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

Abstract

Arabinoxylans (AXs) are major components of graminaceous plant cell walls, including those in the grain and straw of economically important cereals. Despite some recent advances in identifying the genes encoding 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 expressed sequence tags were mapped onto the complete sets of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genes, respectively. It was assumed that genes in cereals involved in AX biosynthesis would be expressed at high levels and that their orthologs in dicotyledonous plants would be expressed at much lower levels. Considering all rice genes encoding putative glycosyl transferases (GTs) 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 Pfam family PF02458 emerged as candidates for the feruloylation of AX. 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-AX beta-1,2-xylosyl transferases.

Figure 1.

Tissue distribution of cereal EST counts for rice loci with 50 or more cereal ESTs in orthologous groups from Table I. Only counts from libraries with tissue information are included and data are presented as a percentage of the total of these for each locus.

Figure 2.

Scheme for mapping of ESTs to genes by sequence similarity. Arabidopsis-rice loci relationships were defined by protein similarity searches (black arrows; BLASTp with bits score >200). The closest matching rice or Arabidopsis gene for every EST was identified by nucleotide similarity search (grey arrow; BLASTn with E < 10⁻⁵) or translated nucleotide similarity search (striped arrow; BLASTx with E < 10⁻⁵). Number of sequences are indicated.