medigraphic.com
ISSN 1027-2852 (Digital)
ISSN 0864-4551 (Impreso)

2011, Número 1

<< Anterior Siguiente >>

Biotecnol Apl 2011; 28 (1)


Glicosilación y Bioinformática: estado actual de las herramientas para predecir glicosilación

Mazola Y, Chinea G, Musacchio A

Idioma: Ingles.
Referencias bibliográficas: 99
Paginas: 6-12
Archivo PDF: 213.17 Kb.


RESUMEN

El desarrollo de algoritmos computacionales para la predicción de sitios potenciales de glicosilación en las proteínas ha sido impulsado en los últimos años. La glicosilación constituye una modificación co-y post-traduccional involucrada en una gran variedad de procesos biológicos críticos. La localización de los sitios potenciales de glicosilación facilita la modificación racional de las funciones relacionadas con la glicosilación en las células. Este manuscrito resume el estado actual de las herramientas bioinformáticas y las bases de datos disponibles para la glicobiología, haciendo énfasis en los predictores de glicosilación. Además, como complemento se incluyen las principales características de los diferentes tipos de glicosilación.


REFERENCIAS (EN ESTE ARTÍCULO)

  1. Ramamurthy B, Hook P, Larsson L. An overview of carbohydrate-protein interactions with specific reference to myosin and ageing. Acta Physiol Scand. 1999; 167:327-9.

  2. Mitra N, Sinha S, Ramya TN, Surolia A. N-linked oligosaccharides as outfitters for glycoprotein folding, form and function. Trends Biochem Sci. 2006;31:156-63.

  3. Mbonye UR, Yuan C, Harris CE, Sidhu RS, Song I, Arakawa T, et al. Two distinct pathways for cyclooxygenase-2 protein degradation. J Biol Chem. 2008;283:8611-23.

  4. Sola RJ, Griebenow K. Effects of glycosylation on the stability of protein pharmaceuticals. J Pharm Sci. 2009;98:1223-45.

  5. Specks U, Fass DN, Finkielman JD, Hummel AM, Viss MA, Litwiller RD, et al. Functional significance of Asn-linked glycosylation of proteinase 3 for enzymatic activity, processing, targeting, and recognition by anti-neutrophil cytoplasmic antibodies. J Biochem. 2007;141:101-12.

  6. Corthay A, Backlund J, Broddefalk J, Michaelsson E, Goldschmidt TJ, Kihlberg J, et al. Epitope glycosylation plays a critical role for T cell recognition of type II collagen in collagen-induced arthritis. Eur J Immunol. 1998;28:2580-90.

  7. Vagin O, Kraut JA, Sachs G. Role of N-glycosylation in trafficking of apical membrane proteins in epithelia. Am J Physiol Renal Physiol. 2009;296:F459-F469.

  8. Couldrey C, Green JE. Metastases: the glycan connection. Breast Cancer Res. 2000;2:321-3.

  9. Corthay A, Backlund J, Holmdahl R. Role of glycopeptide-specific T cells in collagen-induced arthritis: an example how post-translational modification of proteins may be involved in autoimmune disease. Ann Med. 2001;33:456-65.

  10. Freeze HH. Update and perspectives on congenital disorders of glycosylation. Glycobiology. 2001;11:129R-43R.

  11. Varki A, Cummings RD, Esko JD, et al., editors. Essentials of glycobiology. 2nd ed. New York: Cold Spring Harbor Laboratory press; 2008.

  12. Zaia J. Mass spectrometry and the emerging field of glycomics. Chem Biol. 2008;15:881-92.

  13. Chen YZ, Tang YR, Sheng ZY, Zhang Z. Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs. BMC Bioinformatics. 2008;9:101.

  14. Aoki-Kinoshita KF. An introduction to bioinformatics for glycomics research. PLoS Comput Biol. 2008;4:e1000075.

  15. der Lieth CW, Bohne-Lang A, Lohmann KK, Frank M. Bioinformatics for glycomics: status, methods, requirements and perspectives. Brief Bioinform. 2004;5:164-78.

