Proteoglycanomics: tools to unravel the biological function of glycosaminoglycans

Glycosylation is the most frequent PTM and contributes significantly to the function of proteins depending on the type of glycosylation. Especially glycan structures like the glycosaminoglycans are considered to constitute themselves the major function of the glycoconjugate which is therefore termed proteoglycan. Here we review recent views on and novel tools for analysing the proteoglycanome, which are directly related to the type of glycanation under investigation. We define the major function of the proteoglycanome to be its interaction with various proteins in many different (patho-)physiological conditions. This is exemplified by the differential glycosaminoglycan-interactome of healthy versus arthritic patient sera.     

Mutants as tools to understand cellular and molecular drought tolerance mechanisms

The use of mutants: a most promising way to detect genes involved in development or in response to environmental stress. The model species Arabidopsis, particularly amenable to dissect the genetics and molecular mechanisms underlying physiological responses, also offers the advantage of a wide variety of mutants. As far as drought tolerance is concerned, hormonal mutants, impaired in hormone biosynthesis — deficient mutants — or in the signal transduction pathway—responsive mutants—provide a valuable tool to analyse the role of phytohormone interaction in the plant drought behaviour as well as to differentiate the mutant phenotypes with new criteria.These two categories of mutants (in particular the abscisic acid, ABA, mutants) were shown to be affected in developmental processes during seed maturation-in the desiccation phase- and/or in response to environmental stress (drought, ...) in vegetative tissues. The present report will focus on this last aspect: alterations in drought responses in vegetative tissues (adaptive strategies and drought tolerance mechanisms) essentially in Arabidopsis hormonal mutants (ABA-deficient and ABA-insensitive, GA-deficient, auxin and ethylene-insensitive).Some of the results are discussed with regard to the predicted functions of genes affected by the mutations.     

Phosphoproteomics as a tool to unravel plant regulatory mechanisms

Reversible phosphorylation of proteins plays a key role in many regulatory processes that lie at the basis of life. With plants, much research has focused on protein kinases that are involved in the adaptation to different stress conditions, such as pathogen attack and cold. However, the substrates of these kinases are mostly unknown. With the recent advances in phosphoproteomic techniques, the large-scale identification of kinase substrates, including their phosphorylation sites, is finally possible. Studies in mainly non-plant systems have demonstrated the high potential of this method by uncovering numerous novel phosphorylation events. In this minireview, we focus on recent developments in the field of phosphoproteomics that are based on phosphopeptide isolation from complex mixtures by immobilized metal-affinity chromatography coupled to sequence identification by mass spectrometry. Combination of these methods with labelling techniques now allows quantitative analysis of phosphorylation between different samples. We discuss the potential of this technology to uncover entire phosphoproteomes and signalling pathways in plants in the future.     

The use of isothermal titration calorimetry to unravel chemotactic signalling mechanisms

Chemotaxis is based on the action of chemosensory pathways and is typically initiated by the recognition of chemoeffectors at chemoreceptor ligand-binding domains (LBD). Chemosensory signalling is highly complex; aspect that is not only reflected in the intricate interaction between many signalling proteins but also in the fact that bacteria frequently possess multiple chemosensory pathways and often a large number of chemoreceptors, which are mostly of unknown function. We review here the usefulness of isothermal titration calorimetry (ITC) to study this complexity. ITC is the gold standard for studying binding processes due to its precision and sensitivity, as well as its capability to determine simultaneously the association equilibrium constant, enthalpy change and stoichiometry of binding. There is now evidence that members of all major LBD families can be produced as individual recombinant proteins that maintain their ligand-binding properties. High-throughput screening of these proteins using thermal shift assays offer interesting initial information on chemoreceptor ligands, providing the basis for microcalorimetric analyses and microbiological experimentation. ITC has permitted the identification and characterization of many chemoreceptors with novel specificities. This ITC-based approach can also be used to identify signal molecules that stimulate members of other families of sensor proteins.     

Novel protein kinases and molecular mechanisms of autoinhibition

During the past year, crystal structures of the PDK-1, ITK, Aurora-A, c-KIT and FLT-3 protein kinases in complex with several ATP-competitive inhibitors have been determined. Some structures have crystallized in catalytically active conformations, whereas others appear to be in inactive or native conformations. The differences between these two classes of structures provide further understanding of how kinase activity may be self-regulated in the cellular environment and how phosphorylation can modulate signalling at a molecular level. All of these structures provide a basis for designing selective protein kinase inhibitors of use in the treatment of cancer and autoimmune disease.     

