependent formate dehydrogenase. Metab. Eng. 2002, 4:217-229.
3. Branduardi P., Sauer M., De Gioia L., Zampella G., Valli M., Mattanovich D., Porro D. Lactate production yield from engineered yeasts is dependent from the host background, the lactate dehydrogenase source and the lactate export. Microb. Cell Fact. 2006, 5:4.
4. Bugg T.D.H., Ahmad M., Hardiman E.M., Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat. Prod. Rep. 2011, 28:1883-1896.
5. Bugg T.D.H., Ahmad M., Hardiman E.M., Singh R. The emerging role for bacteria in lignin degradation and bio-product formation. Curr. Opin. Biotechnol 2011, 22:394-400.
6. Chandran S.S., Kealey J.T., Reeves C.D. Microbial production of isoprenoids. Process Biochem. 2011, 46:1703-1710.
7. Chundawat S.P.S., Beckham G.T., Himmel M.E., Dale B.E. Deconstruction of lignocellulosic biomass to fuels and chemicals. Annu. Rev. Chem. Biomol. Eng. 2011, 2:121-145.
8. Clark T.J., Phillips R.S., Bundy B.M., Momany C., Neidle E.L. Benzoate decreases the binding of cis,cis-Muconate to the BenM regulator despite the synergistic effect of both compounds on transcriptional activation. J. Bacteriol. 2004, 186:1200-1204.
9. Cosper N.J., Collier L.S., Clark T.J., Scott R.A., Neidle E.L. Mutations in catB, the gene encoding muconate cycloisomerase, activate transcription of the distal ben genes and contribute to a complex regulatory circuit in Acinetobacter sp. strain ADP1. J. Bacteriol. 2000, 182:7044-7052.
10. Crawford R.L. Novel pathway for degradation of protocatechuic acid in Bacillus species. J. Bacteriol. 1975, 121:531-536.
11. 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.
12. Dagley S., Evans W.C., Ribbons D.W. New pathways in the oxidative metabolism of aromatic compounds by microorganisms. Nature 1960, 188:560-566.
13. Dagley S., Gibson D.T. The bacterial degradation of catechol. Biochem. J. 1965, 95:466-474.
14. Davis R., Tao L., Tan E.C.D., Biddy M.J., Beckham G.T., Scarlata C., Jacobson J., Cafferty K., Ross J., Lukas J., Knorr D., Schoen P. Process Design and Economics for the Conversion of Lignocellulosic Biomass to Hydrocarbons: Dilute-Acid and Enzymatic Deconstruction of Biomass to Sugars and Biological Conversion of Sugars to Hydrocarbons. Technical Report 2013, 88-101. NREL/TP-5100-60223, National Renewable Energy Laboratory, Golden, CO.
15. 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.
16. Draths K.M., Frost J.W. Environmentally compatible synthesis of adipic acid from d-glucose. J. Am. Chem. Soc. 1994, 116:399-400.
17. Escapa I.F., Garcia J.L., Bühler B., Blank L.M., Prieto M.A. The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida. Environ. Microbiol. 2012, 14:1049-1063.
18. Eschbach M., Schreiber K., Trunk K., Buer J., Jahn D., Schobert M. Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J. Bacteriol. 2004, 186:4596-4604.
19. Feist C.F., Hegeman G.D. Phenol and benzoate metabolism by Pseudomonas putida: regulation of tangential pathways. J. Bacteriol. 1969, 100:869-877.
20. Feist C.F., Hegeman G.D. Regulation of the meta cleavage pathway for benzoate oxidation by Pseudomonas putida. J. Bacteriol. 1969, 100:1121-1123.
21. Fuchs G., Boll M., Heider J. Microbial degradation of aromatic compounds-from one strategy to four. Nat. Rev. Microbiol. 2011, 9:803-816.
22. Garvie E.I. Bacterial lactate dehydrogenases. Microbiol. Rev. 1980, 44:106-139.
23. Greated A., Lambertsen L., Williams P.A., Thomas C.M. Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ. Microbiol. 2002, 4:856-871.
24. Hara H., Masai E., Miyauchi K., Katayama Y., Fukuda M. Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4, 5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6. J. Bacteriol. 2003, 185:41-50.
25. Harayama S., Rekik M. The meta cleavage operon of TOL degradative plasmid pWW0 comprises 13 genes. Mol. Gen. Genet. 1990, 221:113-120.
26. Harwood C.S., Parales R.E. The beta-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 1996, 50:553-590.
27. Hegeman G.D. Synthesis of the enzymes of the mandelate pathway by Pseudomonas putida. I. Synthesis of enzymes by the wild type. J. Bacteriol. 1966, 91:1140-1154.
28. Holbrook J.J., Liljas A., Steindel S.J., Rossmann M.G. Lactate dehydrogenase. The Enzymes 3rd Ed. 11 1975, Academic Press, New York, 191-292.
29. Jiang G.R., Nikolova S., Clark D.P. Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli. Microbiology (Reading, England) 2001, 147:2437-2446.
30. 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.
31. Kamimura N., Aoyama T., Yoshida R., Takahashi K., Kasai D., Abe T., Mase K., Katayama Y., Fukuda M., Masai E. Characterization of the protocatechuate 4,5-cleavage pathway operon in Comamonas sp. Strain E6 and discovery of a novel pathway gene. Appl. Environ. Microbiol. 2010, 76:8093-8101.
32. Kamimura N., Masai E. The protocatechuate 4, 5-cleavage pathway: overview and new findings. Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve 2014, 207-226. Biodegradative Bacteria. H. Nojiri, M. Tsuda, M. Fukuda, Y. Kamagata (Eds.).
