Radiation and functional specialization of the family-3 glycoside hydrolases

Journal of Molecular Microbiology and Biotechnology

Volumn 5, Issue 3, 2003, Pages 190-198

  Cournoyer, B ^a   Faure, D ^b,c  

^a University of Lyon   (France)

^b INSTITUT DES SCIENCES DU VÉGÉTAL   (France)

^c CNRS   (France)

Author keywords

Glucosidase; Xylosidase; Evolution; Genomics; N Acetylglucosaminidase

Indexed keywords

ENZYME; GLUCOSAMINIDASE; GLUCOSIDASE; GLYCOSIDASE; HYDROLASE; XYLAN 1,4 BETA XYLOSIDASE;

AMINO ACID SEQUENCE; ARTICLE; CELL HETEROGENEITY; COMPARATIVE STUDY; GENE AMPLIFICATION; GENE CLUSTER; GENETIC ANALYSIS; HYDROLYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROKARYOTE; PROTEIN FAMILY; RADIATION; UNINDEXED SEQUENCE; BACTERIAL GENOME; BIOLOGY; COMPUTER PROGRAM; ENZYME SPECIFICITY; GENETICS; GENOME; GENOMICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY;

EUKARYOTA; PROKARYOTA;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; GENOME, FUNGAL; GENOME, PLANT; GENOMICS; GLYCOSIDE HYDROLASES; PHYLOGENY; SOFTWARE; SUBSTRATE SPECIFICITY;

EID: 0042739213     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000070269     Document Type: Article

References (39)

