Advances in qualitative and quantitative plant membrane proteomics

Kota, Uma; Goshe, Michael B.

doi:10.1016/j.phytochem.2011.01.027

Cited by 31 publications

(21 citation statements)

References 177 publications

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“…More recently, this strategy was used efficiently to analyze the proteome of wheat chloroplast protein complexes [25]. BN-PAGE was highly linked to membrane proteomics showing a deep interest to improve the hydrophobic proteome coverage of gel-based approaches [26]. …”

Section: Gel-based Proteomicsmentioning

confidence: 99%

“…In this method, the instrument alternates between low and high collision energies in MS analysis. While the low collision energy scan mode leads to the determination of accurate precursor ion masses, the high-energy scan mode (MS E ) generates accurate peptide fragmentation data [26]. The use of multiplex parallel fragmentation of LC/MS E yields uniformly product ion information of all peptides across their entire chromatographic peaks [134], which provides continuous MS data throughout the entire acquisition.…”

Section: Label-free Quantitative Proteomicsmentioning

confidence: 99%

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Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Abdallah

Dumas‐Gaudot

Renaut³

et al. 2012

International Journal of Plant Genomics

174

175

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Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (MS) to provide a new toolbox of gel-free quantitative techniques. When coupled to MS, the shotgun proteomic pipeline can fuel new routes in sensitive and high-throughput profiling of proteins, leading to a high accuracy in quantification. Although label-based approaches, either chemical or metabolic, gained popularity in quantitative proteomics because of the multiplexing capacity, these approaches are not without drawbacks. The burgeoning label-free methods are tag independent and suitable for all kinds of samples. The challenges in quantitative proteomics are more prominent in plants due to difficulties in protein extraction, some protein abundance in green tissue, and the absence of well-annotated and completed genome sequences. The goal of this perspective assay is to present the balance between the strengths and weaknesses of the available gel-based and -free methods and their application to plants. The latest trends in peptide fractionation amenable to MS analysis are as well discussed.

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Section: Gel-based Proteomicsmentioning

confidence: 99%

Section: Label-free Quantitative Proteomicsmentioning

confidence: 99%

Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Abdallah

Dumas‐Gaudot

Renaut³

et al. 2012

International Journal of Plant Genomics

174

175

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“…Advances in LC (liquid chromatography)-MS have in recent years facilitated the investigation into the qualitative and quantitative proteomics of large numbers of proteins [15,16]. Indeed, MS-based quantification has rapidly made an impact on the analysis of differential protein expression and during the last few years several quantification methods have been proposed [17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%

Proteomic analysis of Mesembryanthemum crystallinum leaf microsomal fractions finds an imbalance in V-ATPase stoichiometry during the salt-induced transition from C3 to CAM

Cosentino

Silvestre

Fischer-Schliebs

et al. 2013

Biochemical Journal

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The halophyte Mesembryanthemum crystallinum adapts to salt stress by salt uptake and switching from C3 photosynthesis to CAM (crassulacean acid metabolism). An important role in this process is played by transport proteins in the tonoplast of the central vacuole. In the present study we examine dynamic changes in the protein composition during salt-stress adaptation in microsomes from M. crystallinum leaves. Plants challenged with 400 mM NaCl accumulate salt by day 4 of treatment and malic acid only at day 12; a switching to CAM hence follows any initial steps of salt adaptation with a delay. Using a label-free and semiquantitative approach, we identified the most dramatic changes between the proteome of control plants and plants harvested after 12 days of the treatment; the abundance of 14 proteins was significantly affected. The proteomic data revealed that the majority of the subunits of V-ATPase (vacuolar H(+)-ATPase) holoenzyme. The salt treatment somewhat decreased the abundance of all subunits in the short term (4 days). Long-term adaptation, including the switching to CAM, goes together with a strong increase in the representation of all detectable subunits. Because this increase is subunit-specific, with the highest rise occurring for subunits E and c, the data suggest that long-term adaptation to salt stress correlates with a change in V-ATPase subunit stoichiometry and highlight the structural plasticity of this holoenzyme.

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“…As there are already a number of excellent reviews covering the developments and perspectives in quantitative proteomics (Aebersold and Mann, 2003; Ong and Mann, 2005; Bantscheff et al, 2007; Schulze and Usadel, 2010) as well as plant proteomics (Gerber et al, 2003; Chen and Harmon, 2006; Thelen and Peck, 2007; Kota and Goshe, 2011; Arsova et al, 2012), this review will focus on the application of 15 N stable isotope-based quantitative and differential PTM proteomics in identification of important PTM protein components during cellular processes and on the investigation of their in vivo functions in plant. The 15 N-stable isotope labeling in Arabidopsis (SILIA)-based quantitative proteomic protocol is first applied onto Arabidopsis grown on a solid-medium (Guo and Li, 2011).…”

Section: Introductionmentioning

confidence: 99%

Quantitation, networking, and function of protein phosphorylation in plant cell

Zhu¹,

Li²

2013

Front. Plant Sci.

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Protein phosphorylation is one of the most important post-translational modifications (PTMs) as it participates in regulating various cellular processes and biological functions. It is therefore crucial to identify phosphorylated proteins to construct a phosphor-relay network, and eventually to understand the underlying molecular regulatory mechanism in response to both internal and external stimuli. The changes in phosphorylation status at these novel phosphosites can be accurately measured using a 15N-stable isotopic labeling in Arabidopsis (SILIA) quantitative proteomic approach in a high-throughput manner. One of the unique characteristics of the SILIA quantitative phosphoproteomic approach is the preservation of native PTM status on protein during the entire peptide preparation procedure. Evolved from SILIA is another quantitative PTM proteomic approach, AQUIP (absolute quantitation of isoforms of post-translationally modified proteins), which was developed by combining the advantages of targeted proteomics with SILIA. Bioinformatics-based phosphorylation site prediction coupled with an MS-based in vitro kinase assay is an additional way to extend the capability of phosphosite identification from the total cellular protein. The combined use of SILIA and AQUIP provides a novel strategy for molecular systems biological study and for investigation of in vivo biological functions of these phosphoprotein isoforms and combinatorial codes of PTMs.

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Advances in qualitative and quantitative plant membrane proteomics

Cited by 31 publications

References 177 publications

Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Gel-Based and Gel-Free Quantitative Proteomics Approaches at a Glance

Proteomic analysis of Mesembryanthemum crystallinum leaf microsomal fractions finds an imbalance in V-ATPase stoichiometry during the salt-induced transition from C3 to CAM

Quantitation, networking, and function of protein phosphorylation in plant cell

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