33. Kasai D., Fujinami T., Abe T., Mase K., Katayama Y., Fukuda M., Masai E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J. Bacteriol. 2009, 191:6758-6768.
34. Kolb E., Fleisher G.A., Larner J. Isolation and characterization of bovine lactate dehydrogenase X. Biochemistry 1970, 9:4372-4380.
35. Lamsen E.N., Atsumi S. Recent progress in synthetic biology for microbial production of C3-C10 alcohols. Front Microbiol. 2012, 3.
36. Lee M., Smith G.M., Eiteman M.A., Altman E. Aerobic production of alanine by Escherichia coli aceF ldhA mutants expressing the Bacillus sphaericus alaD gene. Appl. Microbiol. Biotechnol. 2004, 65:56-60.
37. 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. 2014, 23:62-69.
38. 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. Lignin valorization through integrated biological funneling and chemical catalysis. Proc. Natl. Acad. Sci. 2014, 111:12013-12018.
39. Martínez A.T., Speranza M., Ruiz-Dueñas F.J., Ferreira P., Camarero S., Guillén F., Martínez M.J., Gutiérrez A., del Río J.C. Biodegradation of lignocellulosics: microbial, chemical, and enzymatic aspects of the fungal attack of lignin. Int. Microbiol. 2005, 8:195-204.
40. Marx C.J. Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Res. Notes 2008, 1:1.
41. 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.
42. Nikel P.I., de Lorenzo V. Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene. Metab. Eng. 2013, 15:98-112.
43. Nikel P.I., Martínez-García E., de Lorenzo V. Biotechnological domestication of pseudomonads using synthetic biology. Nat. Rev. Microbiol. 2014, 12:368-379.
44. Noda Y., Nishikawa S., Shiozuka K., Kadokura H., Nakajima H., Yoda K., Katayama Y., Morohoshi N., Haraguchi T., Yamasaki M. Molecular cloning of the protocatechuate 4, 5-dioxygenase genes of Pseudomonas paucimobilis. J. Bacteriol. 1990, 172:2704-2709.
45. Ornston L.N. The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida. IV. Regulation. J. Biol. Chem. 1966, 241:3800-3810.
46. 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.
47. 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. USA 2007, 104:7797-7802.
48. Pérez-Pantoja D., González B., Pieper D.H. Aerobic degradation of aromatic hydrocarbons. Handbook of Hydrocarbon and Lipid Microbiology 2010, 799-837. Springer, Berlin Heidelberg, Berlin, Heidelberg.
49. Phale P.S., Basu A., Majhi P.D., Deveryshetty J., Vamsee-Krishna C., Shrivastava R. Metabolic diversity in bacterial degradation of aromatic compounds. OMICS 2007, 11:252-279.
50. Poblete-Castro I., Binger D., Rodrigues A., Becker J., Martins dos Santos V.A.P., Wittmann C. In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates. Metab. Eng. 2013, 15:113-123.
51. Porro D., Brambilla L., Ranzi B.M., Martegani E., Alberghina L. Development of metabolically engineered Saccharomyces cerevisiae cells for the production of lactic acid. Biotechnol. Prog. 1995, 11:294-298.
52. Ragauskas A.J., Beckham G.T., Biddy M.J., Chandra R., Chen F., Davis M.F., Davison B.H., Dixon R.A., Gilna P., Keller M., Langan P., Naskar A.K., Saddler J.N., Tschaplinski T.J., Tuskan G.A., Wyman C.E. Lignin valorization: improving lignin processing in the biorefinery. Science 2014, 344:1246843.
53. Regenhardt D., Heuer H., Heim S., Fernandez D.U., Strompl C., Moore E., Timmis K.N. Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ. Microbiol. 2002, 4:912-915.
54. Taguchi H., Ohta T. d-lactate dehydrogenase is a member of the d-isomer-specific 2-hydroxyacid dehydrogenase family. Cloning, sequencing, and expression in Escherichia coli of the d-lactate dehydrogenase gene of Lactobacillus plantarum. J. Biol. Chem. 1991, 266:12588-12594.
55. Tarmy E.M., Kaplan N.O. Chemical characterization of d-lactate dehydrogenase from Escherichia coli B. J. Biol. Chem. 1968, 243:2579-2586.
56. Tomar A., Eiteman M.A., Altman E. The effect of acetate pathway mutations on the production of pyruvate in Escherichia coli. Appl. Microbiol. Biotechnol. 2003, 62:76-82.
57. 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 and Environmental Science 2015, 8:617-628.
58. van Duuren J.B.J.H., Wijte D., Karge B., Santos dos V.A.P.M., 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. Prog. 2012, 28:85-92. 10.1002/btpr.709.
59. van Duuren J.B.J.H., Wijte D., Leprince A., Karge B., Puchałka J., Wery J., Santos dos V.A.P.M., Eggink G., Mars A.E. Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield. J. Biotechnol. 2011, 156:163-172.
60. 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.
61. Williams P.A., Sayers J.R. The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 1994, 5:195-217.
62. Zakzeski J., Bruijnincx P.C.A., Jongerius A.L., Weckhuysen B.M. The catalytic valorization of lignin for the production of renewable chemicals. Chem. Rev. 2010, 110:3552-3599.
63. Zhao Y., Yang J., Qin B., Li Y., Sun Y., Su S., Xian M. Biosynthesis of isoprene in Escherichia coli via methylerythritol phosphate (MEP) pathway. Appl. Microbiol. Biotechnol. 2011, 90:1915-1922.
64. Zhu J., Shimizu K. The effect of pfl gene knockout on the metabolism for optically pure d-lactate production by Escherichia coli. Appl. Microbiol. Biotechnol. 2004, 64:367-375.