Biochemical Society Transactions Current Issue

A pore way to die: the role of mitochondria in reperfusion injury and cardioprotection

Andrew P. Halestrap, — 2010-08-01

In addition to their normal physiological role in ATP production and metabolism, mitochondria exhibit a dark side mediated by the opening of a non-specific pore in the inner mitochondrial membrane. This mitochondrial permeability transition pore (MPTP) causes the mitochondria to breakdown rather than synthesize ATP and, if unrestrained, leads to necrotic cell death. The MPTP is opened in response to Ca²⁺ overload, especially when accompanied by oxidative stress, elevated phosphate concentration and adenine nucleotide depletion. These conditions are experienced by the heart and brain subjected to reperfusion after a period of ischaemia as may occur during treatment of a myocardial infarction or stroke and during heart surgery. In the present article, I review the properties, regulation and molecular composition of the MPTP. The evidence for the roles of CyP-D (cyclophilin D), the adenine nucleotide translocase and the phosphate carrier are summarized and other potential interactions with outer mitochondrial membrane proteins are discussed. I then review the evidence that MPTP opening mediates cardiac reperfusion injury and that MPTP inhibition is cardioprotective. Inhibition may involve direct pharmacological targeting of the MPTP, such as with cyclosporin A that binds to CyP-D, or indirect inhibition of MPTP opening such as with preconditioning protocols. These invoke complex signalling pathways to reduce oxidative stress and Ca²⁺ load. MPTP inhibition also protects against congestive heart failure in hypertensive animal models. Thus the MPTP is a very promising pharmacological target for clinical practice, especially once more specific drugs are developed.

Synchrotron radiation circular dichroism (SRCD) spectroscopy: an enhanced method for examining protein conformations and protein interactions

B.A. Wallace,Robert W. Janes, — 2010-08-01

CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins, the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein–protein complex formation involving either induced-fit or rigid-body mechanisms, and protein–lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.

Protein-protein interactions

Mike P. Williamson,Michael J. Sutcliffe, — 2010-08-01

In the present article, we describe the two standard high-throughput methods for identification of protein complexes: two-hybrid screens and TAP (tandem affinity purification) tagging. These methods have been used to characterize the interactome of Saccharomyces cerevisiae, showing that the majority of proteins are part of complexes, and that complexes typically consist of a core to which are bound ‘party’ and ‘dater’ proteins. Complexes typically are merely the sum of their parts. A particularly interesting type of complex is the metabolon, containing enzymes within the same metabolic pathway. There is reasonably good evidence that metabolons exist, but they have not been detected using high-thoughput assays, possibly because of their fragility.

Homomeric protein complexes: evolution and assembly

A.J. Venkatakrishnan,Emmanuel D. Levy,Sarah A. Teichmann, — 2010-08-01

Homo-oligomeric protein complexes are functionally vital and highly abundant in living cells. In the present article, we review our current understanding of their geometry and evolution, including aspects of the symmetry of these complexes and their interaction interfaces. Also, we briefly discuss the pathway of their assembly in solution.

Interaction proteomics: characterization of protein complexes using tandem affinity purification-mass spectrometry

Pamela Völkel,Perrine Le Faou,Pierre-Olivier Angrand, — 2010-08-01

Most cellular processes are carried out by a multitude of proteins that assemble into multimeric complexes. Thus a precise understanding of the biological pathways that control cellular events relies on the identification and on the biochemical characterization of the proteins involved in such multimeric assemblies. Advances in MS have made possible the identification of multisubunit protein complexes isolated from cell lysates with high sensitivity and accuracy, whereas the TAP (tandem affinity purification) methodology efficiently isolates native protein complexes from cells for proteomics analysis. TAP is a generic method based on the sequential utilization of two affinity tags to purify protein assemblies. During the first purification step, the Protein A moiety of the TAP tag is bound to IgG beads, and protein components associated with the TAP-tagged protein are retrieved by TEV (tobacco etch virus) protease cleavage. This enzyme is a sequence-specific protease cleaving a seven-amino-acid recognition site located between the first and second tags. In the second affinity step, the protein complex is immobilized to calmodulin-coated beads via the CBP (calmodulin-binding peptide) of the TAP tag. The CBP–calmodulin interaction is calcium-dependent and calcium-chelating agents are used in the second elution step to release the final protein complex preparation used for protein identification by MS. The TAP–MS approach has proven to efficiently permit the characterization of protein complexes from bacteria, yeast and mammalian cells, as well as from multicellular organisms such as Caenorhabditis elegans, Drosophila and mice.

Calorimetry as a tool for understanding biomolecular interactions and an aid to drug design

John E. Ladbury, — 2010-08-01

The binding of two biomolecules viewed from the atomic level is highly complex. It involves the formation or removal of many individual non-covalent bonds both between the interacting molecules as well as with solvent. Currently, our understanding of the thermodynamic quantification of biomolecular interactions is somewhat naïve. ITC (isothermal titration calorimetry) provides a rapid route to a full thermodynamic characterization of a biomolecular interaction. Armed with these data, what are we really able to understand about complex formation and can any of this information provide a useful tool to aid drug development? Correlations between thermodynamic data and structural detail have been investigated, allowing insight into ways in which these can be used to understand protein–ligand interactions and provide input into the decision-making process in drug development.

Unravelling protein-protein interactions between complement factor H and C-reactive protein using a multidisciplinary strategy

Stephen J. Perkins,Azubuike I. Okemefuna,Ruodan Nan, — 2010-08-01

Experimental studies of protein–protein interactions are very much affected by whether the complexes are fully formed (strong, with nanomolar dissociation constants) or partially dissociated (weak, with micromolar dissociation constants). The functions of the complement proteins of innate immunity are governed by the weak interactions between the activated proteins and their regulators. Complement is effective in attacking pathogens, but not the human host, and imbalances in this process can lead to disease conditions. The inherent complexity in analysing complement interactions is augmented by the multivalency of its main regulator, CFH (complement factor H), for its physiological or pathophysiological ligands. The unravelling of such weak protein–protein or protein–ligand interactions requires a multidisciplinary approach. Synchrotron X-ray solution scattering and constrained modelling resulted in the determination of the solution structure of CFH and its self-associative properties, whereas AUC (analytical ultracentrifugation) identified the formation of much larger CFH multimers through the addition of metals such as zinc. The ligands of CFH, such as CRP (C-reactive protein), also undergo self-association. The combination of X-rays and AUC with SPR (surface plasmon resonance) proved to be essential to identify CRP self-association and revealed how CFH interacts with CRP. We show that CRP unexpectedly binds to CFH at two non-contiguous sites and explain its relevance to age-related macular degeneration.

Insight into protein-protein interactions from analytical ultracentrifugation

Stephen E. Harding,Arthur J. Rowe, — 2010-08-01

Analytical ultracentrifugation is a free solution technique with no supplementary immobilization, columns or membranes required, and can be used to study self-association and hetero-interactions, stoichiometry, reversibility and interaction strength across a very large dynamic range (dissociation constants from 10^{{Minus Sign}12} M to 10^{{Minus Sign}1} M). In the present paper, we review some of the advances that have been made in the two different types of sedimentation experiment – sedimentation equilibrium and sedimentation velocity – for the analysis of protein–protein interactions and indicate how major complications such as thermodynamic and hydrodynamic non-ideality can be dealt with.

