The SUMO1-E67 interacting loop peptide is an allosteric inhibitor of the dipeptidyl peptidases 8 and 9

The intracellular peptidases dipeptidyl peptidase (DPP) 8 and DPP9 are involved in multiple cellular pathways including antigen maturation, cellular homeostasis, energy metabolism, and cell viability. Previously we showed that the small ubiquitin-like protein modifier SUMO1 interacts with an armlike structure in DPP9, leading to allosteric activation of the peptidase. Here we demonstrate that the E67-interacting loop (EIL) peptide, which corresponds to the interaction surface of SUMO1 with DPP9, acts as a noncompetitive inhibitor of DPP9. Moreover, by analyzing the sensitivity of DPP9 arm mutants to the EIL peptide, we mapped specific residues in the arm that are important for inhibition by the EIL, suggesting that the peptide acts as an allosteric inhibitor of DPP9. By modifying the EIL peptide, we constructed peptide variants with more than a 1,000-fold selectivity toward DPP8 (147 nM) and DPP9 (170 nM) over DPPIV (200 μM). Furthermore, application of these peptides to cells leads to a clear inhibition of cellular prolyl peptidase activity. Importantly, in line with previous publications, inhibition of DPP9 with these novel allosteric peptide inhibitors leads to an increase in EGF-mediated phosphorylation of Akt. This work highlights the potential use of peptides that mimic interaction surfaces for modulating enzyme activity.

Insular volume abnormalities associated with different transition probabilities to psychosis

BACKGROUND

Although individuals vulnerable to psychosis show brain volumetric abnormalities, structural alterations underlying different probabilities for later transition are unknown. The present study addresses this issue by means of voxel-based morphometry (VBM).

METHOD

We investigated grey matter volume (GMV) abnormalities by comparing four neuroleptic-free groups: individuals with first episode of psychosis (FEP) and with at-risk mental state (ARMS), with either long-term (ARMS-LT) or short-term ARMS (ARMS-ST), compared to the healthy control (HC) group. Using three-dimensional (3D) magnetic resonance imaging (MRI), we examined 16 FEP, 31 ARMS, clinically followed up for on average 3 months (ARMS-ST, n=18) and 4.5 years (ARMS-LT, n=13), and 19 HC.

RESULTS

The ARMS-ST group showed less GMV in the right and left insula compared to the ARMS-LT (Cohen's d 1.67) and FEP groups (Cohen's d 1.81) respectively. These GMV differences were correlated positively with global functioning in the whole ARMS group. Insular alterations were associated with negative symptomatology in the whole ARMS group, and also with hallucinations in the ARMS-ST and ARMS-LT subgroups. We found a significant effect of previous antipsychotic medication use on GMV abnormalities in the FEP group.

CONCLUSIONS

GMV abnormalities in subjects at high clinical risk for psychosis are associated with negative and positive psychotic symptoms, and global functioning. Alterations in the right insula are associated with a higher risk for transition to psychosis, and thus may be related to different transition probabilities.

SS18-SSX2 and the mitochondrial apoptosis pathway in mouse and human synovial sarcomas

Synovial sarcoma is a deadly malignancy with limited sensitivity to traditional cytotoxic chemotherapy. SS18-SSX fusion oncogene expression characterizes human synovial sarcomas and drives oncogenesis in a mouse model. Elevated expression of BCL2 is considered a consistent feature of the synovial sarcoma expression profile. Our objective was to evaluate the expression of apoptotic pathway members in synovial sarcomas and interrogate the impact of modulating SS18-SSX expression on this pathway. We show in human and murine synovial sarcoma cells that SS18-SSX increases BCL2 expression, but represses other anti-apoptotic genes, including MCL1 and BCL2A1. This repression is achieved by directly suppressing expression via binding through activating transcription factor 2 (ATF2) to the cyclic adenosine monophosphate (AMP) response element (CRE) in the promoters of these genes and recruiting TLE1/Groucho. The suppression of these two anti-apoptotic pathways silences the typical routes by which other tumors evade BH3-domain peptidomimetic pharmacotherapy. We show that mouse and human synovial sarcoma cells are sensitive in vitro to ABT-263, a BH3-peptidomimetic, much more than the other tested cancer cell lines. ABT-263 also enhances the sensitivity of these cells to doxorubicin, a traditional cytotoxic chemotherapy used for synovial sarcoma. We also demonstrate the capacity of ABT-263 to stunt synovial sarcomagenesis in vivo in a genetic mouse model. These data recommend pursuit of BH3-peptidomimetic pharmacotherapy in human synovial sarcomas.

