Analysis of cellular phosphoproteins by two-dimensional gel electrophoresis: applications for cell signaling in normal and cancer cells

Metabolomics-Based Mechanistic Insights into Revealing the Adverse Effects of Pesticides on Plants: An Interactive Review

In plant biology, metabolomics is often used to quantitatively assess small molecules, metabolites, and their intermediates in plants. Metabolomics has frequently been applied to detect metabolic alterations in plants exposed to various biotic and abiotic stresses, including pesticides. The widespread use of pesticides and agrochemicals in intensive crop production systems is a serious threat to the functionality and sustainability of agroecosystems. Pesticide accumulation in soil may disrupt soil-plant relationships, thereby posing a pollution risk to agricultural output. Application of metabolomic techniques in the assessment of the biological consequences of pesticides at the molecular level has emerged as a crucial technique in exposome investigations. State-of-the-art metabolomic approaches such as GC-MS, LC-MS/MS UHPLC, UPLC-IMS-QToF, GC/EI/MS, MALDI-TOF MS, and ¹H-HR-MAS NMR, etc., investigating the harmful effects of agricultural pesticides have been reviewed. This updated review seeks to outline the key uses of metabolomics related to the evaluation of the toxicological impacts of pesticides on agronomically important crops in exposome assays as well as bench-scale studies. Overall, this review describes the potential uses of metabolomics as a method for evaluating the safety of agricultural chemicals for regulatory applications. Additionally, the most recent developments in metabolomic tools applied to pesticide toxicology and also the difficulties in utilizing this approach are discussed.

Phospho-protein Analysis in Adherent Cells Using Flow Cytometry

Protein phosphorylation is one of the most important post-translational modifications, which acts as a reversible on or off switch for the activity of a large number of proteins. Analyzing the phosphorylation status of different proteins can reveal the alterations in the state of the cells in response to cellular damage, cancer and pharmaceutical drugs. Techniques such as mass spectrometry, radiolabeling, 2D-gel electrophoresis and western blotting are used to quantify protein phosphorylation. These assays can quantify phosphorylation in the bulk population of cells, however, flow cytometry can couple cell surface marker expression data with phosphorylation data to understand differential signaling in a sub-population within a heterogeneous population of cells. Our protocol describes the use of flow-cytometry for rapid and single cell-based quantification of intracellular phospho-protein with the help of anti-phospho protein specific antibody.

Application of in vivo MR methods in the study of breast cancer metabolism

In the last two decades, various in vivo MR methodologies have been evaluated for their potential in the study of cancer metabolism. During malignant transformation, metabolic alterations occur, leading to morphological and functional changes. Among various MR methods, in vivo MRS has been extensively used in breast cancer to study the metabolism of cells, tissues or whole organs. It provides biochemical information at the metabolite level. Altered choline, phospholipid and energy metabolism has been documented using proton (¹ H), phosphorus (³¹ P) and carbon (¹³ C) isotopes. Increased levels of choline-containing compounds, phosphomonoesters and phosphodiesters in breast cancer, which are indicative of altered choline and phospholipid metabolism, have been reported using in vivo, in vitro and ex vivo NMR studies. These changes are reversed on successful therapy, which depends on the treatment regimen given. Monitoring the various tumor intermediary metabolic pathways using nuclear spin hyperpolarization of ¹³ C-labeled substrates by dynamic nuclear polarization has also been recently reported. Furthermore, the utility of various methods such as diffusion, dynamic contrast and perfusion MRI have also been evaluated to study breast tumor metabolism. Parameters such as tumor volume, apparent diffusion coefficient, volume transfer coefficient and extracellular volume ratio are estimated. These parameters provide information on the changes in tumor microstructure, microenvironment, abnormal vasculature, permeability and grade of the tumor. Such changes seen during cancer progression are due to alterations in the tumor metabolism, leading to changes in cell architecture. Due to architectural changes, the tissue mechanical properties are altered; this can be studied using magnetic resonance elastography, which measures the elastic properties of tissues. Moreover, these structural MRI methods can be used to investigate the effect of therapy-induced changes in tumor characteristics. This review discusses the potential of various in vivo MR methodologies in the study of breast cancer metabolism.

The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs)

Mass Spectrometry (MS) has revolutionized the way we study biomolecules, especially proteins, their interactions and posttranslational modifications (PTM). As such MS has established itself as the leading tool for the analysis of PTMs mainly because this approach is highly sensitive, amenable to high throughput and is capable of assigning PTMs to specific sites in the amino acid sequence of proteins and peptides. Along with the advances in MS methodology there have been improvements in biochemical, genetic and cell biological approaches to mapping the interactome which are discussed with consideration for both the practical and technical considerations of these techniques. The interactome of a species is generally understood to represent the sum of all potential protein-protein interactions. There are still a number of barriers to the elucidation of the human interactome or any other species as physical contact between protein pairs that occur by selective molecular docking in a particular spatiotemporal biological context are not easily captured and measured.PTMs massively increase the complexity of organismal proteomes and play a role in almost all aspects of cell biology, allowing for fine-tuning of protein structure, function and localization. There are an estimated 300 PTMS with a predicted 5% of the eukaryotic genome coding for enzymes involved in protein modification, however we have not yet been able to reliably map PTM proteomes due to limitations in sample preparation, analytical techniques, data analysis, and the substoichiometric and transient nature of some PTMs. Improvements in proteomic and mass spectrometry methods, as well as sample preparation, have been exploited in a large number of proteome-wide surveys of PTMs in many different organisms. Here we focus on previously published global PTM proteome studies in the Apicomplexan parasites T. gondii and P. falciparum which offer numerous insights into the abundance and function of each of the studied PTM in the Apicomplexa. Integration of these datasets provide a more complete picture of the relative importance of PTM and crosstalk between them and how together PTM globally change the cellular biology of the Apicomplexan protozoa. A multitude of techniques used to investigate PTMs, mostly techniques in MS-based proteomics, are discussed for their ability to uncover relevant biological function.

