Skip to main content

Two main domains with different roles discovered an a new tomato beta-galactosidase

Russian Journal of Bioorganic Chemistry volume 42, pages 522–531 (2016)Cite this article

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.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

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

  1. 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.

    CAS  Article  Google Scholar 

  2. Henrissat, B., Biochem. J., 1991, vol. 280, pp. 309–316.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  3. Henrissat, B. and Bairoch, A., Biochem. J., 1993, vol. 293, pp. 781–788.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. 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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. 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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. Iglesias, N., Abelenda, J.A., Roniño, M., Sampedro, J., Revilla, G., and Zarra, I., Plant Cell Physiol., 2006, vol. 47, pp. 55–63.

    CAS  Article  PubMed  Google Scholar 

  7. De Alcantara, P.H.N., Dietrich, S.M.C., and Buckeridge, M.S., Plant Physiol. Biochem., 1999, vol. 37, pp. 653–663.

    Article  Google Scholar 

  8. 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.

    Article  PubMed  Google Scholar 

  9. Ross, G.S., Wagrzyn, T., MacRae, E.A., and Redgwell, R.J., Plant Physiol., 1994, vol. 106, pp. 521–528.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. Reiter, W.D., and Vanzin, G.F., Plant Mol. Biol., 2001, vol. 47, pp. 95–113.

    CAS  Article  PubMed  Google Scholar 

  11. Esteban, R., Dopico, B., Muñoz, F.J., Romo, S., Martín, I., and Labrador, E., Plant Cell Physiol., 2003, vol. 44, pp. 718–725.

    CAS  Article  PubMed  Google Scholar 

  12. Esteban, R., Labrador, E., and Dopico, B., Plant Sci., 2005, vol. 168, pp. 457–466.

    CAS  Article  Google Scholar 

  13. Sampedro, J., Gianzo, C., Iglesias, N., Guitián, E., Revilla, G., and Zarra, I., Plant Physiol., 2012, vol. 158, pp. 1146–1157.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  14. Kishore, D., and Kayastha, A.M., Food Chem., 2012, vol. 134, pp. 1113–1122.

    CAS  Article  PubMed  Google Scholar 

  15. Rogers, H.J., Maund, S.L., and Johnson, L.H., J. Exp. Bot., 2001, vol. 52, pp. 67–75.

    CAS  Article  PubMed  Google Scholar 

  16. Wu, Z. and Burns, J.K., J. Exp. Bot., 2004, vol. 55, pp. 1483–1490.

    CAS  Article  PubMed  Google Scholar 

  17. Brummell, D.A. and Harpster, M.H., Plant Mol. Biol., 2001, vol. 47, pp. 311–340.

    CAS  Article  PubMed  Google Scholar 

  18. Tateishi, A., Inoue, H., Shiba, H., and Yamaki, S., Plant Cell Physiol., 2001, vol. 42, pp. 492–498.

    CAS  Article  PubMed  Google Scholar 

  19. Lazan, H., Ng, S.Y., Goh, L.Y., and Ali, Z.M., Plant Physiol. Biochem., 2004, vol. 42, pp. 847–853.

    CAS  Article  PubMed  Google Scholar 

  20. 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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. 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.

    CAS  Article  PubMed  Google Scholar 

  22. Tateishi, A., Shiba, H., Ogihara, J., Isobe, K., Nomura, K., Watanabe, K., and Inoue, H., Postharvest Biol. Technol., 2007, vol. 45, pp. 56–65.

    CAS  Article  Google Scholar 

  23. 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.

    Article  Google Scholar 

  24. Kyte, J. and Doolittle, R., J. Mol. Biol., 1982, vol. 157, pp. 105–132.

    CAS  Article  PubMed  Google Scholar 

  25. Von Heijne, G., Eur. J. Biochem., 1983, vol. 133, pp. 17–21.

    Article  Google Scholar 

  26. Bendtsen, J.D., Nielsen, H., Von Heijne, G., and Brunak, S., J. Mol. Biol., 2004, vol. 340, pp. 783–795.

    Article  PubMed  Google Scholar 

  27. Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Bioinformatics, 2002, vol. 18, pp. 298–305.

    CAS  Article  PubMed  Google Scholar 

  28. 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.

    Google Scholar 

  29. Taron, C.H., Benner, J.S., Hornstra, L.J., and Guthrie, E.P., Glycobiology, 1995, vol. 5, pp. 603–610.

    CAS  Article  PubMed  Google Scholar 

  30. Henrissat, B., Biochem. Soc. Trans, 1998, vol. 26, pp. 153–156.

    CAS  Article  PubMed  Google Scholar 

  31. 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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Kardailsky, I.V., Sherrier, D.J., and Brewin, N.J., Plant Physiol., 1996, vol. 111, pp. 49–60.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  33. Smith, D.L. and Gross, K.C., Plant Physiol., 2000, vol. 123, pp. 1173–1183.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Rolin, D., Baldet, P., Just, D., Chevalier, C., Biran, M., and Raymond, P., Aust. J. Plant Physiol., 2000, vol. 27, pp. 61–69.

    CAS  Google Scholar 

  35. 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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Demaurex, N., News Physiol. Sci., 2002, vol. 17, pp. 1–5.

    CAS  PubMed  Google Scholar 

  37. 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.

    Article  PubMed  Google Scholar 

  38. Dwevedi, A., Dubey, V.K., Jagannadham, M.V., and Kayastha, A.M., Appl. Biochem. Biotechnol., 2010, vol. 162, pp. 2294–2312.