Selection of soluble protein expression constructs: the experimental determination of protein domain boundaries

Michael R. Dyson, — 2010-08-01

Proteins can contain multiple domains each of which is capable of possessing a separate independent function and three-dimensional structure. It is often useful to clone and express individual protein domains to study their biochemical properties and for structure determination. However, the annotated domain boundaries in databases such as Pfam or SMART are not always accurate. The present review summarizes various strategies for the experimental determination of protein domain boundaries.

Single-molecule two-colour coincidence detection to probe biomolecular associations

Angel Orte,Richard Clarke,David Klenerman, — 2010-08-01

Two-colour coincidence detection (TCCD) is a form of single-molecule fluorescence developed to sensitively detect and characterize associated biomolecules without any separation, in solution, on the cell membrane and in live cells. In the present short review, we first explain the principles of the method and then describe the application of TCCD to a range of biomedical problems and how this method may be developed further in the future to try to monitor biological processes in live cells.

High-throughput identification of transient extracellular protein interactions

2010-08-01

Protein interactions are highly diverse in their biochemical nature, varying in affinity and are often dependent on the surrounding biochemical environment. Given this heterogeneity, it seems unlikely that any one method, and particularly those capable of screening for many protein interactions in parallel, will be able to detect all functionally relevant interactions that occur within a living cell. One major class of interactions that are not detected by current popular high-throughput methods are those that occur in the extracellular environment, especially those made by membrane-embedded receptor proteins. In the present article, we discuss some of our recent research in the development of a scalable assay to identify this class of protein interaction and some of the findings from its application in the construction of extracellular protein interaction networks.

Proteomic Complex Detection using Sedimentation (ProCoDeS): screening for proteins in stable complexes and their candidate interaction partners

Marcelo P. Segura,Kathryn S. Lilley,Paul Dupree, — 2010-08-01

Over the last few years, our view of cellular organization has changed from one in which enzymes and proteins usually act independently to the situation at present where we commonly accept that many, if not all, enzymes act in close association with others. Co-precipitation using an antibody against a test protein is the standard assay for the identification of members of protein complexes [Musso, Zhang and Emili (2007) Chem. Rev. 107, 3585–3600]. The introduction of TAP (tandem affinity purification) tagging enhanced original approaches in order to analyse protein complexes on a larger scale with reduced false discoveries of interacting partners due to more efficient purification of complexes. However, this technique has some limitations as a high-throughput tool for systems biology: the requirement for genetic manipulation to express the tagged protein excludes studies of non-transformable organisms and intact tissue. In those cases where TAP is applicable, a considerable amount of work is required to generate the baits and to optimize experimental conditions. A technique developed in our laboratories, ProCoDeS (Proteomic Complex Detection using Sedimentation), focuses on the detection of endogenous complexes. Protein samples are separated by centrifugation and then different fractions from the resulting gradient are analysed using quantitative MS. The identification of possible protein partners is based on statistical analysis of the co-fractionation of proteins, without any need for purification of individual complexes. The prospects of ProCoDeS and similar techniques based on quantitative MS for measurement of protein complex composition are reviewed in the present article.

The stressosome: molecular architecture of a signalling hub

Jon Marles-Wright,Richard J. Lewis, — 2010-08-01

The stressosome co-ordinates the response of Bacillus subtilis to the imposition of a variety of physical and environmental insults. These stresses include fluctuations in salt concentration, the presence of ethanol, changes in pH and even the level of UV light. Despite the obvious and significant differences between these quite different physicochemical stimuli, the result is the same: the stressosome is phosphorylated by a key kinase to initiate the {sigma}^B cascade. The phosphorylation of the stressosome initiates a signal transduction system that up-regulates the expression of stress-responsive genes so that the Bacillus can survive the imposition of stress. Hence the stressosome acts as a hub, receiving manifold different stimuli to effect a single outcome. Using single-particle analysis of cryo-electron micrographs, we have been able to reconstruct a series of molecular envelopes of the stressosome. These maps have been interpreted at near-atomic resolution with crystal structures of the individual components of the stressosome to provide the first visualization of this unique signalling hub. The macromolecular structure adopted by the stressosome provides the signalling cascade with the potential for co-operative behaviour, which we have also measured in live bacteria. These experiments are consistent with the tuning of the response of B. subtilis to stress relative to the magnitude of the insult.

Selectivity in a barren landscape: the P450BioI-ACP complex

Max J. Cryle, — 2010-08-01

The cytochromes P450 (P450s) are a superfamily of oxidative haemoproteins that are capable of catalysing a vast range of oxidative transformations, including the oxidation of unactivated alkanes, often with high stereo- and regio-selectivity. Fatty acid hydroxylation by P450s is widespread across both bacteria and higher organisms, with the sites of oxidation and specificity of oxidation varying from system to system. Several key examples are discussed in the present article, with the focus on P450_BioI (CYP107H1), a biosynthetic P450 found in the biotin operon of Bacillus subtilis. The biosynthetic function of P450_BioI is the formation of pimelic acid, a biotin precursor, via a multiple-step oxidative cleavage of long-chain fatty acids. P450_BioI is a member of an important subgroup of P450s that accept their substrates not free in solution, but rather presented by a separate carrier protein. Structural characterization of the P450_BioI–ACP (acyl-carrier protein) complex has recently been performed, which has revealed the basis for the oxidation of the centre of the fatty acid chain. The P450_BioI–ACP structure is the first such P450–carrier protein complex to be characterized structurally, with important implications for other biosynthetically intriguing P450–carrier protein complexes.

Can infrared spectroscopy provide information on protein-protein interactions?

Parvez I. Haris, — 2010-08-01

For most biophysical techniques, characterization of protein–protein interactions is challenging; this is especially true with methods that rely on a physical phenomenon that is common to both of the interacting proteins. Thus, for example, in IR spectroscopy, the carbonyl vibration (1600–1700 cm^{{Minus Sign}1}) associated with the amide bonds from both of the interacting proteins will overlap extensively, making the interpretation of spectral changes very complicated. Isotope-edited infrared spectroscopy, where one of the interacting proteins is uniformly labelled with ¹³C or ¹³C,¹⁵N has been introduced as a solution to this problem, enabling the study of protein–protein interactions using IR spectroscopy. The large shift of the amide I band (approx. 45 cm^{{Minus Sign}1} towards lower frequency) upon ¹³C labelling of one of the proteins reveals the amide I band of the unlabelled protein, enabling it to be used as a probe for monitoring conformational changes. With site-specific isotopic labelling, structural resolution at the level of individual amino acid residues can be achieved. Furthermore, the ability to record IR spectra of proteins in diverse environments means that isotope-edited IR spectroscopy can be used to structurally characterize difficult systems such as protein–protein complexes bound to membranes or large insoluble peptide/protein aggregates. In the present article, examples of application of isotope-edited IR spectroscopy for studying protein–protein interactions are provided.

