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PubMed2004

Requirements of fission yeast septins for complex formation, localization, and function.

Septins are GTP binding proteins important for cytokinesis in many eukaryotes. The Schizosaccaromyces pombe genome sequence predicts orthologues of four of five Saccharomyces cerevisiae septins involved in cytokinesis and these are named Spns1-4p. That spns1-4 are not essential genes permitted the application of a combined genetic and proteomics approach to determine their functional relationships. Our findings indicate that Spns1-4p are present throughout interphase as a diffusely localized approximately 8.5S complex containing two copies of each septin linked together as a chain in the order Spn3p-Spn4p-Spn1p-Spn2p. Septin recruitment to the medial region of the cell is genetically separable from ring formation, and whereas it is normally restricted to mitosis, it can be promoted without activation of the mitotic cell cycle machinery. Coalescence into ring structures requires Spn1p and Spn4p associate with at least one other septin subunit and the expression of Mid2p that is normally restricted to mitosis. This study establishes the functional requirements for septin complex organization in vivo.

Cytoskeletal Proteins↗
PubMed2024

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast.

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein coexpression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship.

Saccharomyces cerevisiae↗
PubMed2006

Recent developments in microarray-based enzyme assays: from functional annotation to substrate/inhibitor fingerprinting.

Recent advances in proteomics have provided impetus towards the development of robust technologies for high-throughput studies of enzymes. The term "catalomics" defines an emerging '-omics' field in which high-throughput studies of enzymes are carried out by using advanced chemical proteomics approaches. Of the various available methods, microarrays have emerged as a powerful and versatile platform to accelerate not only the functional annotation but also the substrate and inhibitor specificity (e.g. substrate and inhibitor fingerprinting, respectively) of enzymes. Herein, we review recent developments in the fabrication of various types of microarray technologies (protein-, peptide- and small-molecule-based microarrays) and their applications in high-throughput characterizations of enzymes.

Animals↗
PubMed2004

The aryl hydrocarbon receptor predisposes hepatocytes to Fas-mediated apoptosis.

Liver homeostasis is achieved by the removal of diseased and damaged hepatocytes and their coordinated replacement to maintain a constant liver cell mass. Cirrhosis, viral hepatitis, and toxic drug effects can all trigger apoptosis in the liver as a means of removing the unwanted cells, and the Fas "death receptor" pathway comprises a major physiological mechanism by which this occurs. The susceptibility to Fas-mediated apoptosis is, in part, a function of the hepatocyte's proteome. The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor known to influence apoptosis, conceivably by regulating the expression of genes involved in apoptotic signaling. In this article, we present evidence demonstrating that AhR expression and function promote apoptosis in liver cells in response to Fas stimulation. Reintroduction of the AhR into the AhR-negative BP8 hepatoma cells as well as into primary hepatocytes from AhR knockout mice increases the magnitude of cell death in response to Fas ligand. Enhanced apoptosis correlates with increased caspase activity and mitochondrial cytochrome c release but not with the expression of several Bcl-2 family proteins. In vivo studies showed that in contrast to wild-type mice, AhR knockout mice are protected from the lethal effects of the anti-Fas Jo2 antibody. Moreover, down-regulation of the aryl hydrocarbon receptor nuclear translocator protein in vivo by adenovirus-mediated RNA interference to suppress AhR activity provided wild-type mice partial protection from Jo2-induced lethality.

Animals↗
PubMed1999

Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database.

FlyNets (http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page.++ +html) is a WWW database describing molecular interactions (protein-DNA, protein-RNA and protein-protein) in the fly Drosophila melanogaster. It is composed of two parts, as follows. (i) FlyNets-base is a specialized database which focuses on molecular interactions involved in Drosophila development. The information content of FlyNets-base is distributed among several specific lines arranged according to a GenBank-like format and grouped into five thematic zones to improve human readability. The FlyNets database achieves a high level of integration with other databases such as FlyBase, EMBL, GenBank and SWISS-PROT through numerous hyperlinks. (ii) FlyNets-list is a very simple and more general databank, the long-term goal of which is to report on any published molecular interaction occuring in the fly, giving direct web access to corresponding s in Medline and in FlyBase. In the context of genome projects, databases describing molecular interactions and genetic networks will provide a link at the functional level between the genome, the proteome and the transcriptome worlds of different organisms. Interaction databases therefore aim at describing the contents, structure, function and behaviour of what we herein define as the interactome world.

Animals↗
PubMed2006

Protein function microarrays based on self-immobilizing and self-labeling fusion proteins.