  16. Frank M, Schloissnig S. Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci. 2010;67:2749-72.

  17. Bause E, Legler G. The role of the hydroxy amino acid in the triplet sequence Asn-Xaa-Thr(Ser) for the N-glycosylation step during glycoprotein biosynthesis. Biochem J. 1981;195:639-44.

  18. Schaffer C, Graninger M, Messner P. Prokaryotic glycosylation. Proteomics. 2001;1:248-61.

  19. Weerapana E, Imperiali B. Asparagine-linked protein glycosylation: from eukaryotic to prokaryotic systems. Glycobiology. 2006;16:91R-101R.

  20. Yurist-Doutsch S, Chaban B, VanDyke DJ, Jarrell KF, Eichler J. Sweet to the extreme: protein glycosylation in Archaea. Mol Microbiol. 2008;68:1079-84.

  21. Helenius A, Aebi M. Intracellular functions of N-linked glycans. Science. 2001;291:2364-9.

  22. Helenius A, Aebi M. Roles of N-linked glycans in the endoplasmic reticulum. Annu Rev Biochem. 2004;73:1019-49.

  23. Jones J, Krag SS, Betenbaugh MJ. Controlling N-linked glycan site occupancy. Biochim Biophys Acta. 2005;1726:121-37.

  24. Munro S. What can yeast tell us about N-linked glycosylation in the Golgi apparatus? FEBS Lett. 2001;498:223-7.

  25. Roitsch T, Lehle L. Structural requirements for protein N-glycosylation. Influence of acceptor peptides on cotranslational glycosylation of yeast invertase and site-directed mutagenesis around a sequon sequence. Eur J Biochem. 1989;181:525-9.

  26. Gavel Y, von Heijne G. Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: implications for protein engineering. Protein Eng. 1990;3:433-42.

  27. Shakin-Eshleman SH, Spitalnik SL, Kasturi L. The amino acid at the X position of an Asn-X-Ser sequon is an important determinant of N-linked core-glycosylation efficiency. J Biol Chem. 1996;271:6363-6.

  28. Kasturi L, Chen H, Shakin-Eshleman SH. Regulation of N-linked core glycosylation: use of a site-directed mutagenesis approach to identify Asn-Xaa-Ser/Thr sequons that are poor oligosaccharide acceptors. Biochem J. 1997;323 ( Pt 2):415-9.

  29. Christlet TH, Biswas M, Veluraja K. A database analysis of potential glycosylating Asn-X-Ser/Thr consensus sequences. Acta Crystallogr D Biol Crystallogr. 1999;55:1414-20.

  30. Petrescu AJ, Milac AL, Petrescu SM, Dwek RA, Wormald MR. Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding. Glycobiology. 2004; 14:103-14.

  31. Ben Dor S, Esterman N, Rubin E, Sharon N. Biases and complex patterns in the residues flanking protein N-glycosylation sites. Glycobiology. 2004;14:95-101.

  32. Kowarik M, Young NM, Numao S, Schulz BL, Hug I, Callewaert N, et al. Definition of the bacterial N-glycosylation site consensus sequence. EMBO J. 2006; 25:1957-66.

  33. Abu-Qarn M, Eichler J. An analysis of amino acid sequences surrounding archaeal glycoprotein sequons. Archaea. 2007;2:73-81.

  34. Nilsson I, von Heijne G. Glycosylation efficiency of Asn-Xaa-Thr sequons depends both on the distance from the C terminus and on the presence of a downstream transmembrane segment. J Biol Chem. 2000;275:17338-43.

  35. Walmsley AR, Hooper NM. Glycosylation efficiency of Asn-Xaa-Thr sequons is independent of distance from the C-terminus in membrane dipeptidase. Glycobiology. 2003;13:641-6.

  36. Bause E. Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes. Biochem J. 1983;209:331-6.

  37. Bause E, Hettkamp H, Legler G. Conformational aspects of N-glycosylation of proteins. Studies with linear and cyclic peptides as probes. Biochem J. 1982;203:761-8.

