Proteomic analysis of salt-responsive ubiquitin-related proteins in rice roots.
BACKGROUND
Ubiquitination of proteins plays an important role in regulating a myriad of physiological functions in plants such as xylogenesis, senescence, cell cycle control, and stress response. However, only a limited number of proteins in plants have been identified as being ubiquitinated in response to salt stress. The relationships between ubiquitination and salt-stress responses in plants are not clear.


METHODS
Rice (Oryza sativa) seedlings from the same genetic background with various salt tolerances exposed to salt stress were studied. The proteins of roots were extracted then analyzed using western blotting against ubiquitin. Differentially expressed ubiquitinated proteins were identified by nanospray liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) and quantified by label-free methods based on the Exponentially Modified Protein Abundance Index (emPAI) and on the peak areas of XIC spectra derived from ubiquitinated peptides. In addition, we performed a gel-based shotgun proteomic analysis to detect the ubiquitinated proteome that may be involved in response to salt stress.


RESULTS
The expressions of ubiquitination on pyruvate phosphate dikinase 1, heat shock protein 81-1, probable aldehyde oxidase 3, plasma membrane ATPase, cellulose synthase A catalytic subunit 4 [UDP-forming] and cyclin-C1-1 were identified and compared before and after salt treatment. The functions of those ubiquitinated proteins were further discussed for defence against salt stress. In addition, a large number of ubiquitinated proteins were successfully identified as well in this study.


CONCLUSIONS
The ubiquitination of proteins affected the protective mechanisms in rice seedlings to resist the salt stress during the initial phase. The findings in the present study also demonstrate that the regulated mechanisms through protein ubiquitination are important for rice seedlings against salt stress.
Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
Chih-Wei
CW
Liu
Yu-Kai
YK
Hsu
Yu-Hsiang
YH
Cheng
Hung-Chen
HC
Yen
Yung-Pei
YP
Wu
Chang-Sheng
CS
Wang
Chien-Chen
CC
Lai
D000595:Amino Acid Sequence; D015153:Blotting, Western; D002853:Chromatography, Liquid; D008969:Molecular Sequence Data; D012275:Oryza / Q000737:chemistry* / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D018517:Plant Roots / Q000737:chemistry / Q000502:physiology; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D055049:Salt Tolerance; D055051:Salt-Tolerant Plants / Q000737:chemistry* / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D012965:Sodium Chloride; D053719:Tandem Mass Spectrometry; D057149:Ubiquitinated Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism
D010940:Plant Proteins; D020543:Proteome; D057149:Ubiquitinated Proteins; D012965:Sodium Chloride