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1.  Interferon-induced ISG15 pathway: an ongoing virus–host battle 
Trends in microbiology  2013;21(4):181-186.
ISG15 is an interferon-induced ubiquitin-like protein that is conjugated to target proteins via the sequential action of three enzymes that are also induced by interferon. Unlike ubiquitin, which is highly conserved, the sequence of ISG15 varies between species. ISG15 conjugation inhibits many viruses, and free (unconjugated) ISG15 can also act as an antiviral protein. Here we focus on the antiviral role of ISG15 conjugation and on countermeasures employed by several viruses. The countermeasure by influenza B virus is unique in that it exhibits species-specificity. Only the antiviral activity of human and non-human primate ISG15s can be blocked, providing one possible explanation for the restriction of influenza B virus to humans.
doi:10.1016/j.tim.2013.01.005
PMCID: PMC3622817  PMID: 23414970
interferon; ISG15; influenza B virus; NS1B protein; species-specificity; ovarian tumor domain
2.  Phosphoinositide Metabolism Links cGMP-Dependent Protein Kinase G to Essential Ca2+ Signals at Key Decision Points in the Life Cycle of Malaria Parasites 
PLoS Biology  2014;12(3):e1001806.
Chemical genetics and a global comparative analysis of phosphorylation and phospholipids in vivo shows that PKG is the upstream regulator that induces calcium signals that enables Plasmodium to progress through its complex life cycle.
Many critical events in the Plasmodium life cycle rely on the controlled release of Ca2+ from intracellular stores to activate stage-specific Ca2+-dependent protein kinases. Using the motility of Plasmodium berghei ookinetes as a signalling paradigm, we show that the cyclic guanosine monophosphate (cGMP)-dependent protein kinase, PKG, maintains the elevated level of cytosolic Ca2+ required for gliding motility. We find that the same PKG-dependent pathway operates upstream of the Ca2+ signals that mediate activation of P. berghei gametocytes in the mosquito and egress of Plasmodium falciparum merozoites from infected human erythrocytes. Perturbations of PKG signalling in gliding ookinetes have a marked impact on the phosphoproteome, with a significant enrichment of in vivo regulated sites in multiple pathways including vesicular trafficking and phosphoinositide metabolism. A global analysis of cellular phospholipids demonstrates that in gliding ookinetes PKG controls phosphoinositide biosynthesis, possibly through the subcellular localisation or activity of lipid kinases. Similarly, phosphoinositide metabolism links PKG to egress of P. falciparum merozoites, where inhibition of PKG blocks hydrolysis of phosphatidylinostitol (4,5)-bisphosphate. In the face of an increasing complexity of signalling through multiple Ca2+ effectors, PKG emerges as a unifying factor to control multiple cellular Ca2+ signals essential for malaria parasite development and transmission.
Author Summary
Malaria, caused by Plasmodium spp. parasites, is a profound human health problem. Plasmodium parasites progress through a complex life cycle as they move between infected humans and blood-feeding mosquitoes. We know that tight regulation of calcium ion levels within the cytosol of the parasite is critical to control multiple signalling events in their life cycle. However, how these calcium levels are controlled remains a mystery. Here, we show that a single protein kinase, the cGMP-dependent protein kinase G (PKG), controls the calcium signals that are critical at three different points of the life cycle: (1) for the exit of the merozoite form of the parasite from human erythrocytes (red blood cells), (2) for the cellular activation that happens when Plasmodium sexual transmission stages are ingested by a blood-feeding mosquito, and (3) for the productive gliding of the ookinete, which is the parasite stage that invades the mosquito midgut. We provide initial evidence that the universal role of PKG relies on the production of lipid precursors which then give rise to inositol (1,4,5)-trisphosphate (IP3), a messenger molecule that serves as a signal for the release of calcium from stores within the parasite. This signalling pathway provides a potential target to block both malaria development in the human host and transmission to the mosquito vector.
doi:10.1371/journal.pbio.1001806
PMCID: PMC3942320  PMID: 24594931
3.  Evolutionary expansion and anatomical specialization of synapse proteome complexity 
Nature neuroscience  2008;11(7):799-806.