Interactions of caeruloplasmin with other proteins participating in inflammation

Vadim B. Vasilyev, — 2010-08-01

The first detailed report of a specific interaction of CP (caeruloplasmin) with another protein described its complex with LF (lactoferrin) in 2000. Since then, several protein–protein interactions involving CP have been reported, mostly concerning iron-containing proteins. The CP–LF complex was studied thoroughly, and evidence of reciprocal effects of CP and LF was obtained. Another specific interaction investigated in detail occurs between CP and MPO (myeloperoxidase). CP–LF, CP–MPO and CP–LF–MPO complexes were found in sera of patients with inflammation. Modelling in vitro allowed understanding of which structural peculiarities of CP and partners allow the modification of their functions in a complex. The present paper reviews the latest data on complexes of CP with LF and MPO, and advances some suggestions about their role in health and disease.

Two days of tau: a meeting focused on its biology and pathology

Efthimios M.C. Skoulakis,Amritpal Mudher, — 2010-08-01

Tauopathies are a clinically diverse group of neurodegenerative dementias involving perturbations of the level or phosphorylation state of the microtubule-binding axonal protein tau. Despite intense effort in recent years, the precise role of tau in the pathology of the various behaviourally and neuropathologically distinct tauopathies, the mechanisms of tau toxicity and the potential functional interaction of tau and amyloid in Alzheimer's disease remain elusive. Nevertheless, novel observations regarding the various aspects of taumisregulation-dependent pathogenesis are emerging from various cellular, vertebrate and invertebrate animal models and are supported by new clinical data. This Focused Meeting brought together scientists working on tau and tauopathies from different disciplines and various experimental models. The aim was to enhance our understanding of the protein itself and disorders associated with its misregulation through synergy.

Proteolytic processing of tau

Yipeng Wang,Sarika Garg,Eva-Maria Mandelkow,Eckhard Mandelkow, — 2010-08-01

Tau aggregation is a hallmark of several neurodegenerative diseases, including AD (Alzheimer's disease), although the mechanism underlying tau aggregation remains unclear. Recent studies show that the proteolysis of tau plays an important role in both tau aggregation and neurodegeneration. On one hand, truncation of tau may generate amyloidogenic tau fragments that initiate the aggregation of tau, which in turn can cause toxicity. On the other hand, truncation of tau may result in tau fragments which induce neurodegeneration through unknown mechanisms, independently of tau aggregation. Blocking the truncation of tau thus may represent a promising therapeutic approach for AD or other tauopathies. In the present paper, we summarize our data on tau cleavage in a cell model of tauopathy and major results on tau cleavage reported in the literature.

Alzheimer's disease neurofibrillary degeneration: pivotal and multifactorial

2010-08-01

Independent of the aetiology, AD (Alzheimer's disease) neurofibrillary degeneration of abnormally hyperphosphorylated tau, a hallmark of AD and related tauopathies, is apparently required for the clinical expression of the disease and hence is a major therapeutic target for drug development. However, AD is multifactorial and heterogeneous and probably involves several different aetiopathogenic mechanisms. On the basis of CSF (cerebrospinal fluid) levels of A{beta}^1–42 (where A{beta} is amyloid {beta}-peptide), tau and ubiquitin, five different subgroups, each with its own clinical profile, have been identified. A successful development of rational therapeutic disease-modifying drugs for AD will require understanding of the different aetiopathogenic mechanisms involved and stratification of AD patients by different disease subgroups in clinical trials. We have identified a novel aetiopathogenic mechanism of AD which is initiated by the cleavage of SET, also known as inhibitor-2 (I₂^PP2A) of PP2A (protein phosphatase 2A) at Asn¹⁷⁵ into N-terminal (I_2NTF) and C-terminal (I_2CTF) halves and their translocation from the neuronal nucleus to the cytoplasm. AAV1 (adeno-associated virus 1)-induced expression of I_2CTF in rat brain induces inhibition of PP2A activity, abnormal hyperphosphorylation of tau, neurodegeneration and cognitive impairment in rats. Restoration of PP2A activity by inhibition of the cleavage of I₂^PP2A/SET offers a promising therapeutic opportunity in AD with this aetiopathogenic mechanism.

From tau phosphorylation to tau aggregation: what about neuronal death?

2010-08-01

Tau pathology is characterized by intracellular aggregates of abnormally and hyperphosphorylated tau proteins. It is encountered in many neurodegenerative disorders, but also in aging. These neurodegenerative disorders are referred to as tauopathies. Comparative biochemistry of the tau aggregates shows that they differ in both tau isoform phosphorylation and content, which enables a molecular classification of tauopathies. In conditions of dementia, NFD (neurofibrillary degeneration) severity is correlated to cognitive impairment and is often considered as neuronal death. Using tau animal models, analysis of the kinetics of tau phosphorylation, aggregation and neuronal death in parallel to electrophysiological and behavioural parameters indicates a disconnection between cognition deficits and neuronal cell death. Tau phosphorylation and aggregation are early events followed by cognitive impairment. Neuronal death is not observed before the oldest ages. A sequence of events may be the formation of toxic phosphorylated tau species, their aggregation, the formation of neurofibrillary tangles (from pre-tangles to ghost tangles) and finally neuronal cell death. This sequence will last from 15 to 25 years and one can ask whether the aggregation of toxic phosphorylated tau species is a protection against cell death. Apoptosis takes 24 h, but NFD lasts for 24 years to finally kill the neuron or rather to protect it for more than 20 years. Altogether, these data suggest that NFD is a transient state before neuronal death and that therapeutic interventions are possible at that stage.

The role of MSUT-2 in tau neurotoxicity: a target for neuroprotection in tauopathy?

Jeanna M. Wheeler,Chris R. Guthrie,Brian C. Kraemer, — 2010-08-01

We previously developed a transgenic Caenorhabditis elegans model of human tauopathy disorders by expressing human tau in nematode worm neurons to explore genetic pathways contributing to tau-induced neurodegeneration. This animal model recapitulates several hallmarks of human tauopathies, including altered behaviour, accumulation of detergent-insoluble phosphorylated tau protein and neurodegeneration. To identify genes required for tau neurotoxicity, we carried out a forward genetic screen for mutations that suppress tau neurotoxicity. We ultimately cloned the sut-2 (suppressor of tau pathology-2) gene, mutations in which alleviate tau neurotoxicity in C. elegans. SUT-2 encodes a novel subtype of CCCH zinc-finger protein conserved across animal phyla. SUT-2 shares significant identity with the mammalian SUT-2 (MSUT-2). We identified components of the aggresome as binding partners of MSUT-2. Thus we hypothesize that MSUT-2 plays a role in the formation and/or clearance of protein aggregates. We are currently exploring the role of MSUT-2 in tauopathy using mammalian systems. The identification of sut-2 as a gene required for tau neurotoxicity in C. elegans suggests new neuroprotective strategies targeting MSUT-2 that may be effective in modulating tau neurotoxicity in human tauopathy disorders.

