Comprehensive analysis of beta-galactosidase protein in plants based on Arabidopsis thaliana

Beta-galactosidases (\BETAgals) (EC 3.2.1.23) have been detected in a wide range of plant organs and tissues and are described by their ability to hydrolyze terminal nonreducing \BETA-D-galactosyl residues from \BETA-D-galactosides. In this study, 92 \BETAgal protein sequences from different plants, 7 animal samples including human and mouse, 3 samples from bacteria including Escherichia coli, and 4 samples from insects including Drosophila melanogaster were aligned. Sequences were analyzed by computational tools to predict the protein properties, such as molecular mass, isoelectric point, signal peptide, motifs, transmembrane domain, and secondary and spatial structure. Protein structure analysis revealed there is a high identity between plants and other organisms. The modeled \BETAgal has a typical spatial structure with catalytic regions. The 3-dimensional model of Arabidopsis thaliana \BETAgal (Accession Number: NP_001154292) was further checked by PROCHECK algorithm, and showed the majority of the amino acid residues were located in the most-favored regions in a Ramachandran plot. This result suggested that the simulated 3-dimensional structure was reliable. Phylogenetic analysis indicated that A. thaliana \BETAgal has a close relationship with some plants' \BETAgal from different families such as Malvaceae, Solanaceae, and Poaceae. According to these results, \BETAgals should be derived from a common ancestor.

Anahtar Kelimeler:

Key words: Arabidopsis thaliana, \BETA-galactosidase, catalytic domain, phylogenetic tree

Comprehensive analysis of beta-galactosidase protein in plants based on Arabidopsis thaliana

Keywords:

Key words: Arabidopsis thaliana, \BETA-galactosidase, catalytic domain, phylogenetic tree,

