Characterization of alternatively spliced products and tissue-specific isoforms of USP28 and USP25

Background: The ubiquitin-dependent protein degradation pathway is essential for the proteolysis of intracellular proteins and peptides. Deubiquitinating enzymes constitute a complex protein family involved in a multitude of cellular processes. The ubiquitin-specific proteases (UBP) are a group of enzymes whose predicted function is to reverse the ubiquitinating reaction by removing ubiquitin from a large variety of substrates. We have lately reported the characterization of human USP25, a specific-ubiquitin protease gene at 21q11.2, with a specific pattern of expression in murine fetal brains and adult testis. Results: Database homology searches at the DNA and protein levels and cDNA library screenings led to the identification of a new UBP member in the human genome, named USP28, at 11q23. This novel gene showed preferential expression in heart and muscle. Moreover, cDNA, expressed sequence tag and RT-PCR analyses provided evidence for alternatively spliced products and tissue-specific isoforms. Concerning function, USP25 overexpression in Down syndrome fetal brains was shown by real-time PCR. Conclusions: On the basis of the genomic and protein sequence as well as the functional data, USP28 and USP25 establish a new subfamily of deubiquitinating enzymes. Both genes have alternatively spliced exons that could generate protein isoforms with distinct tissue-specific activity. The overexpression of USP25 in Down syndrome fetal brains supports the gene-dosage effects suggested for other UBP members related to aneuploidy syndromes.

Comparative genomics of the odorant-binding and chemosensory protein gene families across the arthropoda: origin and evolutionary history of the chemosensory system

Chemoreception is a biological process essential for the survival of animals, as it allows the recognition of important volatile cues for the detection of food, egg-laying substrates, mates or predators, among other purposes. Furthermore, its role in pheromone detection may contribute to evolutionary processes such as reproductive isolation and speciation. This key role in several vital biological processes makes chemoreception a particularly interesting system for studying the role of natural selection in molecular adaptation. Two major gene families are involved in the perireceptor events of the chemosensory system: the odorant-binding protein (OBP) and chemosensory protein (CSP) families. Here, we have conducted an exhaustive comparative genomic analysis of these gene families in twenty Arthropoda species. We show that the evolution of the OBP and CSP gene families is highly dynamic, with a high number of gains and losses of genes, pseudogenes and independent origins of subfamilies. Taken together, our data clearly support the birth-and-death model for the evolution of these gene families with an overall high gene-turnover rate. Moreover, we show that the genome organization of the two families is significantly more clustered than expected by chance and, more important, that this pattern appears to be actively maintained across the Drosophila phylogeny. Finally, we suggest the homologous nature of the OBP and CSP gene families, dating back their MRCA (most recent common ancestor) to 380¿420 Mya, and we propose a scenario for the origin and diversification of these families.

In vivo assessment of use-dependent brain plasticity--beyond the "one trick pony" imaging strategy.

This article has been written as a comment to Dr Thomas and Dr Baker's article "Teaching an adult brain new tricks: A critical review of evidence for training-dependent structural plasticity in humans". We deliberately expand on the key question about the biological substrates underlying use-dependent brain plasticity rather than reiterating the authors' main points of criticism already addressed in more general way by previous publications in the field. The focus here is on the following main issues: i) controversial brain plasticity findings in voxel-based morphometry studies are partially due to the strong dependency of the widely used T1-weighted imaging protocol on varying magnetic resonance contrast contributions; ii) novel concepts in statistical analysis allow one to directly infer topological specificity of structural brain changes associated with plasticity. We conclude that iii) voxel-based quantification of relaxometry derived parameter maps could provide a new perspective on use-dependent plasticity by characterisation of brain tissue property changes beyond the estimation of volume and cortical thickness changes. In the relevant sections we respond to the concerns raised by Dr Thomas and Dr Baker from the perspective of the proposed data acquisition and analysis strategy.

Stable alpha-synuclein oligomers strongly inhibit chaperone activity of the Hsp70 system by weak interactions with J-domain co-chaperones.

