Cutting-edge technology. II. Proteomics: core technologies and applications in physiology

Invited Review: Toxicoproteomics: Proteomics Applied to Toxicology and Pathology

Global measurement of proteins and their many attributes in tissues and biofluids defines the field of proteomics. Toxicoproteomics, as part of the larger field of toxicogenomics, seeks to identify critical proteins and pathways in biological systems that are affected by and respond to adverse chemical and environmental exposures using global protein expression technologies. Toxicoproteomics integrates 3 disciplinary areas: traditional toxicology and pathology, differential protein and gene expression analysis, and systems biology. Key topics to be reviewed are the evolution of proteomics, proteomic technology platforms and their capabilities with exemplary studies from biology and medicine, a review of over 50 recent studies applying proteomic analysis to toxicological research, and the recent development of databases designed to integrate -Omics technologies with toxicology and pathology. Proteomics is examined for its potential in discovery of new biomarkers and toxicity signatures, in mapping serum, plasma, and other biofluid proteomes, and in parallel proteomic and transcriptomic studies. The new field of toxicoproteomics is uniquely positioned toward an expanded understanding of protein expression during toxicity and environmental disease for the advancement of public health.

After genomics, what proteomics tools could help us understand the antimicrobial resistance of Escherichia coli?

Proteomic approaches have been considerably improved during the past decade and have been used to investigate the differences in protein expression profiles of cells grown under a broad spectrum of growth conditions and with different stress factors including antibiotics. In Europe, the most significant disease threat remains the presence of microorganisms that have become resistant to antimicrobials and so it is important that different scientific tools are combined to achieve the largest amount of knowledge in this area of expertise. The emergence and spread of the antibiotic-resistant Gram-negative pathogens, such as Escherichia coli, can lead to serious problem public health in humans. E. coli, a very well described prokaryote, has served as a model organism for several biological and biotechnological studies increasingly so since the completion of the E. coli genome-sequencing project. The purpose of this review is to present an overview of the different proteomic approaches to antimicrobial-resistant E. coli that will be helpful to obtain a better knowledge of the antibiotic-resistant mechanism(s). This can also aid to understand the molecular determinants involved with pathogenesis, which is essential for the development of effective strategies to combat infection and to reveal new therapeutic targets. This article is part of a Special Issue entitled: Proteomics: The clinical link.

EcoProDB: the Escherichia coli protein database

EcoProDB is a web-based database for comparative proteomics of Escherichia coli. The database contains information on E. coli proteins identified on 2D gels along with other resources collected from various databases and published literature, with a special feature of showing the expression levels of E. coli proteins under different genetic and environmental conditions. It also provides comparative information of subcellular localization, theoretical 2D map, experimental 2D map and integrated protein information via an interactive web interface and application such as the Map Browser. Users can also upload their own 2D gels, extract core information associated with the proteins and 2D gel results from different experiments and consequently generate new knowledge and hypotheses for further studies.

AVAILABILITY

EcoProDB database system is accessible at http://eecoli.kaist.ac.kr.

Protein identification by syringe pump-driven reversed-phase LC-MS/MS

In typical mass spectrometry-based protein identification using peptide fragmentation fingerprinting, front-end separation plays a critical role in successful peptide sequencing. This separation step demands a great deal of time and usually is the rate-limiting step for the whole process. Here we provide an alternative separation method, based on a simple nanoflow delivery system, that is able to shorten the separation time considerably. This system consists of a 25-mul syringe connected to a manually packed reversed-phase mini-capillary column that can be directly coupled to an electrospray ionization tandem mass spectrometer. A syringe pump is then used to deliver the peptide mixtures at a nanoscale flow rate. We examined the efficiency and efficacy of this method by analyzing the tryptic peptides of bovine serum albumin and of 10 Escherichia coli proteins separated by two-dimensional gel electrophoresis (2DE). The results showed that identification of each protein could be achieved successfully within 25 min by using the disposable mini-capillary column. Moreover, all 2DE-separated E. coli proteins were identified at high confidence levels. Together, our data suggest that this method is a suitable option for mass spectrometry-based protein identification.

Proteomic Identification of Altered Proteins in Skeletal Muscle During Chronic Potassium Depletion: Implications for Hypokalemic Myopathy

Prolonged potassium depletion is a well-known cause of myopathy. The pathophysiology of hypokalemic myopathy, however, remains unclear. We performed a gel-based, differential proteomics study to define altered proteins in skeletal muscles during chronic potassium depletion. BALB/c mice were fed with normal chow (0.36% K+) or K+-depleted (KD) diet (<0.001% K+) for 8 weeks (n = 5 in each group). Left gastrocnemius muscles were surgically removed from each animal. Histopathological examination showed mild-degree infiltration of polymornuclear and mononuclear cells at the interstitium of the KD muscles. Extracted proteins were resolved with two-dimensional electrophoresis (2-DE), and visualized with Coomassie Brilliant Blue R-250 stain. Quantitative intensity analysis revealed 16 up-regulated protein spots in the KD muscles, as compared to the controls. These differentially expressed proteins were subsequently identified by peptide mass fingerprinting and by quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS). Most of the altered proteins induced by chronic potassium depletion were muscle enzymes that play significant roles in several various metabolic pathways. Other up-regulated proteins included myosin-binding protein H, alpha-B Crystallin, and translationally controlled tumor protein (TCTP). These findings may lead to a new roadmap for research on hypokalemic myopathy, to better understanding of the pathophysiology of this medical disease, and to biomarker discovery.