  38. Yan A, Lennarz WJ. Unraveling the mechanism of protein N-glycosylation. J Biol Chem. 2005;280:3121-4.

  39. Reddy A, Gibbs BS, Liu YL, Coward JK, Changchien LM, Maley F. Glycosylation of the overlapping sequons in yeast external invertase: effect of amino acid variation on site selectivity in vivo and in vitro. Glycobiology. 1999;9:547-55.

  40. NetNGlyc 1.0 Server (Internet; updated 2007 Mar 09; cited 2011 Jan 17). Available from: http://www.cbs.dtu.dk/services/NetNGlyc/.

  41. Caragea C, Sinapov J, Silvescu A, Dobbs D, Honavar V. Glycosylation site prediction using ensembles of Support Vector Machine classifiers. BMC Bioinformatics. 2007;8:438.

  42. Hamby SE, Hirst JD. Prediction of glycosylation sites using random forests. BMC Bioinformatics. 2008;9:500.

  43. Liu Y, Nguyen A, Wolfert RL, Zhuo S. Enhancing the secretion of recombinant proteins by engineering N-glycosylation sites. Biotechnol Prog. 2009;25:1468-75.

  44. Radoslavov G, Jordanova R, Teofanova D, Georgieva K, Hristov P, Salomone-Stagni M, et al. A novel secretory poly-cysteine and histidine-tailed metalloprotein (Ts-PCHTP) from Trichinella spiralis (Nematoda). PLoS One. 2010;5:e13343.

  45. Lu C, Walker WH, Sun J, Weisz OA, Gibbs RB, Witchel SF, et al. Insulin-like peptide 6: characterization of secretory status and posttranslational modifications. Endocrinology. 2006;147:5611-23.

  46. Gupta R, Brunak S. Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput. 2002;7:310-22.

  47. Nothaft H, Szymanski CM. Protein glycosylation in bacteria: sweeter than ever. Nat Rev Microbiol. 2010;8:765-78.

  48. Gentzsch M, Tanner W. Protein-O-glycosylation in yeast: protein-specific mannosyltransferases. Glycobiology. 1997;7:481-6.

  49. Hanisch FG. O-glycosylation of the mucin type. Biol Chem. 2001;382:143-9.

  50. Carraway KL, Hull SR. Cell surface mucin-type glycoproteins and mucin-like domains. Glycobiology. 1991;1:131-8.

  51. Strous GJ, Dekker J. Mucin-type gly-coproteins. Crit Rev Biochem Mol Biol. 1992;27:57-92.

  52. Asker N, Baeckstrom D, Axelsson MA, Carlstedt I, Hansson GC. The human MUC2 mucin apoprotein appears to dimerize before O-glycosylation and shares epitopes with the 'insoluble' mucin of rat small intestine. Biochem J. 1995;308(Pt 3):873-80.

  53. Thanka Christlet TH, Veluraja K. Database analysis of O-glycosylation sites in proteins. Biophys J. 2001;80:952-60.

  54. Wilson IB, Gavel Y, von Heijne G. Amino acid distributions around O-linked glycosylation sites. Biochem J. 1991;275(Pt 2):529-34.

  55. Julenius K, Molgaard A, Gupta R, Brunak S. Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology. 2005;15:153-64.

  56. Li S, Liu B, Zeng R, Cai Y, Li Y. Predicting O-glycosylation sites in mammalian proteins by using SVMs. Comput Biol Chem. 2006;30:203-8.

  57. Kobayashi T, Nishizaki R, Ikezawa H. The presence of GPI-linked protein(s) in an archaeobacterium, Sulfolobus acidocaldarius, closely related to eukaryotes. Biochim Biophys Acta. 1997;1334:1-4.

  58. Eisenhaber B, Bork P, Eisenhaber F. Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes. Protein Eng. 2001;14:17-25.