α-Synuclein aggregation and accumulation in Lewy bodies are implicated in progressive loss of dopaminergic neurons in Parkinson disease and related disorders. In neurons, the Hsp70s and their Hsp40-like J-domain co-chaperones are the only known components of chaperone network that can use ATP to convert cytotoxic protein aggregates into harmless natively refolded polypeptides. Here we developed a protocol for preparing a homogeneous population of highly stable β-sheet enriched toroid-shaped α-Syn oligomers with a diameter typical of toxic pore-forming oligomers. These oligomers were partially resistant to in vitro unfolding by the bacterial Hsp70 chaperone system (DnaK, DnaJ, GrpE). Moreover, both bacterial and human Hsp70/Hsp40 unfolding/refolding activities of model chaperone substrates were strongly inhibited by the oligomers but, remarkably, not by unstructured α-Syn monomers even in large excess. The oligomers acted as a specific competitive inhibitor of the J-domain co-chaperones, indicating that J-domain co-chaperones may preferably bind to exposed bulky misfolded structures in misfolded proteins and, thus, complement Hsp70s that bind to extended segments. Together, our findings suggest that inhibition of the Hsp70/Hsp40 chaperone system by α-Syn oligomers may contribute to the disruption of protein homeostasis in dopaminergic neurons, leading to apoptosis and tissue loss in Parkinson disease and related neurodegenerative diseases.

Fatty acid amide hydrolase deficiency enhances intraplaque neutrophil recruitment in atherosclerotic mice.

OBJECTIVE: Endocannabinoid levels are elevated in human and mouse atherosclerosis, but their causal role is not well understood. Therefore, we studied the involvement of fatty acid amide hydrolase (FAAH) deficiency, the major enzyme responsible for endocannabinoid anandamide degradation, in atherosclerotic plaque vulnerability. METHODS AND RESULTS: We assessed atherosclerosis in apolipoprotein E-deficient (ApoE(-/-)) and ApoE(-/-)FAAH(-/-) mice. Before and after 5, 10, and 15 weeks on high-cholesterol diet, we analyzed weight, serum cholesterol, and endocannabinoid levels, and atherosclerotic lesions in thoracoabdominal aortas and aortic sinuses. Serum levels of FAAH substrates anandamide, palmitoylethanolamide (PEA), and oleoylethanolamide (OEA) were 1.4- to 2-fold higher in case of FAAH deficiency. ApoE(-/-)FAAH(-/-) mice had smaller plaques with significantly lower content of smooth muscle cells, increased matrix metalloproteinase-9 expression, and neutrophil content. Circulating and bone marrow neutrophil counts were comparable between both genotypes, whereas CXC ligand1 levels were locally elevated in aortas of FAAH-deficient mice. We observed enhanced recruitment of neutrophils, but not monocytes, to large arteries of ApoE(-/-) mice treated with FAAH inhibitor URB597. Spleens of ApoE(-/-)FAAH(-/-) mice had reduced CD4+FoxP3+regulatory T-cell content, and in vitro stimulation of splenocytes revealed significantly elevated interferon-γ and tumor necrosis factor-α production in case of FAAH deficiency. CONCLUSIONS: Increased anandamide and related FAAH substrate levels are associated with the development of smaller atherosclerotic plaques with high neutrophil content, accompanied by an increased proinflammatory immune response.

Comparative effects of oleoyl-estrone and a specific b3-adrenergic agonist (CL316, 243) on the expression of genes involved in energy metabolism of rat white adipose tissue

Background: The combination of oleoyl-estrone (OE) and a selective b3-adrenergic agonist (B3A; CL316,243) treatment in rats results in a profound and rapid wasting of body reserves (lipid). Methods: In the present study we investigated the effect of OE (oral gavage) and/or B3A (subcutaneous constant infusion) administration for 10 days to overweight male rats, compared with controls, on three distinct white adipose tissue (WAT) sites: subcutaneous inguinal, retroperitoneal and epididymal. Tissue weight, DNA (and, from these values cellularity), cAMP content and the expression of several key energy handling metabolism and control genes were analyzed and computed in relation to the whole site mass. Results: Both OE and B3A significantly decreased WAT mass, with no loss of DNA (cell numbers). OE decreased and B3A increased cAMP. Gene expression patterns were markedly different for OE and B3A. OE tended to decrease expression of most genes studied, with no changes (versus controls) of lipolytic but decrease of lipogenic enzyme genes. The effects of B3A were widely different, with a generalized increase in the expression of most genes, including the adrenergic receptors, and, especially the uncoupling protein UCP1. Discussion: OE and B3A, elicit widely different responses in WAT gene expression, end producing similar effects, such as shrinking of WAT, loss of fat, maintenance of cell numbers. OE acted essentially on the balance of lipolysislipogenesis and the blocking of the uptake of substrates; its decrease of synthesis favouring lipolysis. B3A induced a shotgun increase in the expression of most regulatory systems in the adipocyte, an effect that in the end favoured again the loss of lipid; this barely selective increase probably produces inefficiency, which coupled with the increase in UCP1 expression may help WAT to waste energy through thermogenesis. Conclusions: There were considerable differences in the responses of the three WAT sites. OE in general lowered gene expression and stealthily induced a substrate imbalance. B3A increasing the expression of most genes enhanced energy waste through inefficiency rather than through specific pathway activation. There was not a synergistic effect between OE and B3A in WAT, but their combined action increased WAT energy waste.

