Plant Physiology Preview
Published on March 9, 2007; 10.1104/pp.106.094995
OPEN ACCESS ARTICLE
Received December 19, 2006
Accepted March 6, 2007
A Novel Bioinformatics Approach Identifies Candidate Genes for the Synthesis and Feruloylation of Arabinoxylan
Rowan Andrew Craig Mitchell *, Paul Dupree , and Peter R. Shewry
Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK; Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
* Corresponding author; email: rowan.mitchell{at}bbsrc.ac.uk.
Arabinoxylans (AX) are major components of graminaceous plant cell walls, including those in the grain and straw of the economically important cereals. Despite some recent advances in identifying the genes encoding the biosynthetic enzymes for a number of other plant cell wall polysaccharides, the genes encoding enzymes of the final stages of AX synthesis have not been identified. We have therefore adopted a novel bioinformatics approach based on estimation of differential expression of orthologous genes between taxonomic divisions of species. Over 3 million public domain cereal and dicot ESTs were mapped onto the complete sets of rice and Arabidopsis genes, respectively. It was assumed that genes in cereals involved in AX biosynthesis would be expressed at high levels and that their orthologues in dicotyledonous plants would be expressed at much lower levels. Considering all rice genes encoding putative glycosyltransferases (GT) predicted to be integral membrane proteins, genes in the GT43, GT47 and GT61 families emerged as much the strongest candidates. When the search was widened to all other rice or Arabidopsis genes predicted to encode integral membrane proteins, cereal genes in the Pfam family PF02458 emerged as candidates for the feruloylation of arabinoxylan. Our analysis, known activities and recent findings elsewhere are most consistent with genes in the GT43 families encoding beta 1,4 xylan synthases, genes in the GT47 family encoding xylan alpha 1,2 or alpha 1,3 arabinosyl transferases and genes in the GT61 family encoding feruloyl-arabinoxylan beta 1,2 xylosyl transferases.
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