PDF

___

Agrawal KM, Bahl OP (1968). Glycosidases of Phaseolus vulgaris. II. Isolation and general properties. J Biol Chem 243: 103–111.
Akasaki M, Suzuki M, Funakoshi I, Yamashina I (1976).
Characterization of beta-galactosidase from a special strain of Aspergillus oryzae. J Biochem 80: 1195–200.
Ali ZM, Armugam S, Lazan H (1995). β-Galactosidase and its significance in ripening mango fruit. Phytochemistry 38: 1109–1114.
Altay G, Altay N, Neal D (2013). Global assessment of network inference algorithms based on available literature of gene/ protein interactions. Turk J Biol 37: 547–555.
Bailey TL, Williams N, Misleh C, Li WW (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34: 369–373.
Bayless TM, Rosensweig NS (1966). A racial difference in incidence of lactase deficiency. JAMA- J Am Med Assoc 197: 968–972.
Blobel G, Dobberstein B (1975). Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma. J Cell Biol 67: 835–851.
Buckeridge MS, Reid JSG (1994). Purification and properties of a novel β-galactosidase or exo-(1→4)-β-D-galactanase from the cotyledons of germinated Lupinus angustifolius L. seeds. Planta 192: 502–511.
Campbell JH, Lengyel JA, Langridge J (1973). Evolution of a second gene for β-galactosidase in Escherichia coli. P Natl Acad Sci USA 70: 1841–1845.
Carey AT, Holt K, Picard S, Wilde R, Tucker GA, Bird CR, Schuch W, Seymour GB (1995). Tomato exo-(1→4)-β-D-galactanase. Isolation, changes during ripening in normal and mutant tomato fruit, and characterization of a related clone. Plant Physiol 1008: 1099–1107.
Carrington CM, Pressy R (1996). β-Galactosidase II activity in relation to changes in cell wall galactosyl composition during tomato ripening. J Am Soc Hortic Sci 121: 132–136.
Combet C, Blanchet C, Geourjon C, Deleage G (2000). NPS@: Network Protein Sequence Analysis. Trends Biochem Sci 25: 147–150.
Conzelmann E, Sandhoff K (1987). Glycolipid and glycoprotein degradation. Adv Enzymol RAMB 60: 89–216.
Cuatrecasas P, Lockwood DH, Caldwell JR (1965). Lactase deficiency in the adult: A common occurrence. Lancet 1: 14–18.
Darabi M, Masoudi-Nejad A, Nemat-Zadeh G (2012). Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae. Mol Biol Rep 39: 8925–8935.
Darabi M, Seddigh S (2013a). Conserved motifs identification of 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) protein in some different species of drosophilidae by bioinformatics tools. Ann Biol Res 4: 158–163.
Darabi M, Seddigh S (2013b). Phylogenetic study of the 3-hydroxy-3- methylglotaryl-Coenzyme A reductase (HMGR) protein in six different family. Eur J Exp Biol 3: 158–164.
De Veau EJI, Gross KC, Huber DJ, Watada AE (1993). Degradation and solubilization of pectin by β-galactosidase purified from avocado mesocarp. Physiol Plantarum 87: 279–285.
Dick AJ, Opoku-Gyamfua A, DeMarco AC (1990). Glycosidases of apple fruit: a multi-functional β-galactosidase. Physiol Plantarum 80: 250–256.
Dimri GP, Lee X, Basile G, Acosta M, Scott G, Roskelley C, Medrano EE, Linskens M, Rubelj I, Pereira-Smith O (1995). A biomarker that identifies senescent human cells in culture and in aging skin in vivo. P Natl Acad Sci USA 92: 9363–9367.
Edwards M, Bowman YJL, Dea ICM, Reid JSG (1988). A β-Dgalactosidase from nasturtium (Tropaeolum majus L.) cotyledons. J Biol Chem 22: 4333–4337.
Fowler AV, Zabin I (1970). The amino acid sequence of beta galactosidase. I. Isolation and composition of tryptic peptides. J Biol Chem 245: 5032–5041.
Geourjon C, Deleage G (1995). SOPMA: significant improvement in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 11: 681–684.
Giannakouros T, Karagiorgos A, Simos G (1991). Expression of β-galactosidase multiple forms during barley (Hordeum vulgare) seed germination. Separation and characterization of enzyme isoforms. Physiol Plantarum 82: 413–418.
Golden KD, John M, Kean EA (1993). β-Galactosidase from Coffea arabica and its role in fruit ripening. Phytochemistry 34: 355–360. Harley SM, Beevers H (1985). Characterization and partial purification of three galactosidases from castor bean endosperm. Phytochemistry 24: 1459–1464.
Hirano Y, Tsumuraya Y, Hashimoto Y (1994). Characterization of spinach leaf α-L-arabinofuranosidases and β-galactosidases and their synergistic action on an endogenous arabinogalactanprotein. Physiol Plantarum 92: 286–296.
