From proteins to proteomics

Exploring the HeLa Dark Mitochondrial Proteome

In the framework of the Human Proteome Project initiative, we aim to improve mapping and characterization of mitochondrial proteome. In this work we implemented an experimental workflow, combining classical biochemical enrichments and mass spectrometry, to pursue a much deeper definition of mitochondrial proteome and possibly mine mitochondrial uncharacterized dark proteins. We fractionated in two compartments mitochondria enriched from HeLa cells in order to annotate 4230 proteins in both fraction by means of a multiple-enzyme digestion (trypsin, chymotrypsin and Glu-C) followed by mass spectrometry analysis using a combination of Data Dependent Acquisition (DDA) and Data Independent Acquisition (DIA). We detected 22 mitochondrial dark proteins not annotated for their function and we provide their relative abundance inside the mitochondrial organelle. Considering this work as a pilot study we expect that the same approach, in different biological system, could represent an advancement in the characterization of the human mitochondrial proteome providing uncharted ground to explore the mitonuclear phenotypic relationships. All spectra have been deposited to ProteomeXchange with PXD014201 and PXD014200 identifier.

The Nuclear Proteome of White and Gray Matter from Schizophrenia Postmortem Brains

Schizophrenia (SCZ) is a serious neuropsychiatric disorder that manifests through several symptoms from early adulthood. Numerous studies over the last decades have led to significant advances in increasing our understanding of the factors involved in SCZ. For example, mass spectrometry-based proteomic analysis has provided important insights by uncovering protein dysfunctions inherent to SCZ. Here, we present a comprehensive analysis of the nuclear proteome of postmortem brain tissues from corpus callosum (CC) and anterior temporal lobe (ATL). We show an overview of the role of deregulated nuclear proteins in these two main regions of the brain: the first, mostly composed of glial cells and axons of neurons, and the second, represented mainly by neuronal cell bodies. These samples were collected from SCZ patients in an attempt to characterize the role of the nucleus in the disease process. With the ATL nucleus enrichment, we found 224 proteins present at different levels, and 76 of these were nuclear proteins. In the CC analysis, we identified 119 present at different levels, and 24 of these were nuclear proteins. The differentially expressed nuclear proteins of ATL are mainly associated with the spliceosome, whereas those of the CC region are associated with calcium/calmodulin signaling.

A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues

Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.

SprayQc: a real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components

With the advent of high-throughput mass spectrometry (MS)-based proteomics, the magnitude and complexity of the performed experiments has increased dramatically. Likewise, investments in chromatographic and MS instrumentation are a large proportion of the budget of proteomics laboratories. Guarding measurement quality and maximizing uptime of the LC-MS/MS systems therefore requires constant care despite automated workflows. We describe a real-time surveillance system, called SprayQc, that continuously monitors the status of the peripheral equipment to ensure that operational parameters are within an acceptable range. SprayQc is composed of multiple plug-in software components that use computer vision to analyze electrospray conditions, monitor the chromatographic device for stable backpressure, interact with a column oven to control pressure by temperature, and ensure that the mass spectrometer is still acquiring data. Action is taken when a failure condition has been detected, such as stopping the column oven and the LC flow, as well as automatically notifying the appropriate operator. Additionally, all defined metrics can be recorded synchronized on retention time with the MS acquisition file, allowing for later inspection and providing valuable information for optimization. SprayQc has been extensively tested in our laboratory, supports third-party plug-in development, and is freely available for download from http://sourceforge.org/projects/sprayqc .

Proteomics: a subcellular look at spermatozoa

BACKGROUND

Male-factor infertility presents a vexing problem for many reproductively active couples. Many studies have focused on abnormal sperm parameters. Recent advances in proteomic techniques, especially in mass spectrometry, have aided in the study of sperm and more specifically, sperm proteins. The aim of this study was to review the current literature on the various proteomic techniques, and their usefulness in diagnosing sperm dysfunction and potential applications in the clinical setting.

METHODS

Review of PubMed database. Key words: spermatozoa, proteomics, protein, proteome, 2D-PAGE, mass spectrometry.