Understanding the origins and evolution of synapses may provide insight into species diversity and organisation of the brain. Using comparative proteomics and genomics we examined the evolution of the postsynaptic density (PSD) and MAGUK associated signalling complexes (MASCs) underlying learning and memory. PSD/MASC orthologues found in yeast perform basic cellular functions regulating protein synthesis and structural plasticity. Striking changes in signalling complexity were observed at the yeast:metazoan and invertebrate:vertebrate boundaries, with expansion of key synapse components, notably receptors, adhesion/cytoskeletal and scaffold proteins. Proteomic comparison of Drosophila and mouse MASCs revealed species-specific adaptation with greater signalling complexity in mouse. Although synapse components were conserved amongst diverse vertebrate species, mapping mRNA and protein expression within the mouse brain showed vertebrate-specific components preferentially contributed to differences between brain regions. We propose that evolution of synapse complexity around a core proto-synapse has contributed to invertebrate–vertebrate differences and to brain specialisation.
doi:10.1038/nn.2135
PMCID: PMC3624047  PMID: 18536710
4.  Epithelioid Malignant Peripheral Nerve Sheath Tumor Arising in a Schwannoma, in a Patient with “Neuroblastoma-like” Schwannomatosis and a Novel Germline SMARCB1 mutation 
Epithelioid malignant peripheral nerve sheath tumors arising in pre-existing schwannomas are extremely rare. We report an unusual example occurring in a patient with multiple schwannomas (schwannomatosis), all but one of which showed “neuroblastoma-like” histology. By immunohistochemistry, both the epithelioid malignant peripheral nerve sheath tumor and the schwannomas showed a complete loss of the Smarcb1 protein. Subsequent genetic evaluation revealed the presence of a novel germline mutation in the SMARCB1/INI1 gene in the patient and three of her children, two of whom were diagnosed with atypical teratoid/rhabdoid tumors of the brain.
doi:10.1097/PAS.0b013e3182380802
PMCID: PMC3241826  PMID: 22082606
Malignant peripheral nerve sheath tumor; schwannoma; schwannomatosis; SMARCB1/INI1
5.  Comparative Study of Human and Mouse Postsynaptic Proteomes Finds High Compositional Conservation and Abundance Differences for Key Synaptic Proteins 
PLoS ONE  2012;7(10):e46683.
Direct comparison of protein components from human and mouse excitatory synapses is important for determining the suitability of mice as models of human brain disease and to understand the evolution of the mammalian brain. The postsynaptic density is a highly complex set of proteins organized into molecular networks that play a central role in behavior and disease. We report the first direct comparison of the proteome of triplicate isolates of mouse and human cortical postsynaptic densities. The mouse postsynaptic density comprised 1556 proteins and the human one 1461. A large compositional overlap was observed; more than 70% of human postsynaptic density proteins were also observed in the mouse postsynaptic density. Quantitative analysis of postsynaptic density components in both species indicates a broadly similar profile of abundance but also shows that there is higher abundance variation between species than within species. Well known components of this synaptic structure are generally more abundant in the mouse postsynaptic density. Significant inter-species abundance differences exist in some families of key postsynaptic density proteins including glutamatergic neurotransmitter receptors and adaptor proteins. Furthermore, we have identified a closely interacting set of molecules enriched in the human postsynaptic density that could be involved in dendrite and spine structural plasticity. Understanding synapse proteome diversity within and between species will be important to further our understanding of brain complexity and disease.
doi:10.1371/journal.pone.0046683
PMCID: PMC3465276  PMID: 23071613
6.  Analysis of Protein Palmitoylation Reveals a Pervasive Role in Plasmodium Development and Pathogenesis 
Cell Host & Microbe  2012;12(2):246-258.