Feasibility of in vivo myelin water imaging using 3D multigradient-echo pulse sequences

Quantitative myelin water imaging is able to show demyelinating processes and, therefore, provides insight into the pathology of white matter diseases such as multiple sclerosis. So far, mapping of the myelin water fraction most often was performed using single-slice multiecho spin-echo sequences. Recently, a different approach using two-dimensional multigradient-echo pulse sequences was suggested. In this work, a solution to three-dimensional in vivo myelin water fraction imaging is presented that applies multigradient-echo pulse sequences and uses non-negative least squares algorithms to analyze the multicomponent T*(2) decay. The suggested method offers not only whole brain coverage but also clinically practicable acquisition times. The obtained myelin water fraction values are low (6.9% for white matter) but are able to detect demyelination in multiple sclerosis lesions. However, the clinical application of the proposed method remains questionable, because further measurements that clarify the possibility of detecting ongoing processes in lesions are needed.

Combined proteomic and transcriptomic analysis identifies differentially expressed pathways associated to Pinus radiata needle maturation

Needle differentiation is a very complex process that leads to the formation of a mature photosynthetic organ from pluripotent needle primordia. The proteome and transcriptome of immature and fully developed needles of Pinus radiata D. Don were compared to described changes in mRNA and protein species that characterize the needle maturation developmental process. A total of 856 protein spots were analyzed, defining a total of 280 spots as differential between developmental stages, from which 127 were confidently identified. A suppressive subtractive library (2048 clones, 274 non redundant contigs) was built, and 176 genes showed to be differentially expressed. The Joint data analysis of proteomic and transcriptomic results provided a broad overview of differentially expressed pathways associated with needle maturation and stress-related pathways. Proteins and genes related to energy metabolism pathways, photosynthesis, and oxidative phosphorylation were overexpressed in mature needles. Amino acid metabolism, transcription, and translation pathways were overexpressed in immature needles. Interestingly, stress related proteins were characteristic of immature tissues, a fact that may be linked to defense mechanisms and the higher growth rate and morphogenetic competence exhibited by these needles. Thus, this work provides an overview of the molecular changes affecting proteomes and transcriptomes during P. radiata needle maturation, having an integrative vision of the functioning and physiology of this process.

Separating two components of body image in anorexia nervosa using fMRI

BACKGROUND

Body image distortion is a key symptom of anorexia nervosa. In behavioral research two components of body image have been defined: attitudes towards the body and body size experience. Neuroimaging studies concerning own body image distortions in anorexia nervosa have revealed an inconsistent pattern of results and are constrained by the fact that no direct distinction between the different parts of body image has been made.

METHOD

The present study therefore set out to investigate the neural correlates of two parts of the own body image using functional magnetic resonance imaging (fMRI): satisfaction rating and size estimation for distorted own body photographs in patients with anorexia nervosa and controls.

RESULTS

Anorectic patients were less satisfied with their current body shape than controls. Patients further demonstrated stronger activation of the insula and lateral prefrontal cortex during the satisfaction rating of thin self-images. This indicates a stronger emotional involvement when patients are presented with distorted images close to their own ideal body size. Patients also overestimated their own body size. We were able to show complex differential modulations in activation of the precuneus during body size estimation in control and anorectic subjects. It could be speculated that a deficit in the retrieval of a multimodal coded body schema in precuneus/posterior parietal cortex is related to body size overestimation.

CONCLUSIONS

We were able to find specific behavioral responses and neural activation patterns for two parts of body image in anorexia nervosa and healthy controls. Thus, the present results underline the importance of developing research and therapeutic strategies that target the two different aspects of body image separately.

Determination of protein stoichiometry within protein complexes using absolute quantification and multiple reaction monitoring

Many cellular processes are driven by protein complexes. Although the identification of protein components in such complexes has become almost a routine matter, accurate determination of their stoichiometry within a protein complex is still a challenge. We have established a method to determine the stoichiometries of protein complexes using absolute quantification (AQUA) with the help of synthetic standard peptides in combination with multiple reaction monitoring (MRM). Our approach is exemplified by the analysis of the human spliceosomal hPrp19/CDC5L complex, which consists of seven individual proteins and plays a crucial role in the assembly of the fully catalytically active spliceosome during pre-mRNA splicing. We evaluated several conditions for complete hydrolysis of the protein complex and found that the denaturing conditions under which hydrolysis is performed are absolutely crucial for accurately determining protein stoichiometries within this complex. In addition, we tested the suitability of different AQUA peptides and further compared different MS techniques to read out the relative signal intensities that were then used in absolute quantification. Our analyses revealed that dependent on the denaturing conditions different stoichiometries within the complex were obtained. The most consistent results were obtained by enzymatic hydrolysis in the presence of acetonitrile in combination with MRM.

Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry

Mass spectrometry allows the elucidation of molecular details of the interaction domains of the individual components in macromolecular complexes subsequent to cross-linking of the individual components. Here, we applied chemical and UV cross-linking combined with tandem mass-spectrometric analysis to identify contact sites of the nuclear import adaptor snurportin 1 to the small ribonucleoprotein particle U1 snRNP in addition to the known interaction of m₃G cap and snurportin 1. We were able to define previously unknown sites of protein–protein and protein–RNA interactions on the molecular level within U1 snRNP. We show that snurportin 1 interacts with its central m₃G-cap-binding domain with Sm proteins and with its extreme C-terminus with stem-loop III of U1 snRNA. The crosslinking data support the idea of a larger interaction area between snurportin 1 and U snRNPs and the contact sites identified prove useful for modeling the spatial arrangement of snurportin 1 domains when bound to U1 snRNP. Moreover, this suggests a functional nuclear import complex that assembles around the m₃G cap and the Sm proteins only when the Sm proteins are bound and arranged in the proper orientation to the cognate Sm site in U snRNA.

Supramolecular structure of the OXPHOS system in highly thermogenic tissue of Arum maculatum

The protein complexes of the mitochondrial respiratory chain associate in defined ways forming supramolecular structures called respiratory supercomplexes or respirasomes. In plants, additional oxidoreductases participate in respiratory electron transport, e.g. the so-called "alternative NAD(P)H dehydrogenases" or an extra terminal oxidase called "alternative oxidase" (AOX). These additional enzymes were previously reported not to form part of respiratory supercomplexes. However, formation of respiratory supercomplexes might indirectly affect "alternative respiration" because electrons can be channeled within the supercomplexes which reduces access of the alternative enzymes towards their electron donating substrates. Here we report an investigation on the supramolecular organization of the respiratory chain in thermogenic Arum maculatum appendix mitochondria, which are known to have a highly active AOX for heat production. Investigations based on mild membrane solubilization by digitonin and protein separation by blue native PAGE revealed a very special organization of the respiratory chain in A. maculatum, which strikingly differs to the one described for the model plant Arabidopsis thaliana: (i) complex I is not present in monomeric form but exclusively forms part of a I + III(2) supercomplex, (ii) the III(2) + IV and I + III(2) + IV supercomplexes are detectable but of low abundance, (iii) complex II has fewer subunits than in A. thaliana, and (iv) complex IV is mainly present as a monomer in a larger form termed "complex IVa". Since thermogenic tissue of A. maculatum at the same time has high AOX and I + III(2) supercomplex abundance and activity, negative regulation of the alternative oxidase by supercomplex formation seems not to occur. Functional implications are discussed.

RNAi and iTRAQ reagents united: targeted quantitation of siRNA-mediated protein silencing in human cells

Bridging the gap between functional genomics and traditional molecular cell biology is a challenge of the next decade. Here, we are aiming to find routines for targeted quantitation of protein silencing in response to RNAi based on complex cellular lysates. A workflow was established adapting siRNA treatment, processing the sample, generating isobaric iTRAQ-reagent-labeled peptides, and analyzing the sample applying MRM-based peptide quantitation to verify protein silencing on a 4000 QTRAP LC/MS/MS mass spectrometer. Subsequently, eight targets were analyzed, mostly with two siRNA designs. Although transcript and protein silencing correlated, the downregulation on the protein level was less pronounced. A time-course analysis of the chaperon HSPA9/mortalin indicated a delayed kinetic of protein versus transcript silencing. Further, the analysis of the functional response on the example of HSD17B4, a multifunctional enzyme essential to generate precursors for cholesterol biosynthesis, confirmed that strong silencing on the transcript level accompanied by moderate reduction of protein is sufficient to generate a physiological significant response. Fifty percent protein silencing resulted in a 3.5-fold induction of low-density lipoprotein and therefore cholesterol uptake in human liver cells. The established routines pave the way for the development of targeted protein quantitation assays suitable for target and biomarker validation.

