Correlation index-based responsible-enzyme gene screening (CIRES), a novel DNA microarray-based method for enzyme gene involved in glycan biosynthesis

PLoS ONE

Volumn 2, Issue 11, 2007, Pages

  Yamamoto, Harumi ^a,b   Takematsu, Hiromu ^a,c   Fujinawa, Reiko ^b   Naito, Yuko ^a,c   Okuno, Yasushi ^a   Tsujimoto, Gozoh ^a   Suzuki, Akemi ^b   Kozutsumi, Yasunori ^a,b,c  

^a KYOTO UNIVERSITY   (Japan)

^b Japan Science and Technology Agency   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GLYCAN; GLYCOSYLTRANSFERASE; PLANT LECTIN; POLYSACCHARIDE;

ARTICLE; CELL SURFACE; CONTROLLED STUDY; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; DNA MICROARRAY; ENZYME ANALYSIS; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC SCREENING; HUMAN; HUMAN CELL; MOLECULAR PROBE; MOLECULAR RECOGNITION; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; STAINING; BIOSYNTHESIS; GENETICS; METABOLISM; METHODOLOGY;

DNA, COMPLEMENTARY; FLOW CYTOMETRY; GENE EXPRESSION PROFILING; GENETIC SCREENING; GLYCOSYLTRANSFERASES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYSACCHARIDES;

EID: 43349084913     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001232     Document Type: Article

References (51)