Summary
Asexual stage Plasmodium falciparum replicates and undergoes a tightly regulated developmental process in human erythrocytes. One mechanism involved in the regulation of this process is posttranslational modification (PTM) of parasite proteins. Palmitoylation is a PTM in which cysteine residues undergo a reversible lipid modification, which can regulate target proteins in diverse ways. Using complementary palmitoyl protein purification approaches and quantitative mass spectrometry, we examined protein palmitoylation in asexual-stage P. falciparum parasites and identified over 400 palmitoylated proteins, including those involved in cytoadherence, drug resistance, signaling, development, and invasion. Consistent with the prevalence of palmitoylated proteins, palmitoylation is essential for P. falciparum asexual development and influences erythrocyte invasion by directly regulating the stability of components of the actin-myosin invasion motor. Furthermore, P. falciparum uses palmitoylation in diverse ways, stably modifying some proteins while dynamically palmitoylating others. Palmitoylation therefore plays a central role in regulating P. falciparum blood stage development.
Graphical Abstract
Highlights
► A global approach identified >400 palmitoylated proteins in Plasmodium falciparum ► Palmitoyl proteins are central to invasion and other virulence-associated processes ► Palmitoylation is required for completion of the P. falciparum asexual life cycle ► P. falciparum uses palmitoylation dynamically for diverse regulatory purposes
doi:10.1016/j.chom.2012.06.005
PMCID: PMC3501726  PMID: 22901544
7.  A Plasmodium Calcium-Dependent Protein Kinase Controls Zygote Development and Transmission by Translationally Activating Repressed mRNAs 
Cell Host & Microbe  2012;12(1-10):9-19.
Summary
Calcium-dependent protein kinases (CDPKs) play key regulatory roles in the life cycle of the malaria parasite, but in many cases their precise molecular functions are unknown. Using the rodent malaria parasite Plasmodium berghei, we show that CDPK1, which is known to be essential in the asexual blood stage of the parasite, is expressed in all life stages and is indispensable during the sexual mosquito life-cycle stages. Knockdown of CDPK1 in sexual stages resulted in developmentally arrested parasites and prevented mosquito transmission, and these effects were independent of the previously proposed function for CDPK1 in regulating parasite motility. In-depth translational and transcriptional profiling of arrested parasites revealed that CDPK1 translationally activates mRNA species in the developing zygote that in macrogametes remain repressed via their 3′ and 5′UTRs. These findings indicate that CDPK1 is a multifunctional protein that translationally regulates mRNAs to ensure timely and stage-specific protein expression.
Highlights
► CDPK1 is an abundant kinase of invasive and noninvasive life-cycle stages ► It functions in gametocyte emergence and zygote-to-ookinete transformation ► CDPK1 mediates transcriptional activation of some silenced mRNAs in the zygote ► CDPK1 is crucial for the mosquito transmission of P. berghei
doi:10.1016/j.chom.2012.05.014
PMCID: PMC3414820  PMID: 22817984
8.  Quantitative Proteomics Reveals the Basis for the Biochemical Specificity of the Cell Cycle Machinery 
Molecular cell  2011;43(3):406-417.
Summary
Cyclin-dependent-kinases comprise the conserved machinery that drives progress through the cell cycle, but how they do this in mammalian cells is still unclear. To identify the mechanisms by which cyclin-cdks control the cell cycle, we performed a time-resolved analysis of the in vivo interactors of cyclins E1, A2 and B1 by quantitative mass spectrometry. This global analysis of context-dependent protein interactions reveals the temporal dynamics of cyclin function in which networks of cyclin-cdk interactions vary according to the type of cyclin and cell cycle stage. Our results explain the temporal specificity of the cell cycle machinery, thereby providing a biochemical mechanism for the genetic requirement for multiple cyclins in vivo, and reveal how the actions of specific cyclins are coordinated to control the cell cycle. Furthermore, we identify key substrates (Wee1 and c15orf42/Sld3) that reveal how cyclin A is able to promote both DNA replication and mitosis.
