Abstract
β-Galactosidases (β-gals) are a wide family of glycosyl hydrolases thought to be involved in the metabolic recycling of galactolipids, glycoproteins, and cell wall polysaccharides in plants. A full-length cDNA, designated STBG2, was isolated and cloned from tomato (Solanum lycopersicum L. cv. Falcato) by reverse transcription–polymerase chain reaction. The cDNA was 2996 bp in length and encoded a typical β-gal protein, designated SlGal2, consisting of 892 residues. A comparison of SlGal2 with its counterpart isoform in the cultivar Rutgers revealed that SlGal2 had identical residues, except for 44 amino acids. Noteworthy, 42 different residues were located in a limited area in the middle of the protein. An alignment of SlGal2 with other plant β-gals clearly showed the existence of a non-conserved short polypeptide, as a connector between the N- and C-terminal domains. A deeper bioinformatic analysis referring to recent experimental findings strongly suggested different roles for the N- and C-terminal domains. As a result, the N-terminal domain is responsible for the catalytic activity and the C-terminal domain is responsible for the stability and the substrate binding of the enzyme. In addition, a substantial difference in physiochemical characteristics of similar β-gals was found to be in their isoelectric points. In conclusion, the differential role of C-terminal domains and also the significant differences in isoelectric points provided insights into the unknown mechanism of substrate specificity of plant β-gals, which in turn will help in protein engineering studies.
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Abbreviations
- β-gal:
-
β-galactosidase
- dpp:
-
day post pollination
- GH:
-
glycosyl hydrolase
- gDNA:
-
genomic DNA
- ORF:
-
open reading frame
- RACE:
-
rapid amplification of cDNA end
- RTPCR:
-
reverse transcription–polymerase chain reaction
- SUElectin:
-
sea urchin egg lectin
- UTR:
-
untranslated region
References
Mwaniki, M.W., Mathooko, F.M., Matsuzaki, M., Hiwasa, K., Tateishi, A., Ushijima, K., Nakano, R., Inaba, A., and Kubo, Y., Postharvest Biol. Technol., 2005, vol. 36, pp. 253–263.
Henrissat, B., Biochem. J., 1991, vol. 280, pp. 309–316.
Henrissat, B. and Bairoch, A., Biochem. J., 1993, vol. 293, pp. 781–788.
Carey, A.T., Holt, K., Picard, S., Wilde, R., Tucker, G.A., Bird, C.R., Shuch, W., and Seymour, G.B., Plant Physiol., 1995, vol. 108, pp. 1099–1107.
Kotake, T., Dina, S., Konishi, T., Kaneko, S., Igarashi, K., Samejima, M., Watanabe, Y., Kimura, K., and Tsumuraya, Y., Plant Physiol., 2005, vol. 138, pp. 1563–1576.
Iglesias, N., Abelenda, J.A., Roniño, M., Sampedro, J., Revilla, G., and Zarra, I., Plant Cell Physiol., 2006, vol. 47, pp. 55–63.
De Alcantara, P.H.N., Dietrich, S.M.C., and Buckeridge, M.S., Plant Physiol. Biochem., 1999, vol. 37, pp. 653–663.
De Alcantara, P.H.N., Martim, L., Silva, C.O., Dietrich, S.M.C., and Buckeridge, M.S., Plant Physiol. Biochem., 2006, vol. 44, pp. 619–627.
Ross, G.S., Wagrzyn, T., MacRae, E.A., and Redgwell, R.J., Plant Physiol., 1994, vol. 106, pp. 521–528.
Reiter, W.D., and Vanzin, G.F., Plant Mol. Biol., 2001, vol. 47, pp. 95–113.
Esteban, R., Dopico, B., Muñoz, F.J., Romo, S., Martín, I., and Labrador, E., Plant Cell Physiol., 2003, vol. 44, pp. 718–725.
Esteban, R., Labrador, E., and Dopico, B., Plant Sci., 2005, vol. 168, pp. 457–466.
Sampedro, J., Gianzo, C., Iglesias, N., Guitián, E., Revilla, G., and Zarra, I., Plant Physiol., 2012, vol. 158, pp. 1146–1157.
Kishore, D., and Kayastha, A.M., Food Chem., 2012, vol. 134, pp. 1113–1122.
Rogers, H.J., Maund, S.L., and Johnson, L.H., J. Exp. Bot., 2001, vol. 52, pp. 67–75.
Wu, Z. and Burns, J.K., J. Exp. Bot., 2004, vol. 55, pp. 1483–1490.