Simultaneous Detection of Phosphoproteins and Total Proteins in SDS-PAGE Using Calcon

A novel fluorescent staining protocol to detect phosphoproteins in sodium dodecyl sulfate-polyacrylamide gels using a fluorescence sensor, 1-(2-hydroxy-1-naphthylazo)-2-naphthol-4-sulfonic acid sodium salt (Calcon), was developed. This method yields results within 135 min, with the sensitivities of 15 ng of α-casein and β-casein, and 62.5 ng of κ-casein, respectively. Since non-phosphoproteins have shown negative signals that are distinctly different from positive signals of phosphoproteins, this detection method allows one to monitor phosphoproteins with high specificity. Furthermore, a total protein profile can be achieved before a destaining step using a scanner with rapid and low-cost without further total protein staining.

Breast Tissue Metabolism by Magnetic Resonance Spectroscopy

Metabolic alterations are known to occur with oncogenesis and tumor progression. During malignant transformation, the metabolism of cells and tissues is altered. Cancer metabolism can be studied using advanced technologies that detect both metabolites and metabolic activities. Identification, characterization, and quantification of metabolites (metabolomics) are important for metabolic analysis and are usually done by nuclear magnetic resonance (NMR) or by mass spectrometry. In contrast to the magnetic resonance imaging that is used to monitor the tumor morphology during progression of the disease and during therapy, in vivo NMR spectroscopy is used to study and monitor tumor metabolism of cells/tissues by detection of various biochemicals or metabolites involved in various metabolic pathways. Several in vivo, in vitro and ex vivo NMR studies using ¹H and ³¹P magnetic resonance spectroscopy (MRS) nuclei have documented increased levels of total choline containing compounds, phosphomonoesters and phosphodiesters in human breast cancer tissues, which is indicative of altered choline and phospholipid metabolism. These levels get reversed with successful treatment. Another method that increases the sensitivity of substrate detection by using nuclear spin hyperpolarization of ¹³C-lableled substrates by dynamic nuclear polarization has revived a great interest in the study of cancer metabolism. This review discusses breast tissue metabolism studied by various NMR/MRS methods.

Characterization of in vivo phosphorylation modification of differentially accumulated proteins in cotton fiber-initiation process

Initiation of cotton fiber from ovule epidermal cells determines the ultimate number of fibers per cotton ovule, making it one of the restriction factors of cotton fiber yield. Previous comparative proteomics studies have collectively revealed 162 important differentially accumulated proteins (DAPs) in cotton fiber-initiation process, however, whether and how post-translational modifications, especially phosphorylation modification, regulate the expression and function of the DAPs are still unclear. Here we reported the successful identification of 17 phosphopeptides from 16 phosphoproteins out of the 162 DAPs using the integrated bioinformatics analyses of peptide mass fingerprinting data and targeted MS/MS identification method. In-depth analyses indicated that 15 of the 17 phosphorylation sites were novel phosphorylation sites first identified in plants, whereas 6 of the 16 phosphoproteins were found to be the phosphorylated isoforms of 6 proteins. The phosphorylation-regulated dynamic protein network derived from this study not only expanded our understanding of the cotton fiber-initiation process, but also provided a valuable resource for future functional studies of the phosphoproteins.

Multiplexed Imaging of Protein Phosphorylation on Membranes Based on Ti(IV) Functionalized Nanopolymers

Accurate protein phosphorylation analysis reveals dynamic cellular signaling events not evident from protein expression levels. The most dominant biochemical assay, western blotting, suffers from the inadequate availability and poor quality of phospho-specific antibodies for phosphorylated proteins. Furthermore, multiplexed assays based on antibodies are limited by steric interference between the antibodies. Here we introduce a multifunctionalized nanopolymer for the universal detection of phosphoproteins that, in combination with regular antibodies, allows multiplexed imaging and accurate determination of protein phosphorylation on membranes.

2D-DIGE screening of high-productive CHO cells under glucose limitation--basic changes in the proteome equipment and hints for epigenetic effects

CHO derivates (Chinese hamster ovary) belong to the most important mammalian cells for industrial recombinant protein production. Many efforts have been made to improve productivity and stability of CHO cells in bioreactor processes. Here, we followed up one barely understood phenomenon observed with process optimizations: a significantly increased cell-specific productivity in late phases of glucose-limited perfusion cultivations, when glucose (and lactate) reserves are exhausted. Our aim was to elucidate the cellular activities connected to the metabolic shift from glucose surplus to glucose limitation phase. With 2D-DIGE, we compared three stages in a perfusion culture of CHO cells: the initial growth with high glucose concentration and low lactate production, the second phase with glucose going to limitation and high lactate level, and finally the state of glucose limitation and also low lactate concentration but increased cell-specific productivity. With our proteomic approach we were able to demonstrate consequences of glucose limitation for the protein expression machinery which also could play a role for a higher recombinant protein production. Most interestingly, we detected epigenetic effects on the level of proteins involved in histone modification (HDAC1/-2, SET, RBBP7, DDX5). Together with shifts in the protein inventory of energy metabolism, cytoskeleton and protein expression, a picture emerges of basic changes in the cellular equipment under long-term glucose limitation of CHO cells.

Targeted Analysis of Protein Phosphorylation by 2D Electrophoresis

Two-dimensional (2D) gel electrophoresis combines isoelectric focusing in the first and SDS polyacrylamide gel electrophoresis in the second dimension to separate complex mixtures of proteins with unequalled resolution and sensitivity. It is well suited for the analysis of posttranslational protein modifications as most of them affect the isoelectric point and, therefore, the focusing behavior of the protein in the first dimension. It is particularly useful for low-abundance proteins, as it provides a first indication of PTMs, before establishing methods for protein isolation. For targeted proteomics of more abundant proteins, 2D electrophoresis itself may be the method of choice for the isolation of posttranslationally modified isoforms of the protein of interest for mass spectrometric analyses. Protein phosphorylation can be detected by use of phospho-specific stains or antibodies, or by comparing spot patterns of a protein sample before and after phosphatase treatment. Here we describe a simple method, combining 2D gel electrophoresis and western blot analysis with dephosphorylation by λ-phosphatase to analyze the phosphorylation status of oxophytodienoic acid reductase 3 in protein extracts from different organs of tomato and Arabidopsis plants.

Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications

Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine.

Phosphoprotein staining for sodium dodecyl sulfate-polyacrylamide gel electrophoresis using fluorescent reagent morin hydrate

A fluorescence-based stain with 3,5,7,2',4'-pentahydroxyflavone (morin hydrate, MH) was designed to stain phosphoproteins in one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Al(3+) was applied as a "fixed bridge," providing an efficient energy transfer channel between phosphoprotein and MH, to produce a strong fluorescent complex for the determination of phosphoprotein. As little as 62.5ng of α-casein (7 or 8 phosphates) and β-casein (5 phosphates), 125ng of ovalbumin (2 phosphates), and κ-casein (1 phosphate) could be visualized with a wide linear dynamic range. In comparison with conventional methods, MH stain is a time-saving method that takes just 90min. It also has good compatibility with routine protein stainings such as Coomassie Brilliant Blue R (CBBR) and SYPRO Ruby for total protein analysis.

A rapid screening assay to search for phosphorylated proteins in tissue extracts

Reversible protein phosphorylation is an essential mechanism in the regulation of diverse biological processes, nonetheless is frequently altered in disease. As most phosphoproteome studies are based on optimized in-vitro cell culture studies new methods are in need to improve de novo identification and characterization of phosphoproteins in extracts from tissues. Here, we describe a rapid and reliable method for the detection of phosphoproteins in tissue extract based on an experimental strategy that employs 1D and 2D SDS PAGE, Western immunoblotting of phosphoproteins, in-gel protease digestion and enrichment of phosphorpeptides using metal oxide affinity chromatography (MOAC). Subsequently, phosphoproteins are identified by MALDI-TOF-MS/MS with the CHCA-TL or DHB ML sample matrix preparation method and further characterized by various bioinformatic software tools to search for candidate kinases and phosphorylation-dependent binding motifs. The method was applied to mouse lung tissue extracts and resulted in an identification of 160 unique phosphoproteins. Notably, TiO(2) enrichment of pulmonary protein extracts resulted in an identification of additional 17 phosphoproteins and 20 phosphorylation sites. By use of MOAC, new phosphorylation sites were identified as evidenced for the advanced glycosylation end product-specific receptor. So far this protein was unknown to be phosphorylated in lung tissue of mice. Overall the developed methodology allowed efficient and rapid screening of phosphorylated proteins and can be employed as a general experimental strategy for an identification of phosphoproteins in tissue extracts.

Alternative visualization of SDS-PAGE separated phosphoproteins by alizarin red S-aluminum (III)-appended complex

A novel fluorescence detection system using a chemosensor for phosphoprotein in gel electrophoretic analysis has been developed. The system employed the alizarin red S-aluminum (III)-appended complex as a fluorescent staining dye to perform the convenient and selective detection of phosphorylated proteins and total proteins in SDS-PAGE, respectively. Therefore, a full and selective map of proteins can be achieved in the same process without resorting to other compatible detection methods. As low as 62.5 ng of α- (seven or eight phosphates) and β-casein (five phosphates), 125 ng of ovalbumin (two phosphates), and κ-casein (one phosphate) can be detected in approximately 135 min, with the linear responses of rigorous quantitation of changes over a 125-4000 ng range. As a result, alizarin red S-aluminum (III) stain may provide a new choice for selective, economic, and convenient visualization of phosphoproteins.

Phosphoproteomics: A possible route to novel biomarkers of breast cancer

Proteomics is rapidly transforming the way that cancer and other pathologies are investigated. The ability to identify hundreds of proteins and to compare their abundance in different clinical samples presents a unique opportunity for direct identification of novel disease markers. Furthermore, recent advances allow us to analyse and compare PTMs. This gives an additional dimension for defining a new class of protein biomarker based not only on abundance and expression but also on the occurrence of covalent modifications specific to a disease state or therapy response. Such modifications are often a consequence of the activation/inactivation of a particular disease related pathway. In this review we evaluate the available information on breast cancer related protein-phosphorylation events, illustrating the rationale for investigating this PTM as a target for breast cancer research with eventual clinical relevance. We present a critical survey of the published experimental strategies to study protein phosphorylation on a system wide scale and highlight recent specific advances in breast cancer phosphoproteomics. Finally we discuss the feasibility of establishing novel biomarkers for breast cancer based on the detection of patterns of specific protein phosphorylation events.

Chemical visualization of phosphoproteomes on membrane

With new discoveries of important roles of phosphorylation on a daily basis, phospho-specific antibodies, as the primary tool for on-membrane detection of phosphoproteins, face enormous challenges. To address an urgent need for convenient and reliable analysis of phosphorylation events, we report a novel strategy for sensitive phosphorylation analysis in the Western blotting format. The chemical reagent, which we termed pIMAGO, is based on a multifunctionalized soluble nanopolymer and is capable of selectively binding to phosphorylated residues independent of amino acid microenvironment, thus offering great promise as a universal tool in biological analyses where the site of phosphorylation is not known or its specific antibody is not available. The specificity and sensitivity of the approach was first examined using a mixture of standard proteins. The method was then applied to monitor phosphorylation changes in in vitro kinase and phosphatase assays. Finally, to demonstrate the unique ability of pIMAGO to measure endogenous phosphorylation, we used it to visualize and determine the differences in phosphorylated proteins that interact with wild-type and kinase dead mutant of Polo-like kinase 1 during mitosis, the results of which were further confirmed by a quantitative phosphoproteomics experiment.

Phosphorylation detection and characterization in ribonucleotides using Raman and Raman optical activity (ROA) spectroscopies

Raman and Raman optical activity (ROA) spectra are presented for adenosine and seven of its derivative ribonucleotides. Both of these spectroscopic techniques are shown to be sensitive to the site and degree of phosphorylation, with a considerable number of marker bands being identified for these ribonucleotides. ROA spectra are shown to provide the most sensitive diagnostic tool for phosphorylation characterization and quantification.