Utilization of dietary glucose in the metabolic syndrome

This review is focused on the fate of dietary glucose under conditions of chronically high energy (largely fat) intake, evolving into the metabolic syndrome. We are adapted to carbohydrate-rich diets similar to those of our ancestors. Glucose is the main energy staple, but fats are our main energy reserves. Starvation drastically reduces glucose availability, forcing the body to shift to fatty acids as main energy substrate, sparing glucose and amino acids. We are not prepared for excess dietary energy, our main defenses being decreased food intake and increased energy expenditure, largely enhanced metabolic activity and thermogenesis. High lipid availability is a powerful factor decreasing glucose and amino acid oxidation. Present-day diets are often hyperenergetic, high on lipids, with abundant protein and limited amounts of starchy carbohydrates. Dietary lipids favor their metabolic processing, saving glucose, which additionally spares amino acids. The glucose excess elicits hyperinsulinemia, which may derive, in the end, into insulin resistance. The available systems of energy disposal could not cope with the excess of substrates, since they are geared for saving not for spendthrift, which results in an unbearable overload of the storage mechanisms. Adipose tissue is the last energy sink, it has to store the energy that cannot be used otherwise. However, adipose tissue growth also has limits, and the excess of energy induces inflammation, helped by the ineffective intervention of the immune system. However, even under this acute situation, the excess of glucose remains, favoring its final conversion to fat. The sum of inflammatory signals and deranged substrate handling induce most of the metabolic syndrome traits: insulin resistance, obesity, diabetes, liver steatosis, hyperlipidemia and their compounded combined effects. Thus, a maintained excess of energy in the diet may result in difficulties in the disposal of glucose, eliciting inflammation and the development of the metabolic syndrome

Metabolic effects of a mixed and a high-carbohydrate low-fat diet in man, measured over 24 h in a respiration chamber.

1. The relation between dietary carbohydrate: lipid ratio and the fuel mixture oxidized during 24 h was investigated in eleven healthy volunteers (six females, and five males) in a respiration chamber. Values of the fuel mixture oxidized were estimated by continuous indirect calorimetry and urinary nitrogen measurements. 2. The subjects, were first given a mixed diet for 7 d and spent the last 24 h of the 7 d period in a respiration chamber for continuous gas-exchange measurement. The fuels oxidized during 2.5 h or moderate exercise were also measured in the respiration chamber. After an interval of 2 weeks from the end of the mixed-diet period, the same subjects were given an isoenergetic high-carbohydrate low-fat diet for 7 d, and the same experimental regimen was repeated. 3. Dietary composition markedly influenced the fuel mixture oxidized during 24 h and this effect was still present 12 h after the last meal in the postabsorptive state. However, the diets had no influence on the substrates oxidized above resting levels during exercise. With both diets, the 24 h energy balance was slightly negative and the energy deficit was covered by lipid oxidation. 4. With the high-carbohydrate low-fat diet, the energy expenditure during sleep was found to be higher than that with the mixed diet. 5. It is concluded that: (a) the composition of the diet did not influence the fuel mixture utilized for moderate exercise, (b) the energy deficit calculated for a 24 h period was compensated by lipid oxidation irrespective of the carbohydrate content of the diet, (c) energy expenditure during sleep was found to be higher with the high-carbohydrate low-fat diet than with the mixed diet.