Brummell, D.A. and Harpster, M.H., Plant Mol. Biol., 2001, vol. 47, pp. 311–340.
Tateishi, A., Inoue, H., Shiba, H., and Yamaki, S., Plant Cell Physiol., 2001, vol. 42, pp. 492–498.
Lazan, H., Ng, S.Y., Goh, L.Y., and Ali, Z.M., Plant Physiol. Biochem., 2004, vol. 42, pp. 847–853.
Macquet, A., Ralet, M.C., Loudet, O., Kronenberger, J., Mouille, G., Marion-Poll, A., and North, H.M., Plant Cell, 2007, vol. 19, pp. 3990–4006.
Ahn, Y.O., Zheng, M., Bevan, D.R., Esen, A., Shiu, S.H., Benson, J., Peng, H.P., Miller, J.T., Cheng, L.I., Poulton, J.E., and Shih, M.C., Phytochemistry, 2007, vol. 68, pp. 1510–1520.
Tateishi, A., Shiba, H., Ogihara, J., Isobe, K., Nomura, K., Watanabe, K., and Inoue, H., Postharvest Biol. Technol., 2007, vol. 45, pp. 56–65.
Bombarely, A., Menda, N., Tecle, I.Y., Buels, R.M., Strickler, S., Fischer-York, T., Pujar, A., Leto, J., Gosselin, J., and Mueller, L.A., Nucleic Acids Res., 2011, vol. 39, pp. 1149–1155.
Kyte, J. and Doolittle, R., J. Mol. Biol., 1982, vol. 157, pp. 105–132.
Von Heijne, G., Eur. J. Biochem., 1983, vol. 133, pp. 17–21.
Bendtsen, J.D., Nielsen, H., Von Heijne, G., and Brunak, S., J. Mol. Biol., 2004, vol. 340, pp. 783–795.
Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Bioinformatics, 2002, vol. 18, pp. 298–305.
Horton, P., Park, K.J., Obayashi, T., and Nakai, K., in Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference (APBC06), Taipei, Taiwan, 2006, pp. 39–48.
Taron, C.H., Benner, J.S., Hornstra, L.J., and Guthrie, E.P., Glycobiology, 1995, vol. 5, pp. 603–610.
Henrissat, B., Biochem. Soc. Trans, 1998, vol. 26, pp. 153–156.
Henrissat, B., Callebaut, I., Fabrega, S., Lehn, P., Mornon, J.P., and Davies, G., Proc. Natl. Acad. Sci. U. S. A., 1995, vol. 92, pp. 7090–7094.
Kardailsky, I.V., Sherrier, D.J., and Brewin, N.J., Plant Physiol., 1996, vol. 111, pp. 49–60.
Smith, D.L. and Gross, K.C., Plant Physiol., 2000, vol. 123, pp. 1173–1183.
Rolin, D., Baldet, P., Just, D., Chevalier, C., Biran, M., and Raymond, P., Aust. J. Plant Physiol., 2000, vol. 27, pp. 61–69.
Fasano, J.M., Swanson, S.J., Blancaflor, E.B., Dowd, P.E., Kao, T.H., and Gilroy, S., Plant Cell, 2001, vol. 13, pp. 907–921.
Demaurex, N., News Physiol. Sci., 2002, vol. 17, pp. 1–5.
Tello-Solís, S.R., Jiménez-Guzmán, J., Sarabia-Leos, C., Gómez-Ruíz, L., Cruz-Guerrero, A.E., Rodríguez-Serrano, G.M., and García-Garibay, M., J. Agric. Food Chem., 2005, vol. 53, pp. 10200–10204.
Dwevedi, A., Dubey, V.K., Jagannadham, M.V., and Kayastha, A.M., Appl. Biochem. Biotechnol., 2010, vol. 162, pp. 2294–2312.
Ogasawara, S., Abe, K., and Nakajima, T., Biosci. Biotechnol. Biochem., 2007, vol. 71, pp. 309–322.
Triantafillidou, D. and Georgatsos, J.G., J. Protein Chem., 2001, vol. 20, pp. 551–562.
Li, S.C., Han, J.W., Chen, K.C., and Chen, C.S., Phytochemistry, 2001, vol. 57, pp. 349–359.
Kang, I.K., Suh, S.G., Gross, K.C., and Byoun, J.K., Plant Physiol., 1994, vol. 105, pp. 975–979.