  59. Menon AK. Structural analysis of glycosylphosphatidylinositol anchors. Methods Enzymol. 1994;230:418-42.

  60. Caras IW, Weddell GN, Davitz MA, Nussenzweig V, Martin DW Jr. Signal for attachment of a phospholipid membrane anchor in decay accelerating factor. Science. 1987;238:1280-3.

  61. Udenfriend S, Kodukula K. How glycosylphosphatidylinositol-anchored membrane proteins are made. Annu Rev Biochem. 1995;64:563-91.

  62. Chatterjee S, Mayor S. The GPI-anchor and protein sorting. Cell Mol Life Sci. 2001;58:1969-87.

  63. Koelsch R, Gottwald S, Lasch J. Release of GPI-anchored membrane aminopeptidase P by enzymes and detergents has some peculiarities. Biochim Biophys Acta. 1994;1190:170-2.

  64. Bergelson JM, Chan M, Solomon KR, St John NF, Lin H, Finberg RW. Decay-accelerating factor (CD55), a glycosylphosphatidylinositol-anchored complement regulatory protein, is a receptor for several echoviruses. Proc Natl Acad Sci USA. 1994;91:6245-8.

  65. Chan CH, Stanners CP. Recent advances in the tumour biology of the GPI-anchored carcinoembryonic antigen family members CEACAM5 and CEACAM6. Curr Oncol. 2007;14:70-3.

  66. Cervello M, Matranga V, Durbec P, Rougon G, Gomez S. The GPI-anchored adhesion molecule F3 induces tyrosine phosphorylation: involvement of the FNIII repeats. J Cell Sci. 1996;109(Pt 3):699-704.

  67. Frieman MB, Cormack BP. Multiple sequence signals determine the distribution of glycosylphosphatidylinositol proteins between the plasma membrane and cell wall in Saccharomyces cerevisiae. Microbiology. 2004;150:3105-14.

  68. Nozaki M, Ohishi K, Yamada N, Kinoshita T, Nagy A, Takeda J. Developmental abnormalities of glycosylphosphatidylinositol-anchor-deficient embryos revealed by Cre/loxP system. Lab Invest. 1999;79:293-9.

  69. Orlean P, Menon AK. Thematic review series: lipid posttranslational modifications. GPI anchoring of protein in yeast and mammalian cells, or: how we learned to stop worrying and love glycophospholipids. J Lipid Res. 2007;48:993-1011.

  70. Eisenhaber B, Bork P, Eisenhaber F. Prediction of potential GPI-modification sites in proprotein sequences. J Mol Biol. 1999;292:741-58.

  71. Kronegg J, Buloz D. Detection/prediction of GPI cleavage site (GPI-anchor) in a protein (DGPI). 1999. Available from: http://129.194.185.165/dgpi/index_en.html

  72. Fankhauser N, Maser P. Identification of GPI anchor attachment signals by a Kohonen self-organizing map. Bioinformatics. 2005;21:1846-52.

  73. Dalley JA, Bulleid NJ. The endoplasmic reticulum (ER) translocon can differentiate between hydrophobic sequences allowing signals for glycosylphosphatidylinositol anchor addition to be fully translocated into the ER lumen. J Biol Chem. 2003;278:51749-57.

  74. Poisson G, Chauve C, Chen X, Bergeron A. FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring. Genomics Proteomics Bioinformatics. 2007;5:121-30.

  75. Pierleoni A, Martelli PL, Casadio R. PredGPI: a GPI-anchor predictor. BMC Bioinformatics. 2008;9:392.

  76. Chou KC, Shen HB. MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem Biophys Res Commun. 2007;360:339-45.

  77. Hofsteenge J, Muller DR, de Beer T, Loffler A, Richter WJ, Vliegenthart JF. New type of linkage between a carbohydrate and a protein: C-glycosylation of a specific tryptophan residue in human RNase Us. Biochemistry. 1994;33:13524-30.

  78. de Beer T, Vliegenthart JF, Loffler A, Hofsteenge J. The hexopyranosyl residue that is C-glycosidically linked to the side chain of tryptophan-7 in human RNase Us is alpha-mannopyranose. Biochemistry. 1995;34:11785-9.

