Proteomic Analysis of Pinus radiata Needles: 2-DE Map and Protein Identification by LC/MS/MS and Substitution-Tolerant Database Searching
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- 作者：Luis Valledor ; Maria A. Castillejo ; Christof Lenz ; Roberto Rodrí ; guez ; Maria J. Cañ ; al ; Jesú ; s Jorrí ; n
- 刊名：Journal of Proteome Research
- 出版年：2008
- 出版时间：July 2008
- 年：2008
- 卷：7
- 期：7
- 页码：2616 - 2631
- 全文大小：6422K
- 年卷期：v.7,no.7(July 2008)
- ISSN：1535-3907
文摘
Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m3 of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. To identify key proteins related to tree growth, productivity and responses to environmental factors, a proteomic approach is being utilized. In this paper, we present the first report of the 2-DE protein reference map of physiologically mature P. radiata needles, as a basis for subsequent differential expression proteomic studies related to growth, development, biomass production and responses to stresses. After TCA/acetone protein extraction of needle tissue, 549 
21 well-resolved spots were detected in Coommassie-stained gels within the 5−8 pH and 10−100 kDa Mr ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.
21 well-resolved spots were detected in Coommassie-stained gels within the 5−8 pH and 10−100 kDa Mr ranges. The analytical and biological variance determined for 450 spots were of 31 and 42%, respectively. After LC/MS/MS analysis of in-gel tryptic digested spots, proteins were identified by using the novel Paragon algorithm that tolerates amino acid substitution in the first-pass search. It allowed the confident identification of 115 out of the 150 protein spots subjected to MS, quite unusual high percentage for a poor sequence database, as is the case of P. radiata. Proteins were classified into 12 or 18 groups based on their corresponding cell component or biological process/pathway categories, respectively. Carbohydrate metabolism and photosynthetic enzymes predominate in the 2-DE protein profile of P. radiata needles.