Tumor Suppressor Density-enhanced Phosphatase-1 (DEP-1) Inhibits the RAS Pathway by Direct Dephosphorylation of ERK1/2 Kinases

Density-enhanced phosphatase-1 (DEP-1) is a trans-membrane receptor protein-tyrosine phosphatase that plays a recognized prominent role as a tumor suppressor. However, the mechanistic details underlying its function are poorly understood because its primary physiological substrate(s) have not been firmly established. To shed light on the mechanisms underlying the anti-proliferative role of this phosphatase, we set out to identify new DEP-1 substrates by a novel approach based on screening of high density peptide arrays. The results of the array experiment were combined with a bioinformatics filter to identify eight potential DEP-1 targets among the proteins annotated in the MAPK pathway. In this study we show that one of these potential targets, the ERK1/2, is indeed a direct DEP-1 substrate in vivo. Pulldown and in vitro dephosphorylation assays confirmed our prediction and demonstrated an overall specificity of DEP-1 in targeting the phosphorylated tyrosine 204 of ERK1/2. After epidermal growth factor stimulation, the phosphorylation of the activation loop of ERK1/2 can be modulated by changing the concentration of DEP-1, without affecting the activity of the upstream kinase MEK. In addition, we show that DEP-1 contains a KIM-like motif to recruit ERK1/2 proteins by a docking mechanism mediated by the common docking domain in ERK1/2. ERK proteins that are mutated in the conserved docking domain become insensitive to DEP-1 de-phosphorylation. Overall this study provides novel insights into the anti-proliferative role of this phosphatase and proposes a new mechanism that may also be relevant for the regulation of density-dependent growth inhibition.DEP-1⁴ (also known as CD148, HPTPη, and PTPRJ) is a class III receptor protein-tyrosine phosphatase, characterized by eight fibronectin type III repeats within the extracellular domain, a trans-membrane region, and a single cytosolic catalytic domain (1, 2). DEP-1 is expressed in all human hematopoietic cell lineages and was shown to negatively regulate T cell activation. In addition, several epithelial cell types display DEP-1 on their cell membranes (3). Homozygous DEP-1 mutant mice die before embryonic day 11.5, displaying severe defects in vascular organization (4). Interestingly, DEP-1 expression levels were found to augment with increased cell density (2), suggesting a role for this tyrosine phosphatase in sensing cell-cell contacts and in density-dependent growth inhibition (5). Moreover, accumulating evidence supports a prominent role for DEP-1 as a tumor suppressor as it negatively regulates cell proliferation and is poorly expressed in many cancer cell lines (6–10). The observed anti-proliferative effect may be accounted for by the ability of DEP-1 to down-regulate growth factor signaling through the dephosphorylation of various receptor tyrosine kinases, such as PDGFR, VEGFR2, and MET (11–13), resulting in quenching of the downstream RAS-MAPK pathway. However, given the complex pleiotropic functions of DEP-1, it is also possible that additional regulatory circuits mediated by yet unknown DEP-1 substrates may play a functional role in contact inhibition and control of cell proliferation.A variety of in vivo and in vitro approaches has led us to propose a number of DEP-1 substrates as mediators of its function. These include PDGFR, p120 catenin (CTND1), hepatocyte growth factor receptor, SRC kinase, VEGFR2, phosphatidylinositol 3-kinase regulatory subunit α (P85A), and RET receptor kinase (5, 11–16).Here we report a novel, unbiased strategy based on the screening of high density phosphopeptide arrays for their ability to bind phosphatase trapping mutants. A large portion of the phosphoproteome could be explored by this approach, thus unveiling a long list of potential substrates. A selected list of potentially relevant substrates has been obtained by applying a bioinformatics context filter. In this study we report the detailed characterization of one of these substrates, and we propose that DEP-1 modulates the RAS pathway by directly dephosphorylating Tyr-204 of ERK1/2. In addition, we show that the efficient removal of the phosphate group from Tyr-204 requires the integrity of a docking site on the ERK1/2 proteins.     

Performance of olive mill solid waste as a constituent of the substrate in commercial cultivation of Agaricus bisporus

The feasibility of using olive mill waste (OMW) as an ingredient in the substrate used for cultivation of Agaricus bisporus (Lange) Sing. was studied in a large-scale cultivation trial, concerning 2500 m² of mushroom growing area, at a specialized mushroom farm. Standard commercial cultivation technique involving compost preparation, spawning, casing and harvesting was used. The performance indicators such as mushroom yield, biological efficiency, market quality as well as horticultural value of the spent compost showed that the compost prepared with OMW was superior to the control compost in all the categories. The OMW-amended substrate supported higher populations of beneficial microorganisms especially, actinomycetes which enabled the breakdown of the compost ingredients. It is suggested that OMW is a suitable ingredient for the preparation of mushroom substrate. We have demonstrated that conversion of OMW (a liability) into value-added mushroom substrate (an asset) is an effective waste management tool in oleaculture.     