  79. Perez-Vilar J, Randell SH, Boucher RC. C-Mannosylation of MUC5AC and MUC5B Cys subdomains. Glycobiology. 2004;14:325-37.

  80. Zanetta JP, Pons A, Richet C, Huet G, Timmerman P, Leroy Y, et al. Quantitative gas chromatography/mass spectrometry determination of C-mannosylation of tryptophan residues in glycoproteins. Anal Biochem. 2004;329:199-206.

  81. Wang LW, Leonhard-Melief C, Haltiwanger RS, Apte SS. Post-translational modification of thrombospondin type-1 repeats in ADAMTS-like 1/punctin-1 by C-mannosylation of tryp-tophan. J Biol Chem. 2009;284:30004-15.

  82. Ihara Y, Manabe S, Kanda M, Kawano H, Nakayama T, Sekine I, et al. Increased expression of protein C-mannosylation in the aortic vessels of diabetic Zucker rats. Glycobiology. 2005;15:383-92.

  83. Julenius K. NetCGlyc 1.0: prediction of mammalian C-mannosylation sites. Glycobiology. 2007;17:868-76.

  84. Krieg J, Hartmann S, Vicentini A, Glasner W, Hess D, Hofsteenge J. Recognition signal for C-mannosylation of Trp-7 in RNase 2 consists of sequence Trp-x-x-Trp. Mol Biol Cell. 1998;9:301-9.

  85. Hofsteenge J, Blommers M, Hess D, Furmanek A, Miroshnichenko O. The four terminal components of the complement system are C-mannosylated on multiple tryptophan residues. J Biol Chem. 1999;274:32786-94.

  86. Gupta R, Birch H, Rapacki K, Brunak S, Hansen JE. O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins. Nucleic Acids Res. 1999;27:370-2.

  87. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 2003;31:365-70.

  88. Lee TY, Hsu JB, Chang WC, Wang TY, Hsu PC, Huang HD. A comprehensive resource for integrating and displaying protein post-translational modifications. BMC Res Notes. 2009;2:111.

  89. Li H, Xing X, Ding G, Li Q, Wang C, Xie L, et al. SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol Cell Proteomics. 2009;8:1839-49.

  90. Garavelli JS. The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics. 2004;4:1527-33.

  91. Doubet S, Bock K, Smith D, Darvill A, Albersheim P. The complex carbohydrate structure database. Trends Biochem Sci. 1989;14:475-7.

  92. Lutteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, der Lieth CW. GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. Glycobiology. 2006;16:71R-81R.

  93. Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, et al. KEGG as a glycome informatics resource. Glycobiology. 2006;16:63R-70R.

  94. Ranzinger R, Herget S, Wetter T, der Lieth CW. GlycomeDB - integration of open-access carbohydrate structure databases. BMC Bioinformatics. 2008;9:384.

  95. Consortium for Functional Glycomics [Internet]. Consortium for Functional Glycomics funded by NIGMS [updated 2007 Apr 05; cited 2011 Jan 17]. Available from: http://www.functionalglycomics.org/static/consortium/consortium.shtml

  96. Imberty A, Delage MM, Bourne Y, Cambillau C, Perez S. Data bank of three-dimensional structures of disaccharides: Part II, N-acetyllactosaminic type N-glycans. Comparison with the crystal structure of a biantennary octasaccharide. Glycoconj J. 1991;8:456-83.

  97. Lutteke T, der Lieth CW. pdb-care (PDB carbohydrate residue check): a program to support annotation of complex carbohydrate structures in PDB files. BMC Bioinformatics. 2004;5:69.

  98. Frank M, Lutteke T,der Lieth CW. GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. Nucleic Acids Res. 2007;35:287-90.

  99. Lutteke T, Frank M, der Lieth CW. Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. Nucleic Acids Res. 2005;33:D242-D246.




2020     |     www.medigraphic.com