| Title: | Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense |
| Author(s): | Zhang Y; Gao P; Xing Z; Jin S; Chen Z; Liu L; Constantino N; Wang X; Shi W; Yuan JS; Dai SY; |
| Address: | "Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub (SSBiH), Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843;" |
| ISSN/ISBN: | 1535-9484 (Electronic) 1535-9476 (Print) 1535-9476 (Linking) |
| Abstract: | "High abundance proteins like ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. To address this challenge, we developed and evaluated Polyethyleneimine Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery" |
| Keywords: | "Animals Genome, Plant Genomics/*methods Host-Pathogen Interactions/genetics Oryza/genetics/metabolism/parasitology Plant Diseases/genetics Plant Proteins/genetics/*isolation & purification/metabolism Plants/*genetics/*metabolism/parasitology Plants, Genet;" |
| Notes: | "MedlineZhang, Yixiang Gao, Peng Xing, Zhuo Jin, Shumei Chen, Zhide Liu, Lantao Constantino, Nasie Wang, Xinwang Shi, Weibing Yuan, Joshua S Dai, Susie Y eng Research Support, Non-U.S. Gov't 2013/08/15 Mol Cell Proteomics. 2013 Nov; 12(11):3431-42. doi: 10.1074/mcp.M112.025213. Epub 2013 Aug 13" |
