A novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan

Plant Physiology

Volumn 144, Issue 1, 2007, Pages 43-53

  Mitchell, Rowan A C ^a   Dupree, Paul ^b   Shewry, Peter R ^a  

^a ROTHAMSTED RESEARCH   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; ENZYMES; GENE ENCODING; GENE EXPRESSION; PLANT CELL CULTURE; POLYSACCHARIDES;

ARABIDOPSIS GENES; ARABINOXYLAN; BIOSYNTHETIC ENZYMES; FERULOYLATION;

CELL MEMBRANES;

BIOSYNTHESIS; CELL WALLS; ENZYMES; GENES;

ARABIDOPSIS; ARABIDOPSIS THALIANA; DICOTYLEDONEAE; ORYZA SATIVA;

EID: 34250654827     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.106.094995     Document Type: Article

References (38)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
2. Aspeborg H, Schrader J, Coutinho PM, Stam M, Kallas A, Djerbi S, Nilsson P, Denman S, Amini B, Sterky F, et al (2005) Carbohydrateactive enzymes involved in the secondary cell wall biogenesis in hybrid aspen. Plant Physiol 137: 983-997
3. Bacic A, Harris PJ, Stone BA (1988) Structure and function of plant cell walls. In J Preiss, ed, The Biochemistry of Plants, Vol 14. Academic Press, San Diego, pp 297-372
4. Bauer S, Vasu P, Persson S, Mort AJ, Somerville CR (2006) Development and application of a suite of polysaccharide-degrading enzymes for analyzing plant cell walls. Proc Natl Acad Sci USA 103: 11417-11422
5. Bencur P, Steinkellner H, Svoboda B, Mucha J, Strasser R, Kolarich D, Hann S, Kollensperger G, Glossl J, Altmann F, et al (2005) Arabidopsis thaliana beta 1,2-xylosyltransferase: an unusual glycosyltransferase with the potential to act at multiple stages of the plant N-glycosylation pathway. Biochem J 388: 515-525
6. Boguski MS, Lowe TMJ, Tolstoshev CM (1993) dbEST - Database for expressed sequence tags. Nat Genet 4: 332-333
7. Boutanaev AM, Kalmykova AI, Shevelyou YY, Nurminsky DI (2002) Large clusters of co-expressed genes in the Drosophila genome. Nature 420: 666-669
8. Bouton S, Leboeuf E, Mouille G, Leydecker MT, Talbotec J, Granier F, Lahaye M, Hofte H, Truong HN (2002) Quasimodo1 encodes a putative membrane-bound glycosyltransferase required for normal pectin synthesis and cell adhesion in Arabidopsis. Plant Cell 14: 2577-2590
9. Brown DM, Zeef LAH, Ellis J, Goodacre R, Turner SR (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17: 2281-2295
10. Burton RA, Wilson SM, Hrmova M, Harvey AJ, Shirley NJ, Stone BA, Newbigin EJ, Bacic A, Fincher GB (2006) Cellulose synthase-like CslF genes mediate the synthesis of cell wall (1,3;1,4)-beta-D-glucans. Science 311: 1940-1942
11. Carpita NC (1996) Structure and biogenesis of the cell walls of grasses. Annu Rev Plant Physiol Plant Mol Biol 47: 445-476
12. Carpita NC, Gibeaut DM (1993) Structural models of primary-cell walls in flowering plants - consistency of molecular-structure with the physicalproperties of the walls during growth. Plant J 3: 1-30
13. Coutinho PM, Deleury E, Davies GJ, Henrissat B (2003) An evolving hierarchical family classification for glycosyltransferases. J Mol Biol 328: 307-317
14. Dhugga KS (2005) Plant Golgi cell wall synthesis: from genes to enzyme activities. Proc Natl Acad Sci USA 102: 1815-1816
15. Egelund J, Skjot M, Geshi N, Ulvskov P, Petersen BL (2004) A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes. Plant Physiol 136: 2609-2620
16. Fondeur-Gelinotte M, Lattard V, Oriol R, Mollicone R, Jacquinet JC, Mulliert G, Gulberti S, Netter P, Magdalou J, Ouzzine M, et al (2006) Phylogenetic and mutational analyses reveal key residues for UDPglucuronic acid binding and activity of beta 1,3-glucuronosyltransferase I (GlcAT-I). Protein Sci 15: 1667-1678
