Biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from Sphingomonas sp. strain 113P3

Microbiology

Volumn 151, Issue 4, 2005, Pages 1255-1262

  Klomklang, Wilailak ^a   Tani, Akio ^a   Kimbara, Kazuhide ^a   Mamoto, Rie ^b   Ueda, Takashi ^b   Shimao, Masayuki ^c   Kawai, Fusako ^a  

^a OKAYAMA UNIVERSITY   (Japan)

^b KOBE GAKUIN UNIVERSITY   (Japan)

^c TOTTORI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID DERIVATIVE; ALCOHOL DEHYDROGENASE; AMINO ACID; DIKETONE; GLYCINE; HYDROLASE; MERCURY; POLYVINYL ALCOHOL; SERINE; SERINE DEHYDRATASE; SIGNAL PEPTIDE; TRIACYLGLYCEROL LIPASE; ZINC ION;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL STRAIN; CYTOPLASM; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME PURIFICATION; ENZYME SUBUNIT; ESCHERICHIA COLI; GENE EXPRESSION; HYDROLYSIS; MESORHIZOBIUM; MOLECULAR CLONING; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOMONAS; RHIZOBIUM; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SINORHIZOBIUM MELILOTI; SPHINGOMONAS;

ALCOHOL OXIDOREDUCTASES; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; CARBOXYLIC ESTER HYDROLASES; CLONING, MOLECULAR; DNA, BACTERIAL; GENES, BACTERIAL; KINETICS; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PERIPLASM; PROTEIN SUBUNITS; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SPHINGOMONAS;

ESCHERICHIA COLI; MESORHIZOBIUM LOTI; POTATO VIRUS A; PSEUDOMONAS; PSEUDOMONAS SP.; PSEUDOMONAS SP. 113; RHIZOBIUM SP.; SINORHIZOBIUM MELILOTI; SPHINGOMONAS SP.;

EID: 17644394208     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.27655-0     Document Type: Article

References (43)