A novel simple extracellular leucine-rich repeat (eLRR) domain protein from rice (OsLRR1) enters the endosomal pathway and interacts with the hypersensitive-induced reaction protein 1 (OsHIR1)

Receptor-like protein kinases (RLKs) containing an extracellular leucine-rich repeat (eLRR) domain, a transmembrane domain and a cytoplasmic kinase domain play important roles in plant disease resistance. Simple eLRR domain proteins structurally resembling the extracellular portion of the RLKs may also participate in signalling transduction and plant defence response. Yet the molecular mechanisms and subcellular localization in regulating plant disease resistance of these simple eLRR domain proteins are still largely unclear. We provided the first experimental evidence to demonstrate the subcellular localization and trafficking of a novel simple eLRR domain protein (OsLRR1) in the endosomal pathway, using both confocal and electron microscopy. Yeast two-hybrid and in vitro pull-down assays show that OsLRR1 interacts with the rice hypersensitive-induced response protein 1 (OsHIR1) which is localized on plasma membrane. The interaction between LRR1 and HIR1 homologs was shown to be highly conserved among different plant species, suggesting a close functional relationship between the two proteins. The function of OsLRR1 in plant defence response was examined by gain-of-function tests using transgenic Arabidopsis thaliana. The protective effects of OsLRR1 against bacterial pathogen infection were shown by the alleviating of disease symptoms, lowering of pathogen titres and higher expression of defence marker genes.

Two-dimensional electrophoresis: an overview

Two-dimensional gel electrophoresis (2DE) separates proteins by molecular charge and molecular size. Proteins are first solubilised in a denaturing buffer containing a neutral chaotrope, a zwitterionic or neutral detergent, and a reducing agent. First-dimension isoelectric keywords, focusing, then subjects proteins to a high voltage within a pH gradient. The amphoteric nature of proteins means each migrates to the pH where the net molecular charge is zero. After equilibration, to ensure complete protein unfolding, the second dimension separates by molecular size. Each protein is therefore resolved at a unique isoelectric point/molecular size coordinate. After visualisation by staining proteome changes are revealed by gel image analysis, and protein spots of interest excised and identified by mass spectrometry sequence analysis combined with database comparison. Variations to this procedure include staining or radio-labelling prior to electrophoresis. Although 2DE does have limitations, the most significant being the resolution of membrane and/or hydrophobic proteins, the potential solutions offered by pre-fractionation or adjustments to the electrophoresis regimen mean this technique is likely to remain central to proteomic research.

Dendritic cell-derived interferon-gamma-induced protein mediates tumor necrosis factor-alpha stimulation of human lung fibroblasts

Lung fibroblast plays a pivotal role in lung repair and remodeling, and also contributes to lung inflammation. The present study investigated differential protein profiling of normal human lung fibroblasts stimulated with tumor necrosis factor (TNF)-alpha. Total proteins from lung fibroblasts were separated by 2-DE, and differentially expressed proteins were identified by MALDI-TOF MS. TNF-alpha was found for the first time to alter the expression levels of myxovirus resistance protein A, interferon-stimulated gene 15, plasminogen activator inhibitor-2, lysyl hydroxylase 2 (isoform a), and prolyl 4-hydroxylase (alpha subunit) in human lung fibroblasts. In particular, dendritic cell-derived interferon-gamma-induced protein (DCIP) was upregulated by TNF-alpha in lung fibroblasts and its biological function is at present unknown. We found that TNF-alpha-induced DCIP expression was dependent on the transcription factor interferon regulatory factor-1. DCIP-selective antisense oligodeoxynucleotide inhibited the expression of TNF-alpha-responsive gene targets including vascular cell adhesion molecule-1, intercellular adhesion molecule-1, IL-6, IL-8, IP-10, and thymic stromal lymphopoietin. In a lipopolysaccharide-induced acute lung injury mouse model, DCIP mRNA level was elevated together with that of TNF-alpha. We have demonstrated for the first time that DCIP is upregulated by TNF-alpha and also mediates TNF-alpha stimulation of human lung fibroblasts. Further studies on the role of DCIP in airway inflammation and remodeling are warranted.

Phospho-proteomic approach to identify new targets of leucine deprivation in muscle cells

The aim of this study was to optimize a protocol that allows identifying changes at the phosphorylation level of specific proteins in response to cell stimulation by leucine starvation. To make possible the identification of differentially phosphorylated proteins by the combination of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), we prepared fraction enriched in phosphoproteins. For that purpose, we adapted the immobilized metal affinity chromatography (IMAC) technique to make it compatible with 2D-PAGE. On the whole, this procedure allowed identifying regulated targets of leucine deprivation: molecular chaperones glucose-regulated protein 58 kDa (GRP58) and BiP (GRP78), RNA helicase DEAD box polypeptide 3, and eukaryotic translation initiation factor 4B (eIF4B).

Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry

Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins.

A novel role for the yeast protein kinase Dbf2p in vacuolar H+-ATPase function and sorbic acid stress tolerance

In Saccharomyces cerevisiae, the serine-threonine protein kinase activity of Dbf2p is required for tolerance to the weak organic acid sorbic acid. Here we show that Dbf2p is required for normal phosphorylation of the vacuolar H(+)-ATPase (V-ATPase) A and B subunits Vma1p and Vma2p. Loss of V-ATPase activity due to bafilomycin treatment or deletion of either VMA1 or VMA2 resulted in sorbic acid hypersensitivity and impaired vacuolar acidification, phenotypes also observed in both a kinase-inactive dbf2 mutant and cells completely lacking DBF2 (dbf2Delta). Crucially, VMA2 is a multicopy suppressor of both the sorbic acid-sensitive phenotype and the impaired vacuolar-acidification defect of dbf2Delta cells, confirming a functional interaction between Dbf2p and Vma2p. The yeast V-ATPase is therefore involved in mediating sorbic acid stress tolerance, and we have shown a novel and unexpected role for the cell cycle-regulated protein kinase Dbf2p in promoting V-ATPase function.