Harnessing the power of yeast to unravel the molecular basis of neurodegeneration

Several neurodegenerative diseases, such as Parkinson's disease (PD), Alzheimer's disease (AD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), or prion diseases, are known for their intimate association with protein misfolding and aggregation. These disorders are characterized by the loss of specific neuronal populations in the brain and are highly associated with aging, suggesting a decline in proteostasis capacity may contribute to pathogenesis. Nevertheless, the precise molecular mechanisms that lead to the selective demise of neurons remain poorly understood. As a consequence, appropriate therapeutic approaches and effective treatments are largely lacking. The development of cellular and animal models that faithfully reproduce central aspects of neurodegeneration has been crucial for advancing our understanding of these diseases. Approaches involving the sequential use of different model systems, starting with simpler cellular models and ending with validation in more complex animal models, resulted in the discovery of promising therapeutic targets and small molecules with therapeutic potential. Within this framework, the simple and well‐characterized eukaryote Saccharomyces cerevisiae, also known as budding yeast, is being increasingly used to study the molecular basis of several neurodegenerative disorders. Yeast provides an unprecedented toolbox for the dissection of complex biological processes and pathways. Here, we summarize how yeast models are adding to our current understanding of several neurodegenerative disorders.     

Penguins as oceanographers unravel hidden mechanisms of marine productivity

A recent concept for investigating marine ecosystems is to employ diving predators as cost‐effective, autonomous samplers of environmental parameters (such as sea‐temperature). Using king penguins during their foraging trips at sea, we obtained an unprecedented high resolution temperature map at depth off the Kerguelen Islands, Southern Ocean, a poorly sampled but productive area. We found clear evidence of a previously unknown subsurface tongue of cold water, flowing along the eastern shelf break. These new results provide a better understanding of regional water circulation and help explain the high primary productivity above the Kerguelen Plateau.     

Multiscale simulation unravel the kinetic mechanisms of inflammasome assembly

In the innate immune system, the host defense from the invasion of external pathogens triggers the inflammatory responses. Proteins involved in the inflammatory pathways were often found to aggregate into supramolecular oligomers, called ‘inflammasome’, mostly through the homotypic interaction between their domains that belong to the death domain superfamily. Although much has been known about the formation of these helical molecular machineries, the detailed correlation between the dynamics of their assembly and the structure of each domain is still not well understood. Using the filament formed by the PYD domains of adaptor molecule ASC as a test system, we constructed a new multiscale simulation framework to study the kinetics of inflammasome assembly. We found that the filament assembly is a multi-step, but highly cooperative process. Moreover, there are three types of binding interfaces between domain subunits in the ASC^PYD filament. The multiscale simulation results suggest that dynamics of domain assembly are rooted in the primary protein sequence which defines the energetics of molecular recognition through three binding interfaces. Interface I plays a more regulatory role than the other two in mediating both the kinetics and the thermodynamics of assembly. Finally, the efficiency of our computational framework allows us to design mutants on a systematic scale and predict their impacts on filament assembly. In summary, this is, to the best of our knowledge, the first simulation method to model the spatial-temporal process of inflammasome assembly. Our work is a useful addition to a suite of existing experimental techniques to study the functions of inflammasome in innate immune system.     

改善血栓形成新的药物组合物及其分子机制

目的：研究α1受体阻断药与山莨菪碱（Ani）形成的药物组合物改善血栓形成的作用及其分子机制。方法：离体大鼠尾动脉血管模型研究α1受体阻断药及其与山莨菪碱的药物组合物的扩血管效应,角又菜胶诱发小鼠尾部血栓模型研究组合物对抗血栓形成的作用及其机制。结果：α1受体阻断药中哌唑嗪（Pra）对血管环舒张率最大,达（82．6±8．9）％,作用强度最强,Ec50值为O．44μmol/L;山莨菪碱和哌唑嗪分别以不同剂量配伍组成组合物,能使角叉菜胶诱发的鼠尾血栓长度（啪）由24．6±4．6缩短到6．94-2．7,成栓率由86．6％下降到50．0％。上述新药物组合物能显著延长血栓小鼠血浆凝血酶原时间（er）,对活化部分凝血活酶时间（APTT）无影响;能抑制血栓小鼠血浆中组织型纤溶酶原激活剂（t-PA）、6-酮一前列腺素F1a（6．Keto．PGF1α）含量的降低和组织纤溶酶原激活剂抑制物-1（PAI-1）、血栓烷B2（TXB2）的增多;并不在于扩血管作用的进一步增强上。结论：山莨菪碱和哌唑嗪组成的药物组合物具有舒张外周血管和改善血栓形成的作用,其抗血栓形成机制分别与影响外源性凝血途径、抑制血小板的活化功能以及促进纤溶功能有关。     