Arenavirus envelope glycoproteins mimic autoprocessing sites of the cellular proprotein convertase subtilisin kexin isozyme-1/site-1 protease.

A crucial step in the arenavirus life cycle is the proteolytic processing of the viral envelope glycoprotein precursor (GPC) by the cellular proprotein convertase (PC) subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P). Here we conducted a systematic and quantitative analysis of SKI-1/S1P processing of peptides derived from the recognition sites of GPCs of different Old World and New World arenaviruses. We found that SKI-1/S1P showed a strong preference for arenaviral sequences resembling its autoprocessing sites, which are recurrent motifs in arenaviral GPCs. The African arenaviruses Lassa, Mobala, and Mopeia resemble the SKI-1/S1P autoprocessing C-site, whereas sequences derived from Clade B New World viruses Junin and Tacaribe have similarities to the autoprocessing B-site. In contrast, analogous peptides derived from cellular SKI-1/S1P substrates were remarkably poor substrates. The data suggest that arenavirus GPCs evolved to mimic SKI-1/S1P autoprocessing sites, likely ensuring efficient cleavage and perhaps avoiding competition with SKI-1/S1P's cellular substrates.

The half-size ABC transporters STR1 and STR2 are indispensable for mycorrhizal arbuscule formation in rice.

The central structure of the symbiotic association between plants and arbuscular mycorrhizal (AM) fungi is the fungal arbuscule that delivers minerals to the plant. Our earlier transcriptome analyses identified two half-size ABCG transporters that displayed enhanced mRNA levels in mycorrhizal roots. We now show specific transcript accumulation in arbusculated cells of both genes during symbiosis. Presently, arbuscule-relevant factors from monocotyledons have not been reported. Mutation of either of the Oryza sativa (rice) ABCG transporters blocked arbuscule growth of different AM fungi at a small and stunted stage, recapitulating the phenotype of Medicago truncatula stunted arbuscule 1 and 2 (str1 and str2) mutants that are deficient in homologous ABCG genes. This phenotypic resemblance and phylogenetic analysis suggest functional conservation of STR1 and STR2 across the angiosperms. Malnutrition of the fungus underlying limited arbuscular growth was excluded by the absence of complementation of the str1 phenotype by wild-type nurse plants. Furthermore, plant AM signaling was found to be intact, as arbuscule-induced marker transcript accumulation was not affected in str1 mutants. Strigolactones have previously been hypothesized to operate as intracellular hyphal branching signals and possible substrates of STR1 and STR2. However, full arbuscule development in the strigolactone biosynthesis mutants d10 and d17 suggested strigolactones to be unlikely substrates of STR1/STR2. Interestingly, rice STR1 is associated with a cis-natural antisense transcript (antiSTR1). Analogous to STR1 and STR2, at the root cortex level, the antiSTR1 transcript is specifically detected in arbusculated cells, suggesting unexpected modes of STR1 regulation in rice.

Analysis of the mechanisms controlling the activity of flp1, a chromosomal passenger protein in the fission Schizosaccharomyces pombe

