# Proteomic Landscape of the Mature Roots in a Rubber-Producing Grass _Taraxacum Kok-saghyz_
## 2 Results
### The Proteins Involved in Natural Rubber Biosynthesis in TKS Roots  
We checked the identified 3592 proteins from the 6M TKS roots and paid special attention to the proteins and enzymes involved in NRB. Our proteomic data demonstrated that a total of 58 unique proteins or gene products were identified at least one time by the three shotgun experiments (Table S6), and four of them, named ACAT7 (spots 157, 183 and 424), HMGR1 (spot 146), DXS3 (spot 257) and DXS8 (spots 199 and 204), were also identified from the 2-DE gel of 6M TKS roots (Figure 1; Table S1). Twenty kinds of proteins were determined from the 58 unique gene products (Table S6), and these proteins are involved in both MVA and MEP pathways for NBR in TKS roots (Figure 7). Genomic sequencing data demonstrated that both cytosolic MVA and plastid MEP pathways are present for NBR, and a total of 102 NBR-related genes have been determined in the genome of TKS [16]. Our proteomic data demonstrated 22 unique proteins were involved in the MVA pathway and 13 proteins in MEP pathway in TKS roots (Figure 7; Table S6). In the MVA pathway, the identified 22 unique proteins belonged to six kinds of essential enzymes for rubber biosynthesis; they are ACAT, HMGS, HMGR, MVK, PMVK and MVD. Among them, seven members for ACAT (from ACAT2 to ACAT8), six members for mevalonate kinase (MVK 1, 2 and 7-11), and five members for phosphomevalonate kinase (PMVK 1 and 2-6), were positively identified from TKS roots by the shotgun method (Table S6). Our proteomics results also showed that, by contrast with rubber tree latex, TKS contains the MEP pathway for NRB in its roots. In the MEP pathway, seven kinds of proteins were identified from 13 unique proteins, including six family members for deoxyxylulose-5-phosphate synthase (DXS 1-3 and 8-10) and two members for D-xylulose 5-phosphate reductoisomerase (DXR 1 and 2).  
In the following step for initiation of the synthesis of isopentenyl pyrophosphate (IPP) to form rubber molecule polymer, which is termed initiator synthesis, four crucial enzymes, including isopentenyl-diphosphate delta-isomerase (IPI 2-4), geranylgeranyl pyrophosphate synthase (GGPS 1-3), geranylgeranyl diphosphate synthase (GPS 3, 5 and 7) and farnesyl diphosphate synthase (FPS 1), were identified from 10 unique proteins.  
In the final rubber elongation process, cis-isoprene transferase (CPT) can help GGPP to generate natural rubber hydrocarbons contain different length of carbons. Four kinds of proteins, named CPT, SRPP, REF, and HRBP, which is a Nogo-B receptor as a HRT1-REF bridging protein, are considered to play crucial roles for natural rubber elongation. In this proteomic study, we identified the above four members from 12 unique proteins. Among them, eight SRPP members (SRPP 1-7 and 9) and two REF members were determined from the 6M TKS roots.  
We checked the annotated genomes of the rubber tree _H. brasiliensis_ and the rubber grass _T. kok-saghyz_, and found 85 and 106 NRB-related proteins from _H. brasiliensis_ and TKS genomes, respectively. It is noteworthy that 58 out of 106 NRB-related unique proteins were identified from the 6M TKS roots, and 13 out of the identified 58 unique proteins were crucial members in the MEP pathway (Table S6). These results revealed that both MVA and MEP pathways are important in controlling NRB and rubber production in the mature TKS roots.