1. Freeze HH (1999) Monosaccharide Metabolism In: Varki A, Cummings R, Esko JD, Freeze HH, Hart GW, Marth J, eds. Essentials of Glycobiology. New York: Cold Spring Harbor Laboratory Press. pp 69-84.
2. Hirschberg CB, Robbins PW, Abeijon C (1998) Transporters of nucleotide sugars, ATP, and nucleotide sulfate in the endoplasmic reticulum and Golgi apparatus Annu Rev Biochem 67: 49-69 9759482.
3. Kornfeld R, Kornfeld S (1985) Assembly of Asparogine-Linked Oligosaccharides Annu Rev Biochem 54: 631-664.
4. Aruffo A, Seed B (1987) Molecular cloning of a CD28 cDNA by a high-efficiency COS cell expression system Proc Natl Acad Sci U S A 84: 8573-7 2825196.
5. Seed B, Aruffo A (1987) Molecular cloning of the CD2 antigen, the T-cell crythrocyte receptor, by a rapid immunoselection procedure Proc Natl Acad Sci U S A 84: 3365-9 2437578.
6. Larsen RD, Rajan VP, Ruff MM, Kukowska-Latallo J, Cummings RD, et al. (1989) Isolation of a cDNA encoding a routine UDPgalactose:beta-D-galactosyl-1, 4-N-acetyl-D-glucosaminide alpha-1,3-galactosyltransferase: expression cloning by gene transfer Proc Natl Acad Sci U S A 86: 8227-31 2510162.
7. Narimatsu H (2004) Construction of a human glycogene library and comprehensive functional analysis Glycoconj J 21: 17-24 15467393.
8. Comelli EM, Head SR, Gilmartin T, Whisenant T, Haslam SM, et al. (2006) A focused microarray approach to functional glycomics: transcriptional regulation of the glycome Glycobiology 16: 117-31 16237199.
9. Takematsu H, Kozutsumi Y (2007) DNA microarray in glycobiology In: Greet-Jan B, Lee YC, Suzuki A, Taniguchi N , Voragen AGJ, eds. Comprehensive Glycoscience vol. 2. Oxford: Elsevier. pp 428-448.
10. Kawano S, Hashimoto K, Miyama T, Goto S, Kanehisa M (2005) Prediction of glycan structures from gene expression data based on glycosyltransferase reactions Bioinformatics 21: 3976-82 16159923.
11. Naito Y, Takematsu H, Koyama S, Miyake S, Yamamoto H, et al. (2007) Germinal center marker GL7 probes activation-dependent repression of N-glycolylneuraminic acid, a sialic, acid species involved in the negative modulation of B cell activation Mol Cell Biol 27: 3008-3022.
12. Fernandes B, Sagman U, Auger M, Demetrio M, Dennis JW (1991) Beta 1-6 branched oligosaccharides as a marker of tumor progression in human breast and colon neoplasia. Cancer Res 51: 718-23 1985789.
13. Yamamoto H, Swoger J, Greene S, Saito T, Hurh J, et al. (2000) Beta 1,6-N-acetylglucosamine-bearing N-glycans in human gliomas: implications for a role in regulating invasivity Cancer Res 60: 134-42 10646865.
14. Granovsky M, Fata J, Pawling J, Muller WJ, Khokha R, et al. (2000) Suppression of tumor growth and metastasis in Mgat5-deficient mice Nat Med 6: 306-12 10700233.
15. Partridge EA, Le Roy C, Di Guglielmo GM, Pawling J, Cheung P, et al. (2004) Regulation of cytokine receptors by Golgi N-glycan processing and endocytosis Science 306: 120-4 15459394.
16. Hennet T, Chui D, Paulson JC, Marth JD (1998) Immune regulation by the ST6Gal sialyltransferase Proc Natl Acad Sci U S A 95: 4504-9 9539767.
17. Kuno A, Uchiyama N, Koseki-Kuno S, Ebe Y, Takashima S, et al. (2005) Evanescent-field fluorescence-assisted lectin microarray: a new strategy for glycan profiling Nat Methods 2: 851-6 16278656.
18. Gillespie W, Paulson JC, Kelm S, Pang M, Baum LG (1993) Regulation of alpha 2,3-sialyltransferase expression correlates with conversion of peanut agglutinin (PNA)+ to PNA- phenotype in developing thymocytes J Biol Chem 268: 3801-4 8440675.
19. Priatel JJ, Chui D, Hiraoka N, Simmons CJ, Richardson KB, et al. (2000) The ST3Gal-I sialyltransferase controls CD8+ T lymphocyte homeostasis by modulating O-glycan biosynthesis Immunity 12: 273-83 10755614.
20. Kaifu R, Osawa T, Jeanloz RW (1975) Synthesis of 2-O-(2-acetamido-2-deoxy-beta -D-glucopyranosyl)-D-mannose, and its interaction with D-mannose-specific lectins Carbohydr Res 40: 111-7 1125946.
21. Shinkawa T, Nakamura K, Yamane N, Shoji-Hosaka E, Kanda Y, et al. (2003) The absence of fucose but not the presence of galactose or bisecting N-acetylglucosamine of human IgG1 complex-type oligosaccharides shows the critical role of enhancing antibody-dependent cellular cytotoxicity J Biol Chem 278: 3466-73 12427744.
22. Wang Y, Inoue S, Gu J, Miyoshi E, Noda K, et al. (2005) Dysregulation of TGF-beta1 receptor activation leads to abnormal lung development and emphysema-like phenotype in core fucose-deficient mice Proc Natl Acad Sci U S A 102: 15791-6 16236725.
23. Matsumoto I, Osawa T (1969) Purification and characterization of an anti-H(O) phytohemagglutinin of Ulex europeus Biochim Biophys Acta 194: 180-9 5353123.
24. Okajima T, Fukumoto S, Miyazaki H, Ishida H, Kiso M, et al. (1999) Molecular cloning of a novel alpha2,3-sialyltransferase (ST3Gal VI) that sialylates type II lactosamine structures on glycoproteins and glycolipids J Biol Chem 274: 11479-86 10206952.
25. Ito N, Imai S, Haga S, Nagaike C, Morimura Y, et al. (1996) Localization of binding sites of Ulex europaeus I, Helix pomatia and Griffonia simplicifolia I-B4 lectins and analysis of their backbone structures by several glycosidases and poly-N -acetyllactosamine-specific lectins in human breast carcinomas Histochem Cell Biol 106: 331-9 8897074.
