CORUM: the comprehensive resource of mammalian protein complexes—2009

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The new CORUM 2.0 release encompasses 2837 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes. The CORUM dataset is built from 3198 different genes, representing ∼16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. Recent developments include mapping of functional annotation to Gene Ontology terms as well as cross-references to Entrez Gene identifiers. In addition, a ‘Phylogenetic Conservation’ analysis tool was implemented that analyses the potential occurrence of orthologous protein complex subunits in mammals and other selected groups of organisms. This allows one to predict the occurrence of protein complexes in different phylogenetic groups. CORUM is freely accessible at (http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html)

Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum

Our current understanding of mitochondrial functioning is largely restricted to traditional model organisms, which only represent a fraction of eukaryotic diversity. The unusual mitochondrion of malaria parasites is a validated drug target but remains poorly understood. Here, we apply complexome profiling to map the inventory of protein complexes across the pathogenic asexual blood stages and the transmissible gametocyte stages of Plasmodium falciparum. We identify remarkably divergent composition and clade-specific additions of all respiratory chain complexes. Furthermore, we show that respiratory chain complex components and linked metabolic pathways are up to 40-fold more prevalent in gametocytes, while glycolytic enzymes are substantially reduced. Underlining this functional switch, we find that cristae are exclusively present in gametocytes. Leveraging these divergent properties and stage dynamics for drug development presents an attractive opportunity to discover novel classes of antimalarials and increase our repertoire of gametocytocidal drugs

Getting a Grip on Complexes

We are witnessing tremendous advances in our understanding of the organization of life. Complete genomes are being deciphered with ever increasing speed and accuracy, thereby setting the stage for addressing the entire gene product repertoire of cells, towards understanding whole biological systems. Advances in bioinformatics and mass spectrometric techniques have revealed the multitude of interactions present in the proteome. Multiprotein complexes are emerging as a paramount cornerstone of biological activity, as many proteins appear to participate, stably or transiently, in large multisubunit assemblies. Analysis of the architecture of these assemblies and their manifold interactions is imperative for understanding their function at the molecular level. Structural genomics efforts have fostered the development of many technologies towards achieving the throughput required for studying system-wide single proteins and small interaction motifs at high resolution. The present shift in focus towards large multiprotein complexes, in particular in eukaryotes, now calls for a likewise concerted effort to develop and provide new technologies that are urgently required to produce in quality and quantity the plethora of multiprotein assemblies that form the complexome, and to routinely study their structure and function at the molecular level. Current efforts towards this objective are summarized and reviewed in this contribution

Protein–protein interactions and genetic diseases: The interactome

AbstractProtein–protein interactions mediate essentially all biological processes. Despite the quality of these data being widely questioned a decade ago, the reproducibility of large-scale protein interaction data is now much improved and there is little question that the latest screens are of high quality. Moreover, common data standards and coordinated curation practices between the databases that collect the interactions have made these valuable data available to a wide group of researchers. Here, I will review how protein–protein interactions are measured, collected and quality controlled. I discuss how the architecture of molecular protein networks has informed disease biology, and how these data are now being computationally integrated with the newest genomic technologies, in particular genome-wide association studies and exome-sequencing projects, to improve our understanding of molecular processes perturbed by genetics in human diseases. This article is part of a Special Issue entitled: From Genome to Function

