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 b-1,4-xylan synthases, genes in the GT47 family encoding xylan a-1,2-or a-1,3-arabinosyl transferases, and genes in the GT61 family encoding feruloyl-AX b-1,2-xylosyl transferases.

Pattern of Deposition of Cell Wall Polysaccharides and Transcript Abundance of Related Cell Wall Synthesis Genes during Differentiation in Barley Endosperm

“…This result suggests arabino-(1→4)-b-D-xylan in this region is in a highly substituted form that the LM11 antibody does not recognize. Consistent with this, members of the GT43 and GT47 gene families, which have been implicated in arabino-(1→4)-b-D-xylan synthesis in other plant systems (Mitchell et al, 2007;York and O'Neill, 2008;Zeng et al, 2008) were transcribed throughout the developmental window used in this study (Fig. 11E).…”

“…We have examined the monosaccharide composition of the endosperm over the course of development, applied the recently generated xyloglucan antibody to early endosperm development, and modified our approach to studying arabino-(1→4)-b-D-xylan using the LM11 antibody. Previous studies identifying genes involved in the synthesis of cell wall polysaccharides have shown that transcript accumulation correlates with the time of polysaccharide synthesis and deposition (Pear et al, 1996;Doblin et al, 2001;Dhugga et al, 2004;Brown et al, 2005;Persson et al, 2005;Cocuron et al, 2007;Mitchell et al, 2007). By coupling our immuno-EM observations with transcript profiles of candidate cell wall synthesis genes, we can now infer which subfamily members of these gene families is functional during key stages of endosperm development.…”

“…(1→3, 1→4)-b-DGlucan was immunologically detected in the walls of transgenic plants and confirmed with biochemical analysis of wall extracts ). The genes encoding the xylan synthases and key side chain glycosyl transferases are largely unconfirmed biochemically but studies of mutant lines and transcript profiles of cereal species accumulating arabino-(1-4)-b-D-xylan implicate the GT43, GT47, and GT61 gene families (Mitchell et al, 2007;Scheller and Ulvskov, 2010). Experimental evidence confirming the role of these genes, particularly the xylan synthases, is an area of intense interest given the importance of plant materials as feedstocks for biofuels and the potential human health benefits from diets inclusive of arabino-…”

“…Although the genes involved in arabino-(1→4)-b-Dxylan biosynthesis have not been biochemically defined unequivocally, there are a number of studies that have implicated glycosyl transferases from the GT43, GT47, and GT61 families in the synthesis of this polysaccharide (Mitchell et al, 2007). The transcript abundance of selected genes from these families were therefore monitored and shown to be present throughout grain development, with relatively high levels of GT43 mRNA (Fig.…”

The Genetics and Transcriptional Profiles of the Cellulose Synthase-Like HvCslF Gene Family in Barley

“…However, it has been shown recently that GAUT1, a type II galacturonyltransferase of the GT8 family, is capable of mediating the synthesis of the homogalacturonan backbone of pectic polysaccharides (Sterling et al, 2006). Similarly, type II GTs have been implicated in the synthesis of the (1,4)-b-D-xylan backbone of heteroxylans of the wall (Lee et al, 2007;Mitchell et al, 2007;Pena et al, 2007).…”