Tau phosphorylation in hippocampus results in toxic gain-of-function

2010-08-01

The MAP (microtubule-associated protein) tau binds to tubulin, the main component of MTs (microtubules), which results in the stabilization of MT polymers. Tau binds to the C-terminal of tubulin, like other MAPs (including motor proteins such as kinesin) and it therefore may compete with these proteins for the same binding site in the tubulin molecule. In pathological conditions, tau is the main component of aberrant protein aggregates found in neurodegenerative disorders known as tauopathies where tau is present in its hyperphosphorylated form. GSK3 (glycogen synthase kinase 3, also known as tau kinase I) has been described as one of the main kinases involved in tau modifications. We have analysed the role of phospho-tau as a neurotoxic agent. We have analysed a transgenic mouse model which overexpresses GSK3{beta}. In this transgenic mouse, a clear degeneration of the dentate gyrus, which increases with age, was found. In a double transgenic mouse, which overexpresses GSK3 and tau at the same time, dentate gyrus degeneration was dramatically increased. This result may suggest that phospho-tau may be toxic inside neurons of the dentate gyrus. Once neuronal degeneration takes place, intracellular tau is secreted to the extracellular space. The present review discusses the toxicity of this extracellular tau for surrounding neurons.

Phosphorylation differentiates tau-dependent neuronal toxicity and dysfunction

2010-08-01

The heterogeneous pathology of tauopathies and the differential susceptibility of different neuronal types to WT (wild-type) and mutant tau suggest that phosphorylation at particular sites rather than hyperphosphorylation mediates toxicity or dysfunction in a cell-type-specific manner. Pan-neuronal accumulation of tau in the Drosophila CNS (central nervous system) specifically affected the MBs (mushroom body neurons), consistent with neuronal type-specific effects. The MB aberrations depended, at least in part, on occupation of two novel phosphorylation sites: Ser²³⁸ and Thr²⁴⁵. The degree of isoform-specific MB aberrations was paralleled by defects in associative learning, as blocking putative Ser²³⁸ and Thr²⁴⁵ phosphorylation yielded structurally normal, but profoundly dysfunctional, MBs, as animals accumulating the mutant protein exhibited strongly impaired associative learning. Similarly dysfunctional MBs were obtained by temporally restricting tau accumulation to the adult CNS, which also altered the tau phosphorylation pattern. Our data clearly distinguish tau-dependent neuronal degeneration and dysfunction and suggest that temporal differences in occupation of the same phosphorylation sites are likely to mediate these distinct effects of tau.

Insights from Drosophila models of Alzheimer's disease

Catherine M. Cowan,David Shepherd,Amritpal Mudher, — 2010-08-01

AD (Alzheimer's disease) is a neurodegenerative disorder characterized by the abnormal hyperphosphorylation and aggregation of the microtubule-associated protein tau and the misfolding and deposition of A{beta} peptide. The mechanisms by which tau and A{beta} become abnormal is not clearly understood, neither is it known what role either protein plays in the neurodegenerative process underlying AD. We have modelled aspects of AD in Drosophila melanogaster to shed light on these processes and to further our understanding of the relationship between tau and amyloid in this disease.

Pathways linking Abeta and tau pathologies

Frank M. LaFerla, — 2010-08-01

A{beta} (amyloid {beta}-peptide) and tau are the main proteins that misfold and accumulate in amyloid plaques and NFTs (neurofibrillary tangles) of Alzheimer's disease and other neurological disorders. Historically, because plaques and NFTs accumulate in diverse cellular compartments, i.e. mainly extracellularly for plaques and intracellularly for NFTs, it was long presumed that the constituent proteins formed these lesions via unrelated pathways. Animal and cell studies over the last decade, however, have provided convincing evidence to show that A{beta} can facilitate the development of tau pathology by altering several cell-dependent and -independent mechanisms. In the present article, results are reviewed from several laboratories that show that modulating A{beta} pathology can directly affect the development of tau pathology, which has significant implications for the treatment of Alzheimer's disease.

Modulation of tau pathology in tau transgenic models

Jean-Pierre Brion,Kunie Ando,Céline Heraud,Karelle Leroy, — 2010-08-01

NFTs (neurofibrillary tangles) in Alzheimer's disease and in tauopathies are hallmark neuropathological lesions whose relationship with neuronal dysfunction, neuronal death and with other lesions [such as A{beta} (amyloid {beta}-peptide) pathology] are still imperfectly understood. Many transgenic mice overexpressing wild-type or mutant tau proteins have been generated to investigate the physiopathology of tauopathies. Most of the mice overexpressing wild-type tau do not develop NFTs, but can develop a severe axonopathy, whereas overexpression of mutant tau leads to NFT formation, synaptic loss and neuronal death in several models. The association between neuronal death and NFTs has, however, been challenged in some models showing a dissociation between tau aggregation and tau toxicity. Cross-breeding of mice developing NFTs with mice developing A{beta} deposits increases NFT pathology, highlighting the relationship between tau and amyloid pathology. On the other hand, tau expression seems to be necessary for expression of a pathological phenotype associated with amyloid pathology. These findings suggest that there is a bilateral cross-talk between A{beta} and tau pathology. These observations are discussed by the presentation of some relevant models developed recently.

Deletion of murine tau gene increases tau aggregation in a human mutant tau transgenic mouse model

2010-08-01

We have reported previously a tau transgenic mouse model (Tg30tau) overexpressing human 4R1N double-mutant tau (P301S and G272V) and that develops AD (Alzheimer's disease)-like NFTs (neurofibrillary tangles) in an age-dependent manner. Since murine tau might interfere with the toxic effects of human mutant tau, we set out to analyse the phenotype of our Tg30tau model in the absence of endogenous murine tau with the aim to reproduce more faithfully a model of human tauopathy. By crossing the Tg30tau line with TauKO (tau-knockout) mice, we have obtained a new mouse line called Tg30×TauKO that expresses only exogenous human double-mutant 4R1N tau. Whereas Tg30×TauKO mice express fewer tau proteins compared with Tg30tau, they exhibit augmented sarkosyl-insoluble tau in the brain and an increased number of Gallyas-positive NFTs in the hippocampus. Taken together, exclusion of murine tau causes accelerated tau aggregation during aging of this mutant tau transgenic model.

NMR spectroscopy of the neuronal tau protein: normal function and implication in Alzheimer's disease

2010-08-01

NMR spectroscopy was used to explore the different aspects of the normal and pathological functions of tau, but proved challenging because the protein contains 441 amino acids and has poor signal dispersion. We have set out to dissect the phosphorylation patterns of tau in order to understand better its role in the aggregation process and microtubule-binding regulation. Our current knowledge on the functional consequences of specific phosphorylations is still limited, mainly because producing and assessing quantitatively phosphorylated tau samples is far from straightforward, even in vitro. We use NMR spectroscopy as a proteomics tool to characterize the phosphorylation patterns of tau, after in vitro phosphorylation by recombinant kinases. The phosphorylated tau can next be use for functional assays or interaction assays with phospho-dependent protein partners, such as the prolyl cis–trans isomerase Pin1.