Highly selective enrichment of phosphorylated peptides using titanium dioxide

The characterization of phosphorylated proteins is a challenging analytical task since many of the proteins targeted for phosphorylation are low in abundance and phosphorylation is typically substoichiometric. Highly efficient enrichment procedures are therefore required. Here we describe a protocol for selective phosphopeptide enrichment using titanium dioxide (TiO2) chromatography. The selectivity toward phosphopeptides is obtained by loading the sample in a 2,5-dihydroxybenzoic acid (DHB) or phthalic acid solution containing acetonitrile and trifluoroacetic acid (TFA) onto a TiO2 micro-column. Although phosphopeptide enrichment can be achieved by using TFA and acetonitrile alone, the selectivity is dramatically enhanced by adding DHB or phthalic acid since these compounds, in conjunction with the low pH caused by TFA, prevent binding of nonphosphorylated peptides to TiO2. Using an alkaline solution (pH > or = 10.5) both monophosphorylated and multiphosphorylated peptides are eluted from the TiO2 beads. This highly efficient method for purification of phosphopeptides is well suited for the characterization of phosphoproteins from both in vitro and in vivo studies in combination with mass spectrometry (MS). It is a very easy and fast method. The entire protocol requires less than 15 min per sample if the buffers have been prepared in advance (not including lyophilization).

A novel method of protein extraction from perennialBupleurum root for 2-DE

The perennial Bupleurum root is thick and woody and contains high levels of interfering compounds. Common protein extraction methods have proved refractory towards the isolation of proteins suitable for 2-DE, due to the presence of interfering compounds. A novel method for extracting proteins suitable for 2-DE was established to overcome these problems. The main characteristic of this protocol is the partitioning of the proteins into the aqueous (fraction A-2), chloroform and isoamyl alcohol phases (A-3), and the interphase (A-1). The proteins are then extracted from each of these phases. From A-1, 85% (extracted protein against total proteins) proteins could be extracted and purified. For fraction A-2, a novel phenol extraction step is employed for the extraction of proteins. Based on the well-resolved 2-DE patterns, our protein preparation is free of interfering compounds. Using these methods (A-1, A-2, and A-3-3), a total of 3662 (1526 + 1128 + 1008) spots could be separated, and a protein yield of about 1.41 mg per 1.0 g fresh root material was obtained. To our knowledge, this is the first time that a protocol for protein extraction from perennial Bupleurum root has been reported that gives reproducible results. The protocol is expected to be applicable to other recalcitrant plant tissues as well.

Frozen tissue biobanks. Tissue handling, cryopreservation, extraction, and use for proteomic analysis

The potential and the limitations of protein analysis of tissue samples are surveyed. The complexity, concentration range and dynamics of the human proteome are reviewed, as is the effect of handling and cryopreservation. Protein extraction, solubilization, resolution and detection are discussed, in relation to the properties of the human proteome.

Phosphoprotein analysis: from proteins to proteomes

Characterization of protein modification by phosphorylation is one of the major tasks that have to be accomplished in the post-genomic era. Phosphorylation is a key reversible modification occurring mainly on serine, threonine and tyrosine residues that can regulate enzymatic activity, subcellular localization, complex formation and degradation of proteins. The understanding of the regulatory role played by phosphorylation begins with the discovery and identification of phosphoproteins and then by determining how, where and when these phosphorylation events take place. Because phosphorylation is a dynamic process difficult to quantify, we must at first acquire an inventory of phosphoproteins and characterize their phosphorylation sites. Several experimental strategies can be used to explore the phosphorylation status of proteins from individual moieties to phosphoproteomes. In this review, we will examine and catalogue how proteomics techniques can be used to answer specific questions related to protein phosphorylation. Hence, we will discuss the different methods for enrichment of phospho-proteins and -peptides, and then the various technologies for their identification, quantitation and validation.

Methods for proteomics in neuroscience

Proteomics reveals complex protein expression, function, interactions and localization in different phenotypes of neuron. As proteomics, regarded as a highly complex screening technology, moves from a theoretical approach to practical reality, neuroscientists have to determine the most-appropriate applications for this technology. Even though proteomics compliments genomics, it is in sheer contrast to the basically constant genome due to its dynamic nature. Neuroscientists have to surmount difficulties particular to the research in neuroscience; such as limited sample amounts, heterogeneous cellular compositions in samples and the fact that many proteins of interest are hydrophobic proteins. The necessity of exclusive technology, sophisticated software and skilled manpower tops the challenge. This review examines subcellular organelle isolation, protein fractionation and separation using two-dimensional gel electrophoresis (2-DGE) as well as multi-dimensional liquid chromatography (LC) followed by mass spectrometry (MS). The methods for quantifying relative gene product expression between samples (e.g., two-dimensional difference in gel electrophoresis (2D-DIGE), isotope-coded affinity tag (ICAT) and iTRAQ) are elaborated. An overview of the techniques used currently to assign post-translational modification status on a proteomics scale is also evaluated. The feasible coverage of the proteome, ability to detect unique cell components such as post-synaptic densities and membrane proteins, resource requirements and quantitative as well as qualitative reliability of different approaches is also discussed. While there are many challenges in neuroproteomics, this field promises many returns in the future.

Development of a simplified, economical polyacrylamide gel staining protocol for phosphoproteins

Pro-Q Diamond (Pro-Q DPS) is a commercially available stain that binds the phosphate moiety of phosphoproteins with high sensitivity and linearity. To conserve consumable costs we demonstrate that threefold diluted Pro-Q DPS offers the same sensitivity and linearity of signal to that obtained with undiluted Pro-Q DPS. The optimal conditions for Pro-Q DPS indicate that fixation, staining, and destaining of gels longer than 1 h, 2 h, and four 30-min incubations, respectively, are not required. The fixation and destaining solutions, but not the threefold diluted Pro-Q DPS, can be re-used without compromising the signal intensity or linear dynamic range. This modified protocol of Pro-Q DPS reduces the cost at least by fourfold, making the stain economically attractive for large-scale analysis of phosphoproteins.