17. Geisler-Lee J, Geisler M, Coutinho PM, Segerman B, Nishikubo N, Takahashi J, Aspeborg H, Djerbi S, Master E, Andersson-Gunneras S, et al (2006) Poplar carbohydrate-active enzymes: gene identification and expression analyses. Plant Physiol 140: 946-962
18. Grabber JH (2005) How do lignin composition, structure, and cross-linking affect degradability? A review of cell wall model studies. Crop Sci 45: 820-831
19. Harholt J, Jensen JK, Sorensen SO, Orfila C, Pauly M, Scheller HV (2006) ARABINAN DEFICIENT 1 is a putative arabinosyltransferase involved in biosynthesis of pectic arabinan in Arabidopsis. Plant Physiol 140: 49-58
20. Harris PJ, Kelderman MR, Kendon MF, McKenzie RJ (1997) Monosaccharide compositions of unlignified cell walls of monocotyledons in relation to the occurrence of wall-bound ferulic acid. Biochem Syst Ecol 25: 167-179
21. Haverty PM, Hsiao LL, Gullans SR, Hansen U, Weng ZP (2004) Limited agreement among three global gene expression methods highlights the requirement for non-global validation. Bioinformatics 20: 3431-3441
22. Iwai H, Masaoka N, Ishii T, Satoh S (2002) A pectin glucuronyltransferase gene is essential for intercellular attachment in the plant meristem. Proc Natl Acad Sci USA 99: 16319-16324
23. Kitagawa H, Tone Y, Tamura J, Neumann KW, Ogawa T, Oka S, Kawasaki T, Sugahara K (1998) Molecular cloning and expression of glucuronyltransferase I involved in the biosynthesis of the glycosaminoglycanprotein linkage region of proteoglycans. J Biol Chem 273: 6615-6618
24. Liepman AH, Wilkerson CG, Keegstra K (2005) Expression of cellulose synthase-like (Csl) genes in insect cells reveals that CslA family members encode mannan synthases. Proc Natl Acad Sci USA 102: 2221-2226
25. McNeil M, Darvill AG, Fry SC, Albersheim P (1984) Structure and function of the primary-cell walls of plants. Annu Rev Biochem 53: 625-663
26. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, et al (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35: D883-D887
27. Persson S, Wei HR, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA 102: 8633-8638
28. Renard C, Thibault JF (1993) Structure and properties of apple and sugarbeet pectins extracted by chelating-agents. Carbohydr Res 244: 99-114
29. Rhee SY, Beavis W, Berardini TZ, Chen GH, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
30. Richmond TA, Somerville CR (2000) The cellulose synthase superfamily. Plant Physiol 124: 495-498
31. Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flugge UI, Kunze R (2003) ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol 131: 16-26
32. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, et al (2002) The bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618
33. Strasser R, Mucha J, Mach L, Altmann F, Wilson IBH, Glossl J, Steinkellner H (2000) Molecular cloning and functional expression of beta 1,2-xylosyltransferase cDNA from Arabidopsis thaliana. FEBS Lett 472: 105-108
34. Wende G, Fry SC (1997a) 2-O-β-D- xylopyranosyl-(5-O-feruloyl)-L-arabinose, a widespread component of grass cell walls. Phytochemistry 44: 1019-1030
35. Wende G, Fry SC (1997b) O-feruloylated, O-acetylated oligosaccharides as side-chains of grass xylans. Phytochemistry 44: 1011-1018
36. Wilkie KCB (1979) The hemicelluloses of grasses and cereals. Adv Carbohydr Chem Biochem 36: 215-264
37. Yang Q, Reinhard K, Schiltz E, Matern U (1997) Characterization and heterologous expression of hydroxycinnamoyl/benzoyl-CoA: anthranilate N-hydroxycinnamoyl/benzoyltransferase from elicited cell cultures of carnation, Dianthus caryophyllus L. Plant Mol Biol 35: 777-789
38. Zhang QS, Shirley N, Lahnstein J, Fincher GB (2005) Characterization and expression patterns of UDP-D-glucuronate decarboxylase genes in barley. Plant Physiol 138: 131-141