ABSTRACT In S. cerevisiae, the protein phosphatase Cdc14pwt is essential far mitotic exit through its contribution to reducing mitotic CDK activity. But Cdc14pwt also acts as a mare general temporal coordinator of mid and late mitotic events by controlling the partitioning of DNA, microtubule stability and cytokinesis. Cdc14pwt orthologs are well conserved from yeasts to humans, and sequence comparison revealed the presence of three domains, A, B and C, of which A and B form the catalytic domain. Cdc14pwt orthologs are regulated (in part) through cell cycle dependent changes in their localization. Some of them are thought to be kept inactive by sequestration in the nucleolus during interphase. This is the case for flp1pwt, the single identified Cdc14pwt ortholog in the fission yeast S. pombe. In early mitosis, flp1pwt leaves the nucleolus and localizes to the kinetochores, the contractile ring and the mitotic spindle, suggesting that it has multiple substrates and regulates many mitotic processes. flp1D cells show a high chromosome loss rate and septation defects, suggesting a role for flp1wt in the fidelity of chromosome transmission and cytokinesis. The aim of this study is to characterize the mechanisms underlying flp1pwt functions and the control of its activity. A structure-function analysis has revealed that the presence of both A and B domains is required for biological function and for proper flp1pwt mitotic localization. In contrast, the C domain of flp1pwt is responsible for its proper nucleolar localization in G2/interphase. My data suggest that dephosphorylation of substrates by flp1pwt is not necessary for any changes in localization of flp1pwt except that at the medial ring. In that particular case, the catalytic activity of flp1pwt is required for efficient localization, therefore revealing an additional level of regulation. All the functions of flp1pwt assayed to date require its catalytic activity, emphasizing the importance of further identification of its substrates. As described for other orthologs, the capability of selfinteraction and phosphorylation status might help to control flp1pwt activity. My data suggest that flp1pwt forms oligomers in vivo and that phosphorylation is not essential far localization changes of the protein. In addition, the hypophosphorylated form of flp1pwt might be specifically involved in the promotion of cytokinesis. The results of this study suggest that multiple modes of regulation including localization, selfassociation and phosphorylation allow a fine-tuning regulation of flp1pwt phosphatase activity, and more generally that of Cdc14pwt family of phosphatases. RESUME Chez la levure S. cerevisiae, la protéine phosphatase Cdc14pwt est essentielle pour la sortie de mitose du fait de sa contribution dans la réduction d'activité des CDK mitotiques. Comme elle contrôle également le partage de l'ADN, la stabilité des microtubules et la cytokinèse, Cdc14pwt est en fait considérée comme un coordinateur temporel général des évènements de milieu et de fin de mitose. Les orthologues de Cdc14pwt sont bien conservés, des levures jusqu'à l'espèce humaine. Des comparaisons de séquence ont révélé la présence de trois domaines A, B et C, les deux premiers constituant le domaine catalytique. Ils sont régulés (en partie) via des changements dans leur localisation, eux-mêmes dépendants du cycle cellulaire. Plusieurs de ces orthologues sont supposés inactivés par séquestration dans le nucléole en interphase, ce qui est le cas de flp1pwt le seul orthologue de Cdc14pwt identifié chez la levure fissipare S, pombe. En début de mitose, flp1pwt quitte le nucléole et localise au niveau des kinetochores, de l'anneau contractile d'actine et du fuseau mitotique, ce qui laisse supposer de multiples substrats et fonctions. Comme les cellules délétées pour le gène flp1wt présentent un taux élevé de perte de chromosome et des défauts de septation, flp1pwt semble jouer un rôle dans la fidélité de la transmission du matériel génétique et la cytokinèse. Le but de cette étude est de caractériser les mécanismes impliqués dans les fonctions assurées par flp1pwt d'une part, et dans le contrôle de son activité d'autre part. Une analyse structure-fonction a révélé que la présence simultanée des deux domaines A et B est requise pour la fonction biologique de flp1pwt et sa localisation correcte pendant la mitose. Par contre, le domaine C de flp1pwt confère une localisation nucléolaire adéquate en G2/interphase. Mes données suggèrent que la déphosphorylation de substrats par flp1pwt est dispensable pour sa localisation correcte excepté celle à l'anneau médian, qui requiert dans ce cas, l'activité catalytique de flp1pwt, révélant ainsi un niveau de régulation supplémentaire. Toutes les fonctions de flp1 pwt testées jusqu'à présent nécessitent également son activité catalytique, ce qui accentue l'importance de l'identification future de ses substrats. Comme cela a déjà été décrit pour d'autres orthologues, la capacité d'auto-intéraction et le niveau de phosphorylation pourraient contrôler l'activité de flp1pwt. En effet, mes données suggèrent que flp1pwt forme des oligomères in vivo et que la phosphorylation n'est pas essentielle pour les changements de localisation observés pour la protéine. De plus, la forme hypophosphorylée de flp1pwt pourrait être spécifiquement impliquée dans la promotion de la cytokinèse. De multiples modes de régulation incluant la localisation, l'auto-association et la phosphorylation semblent permettre un contrôle fin et subtil de l'activité de la phosphatase flp1pwt, et plus généralement celle des protéines de la famille de Cdc14pwt.

Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling.