The Escherichia coli proteome: past, present, and future prospects

Proteomics has emerged as an indispensable methodology for large-scale protein analysis in functional genomics. The Escherichia coli proteome has been extensively studied and is well defined in terms of biochemical, biological, and biotechnological data. Even before the entire E. coli proteome was fully elucidated, the largest available data set had been integrated to decipher regulatory circuits and metabolic pathways, providing valuable insights into global cellular physiology and the development of metabolic and cellular engineering strategies. With the recent advent of advanced proteomic technologies, the E. coli proteome has been used for the validation of new technologies and methodologies such as sample prefractionation, protein enrichment, two-dimensional gel electrophoresis, protein detection, mass spectrometry (MS), combinatorial assays with n-dimensional chromatographies and MS, and image analysis software. These important technologies will not only provide a great amount of additional information on the E. coli proteome but also synergistically contribute to other proteomic studies. Here, we review the past development and current status of E. coli proteome research in terms of its biological, biotechnological, and methodological significance and suggest future prospects.

Teaching molecular genetics: Chapter 3--Proteomics in nephrology

The novel discipline of proteomics has experienced a rapid growth in the recent past and has great potentials for the future. The study of proteins on a genomic scale enables a large number of proteins to be analysed simultaneously. Moreover, proteomic analysis reveals the presence of protein isoforms and post-translational modifications, both of which have the potential to regulate protein complex formation, activity and function. As such, the assessment of the proteome, unlike genomic analysis, provides a view of biological processes at their level of occurrence. The knowledge thus gained is important not only for a better understanding of renal physiology and pathophysiology, but also for the identification of disease markers and the development of new therapies. This review applies the science of proteomics to nephrology: our aim is to give an overview of the discipline, providing background information and outlining the scope, advantages and limitations of proteomics.

Synthesis of Acid-Cleavable Light Isotope-Coded Affinity Tags (ICAT-L) for Potential Use in Proteomic Expression Profiling Analysis

A convenient synthesis of some homologous light isotope-coded affinity tags (ICAT-L) containing an acid-labile moiety between the affinity component biotin and an electrophilic polar linker is described. These light ICAT reagents give smooth mass spectral signals in tandem mass spectrometry (MS/MS) analyses of some commercially available cysteine-containing peptides. However, these ICAT molecules are designed for use in identification and relative quantification of whole or partially purified cellular and tissue proteomes. Since the biotin moiety can be readily cleaved off the reagent after mass tagging, undesired residual fragmentation patterns caused by biotin of derived peptides, as normally observed using biotin-containing ICAT reagents, are effectively eliminated. This strategy should enhance peptide sequence coverage significantly which, in turn, should result in improving the quality of data obtained during data-dependent peptide mass and tandem mass spectral analysis of whole proteomes.

Renal and urinary proteomics: current applications and challenges

During the past few years, proteomics has been extensively applied to various fields of medicine including nephrology. Current applications of renal and urinary proteomics are to better understand renal physiology, to explore the complexity of disease mechanisms, and to identify novel biomarkers and new therapeutic targets. This review provides some examples and perspectives of how proteomics can be applied to nephrology and how experimental data can be linked to physiology, functional significance and clinical applications. In some instances, proteomic analysis can be utilized to generate a new hypothesis from a set of candidates that are obtained from expression studies. The new hypothesis can then be addressed rapidly by conventional molecular biology methods, as demonstrated by identification of an altered renal elastin-elastase system in diabetic nephropathy and alterations in the renal kallikrein-kallistatin pathway in hypoxia-induced hypertension. The strengths and limitations of proteomics in renal research are summarized. Optimization of analytical protocols is required to overcome current limitations. Applications of proteomics to nephrology will then be more fruitful and successful.

Synthesis and self-alkylation of isotope-coded affinity tag reagents

A pair of ICAT reagents, N-(13-iodoacetamido-2,2,3,3,11,11,12,12-octadeutero-4,7,10-trioxa-tridecanyl)biotinamide (8d, ICAT-d(8)) and N-(13-iodoacetamido-4,7,10-trioxa-tridecanyl)biotinamide (8c, ICAT-d(0)), and an alternative pair of ICAT reagents, N-(10-iodoacetamido-2,5,5,6,6,9-hexadeutero-4,7-dioxa-decanyl)biotinamide (8b, s-ICAT-d(6)) and N-(10-iodoacetamido-4,7-dioxa-decanyl)biotinamide (8a, s-ICAT-d(0)), were successfully synthesized. A mixture of sodium borohydride and cobalt(II) chloride reduced the intermediate dinitrile to the diamine without loss of the deuterium labels, which occurred when Raney nickel was the reducing agent. The problem caused by unsymmetrical biotinylation of the intermediate diamine was solved by using the solid-phase method in which one end of the diamine was attached to a chlorotrityl chloride resin, followed by biotinylation of the resin-bound amine. The self-alkylation of ICAT reagents that accounted for their instability and their limitations in the applications was also studied.