Changes in the protein profile of Quercus ilex leaves in response to drought stress and recovery

To characterize the molecular response of holm oak to drought stress and its capacity to recover 9-month-old Quercus ilex seedlings were subjected to three treatments for a 14-d period: (i) continuous watering to field capacity (control plants, W), (ii) no irrigation (drought treatment, D), and (iii) no irrigation for 7d followed by a watering period of 7d (recovery treatment, R). In drought plants, leaf water potential decreased from -0.72 (day 0) to -0.99MPa (day 7), and -1.50MPa (day 14). Shoot relative water content decreased from 49.3% (day 0) to 47.7% (day 7) and 40.8% (day 14). Photosystem II quantum yield decreased from 0.80 (day 0) to 0.72 (day 7) and 0.73 (day 14). Plants subjected to water withholding for 7d reached, after a 7-d rewatering period, values similar to those of continuously irrigated control plants. Changes in the leaf protein pattern in response to drought and recovery treatments were analyzed by using a proteomic approach. Twenty-three different spots were observed when comparing the two-dimensional electrophoresis profile of control to both drought and recovered plants. From these, 14 proteins were identified from tryptic peptides tandem mass spectra by using the new Paragon algorithm present in the ProteinPilot software. The proteins identified belong to the photosynthesis, carbohydrate and nitrogen metabolism, and stress-related protein functional categories.

Variation in the holm oak leaf proteome at different plant developmental stages, between provenances and in response to drought stress

Major proteins of the holm oak leaf proteome have been previously identified using a combination of 2-DE, MS analysis and BLAST similarity search (Jorge et al., Proteomics 2005, 5, 222-234). That study, conducted with field samples from mature trees, revealed the existence of a great variability in the 2-DE protein map, with qualitative as well as quantitative changes, both analytical and biological. A similar study has been carried out with 2-year-old seedlings to analyze and study: (i) changes in the 2-DE protein profile at different tree developmental stages; (ii) the 2-DE protein map variability between three different Spanish provenances; and (iii) variations in the 2-DE protein profile in response to drought stress. Although the protein profile of leaves from seedlings and mature trees was fairly similar, the biological variance found was lower in the former. In the present study, new proteins have been identified. At least four different protein spots differentiated Spanish provenances, two of them identified as an ATP synthase alpha chain, and a 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. Fourteen different protein spots were qualitatively variable between well-watered and drought-stressed seedlings, with some of them corresponding to enzymes of carbohydrate and protein metabolism. Data presented indicated the mobilization of storage proteins and carbohydrates, as well as photosynthesis inhibition under drought conditions.

Identification of protein phosphorylation sites by advanced LC-ESI-MS/MS methods

Phosphorylation, the process by which a phosphate group is attached to a pre-existing protein, is an evolutionarily and metabolically cheap way to change the protein's surface and properties. It is presumably for that reason that it is the most wide-spread protein modification: an estimated 10-30% of all proteins are subject to phosphorylation.MS-based methods are the methods of choice for the identification of phosphorylation sites, however biochemical prefractionation and enrichment protocols will be needed to produce suitable samples in the case of low-stoichiometry phosphorylation. Using emerging MS-based technology, the elucidation of the "phosphoproteome," a comprehensive inventory of phosphorylation sites, will become a realistic goal. However, validating these findings in a cellular context and defining their biological meaning remains a daunting task, which will inevitably require extensive and time-consuming additional biological research.

Blood viscosity modulates tissue perfusion: sometimes and somewhere

Each organ possesses specific properties for controlling microvascular perfusion. Such specificity provides an opportunity to design transfusion fluids that target thrombo-embolic or vasospasm-induced ischemia in a particular organ or that optimize overall perfusion from systemic shock. The role of viscosity in the design of these fluids might be underestimated, because viscosity is rarely monitored or considered in critical care decisions. Studies linking viscosity-dependent changes of microvascular perfusion to outcome-relevant data suggest that whole blood viscosity is negligible as a determinant of microvascular perfusion under physiological conditions when autoregulation is effective. Because autoregulation is driven to maintain oxygen supply constant, the organism will compensate for changes in blood viscosity to sustain oxygen delivery. In contrast, under pathological conditions in the brain and elsewhere, increases of overall viscosity should be avoided - including all the situations where vascular autoregulatory mechanisms are inoperative due to ischemia, structural damage or physiologic dysfunction. As latter conditions are not to identify with high certainty, the risks that accompany therapeutic correction of blood viscosity are outweighing the benefits. The ability to bedside monitor blood viscosity and to link changes in viscosity to outcome parameters in various clinical conditions would provide more solid foundation for evidence-based clinical management.