Question

Someone explain how use of genomics and co-expression analysis can be used to generate hypotheses regarding the biosynthesis of secondary plant cell wall polymers such as xylans and lignin and how these hypotheses may be tested using reverse genetics approaches.

Answer 1

Xylans are the major matrix polysaccharide in the secondary cell walls of angiosperms and consist of a linear beta 1,4 xylan backbone decorated with sugar side chains. In broad leaf angiosperms such as Arabidopsis they are
simply decorated with methyl-glucuronic acid side chains, and in grasses, they also have abundant arabinosyl side chains that can be further decorated with feruloyl esters that form linkages between chains (diferulate bridges) or can link to the lignin in the cell wall. In dicots lignin linkage appears to be through the methylglucuronosyl side chains. Xylan backbone synthesis genes were first identified using co-expression analysis in Arabidopsis by Brown et al. who used microarray analysis to look for genes that showed co-expression with two of the three secondary cell wall cellulose synthase genes. This identified over 100 genes, that they scrutinised for putative glycosyl transferase type structure in the proteins they encode. They obtained knock out mutants in these and identified a
number with irregular xylem phenotypes and then showed that some of these have reduced xylan content. The glucuronic acid xylan transferase genes (GUX) were also identified by a similar coexpression approach in Arabidopsis, which revealed two closely relate GT8 genes, that when they were both knocked out the resulting double mutants lacked glucuronic acid side chains in the xylan, which was easier to extract as it isn