Hruba P, Honys D, Twell D, Capková V, Tupy J (2005). Expression of β-galactosidase and β-xylosidase genes during microspore and pollen development. Planta 220: 931–940.
Jacobson RH, Zhang XJ, DuBose RF, Matthews BW (1994). Threedimensional structure of beta-galactosidase from E. coli. Nature 369: 761–766.
Kalnins A, Otto K, Ruther U, Muller-Hill B (1983). Sequence of the lac Z gene of Escherichia coli. EMBO J 2: 593–597.
Kang IK, Suh SG, Gross KC, Byun JK (1994). N-terminal amino acid sequence of persimmon fruit β-galactosidase. Plant Physiol 105: 975–979.
Kesici K, Tüney İ, Zeren D, Güden M, Sukatar A (2013). Morphological and molecular identification of pennate diatoms isolated from Urla, İzmir, coast of the Aegean Sea. Turk J Biol 37: 530–537.
Kitagawa Y, Kanayama Y, Yamaki S (1995). Isolation of β-galactosidase fractions from Japanese pear: activity against native cell wall polysaccharides. Physiol Plantarum 93: 545–550.
Knee M (1973). Polysaccharides changes in cell wall of ripening apple. Phytochemistry 12: 1543–1549.
Kober L, Zehe C, Bode J (2013). Optimized signal peptides for the development of high expressing CHO cell lines. Biotechnol Bioeng 110: 1164–1173.
Kotake T, Dina S, Konishi T, Kaneko S, Igarashi K, Samejima M, Watanabe Y, Kimura K, Tsumuraya Y (2005). Molecular cloning of a β-galactosidase from radish that specifically hydrolyzes β-1→3- and β-1→6-galactosyl residues of arabinogalactan protein. Plant Physiol 138: 1563–1576.
Li SC, Han JW, Chen KC, Chen CS (2001). Purification and characterization of isoforms of β-galactosidases in mung bean seedlings. Phytochemistry 57: 349–359.
Matthews BW (2005). The structure of E. coli beta-galactosidase. C R Biol 328: 549–556.
McCartney L, Ormerod AP, Gidley MJ, Knox JP (2000). Temporal and spatial regulation of pectic (1→4)-β-D-galactan in cell walls of developing pea cotyledons: implications for mechanical properties. Plant J 22: 105–113.
Moctezuma E, Smith DL, Gross KC (2003). Antisense suppression of a β-galactosidase gene (TBG6) in tomato increases fruit cracking. J Exp Bot 54: 2025–2033.
O’Brien JS (1989). β-Galactosidase deficiency (GM1 gangliosidosis, galactosialidosis, and Morquio syndrome type B); gangliosidesialidase deficiency (mucolipidosis IV). In: Scriver CR, Beaudet AL, Sly WS, Valle D, editors. The Metabolic Basis of Inherited Disease. New York, NY, USA: McGraw-Hill, pp. 1797–1806.
Pressy R (1983). β-Galactosidase in ripening tomatoes. Plant Physiol 71: 132–135.
Ranwala AP, Suematsu C, Masuda H (1992). The role of β-galactosidases in the modification of cell wall components during musk-melon fruit ripening. Plant Physiol 100: 1318– 1325.
Ross CS, Cavin S, Wegrzyn T, MacRae EA, Redgwell RJ (1994). Apple β-galactosidase activity against cell wall polysaccharides and characterization of a related cDNA clone. Plant Physiol 106: 521–528.
Ross GS, Redgwell RJ, MacRae EA (1993). Kiwifruit β-galactosidase: isolation and activity against specific fruit cell-wall polysaccharides. Planta 189: 499–506.
Seddigh S, Bandani AR (2012). Comparison of α and β-galactosidase activity in the three cereal pests, Haplothrips tritici Kurdjumov (Thysanoptera: Phlaeothripidae), Rhopalosiphum padi L. (Hemiptera: Aphididae) and Eurygaster integriceps Puton (Hemiptera: Scutelleridae). Mun Ent Zool 7: 904–908.
Serebriiskii IG, Golemis EA (2000). Uses of lacZ to study gene function: evaluation of beta-galactosidase assays employed in the yeast two-hybrid system. Anal Biochem 285: 1–15.
Sorensen SO, Pauly M, Bush M, Skjøt M, McCann MC, Borkhardt B, Ulvskov P (2000). Pectin engineering: modification of potato pectin by in vivo expression of an endo-1,4-β-D-galactanase. P Natl Acad Sci USA, 97: 7639–7644.
Von Heijne G (1985). Signal sequences: The limits of variation. J Mol Biol 184: 99–105.
Wu A, Liu J (2006). Isolation of the promoter of a cotton betagalactosidase gene GhGal1 and its expression in transgenic tobacco plants. Sci China Ser C 49: 105–114.
Yoshioka H, Kashimura Y, Kaneko K (1994). Solubilization and distribution of neutral sugar residues derived from polyuronides during the softening in apple fruit. J JPN Soc Hortic Sci 63: 173–182.