Functional implications of the association of tau with the plasma membrane

Amy M. Pooler,Diane P. Hanger, — 2010-08-01

Tau is an abundant microtubule-associated protein which regulates the stability of the cytoskeleton. Tau binds microtubules directly through microtubule-binding domains in its C-terminus. However, tau is not only located in the cytosol of cells, but also associated with other intracellular domains, including the plasma membrane, suggesting that tau may have additional functions other than stabilizing the neuronal cytoskeleton. Localization of tau at the cell surface appears to be dependent on interactions of the N-terminal projection domain of tau. Furthermore, membrane-associated tau is dephosphorylated at serine/threonine residues, suggesting that the phosphorylation state of tau regulates its intracellular trafficking. Dephosphorylation of tau may increase the association of tau with trafficking proteins which target tau to the plasma membrane. Thus it is possible that the hyperphosphoryation of tau may contribute to the pathogenesis of Alzheimer's disease by promoting the formation of neurofibrillary tangles from cytosolic tau, and also by inhibiting additional tau functions through disruption of its targeting to the plasma membrane.

Tau cleavage and tau aggregation in neurodegenerative disease

Diane P. Hanger,Selina Wray, — 2010-08-01

Deposition of highly phosphorylated tau in the brain is the most significant neuropathological and biochemical characteristic of the group of neurodegenerative disorders termed the tauopathies. The discovery of tau fragments in these diseases suggests that tau cleavage and tau phosphorylation, both of which induce conformational changes in tau, could each have roles in disease pathogenesis. The identities of the proteases responsible for degrading tau, resulting in the appearance of truncated tau species in physiological and pathological conditions, are not known. Several fragments of tau are reported to have pro-aggregation properties, but the lack of disease-relevant cell models of tau aggregation has hampered investigation of the effects of tau aggregation on normal cellular functioning. In the present paper, we describe our findings of N-terminally truncated tau in the brain in a subgroup of the tauopathies in which tau isoforms containing four microtubule-binding domains predominate. We also discuss the evidence for the involvement of proteases in the generation of tau pathology in neurodegenerative disease, since these enzymes warrant further investigation as potential therapeutic targets in the tauopathies.

Links between ApoE, brain cholesterol metabolism, tau and amyloid beta-peptide in patients with cognitive impairment

Valerio Leoni,Alina Solomon,Miia Kivipelto, — 2010-08-01

Brain neurons remove the excess of cholesterol via conversion into the more polar 24OHC [(24S)-hydroxycholesterol]. 24OHC acts as a signalling molecule inducing ApoE (apolipoprotein E)-mediated cholesterol efflux from astrocytes, by a direct effect on ApoE transcription, protein synthesis and secretion. In CSF (cerebrospinal fluid) collected form from patients with cognitive impairment (Alzheimer's disease and patients with mild cognitive impairment) the levels of ApoE, tau, p-tau (hyperphosphorylated tau) were significantly increased, together with 24OHC, compared with controls. We also found that the levels of tau and p-tau were significantly correlated with ApoE and 24OHC in the same samples. Such a correlation was not found in control patients. Increased levels of cholesterol in membranes and impairment in brain cholesterol metabolism were found to be involved both in APP (amyloid precursor protein) processing and amyloid {beta}-peptide deposition and, recently, in tau pathology. The CSF tau levels are considered to be related to the neurodegenerative process in Alzheimer's disease. During neurodegeneration, the cholesterol accumulated in neurons is converted into 24OHC. The release of 24OHC from neurons induces ApoE secretion by astrocytes, and both are related to the intensity of the neurodegenerative process and neuronal injury. ApoE can also be involved in the scavenging of tau from neurons. The direct correlations between ApoE, 24OHC and tau suggest that cholesterol metabolism may be involved in generation of both tau and amyloid {beta}-peptide and that the ApoE is released by astrocytes in order to counteract this ongoing process.

The ground state of pluripotency

Jason Wray,Tuzer Kalkan,Austin G. Smith, — 2010-08-01

Pluripotency is defined as the capacity of individual cells to initiate all lineages of the mature organism in response to signals from the embryo or cell culture environment. A pluripotent cell has no predetermined programme; it is a blank slate. This is the foundation of mammalian development and of ES (embryonic stem) cell biology. What are the design principles of this naïve cell state? How is pluripotency acquired and maintained? Suppressing activation of ERKs (extracellular-signal-regulated kinases) is critical to establishing and sustaining ES cells. Inhibition of GSK3 (glycogen synthase kinase 3) reinforces this effect. We review the effect of selective kinase inhibitors on pluripotent cells and consider how these effects are mediated. We propose that ES cells represent a ground state, meaning a basal proliferative state that is free of epigenetic restriction and has minimal requirements for extrinsic stimuli. The stability of this state is reflected in the homogeneity of ES cell populations cultured in the presence of small-molecule inhibitors of MEK (mitogen-activated protein kinase/ERK kinase) and GSK3.

Role of stem-cell-derived hepatic endoderm in human drug discovery

Claire N. Medine,Sebastian Greenhough,David C. Hay, — 2010-08-01

Accurate prediction of human drug toxicity is a vital part of the drug discovery process. However, the safety evaluation process is hindered by the availability and quality of primary human liver models with which to study drug toxicity. In an attempt to overcome this limitation, research has focused on deriving human hepatocytes from a number of sources, including progenitors from fetal and adult liver, human cell lines derived from liver tumours, immortalized human hepatocytes and pluripotent stem cells. The major hurdles in developing scalable and high-fidelity human hepatocytes from hepatic cell lines and fetal and adult progenitors have been limited organ availability, homogeneous cell purification, short-term cell culture, and the rapid loss of hepatocyte phenotype and function in culture. Therefore it has been necessary to find alternative sources of human hepatocytes which circumvent these issues. The research in our group has focused on generating human hepatic endoderm from the scalable pluripotent stem cell populations, human embryonic stem cells and induced pluripotent stem cells. We have developed efficient and scalable models of human hepatocyte differentiation from these cell populations. Moreover, stem-cell-derived hepatic endoderm displays many of the functional attributes of primary human hepatocytes. Our research is now focused on developing defined culture systems and improving cell culture microenvironments in order to improve our understanding of the mechanisms regulating human liver development. This will in turn facilitate the generation of broad-range functioning hepatic endoderm in vitro. By taking these approaches, we believe that it will be possible to improve the predictive nature of our in vitro models, revolutionizing the manner in which industry measures human drug toxicity and having an impact on drug attrition.