Poch, O., L’hote, H., Dallery, V., Debeaux, F., Fleer, R., and Sodoyer, R., Gene, 1992, vol. 118, pp. 55–63.
Fabiola, G.F., Krishnaswamy, S., Nagarajan, V., and Pattabi, V., Acta Crystallogr. Sect., 1997, vol. 53, pp. 316–320.
Parisien, M. and Major, F., Proteins: Structur., Function, Bioinformatics, 2007, vol. 68, pp. 824–829.
Taylor, M.E. and Drickamer, K., Introduction to Glycobiology, 2nd ed., Oxford University Press, USA, 2006.
Varki, A., Cummings, R.D., Esko, J.D., Freeze, H.H., Stanley, P., Bertozzi, C.R., Hart, G.W., and Etzler, M.E., Essentials of Glycobiology, 2nd ed., New York: Cold Spring Harbor Laboratories Press, 2009.
Clackson, T. and Wells, J.A., Science, 1995, vol. 267, pp. 383–386.
Bogan, A.A. and Thorn, K.S., J. Mol. Biol., 1998, vol. 280, pp. 1–9.
Gallivan, J.P. and Dougherty, D.A., Proc. Natl. Acad. Sci. U. S. A., 1999, vol. 96, pp. 9459–9464.
Samanta, U., Pal, D., and Chakrabarti, P., Proteins: Structur., Function, Genetics, 2000, vol. 38, pp. 288–300.
Huber, R.E., Hakda, S., Cheng, C., Cupples, C.G., and Edwards, R.A., Biochemistry, 2003, vol. 42, pp. 1796–1803.
Spiwok, V., Lipovová, P., Skálová, T., Buchtelová, E., Hašek, J., and Králová, B., Carbohydrate Res., 2004, vol. 339, pp. 2275–2280.
Martinez-Bilbao, M., Holdsworthz, R.E., Edwardsa, L.A., and Huberl, R.E., J. Biol. Chem., 1991, vol. 266, pp. 4979–4986.
Martinez-Bilbao, M. and Huber, R.E., Biochem. Cell Biol., 1994, vol. 72, pp. 313–319.
Ozeki, Y., Matsui, T., Suzuki, M., and Titani, K., Biochemistry, 1991, vol. 30, pp. 2391–2394.
Hosono, M., Ishikawa, K., Mineki, R., Murayama, K., Numata, C., Ogawa, Y., Takayanagi, Y., and Nitta, K., Biochim. Biophys. Acta, 1999, vol. 1472, pp. 668–675.
Zhang, H.M., and Liu, J.Y., J. Integr. Plant Biol., 2005, vol. 47, pp. 223–232.
Mitcham, E.J., Gross, K.C., and Ng, T.J., Plant Physiol., 1989, vol. 89, pp. 477–481.
Etheridge, N., Trusov, Y., Verbelen, J.P., Botella, J.R., Plant Mol. Biol., 1999, vol. 39, pp. 1113–1126.
De Castro, E., Sigrist, C.J.A., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P.S., Gasteiger, E., Bairoch, A., and Hulo, N., Nucleic Acids Res., 2006, vol. 34, pp. 362–365.
Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., and Bairoch, A., in The Proteomics Protocols Handbook, Totowa, N.J.: Humana Press, Inc., 2005, pp. 571–607.
Bryson, K., McGuffin, L.J., Marsden, R.L., Ward, J.J., Sodhi, J.S., and Jones, D.T., Nucleic Acids Res., 2005, vol. 33, pp. 36–38.
Rost, B. and Sander, C., J. Mol. Biol., 1993, vol. 232, pp. 584–599.
Geourjon, C. and Deleage, G., Comput. Appl. Biosci., 1995, vol. 11, pp. 681–684.
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J., Nucleic Acids Res., 1997, vol. 25, pp. 3389–3402.
Thompson, J.D., Higgins, D.G., and Gibson, T.J., Nucleic Acids Res., 1994, vol. 22, pp. 4673–4680.
Saitou, N. and Nei, M., Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.
Tamura, K., Dudley, J., Nei, M., and Kumar, S., Mol. Biol. Evol., 2007, vol. 24, pp. 1596–1599.
Felsenstein, J., Evolution, 1985, vol. 39, pp. 783–791.
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Ghannad Sabzevary, A., Hosseini, R. Two main domains with different roles discovered an a new tomato beta-galactosidase. Russ J Bioorg Chem 42, 522–531 (2016). https://doi.org/10.1134/S106816201605006X
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DOI: https://doi.org/10.1134/S106816201605006X