RESULTS

Recently employed proteomic methods, such as two-dimensional polyacrylamide gel electrophoresis, mass spectrometry, and differential in gel electrophoresis, have identified numerous sperm-specific proteins. They also have provided a further understanding of protein function involved in sperm processes and for the differentiation between normal and abnormal states. In addition, studies on the sperm proteome have demonstrated the importance of post-translational modifications, and their ability to bring about physiological changes in sperm function. No longer do researchers believe that in order for them to elucidate the biochemical functions of genes, mere knowledge of the human genome sequence is sufficient. Moreover, a greater understanding of the physiological function of every protein in the tissue-specific proteome is essential in order to unravel the biological display of the human genome.

CONCLUSION

Recent advances in proteomic techniques have provided insight into sperm function and dysfunction. Several multidimensional separation techniques can be utilized to identify and characterize spermatozoa. Future developments in bioinformatics can further assist researchers in understanding the vast amount of data collected in proteomic studies. Moreover, such advances in proteomics may help to decipher metabolites which can act as biomarkers in the detection of sperm impairments and to potentially develop treatment for infertile couples.Further comprehensive studies on sperm-specific proteome, mechanisms of protein function and its proteolytic regulation, biomarkers and functional pathways, such as oxidative-stress induced mechanisms, will provide better insight into physiological functions of the spermatozoa. Large-scale proteomic studies using purified protein assays will eventually lead to the development of novel biomarkers that may allow for detection of disease states, genetic abnormalities, and risk factors for male infertility. Ultimately, these biomarkers will allow for a better diagnosis of sperm dysfunction and aid in drug development.

Proteomics reveals potential biomarkers of seed vigor in sugarbeet

To unravel biomarkers of seed vigor, an important trait conditioning crop yield, a comparative proteomic study was conducted with sugarbeet seed samples of varying vigor as generated by an invigoration treatment called hydropriming and an aging treatment called controlled deterioration. Comparative proteomics revealed proteins exhibiting contrasting behavior between seed samples. Thus, 18 proteins were up-regulated during priming and down-regulated during aging and further displayed an up-regulation upon priming of the aged seeds, meaning that down-regulation of these spot volumes during aging was reversible upon subsequent priming. Also, 11 proteins exhibited the converse behavior characterized by a decrease and an increase of the spot volumes during priming and aging of the control seeds, respectively, and a decrease in the spot volumes upon priming of the aged seeds. The results underpinned the role in seed vigor of several metabolic pathways involved in lipid and starch mobilization, protein synthesis or the methyl cycle. They also corroborate previous studies suggesting that the glyoxylate enzyme isocitrate lyase, the capacity of protein synthesis and components of abscisic acid signaling pathways are likely contributors of seed vigor.

Effects of mercury on Dictyostelium discoideum: proteomics reveals the molecular mechanisms of physiological adaptation and toxicity

Dictyostelium discoideum amoebae were exposed to Hg 2 microM corresponding to a sublethal concentration and Hg 10 microM with the first effects on mortality and replication rate. A total of 900 spots were visualized by 2-DE electrophoresis. Two-hundred fifty single proteins were identified by mass spectrometry. Low Hg concentration (2 microM) treatment induced up-regulation of 13 spots, mainly involved in oxidative stress response/detoxification, oxidoreductase activity, and metabolic processes. High Hg concentration (10 microM) treatment showed a different PES with 12 proteins downregulated and only two up-regulated, mainly involved in cellular metabolic processes, metal ion binding, and transferase activity. The analyses for the carbonylation show no changes after 2 microM Hg(2+) treatment and 13 differentially carbonylated proteins after 10 microM Hg(2+) involved in a broad range of cellular processes. Our findings provide insight into the mechanisms of physiological adaptation and toxicity to a low and an high mercury concentration, respectively, of Dictyostelium amoebae.