High throughput approaches in neuroscience

Traditional approaches to understanding biological problems are now being advanced with the use of high throughput technologies, which analyse multiple samples simultaneously, or thousands of analytes in a single sample. The application of these technologies in neurochemistry and neuroscience is beginning to be explored and is assisting in the development of new models of drug action, neuroanatomical investigations, and in identifying molecular pathways involved in neurological and psychiatric disease. Tools such as microarray-based gene expression profiling and 2D and multidimensional proteomic methods are uncovering functional components to a wide variety of neuroscience paradigms and the application of these technologies is set to become standard in analysis.

Injury research in the genomic era

With the development of trauma systems, improved resuscitation, and organ system support, survival after severe injury is common, but is often complicated by nosocomial infection and organ failure. These complications are costly, and can lead to death or disability. Although much is known about the pathophysiology of post-traumatic nosocomial infection and organ failure, findings have been limited by our ability to generate and analyse large amounts of experimental and observational data. However, technological advances in nucleic acid and protein analysis, coupled with increased computational capacity, provide an opportunity to characterise the determinants of and the responses to injury and sepsis on a genome-wide scale. New large-scale collaborative efforts aim to investigate the genome for variation (gene polymorphisms), characterise multiple levels of the biological response to injury (transcriptome and proteome), and relate these to clinical phenotypes. In this article, we summarise recent findings and explore where promising new technologies might have the greatest potential for increasing our knowledge. It will now be important to determine how these recent technological advances can be used and integrated with our existing approaches, to reduce death, disability, and the economic consequences of trauma.

Functional genomics and proteomics: application in neurosciences

The sequencing of the complete genome for many organisms, including man, has opened the door to the systematic understanding of how complex structures such as the brain integrate and function, not only in health but also in disease. This blueprint, however, means that the piecemeal analysis regimes of the past are being rapidly superseded by new methods that analyse not just tens of genes or proteins at any one time, but thousands, if not the entire repertoire of a cell population or tissue under investigation. Using the most appropriate method of analysis to maximise the available data therefore becomes vital if a complete picture is to be obtained of how a system or individual cell is affected by a treatment or disease. This review examines what methods are currently available for the large scale analysis of gene and protein expression, and what are their limitations.

From genomics to proteomics: new directions in molecular neuropsychiatry

Neuropsychiatry, like many other biomedical sciences, has been revolutionized by the advances in genomic technologies over the years. The advent of PCR (polymerase chain reaction) and the sequencing of the human genome have provided invaluable insights into the molecular genetics of the various psychiatric disorders through the study of candidate genes and linkage analyses. However, biological phenotype is dictated by protein expression, which has been shown to stray from the genetic blueprint designated by the genome. Consequently, the field of proteomics has recently emerged as a powerful means of exploring protein structure, function, and expression patterns. The ability to study disease at the gene and protein levels presents a tremendous opportunity for neuropsychiatric research, particularly in terms of the potential for developing therapeutic agents for novel protein targets.

The future of GI and liver research: editorial perspectives: I. Visions of epithelial research

Epithelial cells are gatekeepers that sit at the interface between two compartments. By controlling the flow of molecules and information between two compartments, epithelial cells provide unique benefit to the body. This article provides a brief appraisal of our current knowledge about the functions of gastrointestinal epithelial cells as a functionally diverse set of cells mediating transepithelial transport and as a continually renewing layer of cells. The convergence of new methodologies in laser capture microdissection, microarray analyses, microscopic analyses, and generation of mutant animals provides an exciting template for future research.

Advances in quantitative proteomics via stable isotope tagging and mass spectrometry

The high-throughput identification and accurate quantification of proteins are essential components of proteomic strategies for studying cellular functions and processes. Techniques that are largely based on stable isotope protein or peptide labeling and automated tandem mass spectrometry are increasingly being applied in quantitative proteomic studies. Over the past year, significant progress has been made toward improving and diversifying these technologies with respect to the methods for stable isotope labeling, process automation and data processing and analysis. Advances in stable isotope protein labeling and recent biological studies that used stable isotope based quantitative proteomics techniques are reviewed.

Understanding and controlling the enteric nervous system

The enteric nervous system or the 'Little Brain' of the gut controls gastrointestinal motility and secretion, and is involved in visceral sensation. In this chapter, new developments in understanding the function of the enteric nervous system are described. In particular, the interaction of this system with the interstitial cells of Cajal, the pacemaker cells of the gut, is highlighted. The importance of the interaction between the enteric nervous system and the immune system is discussed, especially in relation to functional bowel disorders and post-operative ileus. Evidence is also provided that neurones can change their function and phenotype, a phenomenon called neuronal plasticity, which contributes to the pathogenesis of visceral hypersensitivity. Finally, new developments in stem cell transplantation are described. All these new insights should lead to a better understanding of the enteric nervous system and hopefully to better ways of controlling it.