1. Aebersold, R. M., Leavitt, J., Saavedra, R. A. & Hood, L. E. (1987). Internal amino acid sequence analysis of proteins separated by one-or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose. Proc Natl Acad Sci U S A 84 6970-6974.
2. Anraku, Y. & Heppel, L. A. (1967). On the nature of the changes induced in Escherichia coli by osmotic shock. J Biol Chem 242, 2561-2569.
3. Bergmeyer, H. U., Gowehn, K. & Grassl, M. (1974). Enzymes as biochemical reagents. in Methods of Enzymatic Analysis, 2nd edn, pp. 425-522. Edited by H. U. Bergmeyer. New York: Academic Press.
4. Brenner, S. (1988). The molecular evolution of genes and proteins: a tale of two serines. Nature 334, 528-530.
5. Garden, A. & Levinthal, C. (1960). A fine-structure genetic and chemical study of the enzyme alkaline phosphatase of E. coli. I. Purification and characterization of alkaline phosphatase. Biochim Biophys Acta 38, 470-483.
6. Hatanaka, T., Asahi, N. & Tsuji, M. (1995a). Purification and characterization of poly(vinyl alcohol) dehydrogenase from Pseudomonas sp. 113P3. Biosci Biotechnol Biochem 59 1813-1816.
7. Hatanaka, T., Kawahara, T., Asahi, N. & Tsuji, M. (1995b). Effects of the structure of poly(vinyl alcohol) on the dehydrogenation reaction by poly(vinyl alcohol) dehydrogenase from Pseudomonas sp. 113P3. Biosci Biotechnol Biochem 59, 1229-1231.
8. Hatanaka, T., Hashimoto, T., Kawahara, T., Takami, M., Asahi, N. & Wada, R. (1996). Biodegradability of oxidized poly(vinyl alcohol). Biosci Biotechnol Biochem 60, 1861-1863.
9. Jendrossek, D., Backhaus, M. & Andermann, M. (1995a). Characterization of the extracellular poly(3-hydroxybutyrate) depolymerase of Comamonas sp. and of its structural gene. Can J Microbiol 41, 160-169.
10. Jendrossek, D., Frisse, A., Behrends, A., Andermann, M., Kratzin, H. D., Stanislawski, T. & Schlegel, H. G. (1995b). Biochemical and molecular characterization of the Pseudomonas lemoignei polyhydroxy-alkanoate depolymerase system. J Bacteriol 177, 596-607.
11. Kasai, Y., Tanimura, T. & Tamura, Z. (1975). Spectrophotometric determination of carboxlic acids by the formation of hydroxamic acids with dicyclohexylcarbodiimide. Anal Chem 47, 34-37.
12. Kawai, F. (1995). Breakdown of plastic and polymers by micro-organisms, In Advances in Biochemical Engineering /Biotechnology vol. 52, pp. 201-225. Edited by A. Fiechter. Berlin: Springer.
13. Kawai, F. (1999). Sphingomonads involved in the biodegradation of xenobiotic polymers. J Ind Microbiol Biotechnol 23, 400-407.
14. Kawai, F. & Enokibara, S. (1996). Symbiotic degradation of polyethylene glycol (PEG) 20,000-phthalate polyester by phthalate ester- and PEG 20,000-utilizing bacteria. J Ferment Bioeng 82 575-579.
15. Kim, B. C., Sohn, C. K., Lim, S. K., Lee, J. W. & Park, W. (2003). Degradation of polyvinyl alcohol by Sphingomonas sp. SA3 and its symbiote. J Ind Microbiol Biotechnol 30, 70-74.
16. Kim, C. H., Lee, J. H., Heo, J. H., Kwon, O. S., Kang, H. A. & Rhee, S. K. (2004). Cloning and expression of a novel esterase gene cpoA from Burkholderia cepacia. J Appl Microbiol 96 1306-1316.
17. Laemmli, U. K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 680-685.
18. Lassy, R. A. L. & Miller, C. G. (2000). Peptidase E, a peptidase specific for N-terminal aspartic dipeptides, is a serine hydrolase. J Bacteriol 182, 2536-2543.
19. Matsumura, S., Tomizawa, N., Toki, A. & Toshima, K. (1998). Enzymatic degradation of poly(vinyl alcohol) and its copolymer. In Biochemical Principles and Mechanisms of Biosynthesis and Biodegradation of Polymers, pp. 230-238. Edited by A. Steinbüchel. Weinheim: Wiley-VCH.
20. Matsumura, S., Tomizawa, N., Toki, A., Nishikawa, K. & Toshima, K. (1999). Novel poly(vinyl alcohol)-degrading enzyme and the degradation mechanism. Macromolecules 32, 7753-7761.
21. Momma, K., Okamoto, M., Mishima, Y., Mori, S., Hashimoto, W. & Murata, K. (2000). A novel bacterial ATP-binding cassette transporter system that allows uptake of macromolecules. J Bacteriol 18, 3998-4004.
22. Ochman, H., Gerber, A. S. & Hart, D. L. (1988). Genetic applications of an inverse polymerase chain reaction. Genetics 120, 621-623.