Protein microarrays are an attractive approach for the high-throughput analysis of protein function, but their impact on proteomics has been limited by the technical difficulties associated with their generation. Here we demonstrate that fusion proteins of O6-alkylguanine-DNA alkyltransferase (AGT) can be used for the simple and reliable generation of protein microarrays for the analysis of protein function. Important features of the approach are the selectivity of the covalent immobilization; this allows for direct immobilization of proteins out of cell extracts, and the option both to label and to immobilize AGT fusion proteins, which allows for direct screening for protein-protein interactions between different AGT fusion proteins. In addition to the identification of protein-protein interactions, AGT-based protein microarrays can be used for the characterization of small molecule-protein interactions or post-translational modifications. The potential of the approach was demonstrated by investigating the post-translational modification of acyl carrier protein (ACP) from E. coli by different phosphopantetheine transferases (PPTases), yielding insights into the role of selected ACP amino acids in the ACP-PPTase interaction.

Carrier Proteins↗
PubMed2003

Novel glyoxysomal protein kinase, GPK1, identified by proteomic analysis of glyoxysomes in etiolated cotyledons of Arabidopsis thaliana.

Glyoxysomes are present in etiolated cotyledons and contain enzymes for gluconeogenesis, which constitutes the major function of glyoxysomes. However, 281 genes seemingly related to peroxisomal functions occur in the Arabidopsis genome, implying that many unidentified proteins are present in glyoxysomes. To better understand the functions of glyoxysomes, we performed glyoxysomal proteomic analysis of etiolated Arabidopsis cotyledons. Nineteen proteins were identified as glyoxysomal proteins, including 13 novel proteins, one of which is glyoxysomal protein kinase 1 (GPK1). We cloned GPK1 cDNA by RT-PCR and characterized GPK1. The amino acid sequence deduced from GPK1 cDNA has a hydrophobic region, a putative protein kinase domain, and a possible PTS1 motif. Immunoblot analysis using fractions collected on a Percoll density gradient confirmed that GPK1 is localized in glyoxysomes. Analysis of suborganellar localization and protease sensitivity showed that GPK1 is localized on glyoxysomal membranes as a peripheral membrane protein and that the putative kinase domain is located inside the glyoxysomes. Glyoxysomal proteins are phosphorylated well in the presence of various metal ions and [g-32P]ATP, and one of them is identified as thiolase by immunoprecipitation. Immuno-inhibition of phosphorylation in glyoxysomes suggested that GPK1 phosphorylates a 40-kDa protein. These results show that protein phosphorylation systems are operating in glyoxysomes.

Amino Acid Sequence↗
PubMed2005

Vernix caseosa as a multi-component defence system based on polypeptides, lipids and their interactions.

Vernix caseosa is a white cream-like substance that covers the skin of the foetus and the newborn baby. Recently, we discovered antimicrobial peptides/proteins such as LL-37 in vernix, suggesting host defence functions of vernix. In a proteomic approach, we have continued to characterize proteins in vernix and have identified 20 proteins, plus additional variant forms. The novel proteins identified, considered to be involved in host defence, are cystatin A, UGRP-1, and calgranulin A, B and C. These proteins add protective functions to vernix such as antifungal activity, opsonizing capacity, protease inhibition and parasite inactivation. The composition of the lipids in vernix has also been characterized and among these compounds the free fatty acids were found to exhibit antimicrobial activity. Interestingly, the vernix lipids enhance the antimicrobial activity of LL-37 in vitro, indicating interactions between lipids and antimicrobial peptides in vernix. In conclusion, vernix is a balanced cream of compounds involved in host defence, protecting the foetus and newborn against infection.

Amino Acid Sequence↗
PubMed2006

Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.

The HUPO Brain Proteome Project is an initiative coordinating proteomics studies to characterise human and mouse brain proteomes. Proteins identified in human brain samples during the project's pilot phase were put into biological context through integration with various annotation sources followed by a bioinformatics analysis. The data set was related to the genome sequence via the genes encoding identified proteins including an assessment of splice variant identification as well as an analysis of tissue specificity of the respective transcripts. Proteins were furthermore categorised according to subcellular localisation, molecular function and biological process, grouped into protein families and mapped to biological pathways they are known to act in. Involvement in pathological conditions was examined based on association with entries in the online version of Mendelian Inheritance in Man and an interaction network was derived from curated protein-proteininteraction data. Overall a non-redundant set of 1804 proteins was identified in human brain samples. In the majority of cases splice variants could be unambiguously identified by unique peptides, including matches to several hypothetical transcripts of known as well as predicted genes.

Alternative Splicing↗
PubMedDate not supplied

Rice proteomics: a cornerstone for cereal food crop proteomes.

