Proteomic analysis of salt-responsive ubiquitin-related proteins in rice roots.

RATIONALE 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.

[1]  M. Caboche,et al.  Higher activity of an aldehyde oxidase in the auxin-overproducing superroot1 mutant of Arabidopsis thaliana. , 1998, Plant physiology.

[2]  Yun Song,et al.  Identification of an Apoplastic Protein Involved in the Initial Phase of Salt Stress Response in Rice Root by Two-Dimensional Electrophoresis1[C][W][OA] , 2008, Plant Physiology.

[3]  Hong Wang,et al.  Gene Expression Profiles during the Initial Phase of Salt Stress in Rice , 2001, Plant Cell.

[4]  C. Slack,et al.  A new enzyme for the interconversion of pyruvate and phosphopyruvate and its role in the C4 dicarboxylic acid pathway of photosynthesis. , 1968, The Biochemical journal.

[5]  C. Patterson,et al.  AtCHIP, a U-Box-Containing E3 Ubiquitin Ligase, Plays a Critical Role in Temperature Stress Tolerance in Arabidopsis1 , 2003, Plant Physiology.

[6]  E. Blumwald,et al.  Sodium transport in plant cells. , 2000, Biochimica et biophysica acta.

[7]  V. Rubio,et al.  The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. , 2003, Genes & development.

[8]  M. Van Montagu,et al.  Low-oxygen stress and water deficit induce cytosolic pyruvate orthophosphate dikinase (PPDK) expression in roots of rice, a C3 plant. , 1998, The Plant journal : for cell and molecular biology.

[9]  W. Griffiths,et al.  Multiple-approaches to the identification and quantification of cytochromes P450 in human liver tissue by mass spectrometry. , 2009, Journal of proteome research.

[10]  A. Altman,et al.  Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance , 2003, Planta.

[11]  K. Mochida,et al.  Genome-wide analysis for identification of salt-responsive genes in common wheat , 2008, Functional & Integrative Genomics.

[12]  M. Estelle,et al.  The F-box protein TIR1 is an auxin receptor , 2005, Nature.

[13]  T. Sun,et al.  Molecular mechanism of gibberellin signaling in plants. , 2004, Annual review of plant biology.

[14]  Zhangcheng Tang,et al.  Proteomic analysis of salt stress‐responsive proteins in rice root , 2005, Proteomics.

[15]  Rongmin Zhao,et al.  Expression of a Constitutively Activated Plasma Membrane H+-ATPase Alters Plant Development and Increases Salt Tolerance1[C][OA] , 2007, Plant Physiology.

[16]  Ivan Dikic,et al.  Ubiquitylation and cell signaling , 2005, The EMBO journal.

[17]  Ken Shirasu,et al.  Role of ubiquitination in the regulation of plant defence against pathogens. , 2003, Current opinion in plant biology.

[18]  Changyu Wang,et al.  Rice Biotech Research at the Taiwan Agricultural Research Institute , 2002 .

[19]  Ching-Huang Lin,et al.  Functional phosphoproteomic profiling of phosphorylation sites in membrane fractions of salt-stressed Arabidopsis thaliana , 2009, Proteome Science.

[20]  Y. Sun,et al.  Small heat shock proteins: molecular structure and chaperone function , 2005, Cellular and Molecular Life Sciences CMLS.

[21]  M. Mann,et al.  Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein*S , 2005, Molecular & Cellular Proteomics.

[22]  P. Busk,et al.  Regulation of abscisic acid-induced transcription , 1998, Plant Molecular Biology.

[23]  D. Nandi,et al.  The ubiquitin-proteasome system , 2006, Journal of Biosciences.

[24]  M. Ishitani,et al.  The Arabidopsis HOS1 gene negatively regulates cold signal transduction and encodes a RING finger protein that displays cold-regulated nucleo--cytoplasmic partitioning. , 2001, Genes & development.

[25]  V. Vitart,et al.  Evidence for a role in growth and salt resistance of a plasma membrane H+-ATPase in the root endodermis. , 2001, The Plant journal : for cell and molecular biology.

[26]  Francisco M. Couto,et al.  Molecular profiling of the human nasal epithelium: A proteomics approach , 2011, Journal of Proteomics.

[27]  M. Mergeay,et al.  Shotgun proteome analysis of Rhodospirillum rubrum S1H: integrating data from gel-free and gel-based peptides fractionation methods. , 2009, Journal of proteome research.

[28]  M. Deyholos,et al.  Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes , 2006, BMC Plant Biology.

[29]  F. Parcy,et al.  Current advances in abscisic acid action and signalling , 1994, Plant Molecular Biology.

[30]  T. Koshiba,et al.  Activity and protein level of AO isoforms in pea plants (Pisum sativum L.) during vegetative development and in response to stress conditions. , 2004, Journal of experimental botany.

[31]  R. Vierstra,et al.  The ubiquitin 26S proteasome proteolytic pathway. , 2004, Annual review of plant biology.