23. Olsvik, O., Rimstad, E., Homes, E., Strockbine, N., Wasteson, Y., Lund, A. & Wachsmuth, K. (1991). A nested PCR followed by magnetic separation of amplified fragments for detection of Escherichia coli Shiga-like toxin genes. Mol Cell Probes 6 429-435.
24. Pelletier, I., Altenbuchner, J. & Mattes, R. (1995). A catalytic triad is required by the non-heme haloperoxidases to perform halogenation. Biochim Biophys Acta 1250, 149-157.
25. Rochelle, P. A., Will, J. A. K., Fry, J. C., Jenkins, G. J. S., Parkes, R. J., Tueley, C. M. & Weightman, A. J. (1995). Extraction and amplification of 16S rRNA genes from deep marine sediments and seawater to assess bacterial community diversity. In Nucleic Acids in the Environment, pp. 219-239. Edited by J. T. Trevors & J. D. van Elsas. New York: Springer.
26. Saegusa, H., Shiraki, M. & Saito, T. (2002). Cloning of an intra-cellular D-(-)-3-hydroxybutyrate-oligomer hydrolase gene from Ralstonia euthopha H16 and identification of the active site serine residue by site-direct mutagenesis. J Biosci Bioeng 94, 106-112.
27. Sakai, K., Hamada, N. & Watanabe, Y. (1985). A new enzyme, β-diketone hydrolase: a component of a poly(vinyl alcohol) degrading enzyme preparation. Agric Biol Chem 49, 1901-1902.
28. Sakai, K., Hamada, N. & Watanabe, Y. (1986). Degradation mechanism of poly(vinyl alcohol) by successive reactions of secondary alcohol oxidase and β-diketone hydrolase from Pseudomonas sp. Agric Biol Chem 50, 989-996.
29. Sakazawa, C., Shimao, M., Taniguchi, Y. & Kato, N. (1981). Symbiotic utilization of polyvinyl alcohol by mixed cultures. Appl Environ Microbiol 41, 261-267.
30. Sambrook, J. & Russell, D. W. (2001). Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
31. Shimao, M., Yamamoto, H., Ninomiya, K., Kato, N., Adachi, O., Ameyama, M. & Sakazawa, C. (1984). Pyrroloquinoline quinone as an essential growth factor for a poly(vinyl alcohol)-degrading symbiont, Pseudomonas sp. VM15C. Agric Biol Chem 48, 2873-2876.
32. Shimao, M., Ninomiya, K., Kuno, O., Kato, N. & Sakazawa, C. (1986). Existence of a novel enzyme, pyrroloquinoline quinone-dependent polyvinyl alcohol dehydrogenase, in a bacterial symbiont, Pseudomonas sp. strain VM15C. Appl Environ Microbiol 51, 268-275.
33. Shimao, M., Tamogami, T., Nishi, K. & Harayama, S. (1996). Cloning and characterization of the gene encoding pyrroloquinoline quinone-dependent poly(vinyl alcohol) dehydrogenase of Pseudomonas sp. strain VM15C. Biosci Biotechnol Biochem 60, 1056-1062.
34. Shimao, M., Tamogami, T., Kishida, S. & Harayama, S. (2000). The gene pvaB encodes oxidized polyvinyl alcohol hydrolase of Pseudomonas sp. strain VM15C and forms an operon with the polyvinyl alcohol dehydrogenase gene pvaA. Microbiology 146 649-657.
35. Silverstein, R. M., Basler, G. C. & Morrill, T. C. (1991). Spectrometric Identification of Organic Compounds, 5th edn. New York: Wiley.
36. Sugimoto, M., Tanabe, M., Hataya, M., Enokibara, S., Duine, J. A. & Kawai, F. (2001). The first step in polyethylene glycol degradation by sphingomonads proceeds via a flavoprotein alcohol dehydrogenase containing flavin adenine dinucleotide. J Bacteriol 183, 6694-6698.
37. Suzuki, T. (1976). Purification and some properties of polyvinyl alcohol-degrading enzyme produced by Pseudomonas O-3. Agric Biol Chem 40, 497-504.
38. Suzuki, T. (1978). Oxidation of secondary alcohol by polyvinyl alcohol-degrading enzyme produced by Pseudomonas O-3. Agric Biol Chem 42, 1187-1194.
39. Tabata, K., Kasuya, K., Abe, H., Masuda, K. & Doi, Y. (1999). Poly(aspartic acid) degradation by a Sphingomonas sp. isolated from freshwater. Appl Environ Microbiol 65, 4268-4270.
40. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
41. Watanabe, Y., Morita, M., Hamada, N. & Tsujisaka, Y. (1975). Formation of hydrogen peroxide by a polyvinyl alcohol degrading enzyme. Agric Biol Chem 39, 2447-2448.
42. Watanabe, Y., Morita, M., Hamada, N. & Tsujisaka, Y. (1976). Purification and properties of a polyvinyl alcohol-degrading enzyme produced by a strain of Pseudomonas. Arch Biochem Biophys 174, 575-581.
43. Zhang, K., Shiraki, M. & Saito, T. (1997). Purification of an extracellular D-(-)-3-hydroxybutyrate oligomer hydrolase from Pseudomonas sp. strain A1 and cloning and sequencing of its gene. J Bacteriol 179, 72-77.