Receptor tyrosine kinase signaling--a proteomic perspective

The RTKs are one of the most important families mediating transmembrane signaling and they participate and are instrumental in regulating a broad range of physiological activities. Indeed, tyrosine kinases in general, and the processes that they control and/or stimulate, provide a rich source of drug targets, particularly in growth related disorders such as cancer (Zwick et al., 2002; Krause and Van Etten, 2005). However, there remain many questions regarding their activation and downstream signaling and the application of proteomic analyses promises to answer many of them. There have been relatively few detailed studies of this type to date and it will require considerably more of them to better define the pathways with respect to both the major and minor PTMs that, along with the protein-protein interactions, are the means to direct the flow of the signals generated. It will take such approaches to define the specificity that characterize the individual families, even appreciating that to some degree all are capable of activating many, if not all, of the principal pathways. It will also be necessary to understand, in the highly complex networks of intracellular phosphorylation (that contain thousands of sites of modification and clearly have not yet been fully determined in any paradigm), exactly which kinases modify which substrates, and to work out the inter-relationships with other modifications such as O-GlcNAcylation and acetylation. Only then will it be possible to determine which modifications are physiologically significant and which are simply background. Along theway, these studies should continue to provide potential drug targets and perhaps improve the current lackluster biomarker discovery track record.

Highlights on the capacities of "Gel-based" proteomics

Gel-based proteomic is the most popular and versatile method of global protein separation and quantification. This is a mature approach to screen the protein expression at the large scale, and a cheaper approach as compared with gel-free proteomics. Based on two independent biochemical characteristics of proteins, two-dimensional electrophoresis combines isoelectric focusing, which separates proteins according to their isoelectric point, and SDS-PAGE, which separates them further according to their molecular mass. The next typical steps of the flow of gel-based proteomics are spots visualization and evaluation, expression analysis and finally protein identification by mass spectrometry. For the study of differentially expressed proteins, two-dimensional electrophoresis allows simultaneously to detect, quantify and compare up to thousand protein spots isoforms, including post-translational modifications, in the same gel and in a wide range of biological systems. In this review article, the limits, benefits, and perspectives of gel-based proteomic approaches are discussed using concrete examples.

Proteomics reveals the overlapping roles of hydrogen peroxide and nitric oxide in the acclimation of citrus plants to salinity

Hydrogen peroxide (H(2)O(2)) and nitric oxide (*NO) are key reactive species in signal transduction pathways leading to activation of plant defense against biotic or abiotic stress. Here, we investigated the effect of pre-treating citrus plants (Citrus aurantium L.) with either of these two molecules on plant acclimation to salinity and show that both pre-treatments strongly reduced the detrimental phenotypical and physiological effects accompanying this stress. A proteomic analysis disclosed 85 leaf proteins that underwent significant quantitative variations in plants directly exposed to salt stress. A large part of these changes was not observed with salt-stressed plants pre-treated with either H(2)O(2) or sodium nitroprusside (SNP; a *NO-releasing chemical). We also identified several proteins undergoing changes either in their oxidation (carbonylation; 40 proteins) and/or S-nitrosylation (49 proteins) status in response to salinity stress. Both H(2)O(2) and SNP pre-treatments before salinity stress alleviated salinity-induced protein carbonylation and shifted the accumulation levels of leaf S-nitrosylated proteins to those of unstressed control plants. Altogether, the results indicate an overlap between H(2)O(2)- and *NO-signaling pathways in acclimation to salinity and suggest that the oxidation and S-nitrosylation patterns of leaf proteins are specific molecular signatures of citrus plant vigour under stressful conditions.

Cold chemical oxidation of proteins

Various methods of protein footprinting use hydrogen peroxide as an oxidant. Its removal by various solid-phase desalting methods, catalase treatment, or freeze drying after the footprinting is critical to ensure no uncontrolled oxidation. Although catalase treatment removes hydrogen peroxide with little loss of protein or additional protein oxidation, we discovered that freeze drying or freezing of the protein in a peroxide solution does lead to protein oxidation. Interestingly, the oxidation is not a result of freeze or thaw processes but is dependent on the temperature and length of time for incubation. After 2 h, apomyoglobin undergoes almost-complete single oxidation at -80 degrees C and double oxidation at -15 degrees C. Minimal oxidation is observed at 4 and 22 degrees C, compared to oxidation at -80 or -15 degrees C. The concentration of hydrogen peroxide is critical; 75 mM (0.2%) is required to oxidize >50% of the protein at -15 degrees C and 100 mM (0.3%) is required at -80 degrees C. In addition to Met, approximately 5% of the tryptophan and tyrosine residues are oxidized, as well as lower amounts of His and Phe. Oxidation of Val 68 and Val 17 (a buried residue) also occurs, with the oxidation of Val 17 likely occurring by electron transfer from one of two of the oxidized aromatic residues that are in contact with Val 17. Here, we describe the need to remove the hydrogen peroxide prior to cold storage of proteins, and we also report some preliminary results pertaining to the mechanism of cold, solid-state oxidation.

