title: Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases.
abstract: BACKGROUND
  Sugarcane 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil. phdjuliana@gmail.com.
authors.forename: Maria Juliana
authors.initials: MJ
authors.lastname: Calderan-Rodrigues
authors.affiliation: Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France. jamet@lrsv.ups-tlse.fr.|CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France. jamet@lrsv.ups-tlse.fr.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Jamet
authors.affiliation: Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France. thibaut.douche@pasteur.fr.|CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France. thibaut.douche@pasteur.fr.
authors.forename: Thibaut
authors.initials: T
authors.lastname: Douché
authors.affiliation: Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil. beatrizcalderan@gmail.com.
authors.forename: Maria Beatriz Rodrigues
authors.initials: MB
authors.lastname: Bonassi
authors.affiliation: Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil. thais.cataldi@usp.br.
authors.forename: Thaís Regiani
authors.initials: TR
authors.lastname: Cataldi
authors.affiliation: Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil. j.g.fonseca@usp.br.
authors.forename: Juliana Guimarães
authors.initials: JG
authors.lastname: Fonseca
authors.affiliation: Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France. sancle@lrsv.ups-tlse.fr.|CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France. sancle@lrsv.ups-tlse.fr.
authors.forename: Hélène
authors.initials: H
authors.lastname: San Clemente
authors.affiliation: Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.|CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
authors.forename: Rafael
authors.initials: R
authors.lastname: Pont-Lezica
authors.affiliation: Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil. calabate@usp.br.
authors.forename: Carlos Alberto
authors.initials: CA
authors.lastname: Labate
mesh_terms: D002473:Cell Wall / Q000737:chemistry*; D006026:Glycoside Hydrolases / Q000378:metabolism*; D010544:Peroxidases / Q000378:metabolism*; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism*; D018547:Plant Stems / Q000737:chemistry; D020543:Proteome; D031786:Saccharum / Q000737:chemistry* / Q000201:enzymology
chemical_list: D010940:Plant Proteins; D020543:Proteome; D010544:Peroxidases; D006026:Glycoside Hydrolases