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 a wide-spreading latex-rich biodiesel plant, of which the high oil content seeds were always under intense studies, but somehow NOT the latex that is considered to be rich in proteins with potential important physiological functions, and secondary metabolites to make a promising source for drug discovery. The proteomic analysis which would make the first step to study these substances was hampered by interfering parts of them. Phenol extraction and TCA/acetone extraction, two major plant proteomic isolation methods, were used and compared for this study. Results: The first J. curcas latex proteome to our knowledge is reported as 459 proteins were identified in total with such two extraction techniques combined. Although phenol extraction (401 proteins) identified much more latex proteins (123 proteins for TCA/acetone), only 65 proteins were commonly isolated by both methods. Biochemical property analysis revealed that relatively more lower-pI-proteins were isolated by TCA/acetone method (pI mode: 4.79, 6.51 for Phenol). Moreover, GO, COG and KEGG analysis showed that certain classes/categories/pathways annotated more proteins than others, and most of them entitled proportionally comparable protein counts of the two methods, however with exemplified exceptions. Conclusions: Large part of proteins were found exclusively identified by either method may due to multiple causes discussed below, indicating a better proteome coverage of plant samples with such context needs combination of multiple isolation methods. In addition, the core biological function of the latex may as speculated be uncovered by certain GO, COG and KEGG classes/categories/pathways annotating more proteins.