Bridging proteomics and systems biology: What are the roads to be traveled?

The comprehensive study of proteomes has become an important part of attempts to uncover the systemic properties of biological systems. Proteomics provides data of a quality which increasingly fulfills strict requirements of systems biology for quantitative and qualitative information. Notably, proteomics can generate rich datasets that describe dynamic changes of proteomes. On the other hand, large-scale modeling requires the development of mathematic tools that are adequate for the processing of largely uncertain biological data. In this review, recent developments that pave the way for the integration of proteomics into systems biology are discussed. These developments include the standardization of data acquisition and presentation, the increased comprehensiveness of proteomics studies in description of functional status, localization and dynamics of proteins, and advanced modeling approaches.

Phosphoproteome Analysis

Protein phosphorylation is directly or indirectly involved in all important cellular events. The understanding of its regulatory role requires the discovery of the proteins involved in these processes and how, where and when protein phosphorylation takes place. Investigation of the phosphoproteome of a cell is becoming feasible today although it still represents a very difficult task especially if quantitative comparisons have to be made. Several different experimental strategies can be employed to explore phosphoproteomes and this review will cover the most important ones such as incorporation of radiolabeled phosphate into proteins, application of specific antibodies against phosphorylated residues and direct staining of phosphorylated proteins in polyacrylamide gels. Moreover, methods to enrich phosphorylated proteins such as affinity chromatography (IMAC) and immunoprecipitation as well as mass spectrometry for identification of phosphorylated peptides and phosphorylation sites are also described.

Functional characterization of two-dimensional gel-separated proteins using sequential staining

Proteins separated by two-dimensional (2-D) gel electrophoresis can be visualized using various protein staining methods. This is followed by downstream procedures, such as image analysis, gel spot cutting, protein digestion, and mass spectrometry (MS), to characterize protein expression profiles within cells, tissues, organisms, or body fluids. Characterizing specific post-translational modifications on proteins using MS of peptide fragments is difficult and labor-intensive. Recently, specific staining methods have been developed and merged into the 2-D gel platform so that not only general protein patterns but also patterns of phosphorylated and glycosylated proteins can be obtained. We used the new Pro-Q Diamond phosphoprotein dye technology for the fluorescent detection of phosphoproteins directly in 2-D gels of mouse leukocyte proteins, and Pro-Q Emerald 488 glycoprotein dye to detect glycoproteins. These two fluorescent stains are compatible with general protein stains, such as SYPRO Ruby stain. We devised a sequential procedure using Pro-Q Diamond (phosphoprotein), followed by Pro-Q Emerald 488 (glycoprotein), followed by SYPRO Ruby stain (general protein stain), and finally silver stain for total protein profile. This multiple staining of the proteins in a single gel provided parallel determination of protein expression and preliminary characterization of post-translational modifications of proteins in individual spots on 2-D gels. Although this method does not provide the same degree of certainty as traditional MS methods of characterizing post-translational modifications, it is much simpler, faster, and does not require sophisticated equipment and expertise in MS.

Rapid enrichment and analysis of yeast phosphoproteins using affinity chromatography, 2D-PAGE and peptide mass fingerprinting

A combination of affinity purification, 2D-PAGE and peptide mass fingerprinting was employed to study the phosphoprotein complement of Saccharomyces cerevisiae. Protein extracts were first passed through a phosphoprotein affinity column, and the phosphoprotein-enriched eluate fractions were then separated on 2D gels and visualized by staining with SYPRO Ruby. Proteins were excised from the gels and identified by peptide mass fingerprinting; 11/13 protein spots identified from a gel of the phosphoprotein-enriched fraction had prior published evidence indicating that they were phosphoproteins. Additional experiments using a specific stain for phosphoproteins, prior incubation of the protein extract with alkaline phosphatase and blotting with monoclonal antibodies to phosphothreonine, phosphoserine and phosphotyrosine demonstrated that the phosphoprotein affinity column was an effective method for enriching phosphoproteins. Further validating the method, growth of yeast in the presence of sorbic acid resulted in altered phosphorylation of 17 proteins, 13 of which had prior published evidence that they were phosphoproteins or had ATP binding activity.

Two-dimensional protein map of an ?ale?-brewing yeast strain: proteome dynamics during fermentation

The first protein map of an ale-fermenting yeast is presented in this paper: 205 spots corresponding to 133 different proteins were identified. Comparison of the proteome of this ale strain with a lager brewing yeast and the Saccharomyces cerevisiae strain S288c confirmed that this ale strain is much closer to S288c than the lager strain at the proteome level. The dynamics of the ale-brewing yeast proteome during production-scale fermentation was analysed at the beginning and end of the first and the third usage of the yeast (called generation in the brewing industry). During the first generation, most changes were related to the switch from aerobic propagation to anaerobic fermentation. Fewer changes were observed during the third generation but certain stress-response proteins such as Hsp26p, Ssa4p and Pnc1p exhibited constitutive expression in subsequent generations. The ale brewing yeast strain appears to be quite well adapted to fermentation conditions and stresses.

Identification of Burkholderia cenocepacia genes required for bacterial survival in vivo

Burkholderia cenocepacia (formerly Burkholderia cepacia complex genomovar III) causes chronic lung infections in patients with cystic fibrosis. In this work, we used a modified signature-tagged mutagenesis (STM) strategy for the isolation of B. cenocepacia mutants that cannot survive in vivo. Thirty-seven specialized plasposons, each carrying a unique oligonucleotide tag signature, were constructed and used to examine the survival of 2,627 B. cenocepacia transposon mutants, arranged in pools of 37 unique mutants, after a 10-day lung infection in rats by using the agar bead model. The recovered mutants were screened by real-time PCR, resulting in the identification of 260 mutants which presumably did not survive within the lungs. These mutants were repooled into smaller pools, and the infections were repeated. After a second screen, we isolated 102 mutants unable to survive in the rat model. The location of the transposon in each of these mutants was mapped within the B. cenocepacia chromosomes. We identified mutations in genes involved in cellular metabolism, global regulation, DNA replication and repair, and those encoding bacterial surface structures, including transmembrane proteins and cell surface polysaccharides. Also, we found 18 genes of unknown function, which are conserved in other bacteria. A subset of 12 representative mutants that were individually examined using the rat model in competition with the wild-type strain displayed reduced survival, confirming the predictive value of our STM screen. This study provides a blueprint to investigate at the molecular level the basis for survival and persistence of B. cenocepacia within the airways.

