Characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathway

Microbial Biotechnology

Volumn 8, Issue 4, 2015, Pages 633-643

  Pick, André ^a   Schmid, Jochen ^a   Sieber, Volker ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GALACTURONIC ACID; GLUCURONIC ACID; MANNURONATE; OXIDOREDUCTASE; POLYSACCHARIDE; POTASSIUM DIHYDROGEN PHOSPHATE; TROMETAMOL; UNCLASSIFIED DRUG; URONATE DEHYDROGENASE; ALDEHYDE DEHYDROGENASE; BACTERIAL DNA; BUFFER;

AGROBACTERIUM TUMEFACIENS; ARTICLE; BACTERIAL GENE; ENZYME ACTIVITY; ENZYME DEGRADATION; ENZYME KINETICS; ENZYME SPECIFICITY; ENZYME STABILITY; NONHUMAN; OCEANICOLA GRANULOSUS; OXIDATIVE DEHYDROGENATION; PH; PROTEIN EXPRESSION; RHODOBACTERACEAE; SEQUENCE ANALYSIS; STREPTOMYCES VIRIDOCHROMOGENES; TEMPERATURE; ALPHAPROTEOBACTERIA; CHEMISTRY; COMPARATIVE STUDY; DNA SEQUENCE; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MOLECULAR GENETICS; PSEUDOMONAS SYRINGAE; STREPTOMYCES;

AGROBACTERIUM TUMEFACIENS; FULVIMARINA; OCEANICOLA; PSEUDOMONAS SYRINGAE; STREPTOMYCES;

ALDEHYDE OXIDOREDUCTASES; ALPHAPROTEOBACTERIA; BUFFERS; DNA, BACTERIAL; ENZYME STABILITY; HYDROGEN-ION CONCENTRATION; KINETICS; MOLECULAR SEQUENCE DATA; PSEUDOMONAS SYRINGAE; SEQUENCE ANALYSIS, DNA; STREPTOMYCES; SUBSTRATE SPECIFICITY; TEMPERATURE;

EID: 84930866517     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/1751-7915.12265     Document Type: Article

References (42)