    CAS  Article  PubMed  Google Scholar 

  39. Ogasawara, S., Abe, K., and Nakajima, T., Biosci. Biotechnol. Biochem., 2007, vol. 71, pp. 309–322.

    CAS  Article  PubMed  Google Scholar 

  40. Triantafillidou, D. and Georgatsos, J.G., J. Protein Chem., 2001, vol. 20, pp. 551–562.

    CAS  Article  PubMed  Google Scholar 

  41. Li, S.C., Han, J.W., Chen, K.C., and Chen, C.S., Phytochemistry, 2001, vol. 57, pp. 349–359.

    CAS  Article  PubMed  Google Scholar 

  42. Kang, I.K., Suh, S.G., Gross, K.C., and Byoun, J.K., Plant Physiol., 1994, vol. 105, pp. 975–979.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. Poch, O., L’hote, H., Dallery, V., Debeaux, F., Fleer, R., and Sodoyer, R., Gene, 1992, vol. 118, pp. 55–63.

    CAS  Article  PubMed  Google Scholar 

  44. Fabiola, G.F., Krishnaswamy, S., Nagarajan, V., and Pattabi, V., Acta Crystallogr. Sect., 1997, vol. 53, pp. 316–320.

    CAS  Google Scholar 

  45. Parisien, M. and Major, F., Proteins: Structur., Function, Bioinformatics, 2007, vol. 68, pp. 824–829.

    CAS  Article  Google Scholar 

  46. Taylor, M.E. and Drickamer, K., Introduction to Glycobiology, 2nd ed., Oxford University Press, USA, 2006.

    Google Scholar 

  47. 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.

    Google Scholar 

  48. Clackson, T. and Wells, J.A., Science, 1995, vol. 267, pp. 383–386.

    CAS  Article  PubMed  Google Scholar 

  49. Bogan, A.A. and Thorn, K.S., J. Mol. Biol., 1998, vol. 280, pp. 1–9.

    CAS  Article  PubMed  Google Scholar 

  50. Gallivan, J.P. and Dougherty, D.A., Proc. Natl. Acad. Sci. U. S. A., 1999, vol. 96, pp. 9459–9464.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  51. Samanta, U., Pal, D., and Chakrabarti, P., Proteins: Structur., Function, Genetics, 2000, vol. 38, pp. 288–300.

    CAS  Article  Google Scholar 

  52. Huber, R.E., Hakda, S., Cheng, C., Cupples, C.G., and Edwards, R.A., Biochemistry, 2003, vol. 42, pp. 1796–1803.

    CAS  Article  PubMed  Google Scholar 

  53. Spiwok, V., Lipovová, P., Skálová, T., Buchtelová, E., Hašek, J., and Králová, B., Carbohydrate Res., 2004, vol. 339, pp. 2275–2280.

    CAS  Article  Google Scholar 

  54. Martinez-Bilbao, M., Holdsworthz, R.E., Edwardsa, L.A., and Huberl, R.E., J. Biol. Chem., 1991, vol. 266, pp. 4979–4986.

    CAS  PubMed  Google Scholar 

  55. Martinez-Bilbao, M. and Huber, R.E., Biochem. Cell Biol., 1994, vol. 72, pp. 313–319.

    CAS  Article  PubMed  Google Scholar 

  56. Ozeki, Y., Matsui, T., Suzuki, M., and Titani, K., Biochemistry, 1991, vol. 30, pp. 2391–2394.

    CAS  Article  PubMed  Google Scholar 

  57. 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.

    CAS  Article  PubMed  Google Scholar 

  58. Zhang, H.M., and Liu, J.Y., J. Integr. Plant Biol., 2005, vol. 47, pp. 223–232.

    CAS  Article  Google Scholar 

  59. Mitcham, E.J., Gross, K.C., and Ng, T.J., Plant Physiol., 1989, vol. 89, pp. 477–481.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  60. Etheridge, N., Trusov, Y., Verbelen, J.P., Botella, J.R., Plant Mol. Biol., 1999, vol. 39, pp. 1113–1126.

    CAS  Article  PubMed  Google Scholar 

  61. 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.

    Article  Google Scholar 

  62. 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.

    Book  Google Scholar 

  63. 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.

    Article  Google Scholar 

  64. Rost, B. and Sander, C., J. Mol. Biol., 1993, vol. 232, pp. 584–599.

    CAS  Article  PubMed  Google Scholar 

  65. Geourjon, C. and Deleage, G., Comput. Appl. Biosci., 1995, vol. 11, pp. 681–684.

    CAS  PubMed  Google Scholar 

  66. 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.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  67. Thompson, J.D., Higgins, D.G., and Gibson, T.J., Nucleic Acids Res., 1994, vol. 22, pp. 4673–4680.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  68. Saitou, N. and Nei, M., Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.

    CAS  PubMed  Google Scholar 

  69. Tamura, K., Dudley, J., Nei, M., and Kumar, S., Mol. Biol. Evol., 2007, vol. 24, pp. 1596–1599.

    CAS  Article  PubMed  Google Scholar 

  70. Felsenstein, J., Evolution, 1985, vol. 39, pp. 783–791.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Agricultural Biotechnology Department, Faculty of Engineering, Imam Khomeini International University, Qazvin, Iran

    A. Ghannad Sabzevary & R. Hosseini

Authors
  1. A. Ghannad Sabzevary
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. Hosseini
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. Hosseini.

Additional information

The article is published in the original.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S106816201605006X

Keywords

  • RT-PCR
  • lectin
  • protein
  • function
  • sequence annotation