Proteomic analysis of latex from Jatropha curcas   L. stems and comparison of two classic proteomic sample isolation methods: The phenol extraction and the TCA/acetone extraction

Background: Jatropha curcas is awide-spreading latex-rich biodiesel plant with high oil content in seeds that have always been under intense studies. However, studies are lacking on the latex component that is considered rich in proteins with potentially important physiological functions and secondary metabolites that are a promising source for new drugs. The proteomic analysis, which would be the first step to study these substances, was hampered by the presence of interfering components. Phenol extraction and Trichloroacetic acid (TCA)/acetone extraction, two major plant proteomic isolation methods, were used and compared in this study.
Results: We identified 459 proteins from the J. curcas latex proteome using the combination of the two extraction techniques. Although more number of latex proteins were identified by the phenol extraction (401 proteins vs. 123 proteins by the TCA/acetone extraction), only 65 proteins were commonly isolated by both methods. Analysis of the biochemical properties revealed that relatively more number of lower isoelectric point (pI) proteins were isolated by the TCA/acetone method (pI mode: 4.79, 6.51 for phenol). Moreover, GO, COG, and KEGG analyses showed that certain classes/categories/pathways annotated more number of proteins than others, and most of them had proportionally comparable protein counts by both the methods, however, with exemplified exceptions.
Conclusions: A large number of proteins were found and exclusively identified by either method, indicating that a better proteome coverage of plant samples in a similar context needs the combined use of multiple isolation methods. In addition, the core biological function of the latex may be uncovered by certain GO, COG, and KEGG classes/categories/pathways that annotate more proteins.

Keywords
Biodiesel plant; Complex contaminants; Greenhouse; Latex collection; Latex proteome; Mass spectrometry; Peptide samples; Plant latex; Plant proteome; Protein; Proteome