Toxoplasma gondii proteomics

Toxoplasma gondii is a ubiquitous, Apicomplexan parasite that, in humans, can cause several clinical syndromes, including encephalitis, chorioretinitis and congenital infection. T. gondii was described a little over 100 years ago in the tissues of the gundi (Ctenodoactylus gundi). There are a large number of applicable experimental techniques available for this pathogen and it has become a model organism for the study of intracellular pathogens. With the completion of the genomes for a type I (GT-1), type II (ME49) and type III (VEG) strains, proteomic studies on this organism have been greatly facilitated. Several subcellular proteomic studies have been completed on this pathogen. These studies have helped elucidate specialized invasion organelles and their composition, as well as proteins associated with the cytoskeleton. Global proteomic studies are leading to improved strategies for genome annotation in this organism and an improved understanding of protein regulation in this pathogen. Web-based resources, such as EPIC-DB and ToxoDB, provide proteomic data and support for studies on T. gondii. This review will summarize the current status of proteomic research on T. gondii.

Characterization of voltage degradation in dynamic field gradient focusing

Dynamic field gradient focusing (DFGF) is an equilibrium gradient method that utilizes an electric field gradient to simultaneously separate and concentrate charged analytes based on their individual electrophoretic mobilities. This work describes the use of a 2-D nonlinear, numerical simulation to examine the impact of voltage loss from the electrodes to the separation channel, termed voltage degradation, and distortions in the electric field on the performance of DFGF. One of the design parameters that has a large impact on the degree of voltage degradation is the placement of the electrodes in relation to the separation channel. The simulation shows that a distance of about 3 mm from the electrodes to the separation channel gives the electric field profile with least amount of voltage degradation. The simulation was also used to describe the elution of focused protein peaks. The simulation shows that elution under constant electric field gradient gives better performance than elution through shallowing of the electric field. Qualitative agreement between the numerical simulation and experimental results is shown. The simulation also illustrates that the presence of a defocusing region at the cathodic end of the separation channel causes peak dispersion during elution. The numerical model is then used to design a system that does not suffer from a defocusing region. Peaks eluted under this design experienced no band broadening in our simulations. Preliminary experimental results using the redesigned chamber are shown.

Use of comparative proteomics to identify potential resistance mechanisms in cancer treatment

Drug resistance is a major problem in successful cancer chemotherapy. Many molecular mechanisms that are responsible for drug resistance are known whereas others have yet to be discovered. Determining the exact mechanism activated in a particular case (clinical or laboratory) is a difficult task. Recently, proteomics has been applied to investigate drug resistance mechanisms in model cancer cell lines. As a result, novel mechanisms of resistance have been discovered and known mechanisms of resistance confirmed. In this paper, we wish to review recent developments and progresses in the application of proteomic tools to identify known and novel drug resistance mechanisms in drug-selected model cancer cell lines. Our combined analyses of multiple proteomic studies of various drug resistant cancer cell lines revealed that many mechanisms of resistance likely exist in any given drug-selected cancer cell line and that common mechanisms of resistance may be selected in a spectrum of cancer cell lines. These observations suggest that combination therapies targeting multiple mechanisms to sensitize drug resistant cancers may be necessary to eradicate cancers in the future.

