4 Annotating Carbohydrate-Active Enzymes in Plant Genomes: Present Challenges
Annual Plant Reviews book series, Volume 41: Plant Polysaccharides
Pedro M. Coutinho,
Bernard Henrissat,
Pedro M. Coutinho
Universities of Aix-Marseille I and II, Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Marseille, 13288, Cédex 9 France
Search for more papers by this authorBernard Henrissat
Universities of Aix-Marseille I and II, Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Marseille, 13288, Cédex 9 France
Search for more papers by this authorPedro M. Coutinho,
Bernard Henrissat,
Pedro M. Coutinho
Universities of Aix-Marseille I and II, Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Marseille, 13288, Cédex 9 France
Search for more papers by this authorBernard Henrissat
Universities of Aix-Marseille I and II, Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Marseille, 13288, Cédex 9 France
Search for more papers by this authorFirst published: 19 April 2018
This article was originally published in 2011 in Plant Polysaccharides, Volume 41 (ISBN 9781405181723) of the Annual Plant Reviews book series, this volume edited by Peter Ulvskov. The article was republished in Annual Plant Reviews online in April 2018.
Manuscript received September 2008
Abstract
There are far more carbohydrate structures than protein folds and, not unexpectedly, sequence-based families of carbohydrate-active enzymes often group together enzymes of different specificity. While this fact illustrates the remarkable plasticity of proteins to evolve novel specificities from pre-existing folds, this is also the source of potential errors during the functional prediction of genes derived from whole genome sequencing efforts. This chapter reviews the problems and the advances associated with the sequence-based classification of plant carbohydrate-active enzymes as used in the CAZy database (www.cazy.org).
References
- Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana . Nature, 408, 796–815.
- Berteau, O., Stenutz, R. (2004) Web resources for the carbohydrate chemist. Carbohydrate Research, 339(5), 929–936.
- Boraston, A.B., Bolam, D.N., Gilbert, H.J., Davies, G.J. (2004) Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochemical Journal, 382, 769–781.
- Campbell, J.A., Davies, G.J., Bulone, V., Henrissat, B. (1997) A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochemical Journal, 326, 929–939.
- Cantarel, B.L., Coutinho, P.M., Rancurel, C., Bernard, T., Lombard, V., Henrissat, B. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res., 37, D233–D238.
- Coutinho, P.M., Henrissat, B. (1999) Carbohydrate-active enzymes: an integrated database approach. In: Recent Advances in Carbohydrate Bioengineering (eds H.J. Gilbert, G. Davies, B. Henrissat, B. Svensson), pp. 3–12. Royal Society of Chemistry, Cambridge.
- Coutinho, P.M., Deleury, E., Davies, G.J., Henrissat, B. (2003) An evolving hierarchical family classification for glycosyltransferases. Journal of Molecular Biology, 328, 307–317.
- Escamilla-Treviño, L.L., Chen, W., Card, M.L., Shih, M.C., Cheng, C.L., Poulton, J.E. (2006) Arabidopsis thaliana β-glucosidases BGLU45 and BGLU46 hydrolyse monolignol glucosides. Phytochemistry, 67, 1651–1660.
- Farrokhi, N., Burton, R.A., Brownfield, L., et al. (2006) Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genes. Plant Biotechnology Journal, 4, 145–167.
- Gachon, C.M., Langlois-Meurinne, M., Saindrenan, P. (2005) Plant secondary metabolism glycosyltransferases: the emerging functional analysis. Trends in Plant Science, 10, 542–549.
- Geisler-Lee, J., Geisler, M., Coutinho, P.M., et al. (2006) Poplar carbohydrate-active enzymes. Gene identification and expression analyses. Plant Physiology, 140, 946–962.
- Gilks, W.R., Audit, B., De Angelis, D., Tsoka, S., Ouzounis, C.A. (2002) Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics, 18, 1641–1649.
- Henrissat, B. (1991) A classification of glycosyl hydrolases based on amino-acid sequence similarities. Biochemical Journal, 280, 309–316.
- Henrissat, B., Bairoch, A. (1993) New families in the classification of glycosyl hydrolases based on amino-acid sequence similarities. Biochemical Journal, 293, 781–788.