Effect of adaptation to ethanol on cytoplasmic and membrane protein profiles of Oenococcus oeni

The practical application of commercial malolactic starter cultures of Oenococcus oeni surviving direct inoculation in wine requires insight into mechanisms of ethanol toxicity and of acquired ethanol tolerance in this organism. Therefore, the site-specific location of proteins involved in ethanol adaptation, including cytoplasmic, membrane-associated, and integral membrane proteins, was investigated. Ethanol triggers alterations in protein patterns of O. oeni cells stressed with 12% ethanol for 1 h and those of cells grown in the presence of 8% ethanol. Levels of inosine-5'-monophosphate dehydrogenase and phosphogluconate dehydrogenase, which generate reduced nicotinamide nucleotides, were decreased during growth in the presence of ethanol, while glutathione reductase, which consumes NADPH, was induced, suggesting that maintenance of the redox balance plays an important role in ethanol adaptation. Phosphoenolpyruvate:mannose phosphotransferase system (PTS) components of mannose PTS, including the phosphocarrier protein HPr and EII(Man), were lacking in ethanol-adapted cells, providing strong evidence that mannose PTS is absent in ethanol-adapted cells, and this represents a metabolic advantage to O. oeni cells during malolactic fermentation. In cells grown in the presence of ethanol, a large increase in the number of membrane-associated proteins was observed. Interestingly, two of these proteins, dTDT-glucose-4,6-dehydratase and D-alanine:D-alanine ligase, are known to be involved in cell wall biosynthesis. Using a proteomic approach, we provide evidence for an active ethanol adaptation response of O. oeni at the cytoplasmic and membrane protein levels.

Use of two-dimensional gel electrophoresis proteome reference maps of dinoflagellates for species recognition of causative agents of harmful algal blooms

The sample preparation procedures established for Prorocentrum triestinum were adapted to cover both thecate and athecate dinoflagellates. Further, whether trichloroacetic acid (TCA) precipitation can be used to fix and preserve the harmful or nuisance species from local waters that they infest was tested. Optimized technical procedures developed were used to generate proteome reference maps for eight other local causative species of harmful algal blooms (HABs): Prorocentrum micans, Prorocentrum minimum, Prorocentrum sigmoides, Prorocentrum dentatum, Scrippsiella trochoidea, Karenia longicanalis, Karenia digitata and Karenia mikimotoi; together with one American species Karenia brevis (Florida, USA). These proteome maps were used to test their ability for species recognition in a mixed culture of dinoflagellates and whether such investigations will provide a comparative view at a global level. Comparisons of proteome profiles were made (i). between closely related species within the same family; (ii). between distantly related species belonging to different types, i.e., gymnodinioids, prorocentroids or peridinioids, or (iii). between different groups, i.e., thecate (armored) dinoflagellate cells against athecate (naked or unarmored) dinoflagellate cells. Species-specific two-dimensional electrophoresis (2-DE) protein profiles were observed in all ten species and it was possible to distinguish between even closely related species within the same family. To demonstrate the extent of reproducibility and usefulness of these 2-DE reference maps, 2-DE has been used to analyze three geographically distinct isolates of Prorocentrum dentatum, and to distinguish species composition in a mixed culture. Application of 2-D PAGE analysis to differentiate between taxonomically confused strains of a single species could be a powerful taxonomic tool.

Soft immobilized pH gradient gels in proteome analysis: a follow-up

As a follow-up of a previous work on two-dimensional map analysis utilizing soft (< 4%T) immobilized pH gradient (IPG) matrices in the first dimension (Candiano et al., Electrophoresis 2002, 23, 292-297), we have further optimized the preparation of such dilute IPG gels. One important step for obtaining an even reswelling of the entire IPG strip along the pH 3-10 interval is a washing step in 100 mM citric acid. It appears as though after rinsing off the excess acid in distilled water, a gradient of this tricarboxylic acid remains trapped into the IPG matrix, from almost nil at the acidic gel region to substantially higher amounts in its basic counterpart. This gradient helps in obtaining a uniform reswelling of the IPG strip, since carboxyl groups are more heavily hydrated than amino groups. The combined effects of uniform reswelling and of diluting the gel matrix favor penetration of large macromolecules (> 200 kDa) and allow for better spot resolution and for the display of a substantially higher number of spots also in the 30-60 000 Da region. A delipidation step in tri-n-butylphosphate:acetone:methanol (1:12:1) appears to substantially improve spot focusing and greatly diminish streaking and smearing of spots in all regions of the pH gradient.

Detection technologies in proteome analysis

Common strategies employed for general protein detection include organic dye, silver stain, radiolabeling, reverse stain, fluorescent stain, chemiluminescent stain and mass spectrometry-based approaches. Fluorescence-based protein detection methods have recently surpassed conventional technologies such as colloidal Coomassie blue and silver staining in terms of quantitative accuracy, detection sensitivity, and compatibility with modern downstream protein identification and characterization procedures, such as mass spectrometry. Additionally, specific detection methods suitable for revealing protein post-translational modifications have been devised over the years. These include methods for the detection of glycoproteins, phosphoproteins, proteolytic modifications, S-nitrosylation, arginine methylation and ADP-ribosylation. Methods for the detection of a range of reporter enzymes and epitope tags are now available as well, including those for visualizing beta-glucuronidase, beta-galactosidase, oligohistidine tags and green fluorescent protein. Fluorescence-based and mass spectrometry-based methodologies are just beginning to offer unparalleled new capabilities in the field of proteomics through the performance of multiplexed quantitative analysis. The primary objective of differential display proteomics is to increase the information content and throughput of proteomics studies through multiplexed analysis. Currently, three principal approaches to differential display proteomics are being actively pursued, difference gel electrophoresis (DIGE), multiplexed proteomics (MP) and isotope-coded affinity tagging (ICAT). New multiplexing capabilities should greatly enhance the applicability of the two-dimensional gel electrophoresis technique with respect to addressing fundamental questions related to proteome-wide changes in protein expression and post-translational modification.