Evaluating the utility of cardiomyocytes from human pluripotent stem cells for drug screening

Emily Dick,Divya Rajamohan,Jonathon Ronksley,Chris Denning, — 2010-08-01

Functional cardiomyocytes can now be derived routinely from hPSCs (human pluripotent stem cells), which collectively include embryonic and induced pluripotent stem cells. This technology presents new opportunities to develop pharmacologically relevant in vitro screens to detect cardiotoxicity, with a view to improving patient safety while reducing the economic burden to industry arising from high drug attrition rates. In the present article, we consider the need for human cardiomyocytes in drug-screening campaigns and review the strategies used to differentiate hPSCs towards the cardiac lineage. During early stages of differentiation, hPSC-cardiomyocytes display gene expression profiles, ultra-structures, ion channel functionality and pharmacological responses reminiscent of an embryonic phenotype, but maturation during extended time in culture has been demonstrated convincingly. Notably, hPSC-cardiomyocytes have been shown to respond in a highly predictable manner to over 40 compounds that have a known pharmacological effect on the human heart. This suggests that further development and validation of the hPSC-cardiomyocyte model as a tool for assessing cardiotoxicity is warranted.

High-content screening of small compounds on human embryonic stem cells

Ivana Barbaric,Paul J. Gokhale,Peter W. Andrews, — 2010-08-01

Human ES (embryonic stem) cells and iPS (induced pluripotent stem) cells have been heralded as a source of differentiated cells that could be used in the treatment of degenerative diseases, such as Parkinson's disease or diabetes. Despite the great potential for their use in regenerative therapy, the challenge remains to understand the basic biology of these remarkable cells, in order to differentiate them into any functional cell type. Given the scale of the task, high-throughput screening of agents and culture conditions offers one way to accelerate these studies. The screening of small-compound libraries is particularly amenable to such high-throughput methods. Coupled with high-content screening technology that enables simultaneous assessment of multiple cellular features in an automated and quantitative way, this approach is proving powerful in identifying both small molecules as tools for manipulating stem cell fates and novel mechanisms of differentiation not previously associated with stem cell biology. Such screens performed on human ES cells also demonstrate the usefulness of human ES/iPS cells as cellular models for pharmacological testing of drug efficacy and toxicity, possibly a more imminent use of these cells than in regenerative medicine.

Human pluripotent stem cells in drug discovery and predictive toxicology

Delphine Laustriat,Jacqueline Gide,Marc Peschanski, — 2010-08-01

Human pluripotent stem cells are a biological resource most commonly considered for their potential in cell therapy or, as it is now called, ‘regenerative medicine’. However, in the near future, their most important application for human health may well be totally different, as they are more and more envisioned as opening new routes for pharmacological research. Pluripotent stem cells indeed possess the main attributes that make them theoretically fully equipped for the development of cell-based assays in the fields of drug discovery and predictive toxicology. These cells are characterized by: (i) an unlimited self-renewal capacity, which make them an inexhaustible source of cells; (ii) the potential to differentiate into any cell phenotype of the body at any stage of differentiation, with probably the notable exception, however, of the most mature forms of many lineages; and (iii) the ability to express genotypes of interest via the selection of donors, whether they be of embryonic origin, through pre-implantation genetic diagnosis, or adults, by genetic reprogramming of somatic cells, so-called iPSCs (induced pluripotent stem cells). In the present review, we provide diverse illustrations of the use of pluripotent stem cells in drug discovery and predictive toxicology, using either human embryonic stem cell lines or iPSC lines.

Identification and characterization of small-molecule ligands that maintain pluripotency of human embryonic stem cells

2010-08-01

hESCs (human embryonic stem cells) offer great potential for pharmaceutical research and development and, potentially, for therapeutic use. However, improvements in cell culture are urgently required to allow the scalable production of large numbers of cells that maintain pluripotency. Supplementing feeder-free conditions with either EHNA [erythro-9-(2-hydroxy-3-nonyl)adenine] or readily synthesized analogues of this compound maintains hESC pluripotency in the absence of exogenous cytokines. When the hESC lines SA121 or SA461 were maintained in feeder-free conditions with EHNA they displayed no reduction in stem-cell-associated markers such as Nanog, Oct4 (octamer-binding protein 4) and SSEA4 (stage-specific embryonic antigen 4) when compared with cells maintained in full feeder-free conditions that included exogenously added bFGF (basic fibroblast growth factor). Spontaneous differentiation was reversibly suppressed by the addition of EHNA, but EHNA did not limit efficient spontaneous or directed differentiation following its removal. We conclude that EHNA or related compounds offers a viable alternative to exogenous cytokine addition in maintaining hESC cultures in a pluripotent state and might be a particularly useful replacement for bFGF for large-scale or GMP (good manufacturing practice)-compliant processes.

The potential of small chemical functional groups for directing the differentiation of kidney stem cells

2010-08-01

In the future, stem-cell-based therapies could offer new approaches to treat kidney disease and reduce the incidence of ESRD (end-stage renal disease), but, as yet, research in this area is only being conducted in rodents and it is not clear whether or when it could be applied to human patients. Drug therapies, on the other hand, have been very effective at delaying the progression of kidney disease, but, for various reasons, current drug regimes are not suitable for all patients. A greater understanding of the molecular mechanisms that underlie disease progression in chronic kidney disease could help to identify novel drug targets. However, progress in this area is currently hindered due to the lack of appropriate in vitro culture systems for important renal cell types, such as proximal tubule cells and podocytes. This problem could be overcome if it were possible to direct the differentiation of kidney stem cells to renal cell types in vitro. In the present review, we highlight the potential of surface gradients of small chemical functional groups to direct the differentiation of kidney stem cells.

Imaging-based chemical screens using normal and glioma-derived neural stem cells

2010-08-01

The development of optimal culture methods for embryonic, tissue and cancer stem cells is a critical foundation for their application in drug screening. We previously described defined adherent culture conditions that enable expansion of human radial glia-like fetal NS (neural stem) cells as stable cell lines. Similar protocols proved effective in the establishment of tumour-initiating stem cell lines from the human brain tumour glioblastoma multiforme, which we termed GNS (glioma NS) cells. Others have also recently derived more primitive human NS cell lines with greater neuronal subtype differentiation potential than NS cells, which have similarities to the early neuroepithelium, named NES (neuroepithelial stem) cells. In the present paper, we discuss the utility of these cells for chemical screening, and describe methods for a simple high-content live-image-based platform. We report the effects of a panel of 160 kinase inhibitors (Inhibitor Select I and II; Calbiochem) on NES cells, identifying three inhibitors of ROCK (Rho-associated kinase) as promoting the expansion of NES cell cultures. For the GNS cells, we screened a panel of 1000 compounds and confirmed our previous finding of a cytotoxic effect of modulators of neurotransmitter signalling pathways. These studies provide a framework for future higher-throughput screens.

Developments in three-dimensional cell culture technology aimed at improving the accuracy of in vitro analyses

Daniel J. Maltman,Stefan A. Przyborski, — 2010-08-01

Drug discovery programmes require accurate in vitro systems for drug screening and testing. Traditional cell culture makes use of 2D (two-dimensional) surfaces for ex vivo cell growth. In such environments, cells are forced to adopt unnatural characteristics, including aberrant flattened morphologies. Therefore there is a strong demand for new cell culture platforms which allow cells to grow and respond to their environment in a more realistic manner. The development of 3D (three-dimensional) alternative substrates for in vitro cell growth has received much attention, and it is widely acknowledged that 3D cell growth is likely to more accurately reflect the in vivo tissue environments from which cultured cells are derived. 3D cell growth techniques promise numerous advantages over 2D culture, including enhanced proliferation and differentiation of stem cells. The present review focuses on the development of scaffold technologies for 3D cell culture.

