Abstract
To study a novel protein family requires a biologist to understand many different types of information. Moreover, the speed of discovery in biology has been expanding exponentially. And, the public knowledge management platforms are not customerized to a research project. It is often cumbersome. To overcome these obstacles, we have set up a knowledge management platform by integrating several databases. Particularly, we have constructed a knowledge management platform on the novel LARGE-liked glycosyltransferases family. The predicted protein structure of a LARGE protein family member contains an N-terminal cytoplasmic domain, a transmembrane region, a coiled-coil motif and a putative catalytic domain with the conserved DXD motif and a conserved protein structural domain, as previously described. Firstly, we have developed workflow to identify the members of the LARGE-liked protein family. We then have integrated DNA sequence, protein sequence, protein domain, protein family based on the CAZY databank, human and animal disease information and references into one knowledge management platform for studying diseases.
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References
Peyrard, M., Seroussi, E., Sandberg-Nordqvist, A.C., Xie, Y.G., Han, F.Y., Fransson, I., Collins, J., Dunham, I., Kost-Alimova, M., Imreh, S., Dumanski, J.P.: The human LARGE gene from 22q12.3-q13.1 is a new, distinct member of the glycosyltransferase gene family. Proc. Natl. Acad. Sci. USA 96, 598–603 (1999)
Grewal, P.K., Holzfeind, P.J., Bittner, R.E., Hewitt, J.E.: Mutant glycosyltransferase and altered glycosylation of alpha-dystroglycan in the myodystrophy mouse. Nat. Genet. 28, 151–154 (2001)
Holzfeind, P.J., Grewal, P.K., Reitsamer, H.A., Kechvar, J., Lassmann, H., Hoeger, H., Hewitt, J.E., Bittner, R.E.: Skeletal, cardiac and tongue muscle pathology, defective retinal transmission, and neuronal migration defects in the Large(myd) mouse defines a natural model for glycosylation-deficient muscle - eye - brain disorders. Hum. Mol. Genet. 11, 2673–2687 (2002)
Longman, C., Brockington, M., Torelli, S., Jimenez-Mallebrera, C., Kennedy, C., Khalil, N., Feng, L., Saran, R.K., Voit, T., Merlini, L., Sewry, C.A., Brown, S.C., Muntoni, F.: Mutations in the human LARGE gene cause MDC1D, a novel form of congenital muscular dystrophy with severe mental retardation and abnormal glycosylation of alpha-dystroglycan. Hum. Mol. Genet. 12, 2853–2861 (2003)
Busch, C., Hofmann, F., Selzer, J., Munro, S., Jeckel, D., Aktories, K.: A common motif of eukaryotic glycosyltransferases is essential for the enzyme activity of large clostridial cytotoxins. J. Biol. Chem. 273, 19566–19572 (1998)
Grewal, P.K., Hewitt, J.E.: Mutation of Large, which encodes a putative glycosyltransferase, in an animal model of muscular dystrophy. Biochim. Biophys. Acta. 1573, 216–224 (2002)
Pang, T.L., Wu, C.J., Chen, P.A., Weng, Y.L., Chen, M.Y.: Dictyostelium gnt15 encodes a protein with similarity to LARGE and plays an essential role in development. Biochem. Biophys. Res. Commun. 360, 83–89 (2007)
Hwa, K.Y., Pang, T.L., Chen, M.Y.: Classification of LARGE-liked GlcNAc-Transferases of Dictyostelium discoideum by Phylogenetic Analysis. In: Frontiers in the Convergence of Bioscience and Information Technologies, pp. 289–293 (2007)
Coutinho, P.M., Deleury, E., Davies, G.J., Henrissat, B.: An evolving hierarchical family classification for glycosyltransferases. J. Mol. Biol. 328, 307–317 (2003)