Malignant breast tumor phospholipid profiles using (31)P magnetic resonance

Biochemical markers improve the classification and staging of breast cancer and may refine management decisions if it can be shown that they correlate with accepted prognostic factors or patient outcome. Using phosphorus-31 magnetic resonance spectroscopy ((31)P MRS), we determined the phospholipid content of 43 malignant breast tumors, correlating the profiles with specific histopathologic and clinical features and hormone receptor status. Among the 14 phospholipids identified, the mean mole percentage of sphingomyelin, phosphatidylcholine, phosphatidylserine, phosphatidic acid, phosphatidylglycerol, and alkylacylphosphatidylcholine predicted cellular infiltration, infiltration type, elastosis, lymphatic invasion, perineural invasion, necrosis, and estrogen receptor positivity. (31)P MRS phospholipid profile data provide statistical correlations among histologic features and molecules known to play important roles in cellular communication, regulation, and processes unique to malignant tissues.

Variants of peroxiredoxins expression in response to hydroperoxide stress

We examined patterns of the proteins that were expressed in human umbilical vein endothelial cells (HUVEC) in response to oxidative stress by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). When HUVEC were exposed to H2O2 at 100 microM for 60 min, the intensities of eight spots increased and those of eight spots decreased on 2D gels, as compared with control gels, after staining with silver. These changes were also observed after exposure of cells to hydroperoxides such as cumene hydroperoxide and tert-butyl hydroperoxide, but not after exposure to other reagents that induce oxidative stress such as S-alkylating compounds, nitric oxide, and salts of heavy metals. Therefore, these proteins were designated hydroperoxide responsive proteins (HPRPs). Microsequencing analysis revealed that these HPRPs corresponded to at least six pairs of proteins. Of these, four pairs of HPRPs were thioredoxin peroxidase I (TPx I), TPx II, TPx III, and the product of human ORF06, all of which belong to the peroxiredoxin (Prx) family and all of which are involved in the elimination of hydroperoxides. The other two pairs corresponded to heat shock protein 27 (HSP27) and glyceraldehyde-3-phosphate dehydrogenase (G3PDH), respectively. The variants that appeared in response to hydroperoxides had molecular masses similar to the respective native forms, but their pI values were lower by 0.2-0.3 pH units than those of the corresponding native proteins. These variants were detected on 2D gels after cells had been exposed to hydroperoxides in the presence of an inhibitor of protein synthesis. All variants were generated within 30 min of exposure to 100 microM H2O2. The variants of TPx I and TPx II appeared within 2 min of the addition of H2O2 to the culture medium. The HPRPs returned to their respective native forms after the removal of stress. Our results indicated that at least six proteins were structurally modified in response to hydroperoxides. Analysis by 2D-PAGE of 32P-labeled proteins revealed that the variant of HSP27 was its phosphorylated form while the other HPRPs were not modified by phosphorylation. Taken together, the results suggest that 2D-PAGE can reveal initial responses to hydroperoxide stress at the level of protein modification. Moreover, it is possible that the variants of four types of Prx might reflect intermediate states in the process of hydroperoxide elimination.

Investigation of Fasciola hepatica sample preparation for two-dimensional electrophoresis

This paper investigates the preparation of Fasciola hepatica samples for two-dimensional electrophoresis (2-DE). Whole samples were prepared by both hot sodium dodecyl sulfate (SDS) solubilisation and precipitation using trichloroacetic acid (TCA) to remove nonprotein contaminants and to inactivate endogenous proteases. Sample preparation had a marked influence on the 2-DE gel profile. TCA precipitation resulted in no measurable improvement in the profile observed, compared to the untreated control. Solubilisation of sample with hot SDS increased the number of protein spots, as did TCA precipitation with the addition of phosphotungstic acid. The preparation of excretory-secretory (ES) products poses problems due to both high salt concentrations and low protein concentration. All precipitation methods used to overcome this gave similar profiles, except acetone alone, which caused depletion of the larger proteins. TCA in acetone gave the best result, similar to that obtained by centrifugal filtration of the sample. Overcrowding of spots in some regions of the 2-DE gel occurred in the whole Fasciola hepatica sample. This problem was alleviated by differential solubilisation, which also resulted in the enrichment of some proteins.

Differential protein phosphorylation in 3T3-L1 adipocytes in response to insulin versus platelet-derived growth factor. No evidence for a phosphatidylinositide 3-kinase-independent pathway in insulin signaling

Insulin regulates glucose metabolism in adipocytes via a phosphatidylinositide 3-kinase (PI3K)-dependent pathway that appears to involve protein phosphorylation. However, the generation of phosphoinositides is not sufficient for insulin action, and it has been suggested that insulin regulation of glucose metabolism may involve both PI3K-dependent and -independent pathways, the latter being insulin specific. To test this hypothesis, we have designed a phosphoprotein screen to study insulin-specific phosphoproteins that may be either downstream or in parallel to PI3K. Nineteen insulin-regulated phosphospots were detected in the cytosol and high speed pellet fractions, only six of which were significantly regulated by platelet-derived growth factor. Importantly, almost all (92%) of the insulin-specific phosphoproteins identified using this approach were sensitive to the PI3K inhibitor wortmannin. Thus, we obtained no evidence for an insulin-specific, PI3K-independent signaling pathway. A large proportion (62%) of the insulin-specific phosphoproteins were enriched in the same high speed pellet fraction to which PI3K was recruited in response to insulin. Thus, our data suggest that insulin specifically stimulates the phosphorylation of a novel subset of downstream targets and this may in part be because of the unique localization of PI3K in response to insulin in adipocytes.