# Proteomic Landscape of the Mature Roots in a Rubber-Producing Grass _Taraxacum Kok-saghyz_
## 3 Discussion  
The First Visual Proteome Based on 2-DE Gel Demonstrated Many Protein Isoforms in the Mature TKS Roots  
The ease and availability of 2-DE combined MS is a classical standard for proteomics study, and it is still a valuable tool to provide a visual proteome for plants [34]. Large amounts of proteomics studies have been performed in many plant species, however, only several proteomic research works were reported on different latex components of the _Para_ rubber tree [2; 35], and only one proteomic analysis was performed to identify 278 unique proteins from the rubber particle phase and pellet  
Figure 7: Schematic diagram of natural rubber biosynthesis (NRB)-related proteins in the 6M TKS roots. A schematic diagram of the identified proteins involved in the mevalonate acid (MVA, left) and methylerythritol phosphate (MEP, right) pathways of NRB is highlighted. In this schematic diagram, the identified proteins involved in NRB from the 6M TKS roots were marked with different color. The name of proteins identified from both 2-DE and shotgun methods was marked in red color. The proteins only determined by shotgun analysis are marked in blue color. The proteins identified from the first (6M-1), second (6M-2) and third (6M-3) shotgun experiments are marked with red, blue and black stars, respectively. phase of the _T. brevicorniculatum_ latex [32]. Our 2-DE gel-based proteomics of TKS roots resulted in 371 abundant protein species (Figure 2; Table S1), but the protein profiles are very different to that in _T. brevicorniculatum_ latex. Compared with the 2-DE gels for a clear aqueous phase and a yellowish pellet phase of the fractionated samples from _T. brevicorniculatum_ latex [32], our 2-DE gel for the mature TKS roots is much clearer and contains more protein spots (Figure 2). Among the identified proteins, 90 unique proteins contained different protein isoforms, which have different experimental M_r_ and _p_I values on the 2-DE gel (Table S1), probably due to the existence of modification protein variants. In the past decade, only 1208 proteins were identified from all the rubber-producing plants, and only several proteomics studies were performed on the rubber particles [36]. In a previous high throughput proteomics study, a total of 186 proteins were positively identified from rubber particles by shotgun tandem MS [28]. After removal of the protein bands corresponding to the RP-abundant REF and SRPP, 137 protein species including 115 unique proteins were identified in a LC-MS/MS based proteome analysis [31]. By investigating the protein profile between LRPs and SRPs, 53 protein spots corresponding to 22 gene products were detected to have significant difference. Among them, most up-regulated proteins in SRPs were identified as SRPP, HMGS, phospholipase D, ethylene response factor, eukaryotic translation initiation factor, etc., but the most abundant proteins in LRPs were REF, glucanase and several hypothetical proteins [27]. Interaction network analysis of rubber particle proteomics revealed the formation of the protein complex consisting of HRT1, REF and HRBP might play crucial roles as a NRB machinery [31], and these proteins are associated with the endoplasmic reticulum [37]. Recently, more than 1600 proteins were identified from total latex of the _Para_ rubber tree by using isobaric tags for relative and absolute quantitation (iTRAQ) method [2] and 1839 unique proteins were determined by LC-MS/MS from the whole translated draft genome of the rubber tree _H. brasiliensis_[24]. Our high throughput shotgun proteomics produced 7481 proteins from at least one independent shotgun experiment and 3545 shared proteins in the three experiments from the 6M TKS roots (Figure 4B; Table S3), which covered almost all the previously identified proteins from the latex-producing plants.