doi:10.1016/j.molcel.2011.05.031
PMCID: PMC3332305  PMID: 21816347
9.  Enhanced Peptide Identification by Electron Transfer Dissociation Using an Improved Mascot Percolator* 
Peptide identification using tandem mass spectrometry is a core technology in proteomics. Latest generations of mass spectrometry instruments enable the use of electron transfer dissociation (ETD) to complement collision induced dissociation (CID) for peptide fragmentation. However, a critical limitation to the use of ETD has been optimal database search software. Percolator is a post-search algorithm, which uses semi-supervised machine learning to improve the rate of peptide spectrum identifications (PSMs) together with providing reliable significance measures. We have previously interfaced the Mascot search engine with Percolator and demonstrated sensitivity and specificity benefits with CID data. Here, we report recent developments in the Mascot Percolator V2.0 software including an improved feature calculator and support for a wider range of ion series. The updated software is applied to the analysis of several CID and ETD fragmented peptide data sets. This version of Mascot Percolator increases the number of CID PSMs by up to 80% and ETD PSMs by up to 60% at a 0.01 q-value (1% false discovery rate) threshold over a standard Mascot search, notably recovering PSMs from high charge state precursor ions. The greatly increased number of PSMs and peptide coverage afforded by Mascot Percolator has enabled a fuller assessment of CID/ETD complementarity to be performed. Using a data set of CID and ETcaD spectral pairs, we find that at a 1% false discovery rate, the overlap in peptide identifications by CID and ETD is 83%, which is significantly higher than that obtained using either stand-alone Mascot (69%) or OMSSA (39%). We conclude that Mascot Percolator is a highly sensitive and accurate post-search algorithm for peptide identification and allows direct comparison of peptide identifications using multiple alternative fragmentation techniques.
doi:10.1074/mcp.O111.014522
PMCID: PMC3412976  PMID: 22493177
10.  APC15 drives the turnover of MCC-Cdc20 to make the Spindle Assembly Checkpoint responsive to kinetochore attachment 
Nature cell biology  2011;13(10):1234-1243.
Faithful chromosome segregation during mitosis depends on the Spindle Assembly Checkpoint (SAC) that monitors kinetochore attachment to the mitotic spindle. Unattached kinetochores generate mitotic checkpoint proteins complexes (MCCs) that bind and inhibit the Anaphase Promoting Complex/Cyclosome (APC/C). How the SAC proficiently inhibits the APC/C but still allows its rapid activation when the last kinetochore attaches to the spindle is important to understand how cells maintain genomic stability. We show that the APC/C subunit APC15 is required for the turnover of the APC/C co-activator Cdc20 and release of MCCs during SAC signalling but not for APC/C activity per se. In the absence of APC15, MCCs and ubiquitylated Cdc20 remain ‘locked’ onto the APC/C, which prevents the ubiquitylation and degradation of Cyclin B1 when the SAC is satisfied. We conclude that APC15 mediates the constant turnover of Cdc20 and MCCs on the APC/C to allow the SAC to respond to the attachment state of kinetochores.
doi:10.1038/ncb2347
PMCID: PMC3188299  PMID: 21926987
11.  Neurotransmitters Drive Combinatorial Multistate Postsynaptic Density Networks 
Science signaling  2009;2(68):ra19.
The mammalian postsynaptic density (PSD) comprises a complex collection of ~1100 proteins. Despite extensive knowledge of individual proteins, the overall organization of the PSD is poorly understood. Here, we define maps of molecular circuitry within the PSD based on phosphorylation of postsynaptic proteins. Activation of a single neurotransmitter receptor, the N-methyl-D-aspartate receptor (NMDAR), changed the phosphorylation status of 127 proteins. Stimulation of ionotropic and metabotropic glutamate receptors and dopamine receptors activated overlapping networks with distinct combinatorial phosphorylation signatures. Using peptide array technology, we identified specific phosphorylation motifs and switching mechanisms responsible for the integration of neurotransmitter receptor pathways and their coordination of multiple substrates in these networks. These combinatorial networks confer high information processing capacity and functional diversity on synapses and their elucidation may provide new insights into disease mechanisms and new opportunities for drug discovery.