26. Furukawa K, Sato T (1999) Beta-1,4-galactosylation of N-glycans is a complex process Biochim Biophys Acta 1473: 54-66 10580129.
27. Crowley JF, Goldstein JJ, Arnarp J, Lonngren J (1984) Carbohydrate binding studies on the lectin from Datura stramonium seeds Arch Biochem Biophys 231: 524-33 6203486.
28. Yamashita K, Totani K, Ohkura T, Takasaki S, Goldstein IJ, et al. (1987) Carbohydrate binding properties of complpx-type oligosaccharides on immobilized Datura stramonium lectin J Biol Chem 262: 1602-7 3805046.
29. Ihara Y, Nishikava A, Taniguchi N (1995) Effects of dibutyryl cAMP and bromodeoxyuridine on expression of N-acetylglucosaminyltransferases III and V in GOTO neuroblastoma cells Glycoconj J 12: 787-94 8748156.
30. Sasai K, Ikeda Y, Eguchi H, Tsuda T, Honke K, et al. (2002) The action of N-acetylglucosaminyltransferase-V is prevented by the bisecting GlcNAc residue at the-catalytic step. FEBS Lett 522: 151 5 12095636.
31. Miyoshi E, Nishikawa A, Ihara Y, Hayashi N, Fusamoto H, et al. (1994) Selective suppression of N-acetylglucosaminyltransferase III activity in a human hepatoblastoma cell line transfected with hepatitis B virus Cancer Res 54: 1854-8 8137300.
32. Sultan AS, Miyoshi E, Ihara Y, Nishikawa A, Tsukada Y, et al. (1997) Bisecting GlcNAc structures act as negative sorting signals for cell surface glycoproteins in forskolin-treated rat hepatoma cells J Biol Chem 272: 2866-72 9006930.
33. Wang WC, Cummings RD (1988) The immobilized leukoagglutinin from the seeds of Maackia amurensis binds with high affinity to complex-type Asn-linked oligosaccharides containing terminal sialic acid-linked alpha-2,3 to penultimate galactose residues J Biol Chem 263: 4576-85 3350806.
34. Konami Y, Yamamoto K, Osawa T, Irimura T (1994) Strong affinity of Maackia amurensis hemagglutinin (MAH) for sialic acid-containing Ser/Thr linked carbohydrate chains of N-terminal octapeptides from human glycophorin A FEBS Lett 342: 334-8 8150094.
35. Knibbs RN, Goldstein IJ, Ratcliffe RM, Shibuya N (1991) Characterization of the carbohydrate binding specificity of the leukoagglutinating lectin from Maackia amurensis. Comparison with other sialic acid-spccific lectins J Bioll Chem 266: 83-8 1985926.
36. Stanley P, Caillibot V, Siminovitch L (1975) Selection and characterization of eight phenotypically distinct lines of lectin-resistant Chinese hamster ovary cell Cell 6: 121-8 1182798.
37. Kitagawa H, Paulson JC (1994) Differential expression of five sialyltransferase genes in human tissues J Biol Chem 269: 17872-8 8027041.
38. Bierhuizen MF, Mattei MG, Fukuda M (1993) Expression of the developmental I antigen by a cloned human cDNA encoding a member of a beta-1,6-N-acetylglucosaminyltransferase gene family Genes Dev 7: 468-78 8449405.
39. Moremen KW (2002) Golgi alpha-mannosidase II deficiency in vertebrate systems: implications for asparagine-linked oligosaccharide processing in mammals Biochim Biophys Acta 1573: 225-35 12417404.
40. Chen Y, Jain RK, Chandrasekaran EV, Matta KL (1995) Use of sialylated or sulfated derivatives and acrylamide copolymers of Gal beta 1,3GalNAc alpha- and GalNAc alpha- to determine the specificities of blood group T- and Tn-specific lectins and the copolymers to measure anti-T and anti-Tn antibody levels in cancer patients Glycoconj J 12: 55-62 7795413.
41. Nakamura-Tsuruta S, Kominami J, Kuno A, Hirabayashi J (2006) Evidence that Agaricus bisporus agglutinin (ABA) has dual sugar-binding specificity Biochem Biophys Res Commun 347: 215-20 16824489.
42. Hakomori S (2004) Carbohydrate-to-carbohydrate interaction in basic cell biology: a brief overview Arch Biochem Biophys 426: 173-81 15158668.
43. Paulson JC, Blixt O, Collins BE (2006) Sweet spots in functional glycomics Nat Chem Biol 2: 238-48 16619023.
44. Fukui S, Feizi T, Galustian C, Lawson AM, Chai W (2002) Oligosaccharide microarrays for high-throughput detection and specificity assignments of carbohydrate-protein interactions Nat Biotechnol. 20: 1011-7 12219077.
45. Blixt O, Head S, Mondala T, Scanlan C, Huflejt ME, et al. (2004) Printed covalent glycan array for ligand profiling of diverse glycan binding proteins Proc Natl Acad Sci U S A 101: 17033-8 15563589.
46. Kamekawa N, Hayama K, Nakamura-Tsuruta S, Kuno A, Hirabayashi J (2006) A combined strategy for glycan profiling: a model study with pyridylaminated oligosaccharides J Biochem (Tokyo) 140: 337-47 16861248.
47. Edwards D (2003) Non-linear normalization and background correction in one-channel cDNA microarray studies Bioinformatics 19: 825-33 12724292.
48. Smyth GK (2005) Limma: linear models for microarray data. In: R. Gentleman VC, S. Dudoit, R. Irizarry, W. Huber, eds. 'Bioinformatics and Computational Biology Solutions using R and Bioconductor'. New York Springer. pp Chapter 23.
49. Team RDC (2004) R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing, http://www.R-project.org.
50. Morita S, Kojima T, Kitamura T (2000) Plat-E: An efficient and stable system for transient packaging of retroviruses Gene Ther 7: 1063-6 10871756.
51. Cummings R (1999) Plant Lectins. In: Varki A, Cummings R, Esko JD, Freeze HH, Hart GW, Marth J. Essentials of Glycobiology. New York: Cold Spring Harbor Iaboratory Press. pp 455-468.