Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases

Abstract

BackgroundSugarcane has been used as the main crop for ethanol production for more than 40 years in Brazil. Recently, the production of bioethanol from bagasse and straw, also called second generation (2G) ethanol, became a reality with the first commercial plants started in the USA and Brazil. However, the industrial processes still need to be improved to generate a low cost fuel. One possibility is the remodeling of cell walls, by means of genetic improvement or transgenesis, in order to make the bagasse more accessible to hydrolytic enzymes. We aimed at characterizing the cell wall proteome of young sugarcane culms, to identify proteins involved in cell wall biogenesis. Proteins were extracted from the cell walls of 2-month-old culms using two protocols, non-destructive by vacuum infiltration vs destructive. The proteins were identified by mass spectrometry and bioinformatics.ResultsA predicted signal peptide was found in 84 different proteins, called cell wall proteins (CWPs). As expected, the non-destructive method showed a lower percentage of proteins predicted to be intracellular than the destructive one (33 % vs 44 %). About 19 % of CWPs were identified with both methods, whilst the infiltration protocol could lead to the identification of 75 % more CWPs. In both cases, the most populated protein functional classes were those of proteins related to lipid metabolism and oxido-reductases. Curiously, a single glycoside hydrolase (GH) was identified using the non-destructive method whereas 10 GHs were found with the destructive one. Quantitative data analysis allowed the identification of the most abundant proteins.ConclusionsThe results highlighted the importance of using different protocols to extract proteins from cell walls to expand the coverage of the cell wall proteome. Ten GHs were indicated as possible targets for further studies in order to obtain cell walls less recalcitrant to deconstruction. Therefore, this work contributed to two goals: enlarge the coverage of the sugarcane cell wall proteome, and provide target proteins that could be used in future research to facilitate 2G ethanol production.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0677-0) contains supplementary material, which is available to authorized users.

Glycoside Hydrolases in Plant Cell Wall Proteomes: Predicting Functions That Could Be Relevant for Improving Biomass Transformation Processes

“…In cell suspension cultures, only 4 GH families were identified among which GH3 was the most populated [28]. In 2-month-old stems, 7 GH families were found, GH3 also being the most represented [29]. Leaves recovered few GHs, from families 19, 27 (young leaves only), 28, and 31 (young leaves only).…”

“…In sugarcane, 49 GHs have been identified in cell wall proteomes [28,29]. They are distributed in 16 GH families.…”

“…Ten GH3s have been identified in sugarcane [28][29][30] and nine GH3s have been identified in B. distachyon [31,32,34]. Half of the sugarcane GH3 are predicted to have a β-glucosidase activity (GO:0008422) (e.g., SCEZLB1007A09, SCEQLR1093F09, and SCQSLR1089A04).…”

Cell Wall Proteomics as a Means to Identify Target Genes to Improve Second‐Generation Biofuel Production

“…Grains were collected at diferent times after lowering , 13 or 1 days [31,61]. The aim of the study was to understand the modiications of cell wall polysaccharides during grain development and illing because they are key determinant of the size and mass of the grain.In the case of sugarcane, three types of materials have been studied Figures C E : 11-dayold cell suspension cultures [62], 2-month-old stems [30], and 4-month-old young or mature leaves and apical or basal internodes [63]. The aim was to identify among CWPs possible targets for cell wall modiication in order to facilitate E2G production.…”

“…Cell walls were resuspended in these bufers and centrifuged at high speed 40,000×g/15 min/ 4°C . The four supernatants were pooled.The same DP with minor modiications was used for sugarcane cell suspension cultures and 2-month-old stems [30,62]. "nother extraction method was tested with young or mature leaves and basal or apical internodes.…”