title: Root proteome of rice studied by iTRAQ provides integrated insight into aluminum stress tolerance mechanisms in plants.
abstract: One of the major limitations to crop growth on acid soils is the prevalence of soluble aluminum ions (Al(3+)). Rice (Oryza sativa L.) has been reported to be highly Al tolerant; however, large-scale proteomic data of rice in response to Al(3+) are still very scanty. Here, we used an iTRAQ-based quantitative proteomics approach for comparative analysis of the expression profiles of proteins in rice roots in response to Al(3+) at an early phase. A total of 700 distinct proteins (homologous proteins grouped together) with >95% confidence were identified. Among them, 106 proteins were differentially expressed upon Al(3+) toxicity in sensitive and tolerant cultivars. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was the most significantly up-regulated biochemical process in response to excess Al(3+). The mRNA levels of eight proteins mapped in the glycolysis/gluconeogenesis were further analyzed by qPCR and the expression levels of all the eight genes were higher in tolerant cultivar than in sensitive cultivar, suggesting that these compounds may promote Al tolerance by modulating the production of available energy. Although the exact roles of these putative tolerance proteins remain to be examined, our data lead to a better understanding of the Al tolerance mechanisms in rice plants through the proteomics approach.
  
  
  CONCLUSIONS
  Aluminum (mainly Al(3+)) is one of the major limitations to the agricultural productivity on acid soils and causes heavy yield loss every year. Rice has been reported to be highly Al tolerant; however, the mechanisms of rice Al tolerance are still not fully understood. Here, a combined proteomics, bioinformatics and qPCR analysis revealed that Al(3+) invasion caused complex proteomic changes in rice roots involving energy, stress and defense, protein turnover, metabolism, signal transduction, transport and intracellular traffic, cell structure, cell growth/division, and transcription. Promotion of the glycolytic/gluconeogenetic pathway in roots appeared crucially important for Al tolerance. These results lead to a better understanding of the Al tolerance mechanisms in rice and help to improve plant performance on acid soils, eventually to increase the crop production.
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address: zhqwang@zju.edu.cn.
authors.forename: Zhan Qi
authors.initials: ZQ
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address: xxy19832002@163.com.
authors.forename: Xiao Yan
authors.initials: XY
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address: gongqiaoqiao331@126.com.
authors.forename: Qiao Qiao
authors.initials: QQ
authors.lastname: Gong
authors.affiliation: Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100101, China. Electronic address: xiec@mail.cbi.pku.edu.cn.
authors.forename: Chen
authors.initials: C
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address: famweo1128@yahoo.com.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Fan
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address: yangjianli@zju.edu.cn.
authors.forename: Jian Li
authors.initials: JL
authors.lastname: Yang
authors.affiliation: UAlbany Proteomics Facility, Center for Functional Genomics, University at Albany, Rensselaer, NY 12144, USA. Electronic address: linq@albany.edu.
authors.forename: Qi Shan
authors.initials: QS
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address: sjzheng@zju.edu.cn.
authors.forename: Shao Jian
authors.initials: SJ
authors.lastname: Zheng
mesh_terms: D000535:Aluminum / Q000494:pharmacology*; D012275:Oryza / Q000378:metabolism*; D010940:Plant Proteins / Q000096:biosynthesis*; D018517:Plant Roots / Q000378:metabolism*; D020543:Proteome / Q000096:biosynthesis*; D040901:Proteomics; D013312:Stress, Physiological / Q000187:drug effects*
chemical_list: D010940:Plant Proteins; D020543:Proteome; D000535:Aluminum
keywords: Aluminum stress; Quantitative proteomics; Rice root; Sensitive; Tolerant