1. Ahn, J.-W., Lee, S.Y., Kim, S., Cho, S.J., Lee, S.B., and Kim, K.-J. (2011) Cloning, expression, purification, crystallization and X-ray crystallographic analysis of glucuronic acid dehydrogenase from Chromohalobacter salexigens. Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 689-691.
2. Ahn, J.-W., Lee, S.Y., Kim, S., Kim, S.M., Lee, S.B., and Kim, K.-J. (2012) Crystal structure of glucuronic acid dehydrogeanse from Chromohalobacter salexigens. Proteins 80: 314-318.
3. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
4. Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., etal. (2012) ExPASy: SIB bioinformatics resource portal, Nucleic Acids Res. 40: W597-W603.
5. Ashwell, G., Wahba, A.J., and Hickman, J. (1958) A new pathway of uronic acid metabolism. Biochim Biophys Acta 30: 186-187.
6. Bateman, D.F., Kosuge, T., and Kilgore, W.W. (1970) Purification and properties of uronate dehydrogenase from Pseudomonas syringae. Arch Biochem Biophys 136: 97-105.
7. Carvalheiro, F., Duarte, L.C., and Girio, F.M. (2008) Hemicellulose biorefineries: a review on biomass pretreatments. J Sci Ind Res 67: 849-864.
8. Chang, Y.F., and Feingold, D.S. (1970) D-glucaric acid and galactaric acid catabolism by Agrobacterium tumefaciens. J Bacteriol 102: 85-96.
9. Chen, W.P., and Kuo, T.T. (1993) A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res 21: 2260.
10. Farmer, J.J., and Eagon, R.G. (1969) Aldohexuronic acid catabolism by a soil aeromonas. J Bacteriol 97: 97-106.
11. Grohmann, K., Manthey, J.A., Cameron, R.G., and Buslig, B.S. (1998) Fermentation of galacturonic acid and pectin-rich materials to ethanol by genetically modified strains of Erwinia. Biotechnol Lett 20: 195-200.
12. Guéraud, F., and Paris, A. (1998) Glucuronidation: a dual control. Vascul Pharmacol 31: 683-688.
13. Guterl, J.-K., Garbe, D., Carsten, J., Steffler, F., Sommer, B., Reiße, S., etal. (2012) Cell-free metabolic engineering: production of chemicals by minimized reaction cascades. ChemSusChem 5: 2165-2172.
14. Jörnvall, H., von Bahr-Lindström, H., Jany, K.-D., Ulmer, W., and Fröschle, M. (1984) Extended superfamily of short alcohol-polyol-sugar dehydrogenases: structural similarities between glucose and ribitol dehydrogenases. FEBS Lett 165: 190-196.
15. Jung, K.A., Lim, S.-R., Kim, Y., and Park, J.M. (2012) Potentials of macroalgae as feedstocks for biorefinery. Bioresour Technol 135: 182-190.
16. Kelley, L.A., and Sternberg, M.J.E. (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4: 363-371.
17. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685.
18. Lahaye, M., and Robic, A. (2007) Structure and functional properties of Ulvan, a polysaccharide from green seaweeds. Biomacromolecules 8: 1765-1774.
19. Laskowski, R.A., and Swindells, M.B. (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51: 2778-2786.
20. Linster, C.L., and Van Schaftingen, E. (2007) Vitamin C. FEBS J 274: 1-22.
21. McRorie, R.A., and Novelli, G.D. (1958) Glucuronate metabolism by Aerobacter aerogenes. Nature 182: 1504-1505.
22. Mojzita, D., Wiebe, M., Hilditch, S., Boer, H., Penttila, M., and Richard, P. (2010) Metabolic engineering of fungal strains for conversion of D-galacturonate to meso-galactarate. Appl Environ Microbiol 76: 169-175.
23. Moon, T.S., Yoon, S.-H., Lanza, A.M., Roy-Mayhew, J.D., and Prather, K.L.J. (2009) Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli. Appl Environ Microbiol 75: 589-595.
24. Mulder, G.J. (1992) Glucuronidation and its role in regulation of biological activity of drugs. Annu Rev Pharmacol Toxicol 32: 25-49.
25. Parkkinen, T., Boer, H., Janis, J., Andberg, M., Penttila, M., Koivula, A., and Rouvinen, J. (2011) Crystal structure of uronate dehydrogenase from Agrobacterium tumefaciens. J Biol Chem 286: 27294-27300.
26. Persson, B., Kallberg, Y., Oppermann, U., and Jörnvall, H. (2003) Coenzyme-based functional assignments of short-chain dehydrogenases/reductases (SDRs). Chem Biol Interact 143-144: 271-278.
27. Richard, P., and Hilditch, S. (2009) D-galacturonic acid catabolism in microorganisms and its biotechnological relevance. Appl Microbiol Biotechnol 82: 597-604.
28. Saha, B.C. (2003) Hemicellulose bioconversion. J Ind Microbiol Biotechnol 30: 279-291.
29. Saha, S.K., Uma, L., and Subramanian, G. (2005) An improved method for marine cyanobacterial DNA isolation. World J Microbiol Biotechnol 21: 877-881.
30. Schrodinger, L.L.C. (2010) The PyMOL molecular graphics system, version 1.3r1.
31. Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W., etal. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539.
32. Spoehr, H.A. (1947) The hydrolysis of alginic acid with formic acid. Arch Biochem 14: 153-155.
33. Stephens, C., Christen, B., Fuchs, T., Sundaram, V., Watanabe, K., and Jenal, U. (2007) Genetic analysis of a novel pathway for D-xylose metabolism in Caulobacter crescentus. J Bacteriol 189: 2181-2185.
34. Studier, F.W. (2005) Protein production by auto-induction in high-density shaking cultures. Protein Expr Purif 41: 207-234.
35. Sutherland, I.W. (2001) Biofilm exopolysaccharides: a strong and sticky framework. Microbiology 147: 3-9.
36. Wagner, G., and Hollmann, S. (1976) Uronic acid dehydrogenase from Pseudomonas Syringae - purification and properties. Eur J Biochem 61: 589-596.
37. Wass, M.N., Kelley, L.A., and Sternberg, M.J.E. (2010) 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res 38: W469-W473.
38. Watanabe, S., Kodaki, T., and Makino, K. (2006a) A novel α-ketoglutaric semialdehyde dehydrogenase: evolutionary insight into an alternative pathway of bacterial l-arabinose metabolism. J Biol Chem 281: 28876-28888.
39. Watanabe, S., Shimada, N., Tajima, K., Kodaki, T., and Makino, K. (2006b) Identification and characterization of L-arabonate dehydratase, l-2-keto-3-deoxyarabonate dehydratase, and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism. J Biol Chem 281: 33521-33536.
40. Werpy, T.A., Holladay, J.E., and White, J.F. (2004) Top value added chemicals from biomass: I. Results of screening for potential candidates from sugars and synthesis gas. Pacific Northwest National Laboratory (PNNL) and National Renewable Energy Laboratory (NREL). 1-477.
41. Yoon, S.-H., Moon, T.S., Iranpour, P., Lanza, A.M., and Prather, K.J. (2009) Cloning and characterization of uronate dehydrogenases from two Pseudomonads and Agrobacterium tumefaciens strain C58. J Bacteriol 191: 1565-1573.
42. Zajic, J.E. (1959) Hexuronic dehydrogenase of Agrobacterium tumefaciens. J Bacteriol 78: 734-735.