doi:10.1126/scisignal.2000102
PMCID: PMC3280897  PMID: 19401593
12.  OpenKnowledge for peer-to-peer experimentation in protein identification by MS/MS 
Background
Traditional scientific workflow platforms usually run individual experiments with little evaluation and analysis of performance as required by automated experimentation in which scientists are being allowed to access numerous applicable workflows rather than being committed to a single one. Experimental protocols and data under a peer-to-peer environment could potentially be shared freely without any single point of authority to dictate how experiments should be run. In such environment it is necessary to have mechanisms by which each individual scientist (peer) can assess, locally, how he or she wants to be involved with others in experiments. This study aims to implement and demonstrate simple peer ranking under the OpenKnowledge peer-to-peer infrastructure by both simulated and real-world bioinformatics experiments involving multi-agent interactions.
Methods
A simulated experiment environment with a peer ranking capability was specified by the Lightweight Coordination Calculus (LCC) and automatically executed under the OpenKnowledge infrastructure. The peers such as MS/MS protein identification services (including web-enabled and independent programs) were made accessible as OpenKnowledge Components (OKCs) for automated execution as peers in the experiments. The performance of the peers in these automated experiments was monitored and evaluated by simple peer ranking algorithms.
Results
Peer ranking experiments with simulated peers exhibited characteristic behaviours, e.g., power law effect (a few dominant peers dominate), similar to that observed in the traditional Web. Real-world experiments were run using an interaction model in LCC involving two different types of MS/MS protein identification peers, viz., peptide fragment fingerprinting (PFF) and de novo sequencing with another peer ranking algorithm simply based on counting the successful and failed runs. This study demonstrated a novel integration and useful evaluation of specific proteomic peers and found MASCOT to be a dominant peer as judged by peer ranking.
Conclusion
The simulated and real-world experiments in the present study demonstrated that the OpenKnowledge infrastructure with peer ranking capability can serve as an evaluative environment for automated experimentation.
doi:10.1186/1759-4499-3-3
PMCID: PMC3377912  PMID: 22192521
13.  Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type β-Propeller Domains 
SUMMARY
Folding and trafficking of low density lipoprotein receptor (LDLR) family members, which play essential roles in development and homeostasis, is mediated by specific chaperones. The Boca/Mesd chaperone family specifically promotes folding and trafficking of the YWTD β-propeller-EGF domain pair found in the ectodomain of all LDLR members. Limited proteolysis, NMR spectroscopy, analytical ultracentrifugation and x-ray crystallography were used to define a conserved core comprised of a structured domain that is preceded by a disordered N-terminal region. High-resolution structures of the ordered domain were determined for homologous proteins from three metazoans. Seven independent protomers reveal a novel ferrodoxin-like superfamily fold with two distinct β-sheet topologies. A conserved hydrophobic surface forms a dimer interface in each crystal, but these differ substantially at the atomic level, indicative of non-specific hydrophobic interactions that may play a role in the chaperone activity of Boca/Mesd family.
doi:10.1016/j.str.2010.11.017
PMCID: PMC3099344  PMID: 21397184
boca; crystal structure; mesd; molecular chaperone; protein folding; YWTD propeller; LDLR; LRP
14.  Characterisation of the proteome, diseases and evolution of the human postsynaptic density 
Nature neuroscience  2010;14(1):19-21.
The postsynaptic density from human neocortex (hPSD) was isolated and 1461 proteins identified. hPSD mutations cause 133 neurological and psychiatric diseases and show enrichment in cognitive, affective and motor phenotypes underpinned by sets of genes. Strong protein sequence conservation within mammalian lineages, particularly in hub proteins, indicates conserved function and organisation in primate and rodent models. The hPSD is a key structure for nervous system disease and behaviour.