Proteomics-a systematic study of proteins present in a cell, tissue, organ, or organism at a particular moment during the life cycle-that began with classical two-dimensional electrophoresis and its advancement during the 1990s, has been revolutionized by a series of tremendous technological developments in mass spectrometry (MS), a core technology. Proteomics is exerting its influence on biological function of genes and genomes in the era (21st century) of functional genomics, and for this reason yeast, bacterial, and mammalian systems are the best examples. Although plant proteomics is still in its infancy, evolving proteomic technologies and the availability of the genome sequences of Arabidopsis thaliana (L.) Heyhn, and rice (Oryza sativa L.), model dicotyledoneous and monocotyledoneous (monocot) species, respectively, are propelling it towards new heights, as evidenced by the rapid spurt in worldwide plant proteome research. Rice, with an immense socio-economic impact on human civilization, is a representative model of cereal food crops, and we consider it as a cornerstone for functional genomics of cereal plants. In this review, we look at the history and the current state of monocot proteomes, including barley, maize, and wheat, with a central focus on rice, which has the most extensive proteomic coverage to date. On one side, we highlight advances in technologies that have generated enormous amount of interest in plant proteomics, and the other side summarizes the achievements made towards establishing proteomes during plant growth & development and challenge to environmental factors, including disease, and for studying genetic relationships. In light of what we have learned from the proteomic journey in rice and other monocots, we finally reveal and assess their impact in our continuous strive towards completion of their full proteomes.

Crops, Agricultural↗
PubMed2005

Application of metal-chelate affinity chromatography to the study of the phosphoproteome.

With the increasing importance of proteome analysis, studying the phosphoproteome is a priority for functional studies. Therefore, a rational approach to simplifying the proteome is needed. In this work, we examined the use of immobilized metal affinity chromatography (IMAC) using ferric ions-chelated column for enriching crude cell extracts in phosphoproteins. The adsorption of the proteins on Fe(3+) was obtained at an acidic pH 5.6, and their elution at a more basic pH in Tris buffer. To evaluate the separation, western blots were performed with either anti-phosphotyrosine or anti-phosphoserine/threonine. The analysis of the eluates demonstrated the selectivity of the separation, particularly for proteins phosphorylated on serine or threonine. In conclusion, the advantages and the limits of this approach are discussed.

Blotting, Western↗
PubMed2005

Proteomics and diabetic nephropathy.

Diabetes mellitus is acknowledged to be a group of metabolic diseases and heterogeneous in natural history, pathogenesis, response to treatment, and disease progression and remission. Diabetic nephropathy (DN) accounts for approximately 40% of all newly diagnosed cases of end-stage renal disease. The complexity of diabetes and its complications requires a broad-based, unbiased, scientific approach such as proteomics. Recently, proteomics (the systematic analysis of protein identity, quantity, and function) has been applied to the study of DN. Proteomic investigations into diabetic kidney disease have identified new mechanisms of diabetic renal pathology, as well as potential urinary markers of DN. Other current proteomic advances in understanding DN include identifying the role of advanced glycation end products in decreased mitochondrial respiration and also the rapid development of mass spectrometric methods for protein and peptide markers of DN development and markers to pharmacologic therapies. Proteomic analysis has only recently been applied to the study of DN, yet it has shown substantial potential.

Animals↗
PubMed2005

Novel biological networks modulated by complement.

The almost complete deciphering of the human genome has paved the way for the application of new technology platforms in understanding the contribution of complex biological pathways to human pathophysiology and disease. In the post-genomic era, the concept of systems biology has gained significant momentum and biomedical research is now being conducted on an integrated and cross-disciplinary platform that pulls together its resources from diverse fields such as computational biology, bioinformatics, functional genomics, structural biology, and proteomics. In this perspective, the identity of established biologic systems is being re-examined in the light of novel findings that suggest novel associations between otherwise unrelated pathways and individual proteins. Complement exemplifies such a system that, transcending its innate immune identity, has forged functional associations with multiple pathways and networks in modulating basic biologic processes. In the present article, we provide a global overview of these unusual system associations of complement with the aid of a powerful and high-throughput bioinformatics platform. Using a novel approach called systems literature analysis that allows the rapid extraction of text-based associations between genes and pathways from the ever expanding scientific article database, we have selected a broad range of biologic processes modulated by complement proteins and have constructed an integrated map of complement-mediated networks that incorporates well over 85 diverse biologic pathways. Expanding the complement cascade beyond its approximately 35 designated components, we discuss protein-protein interactions involving novel ligands and associations with signaling cascades and cellular networks that affect both inflammatory and non-inflammatory processes. This integrated consideration of complement within a unified 'systems biology' framework underscores the concept that innate immunity goes well beyond the protection of 'self' extending links to critical developmental, homeostatic, and metabolic processes.

Complement System Proteins↗
PubMed2006

Identification of putative in vivo substrates of calpain 3 by comparative proteomics of overexpressing transgenic and nontransgenic mice.

