Patterns of expression of cell wall related genes in sugarcane

Abstract

Our search for genes related to cell wall metabolism in the sugarcane expressed sequence tag (SUCEST) database (http://sucest.lbi.dcc.unicamp.br) resulted in 3,283 reads (1% of the total reads) which were grouped into 459 clusters (potential genes) with an average of 7.1 reads per cluster. To more clearly display our correlation coefficients, we constructed surface maps which we used to investigate the relationship between cell wall genes and the sugarcane tissues libraries from which they came. The only significant correlations that we found between cell wall genes and/or their expression within particular libraries were neutral or synergetic. Genes related to cellulose biosynthesis were from the CesA family, and were found to be the most abundant cell wall related genes in the SUCEST database. We found that the highest number of CesA reads came from the root and stem libraries. The genes with the greatest number of reads were those involved in cell wall hydrolases (e.g. β-1,3-glucanases, xyloglucan endo-β-transglycosylase, β-glucosidase and endo-β-mannanase). Correlation analyses by surface mapping revealed that the expression of genes related to biosynthesis seems to be associated with the hydrolysis of hemicelluloses, pectin hydrolases being mainly associated with xyloglucan hydrolases. The patterns of cell wall related gene expression in sugarcane based on the number of reads per cluster reflected quite well the expected physiological characteristics of the tissues. This is the first work to provide a general view on plant cell wall metabolism through the expression of related genes in almost all the tissues of a plant at the same time. For example, developing flowers behaved similarly to both meristematic tissues and leaf-root transition zone tissues. Besides providing a basis for future research on the mechanisms of plant development which involve the cell wall, our findings will provide valuable tools for plant engineering in the near future.

Sugarcane Genetics and Genomics

“…An in silico analysis of tissue expression patterns for cell wall-related genes done with 459 SASs from the SUCEST database reflected the expected physiological characteristics of the tissues (Lima et al 2001). Compared with different cDNA libraries, 1,234 of the 43,141 SUCEST SASs were suggested to be tissue-specific (Arruda 2001;Vettore et al 2003).…”

Apparent Induction of Xylanase by Bacillus pumilus PU4-2 using Pretreated Substrates

“…B. pumilus PU4-2 was a strain which was isolated by Purwadaria et al (2004a) from the gut of Termitidae that had xylanolytic activity. Besides microorganisms, plants (Lima et al 2001) can also produce xylanase. Microbial xylanases are preferred because of their high specificity in enzyme reactions, the mild reaction condition used and the absence of substrate loss due to chemical modifications (Wong et al 1988).…”

Carbon sequestration in the rain forest: alternatives using environmentally friendly biotechnology

“…By usage of conserved domains that appear to be present in most plants, we now know that CesA is a large gene family (Carpita and Vergara, 1998) and some members might be future targets to increase C sequestration in plants. Our research group found many members of the CesA family in sugar-cane (SUCEST-FAPESP; Lima et al 2001) and some are good candidates to study the effects on C sequestration in the near future, by studying the responses to high CO of 2 transgenic plants produced either by overexpression or suppression of specific CesA genes.…”