doi:10.1038/nn.2719
PMCID: PMC3040565  PMID: 21170055
17.  Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins 
The molecular complexity of mammalian proteomes demands new methods for mapping the organization of multiprotein complexes. Here, we combine mouse genetics and proteomics to characterize synapse protein complexes and interaction networks. New tandem affinity purification (TAP) tags were fused to the carboxyl terminus of PSD-95 using gene targeting in mice. Homozygous mice showed no detectable abnormalities in PSD-95 expression, subcellular localization or synaptic electrophysiological function. Analysis of multiprotein complexes purified under native conditions by mass spectrometry defined known and new interactors: 118 proteins comprising crucial functional components of synapses, including glutamate receptors, K+ channels, scaffolding and signaling proteins, were recovered. Network clustering of protein interactions generated five connected clusters, with two clusters containing all the major ionotropic glutamate receptors and one cluster with voltage-dependent K+ channels. Annotation of clusters with human disease associations revealed that multiple disorders map to the network, with a significant correlation of schizophrenia within the glutamate receptor clusters. This targeted TAP tagging strategy is generally applicable to mammalian proteomics and systems biology approaches to disease.
doi:10.1038/msb.2009.27
PMCID: PMC2694677  PMID: 19455133
gene targeting; postsynaptic complexes; postsynaptic density-95; schizophrenia; tandem affinity purification
19.  Mapping similarities in mTOR pathway perturbations in mouse lupus nephritis models and human lupus nephritis 
Arthritis Research & Therapy  2008;10(6):R127.
Introduction
Treatment with sirolimus, a mammalian target of rapamycin (mTOR) inhibitor, has been shown to be efficacious in the MRL/lpr and NZB × NZW F1 mouse models of lupus nephritis, indicating a critical role for the mTOR pathway in both models. This type of demonstration of efficacy in animal models is usually a pre-requisite for advancement into clinical development. However, efficacy in an animal model often has not translated to the desired activity in the clinic. Therefore, a more profound understanding of the mechanistic similarities and differences between various animal models and human diseases is highly desirable.
Methods
Transcriptional profiling was performed on kidneys from mice with lupus nephritis; from mice who had efficacious drug treatment; and from mice before they developed nephritis. Analysis of variance with false discovery rate adjusted to p < 0.05 and an average fold change of two or more was used to identify transcripts significantly associated with disease and response to therapy. Pathway analyses (using various bioinformatics tools) were carried out to understand the basis for drug efficacy in the mouse model. The relevance in human lupus of the pathways identified in the mouse model was explored using information from several databases derived from the published literature.
Results
We identified a set of nephritis-associated genes in mouse kidney. Expression of the majority of these returned to asymptomatic levels on sirolimus treatment, confirming the correlation between expression levels and symptoms of nephritis. Network analysis showed that many of these nephritis genes are known to interact with the mTOR pathway. This led us to ask what human diseases are linked to the mTOR pathway. We constructed the mTOR pathway interactome consisting of proteins that interact with members of the mTOR pathway and identified a strong association between mTOR pathway genes and genes reported in the literature as being involved in human lupus.
Conclusions
Our findings implicate the mTOR pathway as a critical contributor to human lupus. This broad pathway-based approach to understanding the similarities in, and differences between, animal models and human diseases may have broader utility.
doi:10.1186/ar2541
PMCID: PMC2656226  PMID: 18980674
21.  Generating ‘Omic Knowledge’: The Role of Informatics in High Content Screening 
High Content Screening (HCS) and High Content Analysis (HCA) have emerged over the past 10 years as a powerful technology for both drug discovery and systems biology. Founded on the automated, quantitative image analysis of fluorescently labeled cells or engineered cell lines, HCS provides unparalleled levels of multi-parameter data on cellular events and is being widely adopted, with great benefits, in many aspects of life science from gaining a better understanding of disease processes, through better models of toxicity, to generating systems views of cellular processes. This paper looks at the role of informatics and bioinformatics in both enabling and driving HCS to further our understanding of both the genome and the cellome and looks into the future to see where such deep knowledge could take us.
doi:10.2174/138620709789383259
PMCID: PMC2885606  PMID: 19531005
High content screening; HCS; high content analysis; HCA; genomics; informatics; bioinformatics; ontology; systems biology; drug discovery.

Results 1-21 (21)