Hsp70s are highly conserved ATPase molecular chaperones mediating the correct folding of de novo synthesized proteins, the translocation of proteins across membranes, the disassembly of some native protein oligomers, and the active unfolding and disassembly of stress-induced protein aggregates. Here, we bring thermodynamic arguments and biochemical evidences for a unifying mechanism named entropic pulling, based on entropy loss due to excluded-volume effects, by which Hsp70 molecules can convert the energy of ATP hydrolysis into a force capable of accelerating the local unfolding of various protein substrates and, thus, perform disparate cellular functions. By means of entropic pulling, individual Hsp70 molecules can accelerate unfolding and pulling of translocating polypeptides into mitochondria in the absence of a molecular fulcrum, thus settling former contradictions between the power-stroke and the Brownian ratchet models for Hsp70-mediated protein translocation across membranes. Moreover, in a very different context devoid of membrane and components of the import pore, the same physical principles apply to the forceful unfolding, solubilization, and assisted native refolding of stable protein aggregates by individual Hsp70 molecules, thus providing a mechanism for Hsp70-mediated protein disaggregation.

Leishmania metacaspase: an arginine-specific peptidase.

The purpose of this chapter is to give insights into metacaspase of Leishmania protozoan parasites as arginine-specific cysteine peptidase. The physiological role of metacaspase in Leishmania is still a matter of debate, whereas its peptidase enzymatic activity has been well characterized. Among the different possible expression systems, metacaspase-deficient yeast cells (Δyca1) have been instrumental in studying the activity of Leishmania major metacaspase (LmjMCA). Here, we describe techniques for purification of LmjMCA and its activity measurement, providing a platform for further identification of LmjMCA substrates.

Identification of GPx8 as a novel cellular substrate of the hepatitis C virus NS3-4A protease

Background: The hepatitis C virus (HCV) NS3-4A protease is not only an essential component of the viral replication complex and a prime target for a ntiviral intervention but also a key player i n the persistence and pathogenesis of HCV. It cleaves and thereby inactivates two crucial adaptor proteins in viral RNA sensing and innate immunity (MAVS and TRIF) as well as a phosphatase involved in growth factor signaling (TCPTP). T he aim of this study was to identify novel cellular substrates o f the N S3-4A protease and to investigate their role in the replication and pathogenesis of HCV. Methods: Cell lines inducibly expressing t he NS3-4A protease were analyzed in basal as well as interferon-α-stimulated states by stable isotopic l abeling using amino acids in cell culture (SILAC) coupled with protein separation and mass spectrometry. Candidates fulfilling stringent criteria for potential substrates or products of the NS3-4A protease were further i nvestigated in different experimental systems as well a s in liver biopsies from patients with chronic hepatitis C. Results: SILAC coupled with protein separation and mass spectrometry yielded > 5000 proteins of which 18 candidates were selected for further analyses. These allowed us to identify GPx8, a membrane-associated peroxidase involved in disulfide bond formation in the endoplasmic reticulum, as a n ovel cellular substrate of the H CV NS3-4A protease. Cleavage occurs at cysteine in position 11, removing the cytosolic tip of GPx8, and was observed in different experimental systems as well as in liver biopsies from patients with chronic hepatitis C. Further functional studies, involving overexpression and RNA silencing, revealed that GPx8 is a p roviral factor involved in viral particle production but not in HCV entry or HCV RNA replication. Conclusions: GPx8 is a proviral host factor cleaved by the HCV NS3-4A protease. Studies investigating the consequences of GPx8 cleavage for protein function are underway. The identification of novel cellular substrates o f the HCV N S3-4A protease should yield new insights i nto the HCV life cycle and the pathogenesis of hepatitis C and may reveal novel targets for antiviral intervention.

Comparison of the proliferative activity of neuroblasts from chick embryo cerebral hemispheres of different ages in culture.

Dissociated cerebral hemisphere cells from 4- to 7-day-old chick embryos were cultured either on a collagen or a polylysine substrate in a serum-containing medium. Neurons were characterized by the demonstration of acetylcholinesterase, the presence of D2/N-CAM glycoprotein and neurofilament proteins. The proliferation of neuronal precursor cells was shown by morphological observations, autoradiographic analysis and measurements of [3H]-thymidine incorporation. Neuronal precursors derived from the 6-day-old embryos showed the highest proliferative activity. Neuroblast proliferation was found to be dependent on the culture substrates (i.e. polylysine or collagen), which yielded either isolated cells or cell aggregates, and the latter favored the mitogenic effect.