1. Arai, T., and Matsui, K. 1997. A purified protein from Salmonella typhimurium inhibits high-affinity interleukin-2 receptor expression on CTLL-2 cells. FEMS Immunol. Med. Microbiol. 17:155-160.
2. Bowyer, P., Clarke, B.R., Lunness, P., Daniels, M.J., and Osbourn, A.E. 1995. Host range of a plant pathogenic fungus determined by a saponin detoxifying enzyme. Science 267:371-374.
3. Bush, J., Richardson, J., and Cardelli, J. 1994. Molecular cloning and characterization of the full-length cDNA encoding the developmentally regulated lysosomal enzyme β-glucosidase in Dictyostelium discoideum. J. Biol. Chem. 269:1468-1476.
4. Cheng, Q., Li, H., Merdek, K., and Park, J.T. 2000. Molecular characterization of the β-N-acetylglucosaminidase of Escherichia coli and its role in cell wall recycling. J. Bacteriol. 182:4836-4840.
5. Chir, J., Withers, S., Wan, C.F., and Li, Y.K. 2002. Identification of the two essential groups in the family 3 β-glucosidase from Flavobacterium meningosepticum by labelling and tandem mass spectrometric analysis. Biochem. J. 365:857-863.
6. Coutinho, P.M., and Henrissat, B. 1999. Life with no sugars? J. Mol. Microbiol. Biotechnol. 1:307-308.
7. Dan, S., Marton, I., Dekel, M., Bravdo, B.A., He, S., Withers, S.G., and Shoeyov, O. 2000. Cloning, expression, characterization, and nucleophile identification of family-3 Aspergillus niger β-glucosidase. J. Biol. Chem. 275:4973-4980.
8. Deepe, G.S., Jr., and Gibbons, R. 2001. Protective efficacy of H antigen from Histoplasma capsulatum in a murine model of pulmonary histoplasmosis. Infect. Immun. 69:3128-3134.
9. Eisen, J.A. 1998. Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8:163-167.
10. Faure, D. 2002. The family-3 glycoside hydrolases: From housekeeping functions to host-microbe interactions. Appl. Environ. Microbiol. 68:1485-1490.
11. Faure, D., Desair, J., Veijers, V., Bekri, M.A., Proost, P., Henrissat, B., and Vanderleyden, J. 1999. Growth of Azospirillum irakense KBCI on the aryl β-glucoside, salicin, requires either SalA or SalB. J. Bacteriol. 181:3003-3009.
12. Faure, D., Henrissat, B., Ptacek, D., Bekri, A., and Vanderleyden, J. 2001. The celA gene, encoding a glycosyl hydrolase family 3 β-glucosidase in Azospirillum irakense, is required for optimal growth on cellobiosides. Appl. Environ. Microbiol. 67:2380-2383.
13. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
14. Galtier, N., Gouy, M., and Gautier, C. 1996: SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12:543-548.
15. Goyal, A.K., and Eveleigh, D.E. 1996. Cloning, sequencing and analysis of the ggh-A gene encoding a 1,4-b-D-glucan glucohydrolase from Microbispora bispora. Gene 172:93-98.
16. Harvey, A.J., Hrmova, M., De Gori, R., Varghese, J.N., and Fincher, G.B. 2000. Comparative modeling of the three-dimensional structures of family 3 glycoside hydrolases. Proteins 41:257-269.
17. Henrissat, B., and Bairoch, A. 1996. Updating the sequence-based classification of glycosyl hydrolases. Biochem. J. 316:695-696.
18. Hessler, P.E., Larsen, P.E., Constantinou, A.I., Schram, K.H., Weber, J.M. 1997. Isolation of isoflavones from a soy-based fermentations of the erythromycin-producing bacterium Saccharopolyspora erythraea. Appl. Microbiol. Biotechnol. 47:398-404.
19. Hrmova, M., De Gori, R., Smith, B.J., Fair-weather, J.K., Driguez, H., Varghese, J.N., and Fincher, G.B. 2002. Structural basis for broad substrate specificity in higher plant β-D-glucan gluco-hydrolases. Plant Cell 14:1033-1052.
20. Hrmova, M., Harvey, A.J., Wang, J., Shirley, N.J., Jones, G.P., Stones, B.A., Hoj, P.B., and Fincher, G.B. 1996. Barley β-D-glucan exohydrolases with β-D-glucosidase activity. J. Biol. Chem. 271:5277-5286.
21. Hung, C.Y., Yu, J.J., Lehmann, P.F., and Cole, G.T. 2001. Cloning and expression of the gene which encodes a tube precipitin antigen and wall-associated β-glucosidase of Coccidioides immitis. Infect. Immun. 69:2211-2222.
22. Kim, J.B., Olek, A.T., and Carpita, N.C. 2000. Cell wall and membrane-associated exo-β-D-glucanases from developing maize seedlings. Plant Physiol. 123:471-485.
23. Li, Y.K., Chir, J., and Chen, F.Y. 2001. Catalytic mechanism of a family-3 β-glucosidase and mutagenesis study on residue Asp-247. Biochem. J. 355:835-840.
24. Lin L.L., Rumbak, E., Zappe, H., Thomson, J.A., and Woods, D.R. 1990. Cloning, sequencing and analysis of expression of a Butyrivibrio fibrisolvens gene encoding a β-glucosidase. J. Gen. Microbiol. 136:1567-1576.
25. Mach, R.L., Seiboth, B., Myasnikov, A., Gonzalez, R., Strauss, J., Harkki, A.M., and Kubicek, C.P. 1995. The bgl1 gene of Trichoderma reesei QM 9414 encodes an extracellular, cellobiose-inducible β-glucosidase involved in cellulase induction by sophorose. Mol. Microbiol. 15:687-697.
26. Osbourn, A., Bowyer, P., Lunness, P., Clarke, B., and Daniels, M. 1995. Fungal pathogens of oat roots and tomato leaves employ closely related enzymes to detoxify different host plant saponins. Mol. Plant Microbe Interact. 8:971-978.
27. Perez-Gonzalez, J.A., van Peij, N.N., Bezoen, A., MacCabe, A.P., Ramon, D., and de Graaff, L.H. 1998. Molecular cloning and transcriptional regulation of the Aspergillus nidulans xlnD gene encoding a β-xylosidase. Appl. Environ. Microbiol. 64:1412-1419.
28. Perrière, G., and Gouy, M. 1996. WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78:364-369.
29. Peij, N.N. van, Brinkmann, J., Vrsanska, M., Visser, J., and de Graaff, L.H. 1997. β-Xylosidase activity, encoded by xlnD, is essential for complete hydrolysis of xylan by Aspergillus niger but not for induction of the xylanolytic enzyme spectrum. Eur. J. Biochem. 245:164-173.
30. Quiros, L.M., Aguirrezabalaga, I., Olano, C., Mendez, C., and Salas, J.A. 1998. Two glycosyltransferase and a glycosidase are involved in oleandomycin modification during its biosynthesis by Streptomyces antibioticus. Mol. Microbiol. 28:1177-1185.
31. Rixon, J.E., Ferreira, L.M.A., Durrant, A.J., Laurie, J.I., Hazlewood, G.P., and Gilbert, H.J. 1992. Characterization of the gene celD and its encoded product 1,4-β-D-glucan glucohydrolase D from Pseudomonas fluorescens subsp. cellulosa. Biochem. J. 285:947-955.
32. Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
33. She, Q., Singh, R.K., Confalonieri, F., Zivanovic, Y., Allard, G. Awayez, M.J., Chan-Weiher, C.C., Clausen, I.G., Curtis, B.A., De Moors, A., Erauso, G., Fletcher, C., Gordon, P.M., Heikamp-de Jong, I., Jeffries, A.C., Kozera, C.J., Medina, N., Peng, X., Thi-Ngoc, H.P., Redder, P., Schenk, M.E., Theriault, C., Tolstrup, N., Charlebois, R.L., Doolittle, W.F., Duguet, M., Gaasterland, T., Garrett, R.A., Ragan, M.A., Sensen, C.W., and Van der Oost, J. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98:7835-7840.
34. Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33-36.
35. Tsujibo, H.T., Fujimoto, K., Tanno, H., Miyamoto, K., Miyamoto, K., Imada, C., Okami, Y., and Inamori, Y. 1994. Gene sequence, purification and characterization of N-acetyl-β-glucosaminidase from a marine bacterium, Alteromonas sp. Strain O-7. Gene 146:111-115.
36. Tsujibo, H.T., Hatano, N., Mikami, T., Hirasawa, A., Miyamoto, K., and Inamori, Y. 1998. A novel β-N-acetylglucosaminidase from Streptomyces thermoviolaceus OPC-520:gene cloning, expression and assigment to family 3 of the glycosyl hydrolases. Appl. Environ. Microbiol. 64:2920-2924.
37. Varghese, J.N., Hrmova, M., and Fincher, G.B. 1999. Three-dimensional structure of a barley β-D-glucan exohydrolase, a family 3 glycosyl hydrolase. Structure Fold. Des. 7:179-190.
38. Vroemen, S., Heldens, J., Boyd, C., Henrissat, B., and Keen, N.T. 1995. Cloning and characterization of the bgxA gene from Erwinia chrysanthemi D1 which encodes a β-glucosidases/xylosidase enzyme. Mol. Gen. Genet. 246:465-477.
39. Zverlov, V.V., Volkov, I.Y., Velikodvorskaya, T.V., and Schwarz, W.H. 1997: Thermotoga neapolitana bglB gene, upstream of lamA, encodes a highly thermostable β-glucosidase that is a laminaribiase. Microbiology 143:3537-3542.