From single proteins to supercomplexes : a proteomic view on plant mitochondria

The primary function of plant mitochondria is respiration, which is why they are often referred to as “powerhouses of the cell”. Besides their central role in energy metabolism, plant mitochondria are also involved in the photorespiratory C2 cycle and in the provision of carbon skeletons to support efficient nitrogen assimilation. All these functions are catalyzed by mitochondrial proteins. Their composition, abundance and interactions in plant mitochondria are the subject of this thesis. In yeast, Trypanosomes, and several mammalian cell types, mitochondria are organized as extensive mitochondrial networks, resulting in a situation where a cell only hosts few but large mitochondria. In plants, hundreds of small mitochondria are only connected by fusion and fission over time but not physically. Hence, the organelles form individual, functional units. Paradoxically, their biochemical and physiological characterization focuses on large organelle populations and thereby disregards the properties of the individual mitochondrion. This partially is based on the fact that cell biological approaches capturing structural features of plant mitochondria often are of limited value for understanding their physiological properties. Chapter 2.1 of this thesis models the protein content of a single mitochondrion by combining proteomics with classical cell biology. Besides other insights into the function of a single plant mitochondrion, it could be shown that proteins involved in ATP synthesis and transport make up nearly half of the plant mitochondrial proteome. The five protein complexes of the OXPHOS system contribute most to this segment of the mitochondrial proteome, underlining the overall importance of mitochondrial ATP synthesis for the entire plant cell. Despite the central function of OXHPOS components in plants, certain unicellular parasites and yeasts apparently do not need a complete OXPHOS system. Intriguingly, it recently has been reported that the mitochondrial genome of the multicellular parasitic flowering plant Viscum album (European mistletoe) is reduced and lacks the genes encoding the mitochondrially encoded subunits of complex I. This implies that the corresponding genes either have been lost or, alternatively, were transferred to the nuclear genome. The consequences for the mitochondrial respiratory chain were so far unknown. Chapter 2.2 presents data suggesting that V. album indeed lacks mitochondrial complex I. The absence of complex I is accompanied by a rearrangement of the respiratory chain including (i) stable supercomplexes composed of complexes III2 and IV, and (ii) the occurrence of numerous alternative oxidoreductases. Mitochondria of V. album also possess less cristae than mitochondria from non-parasitic plants, which can be explained by low amounts of ATP synthase dimers. The mitochondrial proteome consists of proteins encoded in the nucleus or in the rudimentary mitochondrial genome. The few proteins encoded on the mitochondrial genome are translated by mitochondrial ribosomes. While structure and composition of these mitoribosomes are well established in yeast and mammals, the current knowledge of plant mitoribosomes is negligible. Isolation of plant mitoribosomes is difficult due to their sedimentation coefficient, which is very close to that of cytosolic ribosomes, their interaction with the inner mitochondrial membrane, and the attachment of cytosolic ribosomes to the mitochondrial surface. As part of this dissertation, plant mitoribosomes were analyzed via a novel complexome profiling strategy (chapter 2.3). This revealed an unconventional molecular mass of the small ribosomal subunit of plants. In addition, several pentatricopeptide repeat (PPR) proteins were discovered to form part of both, the large and the small mitoribosomal subunit

From condition-specific interactions towards the differential complexome of proteins

While capturing the transcriptomic state of a cell is a comparably simple effort with modern sequencing techniques, mapping protein interactomes and complexomes in a sample-specific manner is currently not feasible on a large scale. To understand crucial biological processes, however, knowledge on the physical interplay between proteins can be more interesting than just their mere expression. In this thesis, we present and demonstrate four software tools that unlock the cellular wiring in a condition-specific manner and promise a deeper understanding of what happens upon cell fate transitions. PPIXpress allows to exploit the abundance of existing expression data to generate specific interactomes, which can even consider alternative splicing events when protein isoforms can be related to the presence of causative protein domain interactions of an underlying model. As an addition to this work, we developed the convenient differential analysis tool PPICompare to determine rewiring events and their causes within the inferred interaction networks between grouped samples. Furthermore, we present a new implementation of the combinatorial protein complex prediction algorithm DACO that features a significantly reduced runtime. This improvement facilitates an application of the method for a large number of samples and the resulting sample-specific complexes can ultimately be assessed quantitatively with our novel differential protein complex analysis tool CompleXChange.Das Transkriptom einer Zelle ist mit modernen Sequenzierungstechniken vergleichsweise einfach zu erfassen. Die Ermittlung von Proteininteraktionen und -komplexen wiederum ist in großem Maßstab derzeit nicht möglich. Um wichtige biologische Prozesse zu verstehen, kann das Zusammenspiel von Proteinen jedoch erheblich interessanter sein als deren reine Expression. In dieser Arbeit stellen wir vier Software-Tools vor, die es ermöglichen solche Interaktionen zustandsbezogen zu betrachten und damit ein tieferes Verständnis darüber versprechen, was in der Zelle bei Veränderungen passiert. PPIXpress ermöglicht es vorhandene Expressionsdaten zu nutzen, um die aktiven Interaktionen in einem biologischen Kontext zu ermitteln. Wenn Proteinvarianten mit Interaktionen von Proteindomänen in Verbindung gebracht werden können, kann hierbei sogar alternatives Spleißen berücksichtigen werden. Als Ergänzung dazu haben wir das komfortable Differenzialanalyse-Tool PPICompare entwickelt, welches Veränderungen des Interaktoms und deren Ursachen zwischen gruppierten Proben bestimmen kann. Darüber hinaus stellen wir eine neue Implementierung des Proteinkomplex-Vorhersagealgorithmus DACO vor, die eine deutlich reduzierte Laufzeit aufweist. Diese Verbesserung ermöglicht die Anwendung der Methode auf eine große Anzahl von Proben. Die damit bestimmten probenspezifischen Komplexe können schließlich mit unserem neuartigen Differenzialanalyse-Tool CompleXChange quantitativ bewertet werden

Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment

High resolution mapping of the proteomic environment and proteomic hyperlinks in fission and budding yeast reveals that divergent hyperlinks are due to gene duplications

The energy biology of European Mistletoe (Viscum album)

The hemiparasitic European mistletoe (Viscum album) is known for its extraordinary way of life. Not only its huge genome of about 90 Gbp is noticeable, but also the absence of mitochondrial complex I of the Oxidative Phosphorylation system. Since a large genome indicates a high energy demand during cellular division, absence of complex I, which strongly contributes to the proton gradient across the inner mitochondrial membrane and thus to ATP production, is to be considered remarkable. How can V. album accomplish its energy metabolism? This is the central research question of this thesis. To this end, the transcriptome of V. album was first sequenced to provide the basis for efficient proteome analysis. RNA was isolated from mistletoe leaves, flowers, and stems harvested in summer and winter. The RNA was next transcribed into cDNA and sequenced as a pooled sample via the PacBio sequencing strategy. The resulting initial Viscum album Gene Space (VaGs) database showed 78% completeness based on Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. To further develop this database, additional Illumina sequencing of the individual samples (summer and winter) was performed. The resulting Viscum album Gene Space database II (VaGsII) has a completeness of 93% and contains sequences of 90,039 transcripts. Based on these sequences, a GC content of 50% could be calculated. This is an unusually high GC content, as in other dicotyledonous plants the GC content usually ranges between 43-45 %. Due to the resulting enhanced stability of the DNA, an increased energy requirement must also be anticipated for DNA replication and transcription. In addition to the absence of the mitochondrial genes encoding subunits of complex I, the absence of almost all nuclear genes encoding complex I subunits could be shown. Furthermore, by re-evaluating an existing complexome dataset of V. album mitochondria using the new VaGs II database, more than 1,000 additional mitochondrial proteins could be identified with respect to the original evaluation. Besides the mitochondria, also the chloroplasts were examined in more detail to determine their contribution to the energy metabolism of V. album cells through photosynthesis and photophosphorylation. In the course of this examination, a complete absence of the NDH complex (NADH dehydrogenase- like complex, chloroplast pendant of mitochondrial complex I), which contributes to cyclic electron transport around photosystem I, was proven on the proteome level. In addition, PGR5 and PGRL1, two proteins which were shown to be alternatively involved in cyclic electron transport around photosystem I, were found to be of reduced abundance in V. album compared to the model plant Arabidopsis thaliana. Abundance of the chloroplast ATP synthase complex is comparable to A. thaliana; however, its stability clearly is increased in V. album. Also, the photosystem II is of similar abundance in A. thaliana and V. album, in contrast to the photosystem I, which is of comparatively low abundance in V. album. It can be concluded that both, linear and cyclic electron transport and thus ATP synthesis by photophosphorylation are comparatively low in V. album. In summary, it can be concluded that: 1. V. album has an even higher energy demand than previously thought due to its high GC content. 2. ATP production in mitochondria and chloroplasts is limited due to the absence or reduced abundance of some of the involved proteins and protein complexes. How sufficient amounts of ATP are provided in V. album cells is therefore still not entirely clear. It is hypothesized that the slow growth and reduced cell division rate of V. album might reduce its energy demand. In addition, sugar compounds transported in the host xylem in spring may be a source of energy for V. album. This may also explain the strong growth rate of V. album in spring. Further research is needed to understand the way of life of this very particular plant

SS18 Together with Animal-Specific Factors Defines Human BAF-Type SWI/SNF Complexes

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