Developing tools to unravel the biological secrets of Rosellinia necatrix, an emergent threat to woody crops

White root rot caused by Rosellinia necatrix is one of the most destructive diseases of many woody plants in the temperate regions of the world, particularly in Europe and Asia. Recent outbreaks of R. necatrix around the globe have increased the interest in this pathogen. Although the ecology of the disease has been poorly studied, recent genetic and molecular advances have opened the way for future detailed studies of this fungus. TAXONOMY: Rosellinia necatrix Prilleux. Kingdom Fungi; subdivision Ascomycotina; class Euascomycetes; subclass Pyrenomycetes; order Sphaeriales, syn. Xylariales; family Xylariaceae; genus Rosellinia. IDENTIFICATION: Fungal mycelium is present on root surfaces and under the bark, forming mycelium fans, strands or cords. A typical presence of pear-shaped or pyriform swellings can be found above the hyphal septum (with diameters of up to 13 μm). Sclerotia are black, hard and spherical nodules, several millimetres in diameter. Black sclerotia crusts may also form on roots. On synthetic media, it forms microsclerotia: irregular rough bodies composed of a compact mass of melanized, interwoven hyphae with no differentiated cells. Chlamydospores are almost spherical (15 μm in diameter). Synnemata, also named coremia (0.5-1.5 mm in length), can be formed from sclerotia or from mycelial masses. Conidia (3-5 μm in length and 2.5-3 μm in width) are very difficult to germinate in vitro. Ascospores are monostichous, situated inside a cylindrical, long-stalked ascus. They are ellipsoidal and cymbiform (36-46 μm in length and 5.5-6.3 μm in width). HOST RANGE: This fungus can attack above 170 different plant hosts from 63 genera and 30 different families, including vascular plants and algae. Some are of significant economic importance, such as Coffea spp., Malus spp., Olea europaea L., Persea americana Mill., Prunus spp. and Vitis vinifera L. DISEASE SYMPTOMS: Rosellinia necatrix causes white (or Dematophora) root rot, which, by aerial symptoms, shows a progressive weakening of the plant, accompanied by a decline in vigour. The leaves wilt and dry, and the tree can eventually die. White cottony mycelium and mycelial strands can be observed in the crown and on the root surface. On woody plant roots, the fungus can be located between the bark and the wood, developing typical mycelium fans, invading the whole root and causing general rotting. DISEASE CONTROL: Some approaches have been attempted involving the use of tolerant plants and physical control (solarization). Chemical control in the field and biological control methods are still under development.     

Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes

Rearrangements of our genome can be responsible for inherited as well as sporadic traits. The analyses of chromosome breakpoints in the proximal short arm of Chromosome 17 (17p) reveal nonallelic homologous recombination (NAHR) as a major mechanism for recurrent rearrangements whereas nonhomologous end-joining (NHEJ) can be responsible for many of the nonrecurrent rearrangements. Genome architectural features consisting of low-copy repeats (LCRs), or segmental duplications, can stimulate and mediate NAHR, and there are hotspots for the crossovers within the LCRs. Rearrangements introduce variation into our genome for selection to act upon and as such serve an evolutionary function analogous to base pair changes. Genomic rearrangements may cause Mendelian diseases, produce complex traits such as behaviors, or represent benign polymorphic changes. The mechanisms by which rearrangements convey phenotypes are diverse and include gene dosage, gene interruption, generation of a fusion gene, position effects, unmasking of recessive coding region mutations (single nucleotide polymorphisms, SNPs, in coding DNA) or other functional SNPs, and perhaps by effects on transvection.     

Hijacking nature—new approaches to unravel enzyme mechanisms and engineer improved biocatalysts

The second EMBO conference on ‘Catalytic Mechanisms by Biological Systems’ took place in Groningen, the Netherlands, in October 2012. Structural, molecular and computational biologists, as well as chemists, biophysicists and engineers discussed technologies to improve our mechanistic understanding of enzymes, as well as the design of robust biocatalysts.     

Caveolae--from ultrastructure to molecular mechanisms

Almost 50 years after the first sighting of small pits that covered the surface of mammalian cells, investigators are now getting to grips with the detailed workings of these enigmatic structures that we now know as caveolae.