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Author (up) Kim, D.S.; Cho, D.S.; Park, W.-M.; Na, H.J.; Nam, H.G. file  url
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  Title Proteomic pattern-based analyses of light responses in Arabidopsis thaliana wild-type and photoreceptor mutants Type Journal Article
  Year 2006 Publication Proteomics Abbreviated Journal Proteomics  
  Volume 6 Issue 10 Pages 3040-3049  
  Keywords Arabidopsis/metabolism/*radiation effects; Arabidopsis Proteins/*biosynthesis; Cluster Analysis; Electrophoresis, Gel, Two-Dimensional; *Light; Photosynthetic Reaction Center Complex Proteins/*genetics/physiology; Phytochrome/genetics/physiology; Proteome/*biosynthesis; Signal Transduction  
  Abstract Light critically affects the physiology of plants. Using two-dimensional gel electrophoresis, we used a proteomics approach to analyze the responses of Arabidopsis thaliana to red (660 nm), far-red (730 nm) and blue (450 nm) light, which are utilized by type II and type I phytochromes, and blue light receptors, respectively. Under specific light treatments, the proteomic profiles of 49 protein spots exhibited over 1.8-fold difference in protein abundance, significant at p <0.05. Most of these proteins were metabolic enzymes, indicating metabolic changes induced by light of specific wavelengths. The differentially-expressed proteins formed seven clusters, reflecting co-regulation. We used the 49 differentially-regulated proteins as molecular markers for plant responses to light, and by developing a procedure that calculates the Pearson correlation distance of cluster-to-cluster similarity in expression changes, we assessed the proteome-based relatedness of light responses for wild-type and phytochrome mutant plants. Overall, this assessment was consistent with the known physiological responses of plants to light. However, we also observed a number of novel responses at the proteomic level, which were not predicted from known physiological changes.  
  Call Number Serial 275  
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Author (up) Lee, W.; Kim, K.R.; Singaravelu, G.; Park, B.-J.; Kim, D.H.; Ahnn, J.; Yoo, Y.J. file  url
doi  openurl
  Title Alternative chaperone machinery may compensate for calreticulin/calnexin deficiency in Caenorhabditis elegans Type Journal Article
  Year 2006 Publication Proteomics Abbreviated Journal Proteomics  
  Volume 6 Issue 4 Pages 1329-1339  
  Keywords Animals; Animals, Genetically Modified; Caenorhabditis elegans/genetics/growth & development/*metabolism; Calnexin/*deficiency; Calreticulin/*deficiency; Electrophoresis, Gel, Two-Dimensional; Endoplasmic Reticulum/metabolism; HSP70 Heat-Shock Proteins/*metabolism; Mutation/genetics; Peptide Mapping; Protein Disulfide-Isomerases/*metabolism; Proteomics; Reverse Transcriptase Polymerase Chain Reaction; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization  
  Abstract Proper folding and maintenance of the native structure are central to protein function and are assisted by a family of proteins called chaperones. Calreticulin and calnexin are ER resident chaperones well conserved from worm to human. Calreticulin/calnexin knock-out mice exhibit a severe phenotype, whereas in Caenorhabditis elegans, calreticulin [crt-1(jh101)]- and calnexin [cnx-1(nr2009)]-null mutant worms exhibit only a mild phenotype, suggesting the possible existence of alternative chaperone machinery that can compensate for the deficiency of calreticulin and/or calnexin. In order to rapidly identify the compensatory chaperone components involved in this process, we analyzed the proteome of crt-1(jh101) mutants and [crt-1(jh101);cnx-1(nr2009)] double mutants. When grown at 20 degrees C, we found that five proteins were up-regulated and two proteins were down-regulated in crt-1(jh101) mutants; nine proteins were up-regulated and five proteins were down-regulated in [crt-1(jh101);cnx-1(nr2009)] double mutants. In addition, elevation of the cultivation temperature to 25 degrees C, which is still permissive to growth but causes specific defects in mutants, led to the identification of several additional proteins. Interestingly, the consistent increment of heat shock protein-70 family members (hsp70) together with protein disulfide isomerase (PDI) at all the examined conditions suggests the possible compensatory function imparted by hsp70 and PDI family members in the absence of calreticulin and/or calnexin.  