- Henrissat, B., Bairoch, A. (1996) Updating the sequence-based classification of glycosyl hydrolases. Biochemical Journal, 316, 695–696.
- Henrissat, B., Claeyssens, M., Tomme, P., Lemesle, L. & Mornon, J.P. (1989) Cellulase families revealed by hydrophobic cluster analysis. Gene, 81, 83–95.
- Henrissat, B., Coutinho, P.M., Davies, G.J. (2001) A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana . Plant Molecular Biology, 47(1–2), 55–72.
- Kacser, H., Beeby, R. (1984) Evolution of catalytic proteins or on the origin of enzyme species by means of natural selection. Journal of Molecular Evolution, 20, 38–51.
- Koch, K.E. (1996) Carbohydrate-modulated gene expression in plants. Annual Reviews in Plant Physiology and Plant Molecular Biology, 47, 509–540.
- Lairson, L.L., Withers, S.G. (2004) Mechanistic analogies amongst carbohydrate modifying enzymes. Chemical Communications (Camb.), 20, 2243–2248.
- Laine, R.A. (1994), A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 × 1012 structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems. Glycobiology, 4, 759–767.
- Lanot, A., Hodge, D., Jackson, R.G., et al. (2006) The glucosyltransferase UGT72E2 is responsible for monolignol 4-O-glucoside production in Arabidopsis thaliana . Plant Journal, 48, 286–295.
- MacGregor, E.A., Svensson, B. (1989) A super-secondary structure predicted to be common to several α-1,4-d-glucan-cleaving enzymes. Biochemical Journal, 259, 145–152.
- Minic, Z., Jamet, E., Négroni, L., Arsene der Garabedian, P., Zivy, M., Jouanin, L. (2007) A sub-proteome of Arabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases. Journal of Experimental Botany, 58(10), 2503–2512.
- Mitchell, R.A., Dupree, P., Shewry, P.R. (2007) A novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan. Plant Physiology, 144, 43–53.
- Nedelcu, A.M., Borza, T., Lee, R.W. (2006) A land plant-specific multigene family in the unicellular Mesostigma argues for its close relationship to Streptophyta . Molecular and Biological Evolution, 23, 1011–1015.
- Ouzounis, C.A., Karp, P.D. (2002) The past, present and future of genome-wide re-annotation. Genome Biology, 3, comment2001.1–2001.6.
-
Rees, D.A.
(1977)
Polysaccharide Shapes.
Chapman & Hall,
London.
10.1007/978-94-011-6906-6 Google Scholar
- Scheible, W.R., Pauly, M. (2004) Glycosyltransferases and cell wall biosynthesis: novel players and insights. Current Opinion in Plant Biology, 7, 285–295.
- Stam, M.R., Danchin, E.G., Rancurel, C., Coutinho, P.M., Henrissat, B. (2006) Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Engineering, Design, Selection, 19, 555–562.
- Svensson, B. (1988) Regional distant sequence homology between amylases, α-glucosidases and transglucanosylases. FEBS Letters, 230, 72–76.
- Tuskan, G.A., Difazio, S., Jansson, S., et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. and Gray). Science, 313, 1596–1604.
- Valencia, A. (2005) Automatic annotation of protein function. Current Opinion in Structural Biology, 15, 267–274.
- Varki, A. (1999) Essentials in Glycobiology, CSHL Press, Cold Spring Harbour, NY.
- Ward, O.P., Moo-Young, M. (1989) Enzymatic degradation of cell wall and related plant polysaccharides. Critical Reviews in Biotechnology, 8, 237–274.
- Webb, E.C. (1992) Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on Nomenclature and Classification of Enzymes by the Reactions they Catalyse. Academic Press, San Diego, CA.
- Wheeler, D.L., Chappey, C., Lash, A.E., et al. (2000) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 28, 10–14.
- Yokoyama, R., Nishitani, K. (2004) Genomic basis for cell-wall diversity in plants. A comparative approach to gene families in rice and Arabidopsis . Plant Cell Physiology, 45, 1111–1121.
- Yu, J., Hu, S., Wang, J., et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79–92.
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