Alternative polyadenylation of antisense RNAs and flowering time control

2010-08-01

Flowering time is controlled by precision in gene regulation mediated by different pathways. Two Arabidopsis thaliana components of the autonomous flowering pathway, FCA and FPA, function as genetically independent trans-acting regulators of alternative cleavage and polyadenylation. FCA and FPA directly associate with chromatin at the locus encoding the floral repressor FLC, but appear to control FLC transcription by mediating alternative polyadenylation of embedded non-coding antisense RNAs. These findings prompt the re-examination of how other factors control FLC expression, as it is formally possible that they function primarily to control alternative processing of antisense RNAs. As co-expressed sense and antisense gene pairs are widespread in eukaryotes, alternative processing of antisense RNAs may represent a significant form of gene regulation.

snRNA 3' end formation: the dawn of the Integrator complex

Jiandong Chen,Eric J. Wagner, — 2010-08-01

The ubiquitously expressed uridine-rich snRNAs (small nuclear RNAs) are essential for the removal of introns, proper expression of histone mRNA and biosynthesis of ribosomal RNA. Much is known about their assembly into snRNP (small nuclear ribonucleoprotein) particles and their ultimate function in the expression of other genes; however, in comparison, less is known about the biosynthesis of these critical non-coding RNAs. The sequence elements necessary for 3′ end formation of snRNAs have been identified and, intriguingly, the processing of snRNAs is uniquely dependent on the snRNA promoter, indicating that co-transcriptional processing is important. However, the trans-acting RNA-processing factors that mediate snRNA processing remained elusive, hindering overall progress. Recently, the factors involved in this process were biochemically purified, and designated the Integrator complex. Since their initial discovery, Integrator proteins have been implicated not only in the production of snRNA, but also in other cellular processes that may be independent of snRNA biogenesis. In the present study, we discuss snRNA biosynthesis and the roles of Integrator proteins. We compare models of 3′ end formation for different classes of RNA polymerase II transcripts and formulate/propose a model of Integrator function in snRNA biogenesis.

Rrp47 and the function of the Sas10/C1D domain

Phil Mitchell, — 2010-08-01

The Sas10/C1D domain is found in a small group of eukaryotic proteins that have functions in RNA processing events, translational control and DNA repair mechanisms. The domain is predicted to be {alpha}-helical in nature and comprises approx. 80 amino acid residues. Whereas the Sas10/C1D domain has yet to be functionally characterized, available results suggest that this domain forms a binding surface for specific interactions with other proteins and can concomitantly interact with RNA or DNA. This property of the Sas10/C1D domain may facilitate this family of proteins to dock other proteins on to nucleic acid substrates.

Biogenesis of the signal recognition particle

Eileen Leung,Jeremy D. Brown, — 2010-08-01

Assembly of ribonucleoprotein complexes is a facilitated quality-controlled process that typically includes modification to the RNA component from precursor to mature form. The SRP (signal recognition particle) is a cytosolic ribonucleoprotein that catalyses protein targeting to the endoplasmic reticulum. Assembly of SRP is largely nucleolar, and most of its protein components are required to generate a stable complex. A pre-SRP is exported from the nucleus to the cytoplasm where the final protein, Srp54p, is incorporated. Although this outline of the SRP assembly pathway has been determined, factors that facilitate this and/or function in quality control of the RNA are poorly understood. In the present paper, the SRP assembly pathway is summarized, and evidence for the involvement of both the Rex1p and nuclear exosome nucleases and the TRAMP (Trf4–Air2–Mtr4p polyadenylation) adenylase in quality control of SRP RNA is discussed. The RNA component of SRP is transcribed by RNA polymerase III, and both La, which binds all newly transcribed RNAs generated by this enzyme, and the nuclear Lsm complex are implicated in SRP RNA metabolism.

Secondary structure of U6 small nuclear RNA: implications for spliceosome assembly

Elizabeth A. Dunn,Stephen D. Rader, — 2010-08-01

U6 snRNA (small nuclear RNA), one of five RNA molecules that are required for the essential process of pre-mRNA splicing, is notable for its high level of sequence conservation and the important role it is thought to play in the splicing reaction. Nevertheless, the secondary structure of U6 in the free snRNP (small nuclear ribonucleoprotein) form has remained elusive, with predictions changing substantially over the years. In the present review we discuss the evidence for existing models and critically evaluate a fundamental assumption of these models, namely whether the important 3′ ISL (3′ internal stem–loop) is present in the free U6 particle, as well as in the active splicing complex. We compare existing models of free U6 with a newly proposed model lacking the 3′ ISL and evaluate the implications of the new model for the structure and function of U6's base-pairing partner U4 snRNA. Intriguingly, the new model predicts a role for U4 that was unanticipated previously, namely as an activator of U6 for assembly into the splicing machinery.

Brr2p RNA helicase with a split personality: insights into structure and function

Daniela Hahn,Jean D. Beggs, — 2010-08-01

RNA helicases are involved in many cellular processes. Pre-mRNA splicing requires eight different DExD/H-box RNA helicases, which facilitate spliceosome assembly and remodelling of the intricate network of RNA rearrangements that are central to the splicing process. Brr2p, one of the spliceosomal RNA helicases, stands out through its unusual domain architecture. In the present review we highlight the advances made by recent structural and biochemical studies that have important implications for the mechanism and regulation of Brr2p activity. We also discuss the involvement of human Brr2 in retinitis pigmentosa, a degenerative eye disease, and how its functions in splicing might connect to the molecular pathology of the disease.

The function of the NineTeen Complex (NTC) in regulating spliceosome conformations and fidelity during pre-mRNA splicing

Rebecca Hogg,Joanne C. McGrail,Raymond T. O'Keefe, — 2010-08-01

The NineTeen Complex (NTC) of proteins associates with the spliceosome during pre-mRNA splicing and is essential for both steps of intron removal. The NTC and other NTC-associated proteins are recruited to the spliceosome where they participate in regulating the formation and progression of essential spliceosome conformations required for the two steps of splicing. It is now clear that the NTC is an integral component of active spliceosomes from yeast to humans and provides essential support for the spliceosomal snRNPs (small nuclear ribonucleoproteins). In the present article, we discuss the identification and characterization of the yeast NTC and review recent work in yeast that supports the essential role for this complex in the regulation and fidelity of splicing.