  Call Number Serial 521  
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Author (up) Rudolph, B.; Gebendorfer, K.M.; Buchner, J.; Winter, J. file  url
doi  openurl
  Title Evolution of Escherichia coli for growth at high temperatures Type Journal Article
  Year 2010 Publication The Journal of Biological Chemistry Abbreviated Journal J Biol Chem  
  Volume 285 Issue 25 Pages 19029-19034  
  Keywords Chaperonin 10/metabolism; Chaperonin 60/metabolism; Chaperonins/chemistry; Electrophoresis, Gel, Two-Dimensional/methods; Escherichia coli/*genetics; Escherichia coli Proteins/metabolism; Evolution, Molecular; Heat-Shock Proteins/metabolism; Hot Temperature; Models, Biological; Mutation; Proteins/chemistry; Proteomics/methods; Temperature; Time Factors  
  Abstract Evolution depends on the acquisition of genomic mutations that increase cellular fitness. Here, we evolved Escherichia coli MG1655 cells to grow at extreme temperatures. We obtained a maximum growth temperature of 48.5 degrees C, which was not increased further upon continuous cultivation at this temperature for >600 generations. Despite a permanently induced heat shock response in thermoresistant cells, only exquisitely high GroEL/GroES levels are essential for growth at 48.5 degrees C. They depend on the presence of lysyl-tRNA-synthetase, LysU, because deletion of lysU rendered thermoresistant cells thermosensitive. Our data suggest that GroEL/GroES are especially required for the folding of mutated proteins generated during evolution. GroEL/GroES therefore appear as mediators of evolution of extremely heat-resistant E. coli cells.  
  Call Number Serial 311  
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Author (up) Zhang, Q.; Riechers, D.E. file  url
doi  openurl
  Title Proteomic characterization of herbicide safener-induced proteins in the coleoptile of Triticum tauschii seedlings Type Journal Article
  Year 2004 Publication Proteomics Abbreviated Journal Proteomics  
  Volume 4 Issue 7 Pages 2058-2071  
  Keywords Chromatography, Liquid; Cotyledon/chemistry/metabolism; Databases as Topic; Electrophoresis, Gel, Two-Dimensional; Electrophoresis, Polyacrylamide Gel; Glutathione Transferase/metabolism; Herbicides/chemistry/*metabolism; Hydrogen-Ion Concentration; Image Processing, Computer-Assisted; Immunoblotting; Mass Spectrometry; Poaceae/metabolism; Proteins/chemistry; Proteome; Proteomics/*methods; Seedling/metabolism; Seeds/*metabolism; Silver Staining; Tritium/*metabolism  
  Abstract Proteomic methods such as two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry, as well as immunoblotting, were used to identify herbicide safener-induced proteins in the coleoptile of Triticum tauschii, a diploid wheat containing the D genome also found in the cultivated, hexaploid wheat Triticum aestivum. The herbicide safener fluxofenim dramatically increased protein abundance in the molecular weight (M(r)) range of 24 to 30 kDa, as well as a few higher M(r) proteins, in the coleoptile of T. tauschii seedlings. In total, twenty proteins were identified in this study. Eleven proteins were highly safener induced and only weakly expressed in the control; seven proteins were new safener induced proteins that were not detected in the control. Two other proteins were constitutively expressed in both the control and safener-treated coleoptiles. Among the eighteen inducible proteins, fifteen were glutathione S-transferase (GST) subunits that fall into three subclasses: eight proteins were from the tau subclass, six proteins were from the phi subclass, and one protein was from the lambda class. Another three safener inducible proteins showed homology to the aldo/keto reductase family and with proteins that have roles in glycolysis and the Krebs cycle. Two constitutively expressed proteins were identified, one having highest homology to the dehydroascorbate reductase subclass of GSTs and one with an ascorbate peroxidase. Immunoblot analyses, using two different antisera raised against the same GST protein but differing in their specificity, were used to further characterize the GST proteins expressed in response to safener treatment. Results from immunoblotting, combined with mass spectral analysis, showed that post-translational modification of GST proteins in control and safener-treated coleoptiles may occur.  
  Call Number Serial 397  
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