Proteomic-based analysis of nuclear signaling: PLCbeta1 affects the expression of the splicing factor SRp20 in Friend erythroleukemia cells

An extensive body of evidence links inositide-specific phospholipase C (PLC) to the nucleus and the main isoform located in the nucleus is PLCbeta(1). Constitutive overexpression of nuclear PLCbeta(1) has been previously shown to inhibit Friend erythroleukemia cells differentiation and to induce cell cycle progression targeting cyclin D3. The aim of this study was to identify new proteins regulated by PLCbeta(1) overexpression, given the role exerted by its signaling in the nucleus during cell growth and differentiation. To identify novel downstream effectors of nuclear PLCbeta(1)-dependent signaling in Friend erythroleukemia cells, we performed the high-resolution 2-DE-based proteomic analysis. Using a proteomic approach we found that SRp20, a member of the highly conserved SR family of splicing regulators, was down-regulated in cells overexpressing nuclear PLCbeta(1) as compared with wild-type cells. Reduction in SRp20 was confirmed by 2-D Western blotting. Moreover, we have shown that nuclear PLCbeta(1) is bound to the SRp20 splicing factor. Indeed, by immunoprecipitation and subcellular fractioning, we have demonstrated that endogenous PLCbeta(1) and SRp20 physically interact in the nucleus. Here we show the existence of a PLCbeta(1)-specific target, the splicing factor SRp20, whose expression is specifically down-regulated by the nuclear signaling evoked by PLCbeta(1).

Integrating forward and reverse proteomics to unravel protein function

To date, proteomics approaches have aimed to either identify novel proteins or change in protein expression/modification in various organisms under normal or disease conditions. One major aspect of functional proteomics is to identify protein biological properties in a given context, however, forward proteomics approaches alone cannot complete this goal. Indeed, with the increasing successes of such proteomics-based research strategies and the subsequent increasing amounts of proteins identified with unknown molecular functions, approaches allowing for systematic analyses of protein functions are desired. In this review, we propose to depict the complementarities of forward and reverse proteomics approaches in the definite understanding of protein functions. This dual strategy requires a data integration loop which allows for systematic characterization of protein function(s). The details of the integrative process combining both in silico and experimental resources and tools are presented. Altogether, we believe that the integration of forward and reverse proteomics approaches supported by bioinformatics will provide an efficient path towards systems biology.

Focused Proteomics in Post-Mortem Human Spinal Cord

With a highly sensitive electrospray ionization-Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) system, proteins were identified in minimal amounts of spinal cord from patients with the neurodegenerative disease amyotrophic lateral sclerosis (ALS) and compared to proteins in spinal cord from control subjects. The results show 18 versus 16 significantly identified (p < 0.05) proteins, respectively, all known to be found in the central nervous system. The most abundant protein in both groups was the glial fibrillary acidic protein, GFAP. Other proteins were, for example, hemoglobin alpha- and beta chain, myelin basic protein, thioredoxin, alpha enolase, and choline acetyltransferase. This study also includes the technique of laser microdissection in combination with pressure catapulting (LMPC) for the dissection of samples and specific neurons. Furthermore, complementary experiments with nanoLC-matrix assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF-TOF MS) confirmed the results of the ESI-FTICR MS screening and provided additional results of further identified proteins.

Prediction of viable circular permutants using a graph theoretic approach

MOTIVATION

In recent years graph-theoretic descriptions have been applied to aid the analysis of a number of complex biological systems. However, such an approach has only just begun to be applied to examine protein structures and the network of interactions between residues with promising results. Here we examine whether a graph measure known as closeness is capable of predicting regions where a protein can be split to form a viable circular permutant. Circular permutants are a powerful experimental tool to probe folding mechanisms and more recently have been used to design split enzyme reporter proteins.

RESULTS

We test our method on an extensive set of experiments carried out on dihydrofolate reductase in which circular permutants were constructed for every amino acid position in the sequence, together with partial data from studies on other proteins. Results show that closeness is capable of correctly identifying significantly more residues which are suitable for circular permutation than solvent accessibility. This has potential implications for the design of successful split enzymes having particular importance for the development of protein-protein interaction screening methods and offers new perspectives on protein folding. More generally, the method illustrates the success with which graph-theoretic measures encapsulate the variety of long and short range interactions between residues during the folding process.