Heinrichs, D.E., Yethon, J.A., Whitfield, C.: Molecular basis for structural diversity in the core regions of the lipopolysaccharides of Escherichia coli and Salmonella enteric. Mol. Microbiol. 30, 221–232 (1998)
Sasaki, K., Kurata-Miura, K., Ujita, M., Angata, K., Nakagawa, K., Sekine, S., Nishi, T., Fukuda, M.: Expression cloning of cDNA encoding a human beta-1,3-N-acetyl- glucosaminyltransferase that is essential for poly-N-acetyllactosamine synthesis. Proc. Natl. Acad. Sci. USA 94, 14294–14299 (1997)
Kanagawa, M., Saito, F., Kunz, S., Yoshida-Moriguchi, S., Barresi, R., Kobayashi, Y.M., Muschler, J., Dumanski, J.P., Michele, D.E., Oldstone, M.B., Campbell, K.P.: Molecular recognition by LARGE is essential for expression of functional dystroglycan. Cell 117, 953–964 (2004)
Barresi, R., Michele, D.E., Kanagawa, M., Harper, H.A., Dovico, S.A., Satz, J.S., Moore, S.A., Zhang, W., Schachter, H., Dumanski, J.P., Cohn, R.D., Nishino, I., Campbell, K.P.: LARGE can functionally bypass alpha-dystroglycan glycosylation defects in distinct congenital muscular dystrophies. Nat. Med. 10, 696–703 (2004)
Patnaik, S.K., Stanley, P.: Mouse large can modify complex N- and mucin O-glycans on alpha-dystroglycan to induce laminin binding. J. Biol. Chem. 280, 20851–20859 (2005)
Fujimura, K.: LARGE2 facilitates the maturation of alpha-dystroglycan more effectively than LARGE. Biochem. Biophys. Res. Commun. 329, 1162–1171 (2005)
Przybył, M., Pocheć, E., Link-Lenczowski, P., Lityńska, A.: Beta1-6 branching of cell surface glycoproteins contribute to uveal melanoma progression by up-regulating cell motility. Mol. Vis. 26, 625–636 (2008)
Abbott, K.L., Aoki, K., Lim, J.M., Porterfield, M., Johnson, R., O’Regan, R.M., Wells, L., Tiemeyer, M., Pierce, M.: Targeted glycoproteomic identification of biomarkers for human breast carcinoma. J. Proteome Res. 7, 1470–1480 (2008)
Kim, Y.S., Hwang, S.Y., Kang, H.Y., Sohn, H., Oh, S., Kim, J.Y., Yoo, J.S., Kim, Y.H., Kim, C.H., Jeon, J.H., Lee, J.M., Kang, H.A., Miyoshi, E., Taniguchi, N., Yoo, H.S., Ko, J.H.: Functional proteomics study reveals that N-Acetylglucosaminyltransferase V reinforces the invasive/metastatic potential of colon cancer through aberrant glycosylation on tissue inhibitor of metalloproteinase-1. Mol. Cell Proteomics 7, 1–14 (2007)
Abbott, K.L., Nairn, A.V., Hall, E.M., Horton, M.B., McDonald, J.F., Moremen, K.W., Dinulescu, D.M., Pierce, M.: Focused glycomic analysis of the N-linked glycan biosynthetic pathway in ovarian cancer. Proteomics 8, 3210–3220 (2008)
Jin, X.L., Liu, H.B., Zhang, Y., Wang, B.S., Chen, H.L.: Alteration in N -acetylglucosaminyltransferase activities and glycan structure in tissue and bile glycoproteins from extrahepatic bile duct carcinoma. Glycoconj. J. 20, 399–406 (2004)
Guo, J.M., Zhang, X.Y., Chen, H.L., Wang, G.M., Zhang, Y.K.: Structural alterations of sugar chains in urine fibronectin from bladder cancer patients and its enzymatic mechanism. J. Cancer Res. Clin. Oncol. 127, 512–519 (2001)
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Hwa, Ky., Lin, WM., Lee, CP., Chen, MY. (2009). Knowledge Management on the Novel LAGE-Like GlcNAc-Transferase Protein Family. In: Ślęzak, D., Arslan, T., Fang, WC., Song, X., Kim, Th. (eds) Bio-Science and Bio-Technology. BSBT 2009. Communications in Computer and Information Science, vol 57. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-10616-3_19
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DOI: https://doi.org/10.1007/978-3-642-10616-3_19
Publisher Name: Springer, Berlin, Heidelberg
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