Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense.
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.
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;
Yixiang
Y
Zhang
Peng
P
Gao
Zhuo
Z
Xing
Shumei
S
Jin
Zhide
Z
Chen
Lantao
L
Liu
Nasie
N
Constantino
Xinwang
X
Wang
Weibing
W
Shi
Joshua S
JS
Yuan
Susie Y
SY
Dai
D000818:Animals; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D054884:Host-Pathogen Interactions / Q000235:genetics; D012275:Oryza / Q000235:genetics / Q000378:metabolism / Q000469:parasitology; D010935:Plant Diseases / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D010944:Plants / Q000235:genetics* / Q000378:metabolism* / Q000469:parasitology; D030821:Plants, Genetically Modified; D040901:Proteomics / Q000379:methods*; D012273:Ribulose-Bisphosphate Carboxylase / Q000302:isolation & purification*; D018411:Spodoptera / Q000472:pathogenicity
D010940:Plant Proteins; D012273:Ribulose-Bisphosphate Carboxylase