[32]  Zhaohua Peng,et al.  Proteome and phosphoproteome differential expression under salinity stress in rice (Oryza sativa) roots. , 2007, Journal of proteome research.

[33]  M. Van Montagu,et al.  Small heat shock proteins and stress tolerance in plants. , 2002, Biochimica et biophysica acta.

[34]  Yuxiang Cheng,et al.  rHsp90 gene expression in response to several environmental stresses in rice (Oryza sativa L.). , 2006, Plant physiology and biochemistry : PPB.

[35]  K. Mann.  The chicken egg white proteome , 2007, Proteomics.

[36]  N. Yamamoto,et al.  Purification and Properties of Flavin- and Molybdenum-Containing Aldehyde Oxidase from Coleoptiles of Maize , 1996, Plant physiology.

[37]  T. Colmer,et al.  Arabidopsis–rice–wheat gene orthologues for Na+ transport and transcript analysis in wheat–L. elongatum aneuploids under salt stress , 2007, Molecular Genetics and Genomics.

[38]  W. Hurkman,et al.  Solubilization of plant membrane proteins for analysis by two-dimensional gel electrophoresis. , 1986, Plant physiology.

[39]  Bo Yang,et al.  Comparative proteomic analysis of NaCl stress-responsive proteins in Arabidopsis roots. , 2007, Journal of experimental botany.

[40]  E. Vierling.  The Roles of Heat Shock Proteins in Plants , 1991 .

[41]  R. Sunkar,et al.  Drought and Salt Tolerance in Plants , 2005 .

[42]  C. Guy,et al.  Comprehensive expression profile analysis of the Arabidopsis Hsp70 gene family. , 2001, Plant physiology.

[43]  H. Bohnert,et al.  PLANT CELLULAR AND MOLECULAR RESPONSES TO HIGH SALINITY. , 2000, Annual review of plant physiology and plant molecular biology.

[44]  Steven P Gygi,et al.  A proteomics approach to understanding protein ubiquitination , 2003, Nature Biotechnology.

[45]  W. D. De Vos,et al.  Interaction of the Tobacco Lectin with Histone Proteins1[C][W][OA] , 2011, Plant Physiology.

[46]  G. Agrawal,et al.  Gene transcription in the leaves of rice undergoing salt-induced morphological changes (Oryza sativa L.). , 2007, Molecules and cells.

[47]  R. Linforth,et al.  The wilty tomato mutants flacca and sitiens are impaired in the oxidation of ABA‐aldehyde to ABA , 1988 .

[48]  Jian-Kang Zhu,et al.  Disruption of the cellulose synthase gene, AtCesA8/IRX1, enhances drought and osmotic stress tolerance in Arabidopsis. , 2005, The Plant journal : for cell and molecular biology.

[49]  Monika S. Doblin,et al.  Cellulose biosynthesis in plants: from genes to rosettes. , 2002, Plant & cell physiology.

[50]  L. Lopez-Molina,et al.  AFP is a novel negative regulator of ABA signaling that promotes ABI5 protein degradation. , 2003, Genes & development.

[51]  J. M. Dow,et al.  Genome scale analysis of diffusible signal factor regulon in Xanthomonas campestris pv. campestris: identification of novel cell–cell communication‐dependent genes and functions , 2006, Molecular microbiology.

[52]  S. Raab,et al.  Identification of a novel E3 ubiquitin ligase that is required for suppression of premature senescence in Arabidopsis. , 2009, The Plant journal : for cell and molecular biology.

[53]  Yiyue Zhang,et al.  SDIR1 Is a RING Finger E3 Ligase That Positively Regulates Stress-Responsive Abscisic Acid Signaling in Arabidopsis[W] , 2007, The Plant Cell Online.

[54]  B. Bartel,et al.  Auxin: regulation, action, and interaction. , 2005, Annals of botany.

[55]  J. Cock,et al.  Laboratory manual for physiological studies of rice , 1971 .

[56]  W. Kraus,et al.  Clickable NAD analogues for labeling substrate proteins of poly(ADP-ribose) polymerases. , 2010, Journal of the American Chemical Society.

[57]  N. Paniego,et al.  Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis , 2008, BMC Plant Biology.

[58]  R. Hille,et al.  The mononuclear molybdenum enzymes. , 1996, Chemical reviews.

[59]  A. Millar,et al.  Novel Proteins, Putative Membrane Transporters, and an Integrated Metabolic Network Are Revealed by Quantitative Proteomic Analysis of Arabidopsis Cell Culture Peroxisomes1[W][OA] , 2008, Plant Physiology.

[60]  J. Trent.  A review of acquired thermotolerance, heat‐shock proteins, and molecular chaperones in archaea , 1996 .

[61]  Xiaoping Zhou,et al.  Expression analysis of nine rice heat shock protein genes under abiotic stresses and ABA treatment. , 2009, Journal of plant physiology.