Calpain 3 (CAPN3) is a calcium-dependent protease, mutations in which cause limb girdle muscular dystrophy type 2A. To explore the physiological function of CAPN3, we compared the proteomes of transgenic mice that overexpress CAPN3 (CAPN3 Tg) and their nontransgenic (non-Tg) counterparts. We first examined known muscular dystrophy-related proteins to determine if overexpression of CAPN3 results in a change in their distribution or concentration. This analysis did not identify any known muscular dystrophy proteins as substrates of CAPN3. Next, we used a proteomic approach to compare and identify differentially represented proteins in 2-DE of CAPN3 Tg and non-Tg mice. LC-MS/MS analysis led to the identification of ten possible substrates for CAPN3, classified into two major functional categories: metabolic and myofibrillar. Myosin light chain 1 (MLC1) was focused upon because our previous studies suggested a role for CAPN3 in sarcomere remodeling. In this study, CAPN3 was shown to proteolyze MLC1 in vitro. These studies are the first to identify possible substrates for CAPN3 in an in vivo system and support a role for CAPN3 in sarcomere remodeling by cleavage of myofibrillar proteins such as MLC1. In addition, these data also suggest a role for CAPN3 in mitochondrial protein turnover.

Animals↗
PubMed2004

Platelets: signaling cells in the immune continuum.

Platelets have intricate signaling mechanisms and participate in a breadth of cellular interactions. This diversity is frequently unrecognized. In addition to being the chief cellular effectors of haemostasis, platelets are innate inflammatory cells that have previously unrecognized molecular pathways and synthetic capacities, which can link innate and adaptive responses in the immune continuum. Characterization of these features and parallel in vivo observations identify new sentinel, surveillance and information-transfer functions. Recent observations indicate that platelets have key roles in adaptive responses to microbial and antigen challenge, in addition to their well known acute defensive activities in tissue injury, and suggest that these mechanisms can be dysregulated in disease. Ongoing characterization of the platelet transcriptome, secretome and proteome also suggest that additional functions of platelets relevant to innate and adaptive immunity remain to be discovered. This Review is the third in a series on interactions between haemostasis and inflammation.

Animals↗
PubMed2003

A comparative proteomics resource: proteins of Arabidopsis thaliana.

Using an integrative genome annotation pipeline (iGAP) for proteome-wide protein structure and functional domain assignment, we analyzed all the proteins of Arabidopsis thaliana. Three-dimensional structures at the level of the domain are assigned by fold recognition and threading based on a novel fold library that extends common domain classifications. iGAP is being applied to proteins from all available proteomes as part of a comparative proteomics resource. The database is accessible from the web.

Arabidopsis↗
PubMed2005

Proteomics of ischemia/reperfusion injury in rabbit myocardium reveals alterations to proteins of essential functional systems.

Brief periods of myocardial ischemia prior to timely reperfusion result in prolonged, yet reversible, contractile dysfunction of the myocardium, or "myocardial stunning". It has been hypothesized that the delayed recovery of contractile function in stunned myocardium reflects damage to one or a few key sarcomeric proteins. However, damage to such proteins does not explain observed physiological alterations to myocardial oxygen consumption and ATP requirements observed following myocardial stunning, and therefore the impact of alterations to additional functional groups is unresolved. We utilized two-dimensional gel electrophoresis and mass spectrometry to identify changes to the protein profiles in whole cell, cytosolic- and myofilament-enriched subcellular fractions from isolated, perfused rabbit hearts following 15 min or 60 min low-flow (1 mL/min) ischemia. Comparative gel analysis revealed 53 protein spot differences (> 1.5-fold difference in visible abundance) in reperfused myocardium. The majority of changes were observed to proteins from four functional groups: (i) the sarcomere and cytoskeleton, notably myosin light chain-2 and troponin C; (ii) redox regulation, in particular several components of the NADH ubiquinone oxidoreductase complex; (iii) energy metabolism, encompassing creatine kinase; and (iv) the stress response. Protein differences appeared to be the result of isoelectric point shifts most probably resulting from chemical modifications, and molecular mass shifts resulting from proteolytic or physical fragmentation. This is consistent with our hypothesis that the time course for the onset of injury associated with myocardial stunning is too brief to be mediated by large changes to gene/protein expression, but rather that more subtle, rapid and potentially transient changes are occurring to the proteome. The physical manifestation of stunned myocardium is therefore the likely result of the summed functional impairment resulting from these multiple changes, rather than a result of damage to a single key protein.

Amino Acid Sequence↗
PubMed2003

Analysis of protein interactions using fluorescence technologies.

Biophotonics techniques, especially those involving fluorescence, are widely used in proteomics to characterize the in vitro interactions between proteins in high-throughput mode. On the other hand, fluorescence-based imaging studies often show that protein activity is regulated through large protein complexes that transiently form at specific sites in the cell. One could therefore argue that a systematic functional analysis of the human proteome requires technologies that are capable of time and spatially resolved, multiplexed analysis of protein interactions within cells.

Fluorescence Resonance Energy Transfer↗