A 2-D liquid-phase chromatography for proteomic analysis in plant tissues☆

Pirondini, Andrea; Visioli, Giovanna; Malcevschi, Alessio; Marmiroli, Nelson

doi:10.1016/j.jchromb.2006.01.033

Cited by 36 publications

(27 citation statements)

References 42 publications

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“…To identify stress-responsive proteins potentially contributing to waterlogging and high temperature tolerance, seedlings of L6138 and L0994 were subjected to C, F, H, and HF conditions for 72 h. The leaves were used to extract total proteins for PF2D protein profiling (Soldi et al 2005;Pirondini et al 2006). After comparing stress conditions (F, H, and HF) to controls (C), overall there were 31 and 19 peaks showing distinct differences in L0994 ( Supplementary Fig.…”

Section: Comparison Of Overall Changes In Protein Levels Among Stressmentioning

confidence: 99%

Physiological and proteomic analysis in two wild tomato lines under waterlogging and high temperature stress

Lin

Syu

et al. 2015

J. Plant Biochem. Biotechnol.

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Tomato yields are reduced under waterlogging and high temperature stress condition. Ascorbic acid (ASA) was shown to be involved in tolerance to waterlogging and heat stresses in tomato. Among 44 wild tomato lines treated with waterlogging at 38°C, L6138 (Solanum peruvianum) showed highest ASA, shoot growth, chlorophyll content and chlorophyll fluorescence in comparison to other tomato lines. Further leaf proteins in L6138 and L0994 under waterlogging at 38°C for 72 h were analyzed by two-dimensional protein fractionation system. Different protein peaks were analyzed by comparative proteomic analysis and database searching. Fifty protein peaks expressed in response to stress treatment were identified, among which 27 proteins from L0994 and 17 proteins from L6138 were successfully sequenced. Differentially proteins expressed have major functions in protein structure maintenance, metabolism, secretion, translation, biosynthesis, signal transduction, degradation, and photosynthesis under stress. ASA might be played a role in tolerance to waterlogging and heat stress by maintaining RNA transcription, protein structure, and metabolism. In this study, we utilized a physiological and proteomic approach to discover the changes in protein expression profiles of tomatoes in response to heat and flood stresses.

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Section: Comparison Of Overall Changes In Protein Levels Among Stressmentioning

confidence: 99%

Physiological and proteomic analysis in two wild tomato lines under waterlogging and high temperature stress

Lin

Syu

et al. 2015

J. Plant Biochem. Biotechnol.

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“…Based on ESI MS/MS analysis, an average of five proteins were present in each reversed phase fraction (0.25 min; range, 1-35 proteins per fraction) (data not shown). Thus, for protein mixtures with the same or greater complexity as the IMM, analysis by MALDI-TOF MS is of limited utility (16,36). A more useful approach would be to utilize ESI MS/MS unless there is additional data (e.g.…”

Section: Fig 1 2-de Analysis Of Rat Liver Inner Mitochondrial Membrmentioning

confidence: 99%

Expanding the Subproteome of the Inner Mitochondria Using Protein Separation Technologies

McDonald

Sheng

Stanley

et al. 2006

Molecular & Cellular Proteomics

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Currently no single proteomics technology has sufficient analytical power to allow for the detection of an entire proteome of an organelle, cell, or tissue. One approach that can be used to expand proteome coverage is the use of multiple separation technologies especially if there is minimal overlap in the proteins observed by the different methods. Using the inner mitochondrial membrane subproteome as a model proteome, we compared for the first time the ability of three protein separation methods (twodimensional liquid chromatography using the ProteomeLab TM PF 2D Protein Fractionation System from Beckman Coulter, one-dimensional reversed phase high performance liquid chromatography, and two-dimensional gel electrophoresis) to determine the relative overlap in protein separation for these technologies. Data from these different methods indicated that a strikingly low number of proteins overlapped with less than 24% of proteins common between any two technologies and only 7% common among all three methods. Utilizing the three technologies allowed the creation of a composite database totaling 348 non-redundant proteins. 82% of these proteins had not been observed previously in proteomics studies of this subproteome, whereas 44% had not been identified in proteomics studies of intact mitochondria. Each protein separation method was found to successfully resolve a unique subset of proteins with the liquid chromatography methods being more suited for the analysis of transmembrane domain proteins and novel protein discovery. We also demonstrated that both the one-and two-dimensional LC allowed for the separation of the ␣-subunit of F 1 F 0 ATP synthase that differed due to a change in pI or hydrophobicity. The eukaryotic proteome is a compilation of proteins that represents the integration of numerous cellular processes that begin with the variable transcription of genes to mRNA. These products are then translated to proteins, which may in turn be potentially co-and/or post-translationally modified to produce an array of proteins (1, 2). Due to the large number of unique protein species produced coupled with differences in their relative abundance, there is as of yet no single proteomics technology that has the analytical capacity or sensitivity to realize the goal of complete proteome coverage. One strategy to maximize proteome coverage is to combine synergistic proteomics technologies, particularly if each technology reveals a unique subset of proteins. Using the inner mitochondrial membrane as a model subproteome, we compared the ability of three protein separation methods (two-dimensional LC (2-DLC 1 with the PF2D), one-dimensional reversed phase HPLC (1-DLC; reversed phase high performance liquid chromatography (RP-HPLC)), and two-dimensional gel electrophoresis (2-DE) to determine the relative overlap in protein separation for these technologies.2-DE, a classical proteomics technology that separates proteins based on their pI and molecular weight, has a practical dynamic range of 10 4 orders of magnitude (for r...

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“…The main advantage of LC is that crude protein extracts can be analysed after few purification steps thus achieving a higher level of reproducibility than most of the chemical procedures, allowing a better comparison of protein patterns (Lambert 2005). The use of LC or two-dimensional liquid chromatography (2D-LC) separations is a robust methods for characterizing large numbers of total plant protein samples and proteins from plant organelles or sub-cellular compartments, followed by selective intact-protein analysis by MS (Pirondini et al 2006) Among the different LC approaches a 2D-LC separation technique called PF-2D, based on chromatofocusing (CF) in the first dimension and high performance reversed phase (HPRP) liquid chromatography in the second dimension, has been recently developed allowing a fine separation of high amount of heterogeneous proteins. A dedicated software package then converts complex chromatograms of a large number of fractions into easily visualized 2-D maps, "virtual gels", in which pH is plotted against the retention time ( Figure 4).…”

Section: Protein Separationmentioning

confidence: 99%

“…A dedicated software package then converts complex chromatograms of a large number of fractions into easily visualized 2-D maps, "virtual gels", in which pH is plotted against the retention time ( Figure 4). (Pirondini et al 2006) In silico analysis of different "virtual gels" can be used to generate a complete catalogue of the qualitative and quantitative differences existing between different proteomes. Such an approach has been successfully applied to the identification of proteins involved in plant proteomic response to heavy metals and viruses (Larson et al 2008, Visioli et al 2010.…”

Section: Protein Separationmentioning

confidence: 99%