Human papillomavirus regulation of SR proteins

Melanie McFarlane,Sheila V. Graham, — 2010-08-01

Splicing is a cellular process essential for mRNA biogenesis. There are two types of splicing: constitutive and alternative splicing. During constitutive splicing, non-coding intron sequences are removed and exonic coding sequences are spliced together to form mature mRNAs. Alternative splicing can maximize the coding capacity of the genome by specific alternative selection of exons from multi-exon metazoan pre-mRNAs. Splicing is a tightly regulated process, so when control is lost disease may occur. SR proteins (serine/arginine-rich proteins) are a family of highly conserved splicing regulators that are also involved in other steps in RNA biogenesis and expression. Many viruses have evolved to utilize the cellular splicing machinery to enhance their proteome from a limited number of genes. HPV (human papillomavirus) is an example of one such virus. The HPV transcription/replication factor E2 (early 2) specifically up-regulates expression of the SR proteins SF2/ASF (splicing factor 2/alternative splicing factor), SRp20 and SC35 in infected epithelial cells. These SR proteins are essential for viral RNA processing. SF2/ASF is a proto-oncogene that is also up-regulated in a number of cancers. For example, SF2/ASF, together with SRp20 and SC35 is selectively up-regulated in cervical tumours caused by persistent oncogenic HPV infection. However, the mode of SR protein up-regulation in tumours is different to the E2-directed transcriptional regulation in normal transient HPV infection. SR proteins could provide excellent targets for HPV antiviral therapy as well as anticancer therapy.

Determinants of ELAV gene-specific regulation

Matthias Soller,Min Li,Irmgard U. Haussmann, — 2010-08-01

How RNA-binding proteins recognize their complement of targets in a complex cellular environment remains poorly understood. Sequence degeneracy and redundancy of short motifs at genomic scales have mostly eluded predictions of specific target genes for gene-specific ELAV (embryonic lethal abnormal visual system)/Hu proteins that bind ubiquitous AU-rich motifs. Using the genetic tools of Drosophila, we have analysed binding properties of ELAV in vitro and ELAV-dependent regulation of its major target ewg (erect wing) in neurons. These studies reveal that an integral part of ELAV gene-specific regulation involves combinatorial binding to variably spaced short U-rich motifs on an extensive binding site.

The evolution of spliced leader trans-splicing in nematodes

2010-08-01

Spliced leader trans-splicing occurs in many primitive eukaryotes including nematodes. Most of our knowledge of trans-splicing in nematodes stems from the model organism Caenorhabditis elegans and relatives, and from work with Ascaris. Our investigation of spliced leader trans-splicing in distantly related Dorylaimia nematodes indicates that spliced-leader trans-splicing arose before the nematode phylum and suggests that the spliced leader RNA gene complements in extant nematodes have evolved from a common ancestor with a diverse set of spliced leader RNA genes.

Inhibition of translation initiation following glucose depletion in yeast facilitates a rationalization of mRNA content

Jennifer Lui,Susan G. Campbell,Mark P. Ashe, — 2010-08-01

Glucose is the preferred carbon source for most eukaryotes and so it is important that cells can sense and react rapidly to fluctuations in glucose levels. It is becoming increasingly clear that the regulation of gene expression at the post-transcriptional level is important in the adaptation to changes in glucose levels, possibly as this could engender more rapid alterations in the concentrations of key proteins, such as metabolic enzymes. Following the removal of glucose from yeast cells a rapid inhibition of translation is observed. As a consequence, mRNPs (messenger ribonucleoproteins) relocalize into cytoplasmic granules known as P-bodies (processing bodies) and EGP-bodies. mRNA decay components localize into P-bodies, and thus these assemblies are likely to represent sites where mRNAs are targeted for degradation. In contrast, EGP-bodies lack any decay components and contain the eukaryotic translation initiation factors eIF4E, eIF4G and Pab1p, as well as other RNA-binding proteins. Therefore EGP-bodies probably constitute sites where mRNAs are earmarked for storage. So, it is possible that cells distinguish between transcripts and target them to either P-bodies or EGP-bodies depending on their functional value. The localization of mRNAs into these granules following glucose starvation may serve to preserve mRNAs that are involved in the diauxic shift to ethanol growth and entry into stationary phase, as well as to degrade mRNAs that are solely involved in glucose fermentation.

Functions of microRNAs in Drosophila development

Christopher I. Jones,Sarah F. Newbury, — 2010-08-01

Control of mRNA translation and degradation has been shown to be key in the development of complex organisms. The core mRNA degradation machinery is highly conserved in eukaryotes and relies on processive degradation enzymes gaining access to the mRNA. Control of mRNA stability in eukaryotes is also intimately linked to the regulation of translation. A key question in the control of mRNA turnover concerns the mechanisms whereby particular mRNAs are specifically degraded in response to cellular factors. Recently, microRNAs have been shown to bind specifically to mRNAs and regulate their expression via repression of translation and/or degradation. To understand the molecular mechanisms during microRNA repression of mRNAs, it is necessary to identify their biologically relevant targets. However, computational methods have so far proved unreliable, therefore verification of biologically important targets at present requires experimental analysis. The present review aims to outline the mechanisms of mRNA degradation and then focus on the role of microRNAs as factors affecting particular Drosophila developmental processes via their post-transcriptional effects on mRNA degradation and translation. Examples of experimentally verified targets of microRNAs in Drosophila are summarized.

What are natural antisense transcripts good for?

Andreas Werner,Daniel Swan, — 2010-08-01

NATs (natural antisense transcripts) are important regulators of eukaryotic gene expression. Interference between the expression of protein-coding sense transcripts and the corresponding NAT is well documented. In the present review, we focus on an additional, higher-order role of NATs that is currently emerging. The recent discovery of endogenous siRNAs (short interfering RNAs), as well as NAT-induced transcriptional gene silencing, are key to the proposed novel function of NATs.

3' uridylation and the regulation of RNA function in the cytoplasm

Chris J. Norbury, — 2010-08-01

Degradation of cytoplasmic mRNAs is an important aspect of the regulation of gene function in eukaryotes. Much of what is currently known about the underlying pathways of mRNA decay is derived from studies of the budding yeast Saccharomyces cerevisiae, in which mRNA turnover is initiated by deadenylation, followed either by decapping and 5′{Rightwards Arrow}3′ degradation or by further 3′{Rightwards Arrow}5′ exonucleolysis. Our studies using RNA cRACE (circularization-based rapid amplification of cDNA ends) techniques indicate that mRNA decapping in the fission yeast Schizosaccharomyces pombe often does not require prior deadenylation. Furthermore, the poly(A) polymerase-related, cytoplasmic enzyme Cid1 catalyses uridylation of a variety of functionally diverse poly(A)⁺ mRNAs and hence stimulates decapping as part of a novel mRNA turnover pathway. The pathways initiated by uridylation and deadenylation stimulate decapping in a partially redundant fashion, but urg1 mRNA is stabilized in mutants lacking cid1. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the Lsm1–7 complex in recognition of the 3′ uridylation tag and recruitment of the decapping machinery. Recent reports from other groups suggest that in metazoans, which unlike budding yeast contain Cid1 orthologues, 3′ uridylation by such enzymes is used to regulate miRNA (microRNA) and siRNA (small interfering RNA) biogenesis and activity. It has further been suggested that uridylation is an important regulatory modification of non-polyadenylated replication-dependent histone mRNAs. This modification may also form the basis of a widespread mechanism for the initiation of the decay of polyadenylated mRNAs in organisms other than fission yeast.