Novel potent and highly selective human A(3) adenosine receptor antagonists belonging to the 4-amido-2-arylpyrazolo[3,4-c]quinoline series: molecular docking analysis and pharmacological studies

The study of novel 2-arylpyrazolo[3,4-c]quinolin-4-(hetero)arylamides, designed as human (h) A(3) adenosine receptor antagonists, is reported. The new derivatives are endowed with nanomolar hA(3) receptor affinity and high selectivity versus hA(1), hA(2A) and hA(2B) receptors. Among the (hetero)aroyl residues introduced on the 4-amino group, the 2-furyl and 4-pyridyl rings turned out to be the most beneficial for hA(3) affinity (K(i)=3.4 and 5.0nM, respectively). An intensive molecular docking study to a rhodopsin-based homology model of the hA(3) receptor was carried out to obtain a 'structure-based pharmacophore model' that proved to be helpful for the interpretation of the observed affinities of the new hA(3) pyrazoloquinoline antagonists.     

CytokineDB: a database collecting biological information

Cytokines are subdivided in 12 sub-families and are described as multi-functional molecules that play an important biological activity in host defense system against pathogens, in homeostasis, tissue repair, cell growth and development. CytokineDB is an annotated database that collects biological information regarding the cytokines family in human and will be periodically updated by including new biological information. This database is freely available online and can be accessed at the URL: http://www.cro-m.eu/CytokineDB/     

Identification and characterization of protease inhibitors in Diplotaxis species

PCR analysis of the genomes of two wild Brassicaceae plants, Diplotaxis muralis and Diplotaxis tenuifolia, demonstrated the presence of several genes coding for potential protease inhibitors, classifiable within the mustard inhibitor family (MSI). This is a small family of plant protease inhibitors named after the mustard trypsin inhibitor MTI-2, the first protease inhibitor characterized in Brassicaceae. From identified sequences two recombinant inhibitors were expressed in Pichia pastoris. In comparison with MTI-2, they show a reduced activity against bovine trypsin. However, when tested against trypsin-like proteases present in the guts of Helicoverpa zea larvae, the Diplotaxis inhibitors and MTI-2 show similar activities, indicating that the usually adopted procedure of reporting activity of plant protease inhibitors against bovine trypsin may lead to wrong estimation of their effect on insect proteases. This issue is of particular relevance when planning the use of PI genes for developing insect resistant plants.     

African Dacus (Diptera: Tephritidae: Molecular data and host plant associations do not corroborate morphology based classifications

The genus Dacus Fabricius includes economically important pest fruit flies distributed in the Afrotropical and Indo-Australian regions. Two recent revisions based on morphological characters proposed new and partially discordant classifications synonymizing/revalidating several subgeneric names and forming species groups. Regardless these efforts, the phylogenetic relationships among Dacus species remained largely unresolved mainly because of the difficulties in assigning homologous character states. Therefore we investigated the phylogeny of African Dacus by sequencing 71 representatives of 32 species at two mitochondrial (COI, 16S) and one nuclear (period) gene fragments. Phylogenetic relationships were inferred through Bayesian and Maximum Parsimony methods and hypotheses about the monophyly of Dacus subgenera were tested by Shimodaira–Hasegawa tests. The congruence tests and the analyses of the single gene fragments revealed that the nuclear gene supports similar conclusions as the two mitochondrial genes. Levels of intra- and inter-specific differentiation of Dacus species were highly variable and, in some cases, largely overlapping. The analyses of the concatenated dataset resolved two major bootstrap-supported groups as well as a number of well-supported clades and subclades that often comprised representatives of different subgenera. Additionally, specimens of Dacus humeralis from Eastern and Western African localities formed separate clades, suggesting cryptic differentiation within this taxon. The comparisons between the molecular phylogeny and the morphological classification revealed a number of discrepancies and, in the vast majority of cases, the molecular data were not compatible with the monophyly of the currently recognised subgenera. Conversely, the molecular data showed that Apocynaceae feeders are a monophyletic sister group of species feeding on both Cucurbitaceae and Passifloraceae (these latter being also monophyletic). These results show a clear association between the molecular phylogeny of African Dacus and the evolution of host plant choice and provide a basis towards a more congruent taxonomy of this genus.     

Genome organization of Bowman–Birk inhibitor in common bean (Phaseolus vulgaris L.)

A BAC library from common bean has been used in order to isolate the entire multigene Bowman–Birk serine protease inhibitor family and to study its genome organization. Using a previously isolated trypsin/chymotrypsin inhibitor nucleotide sequence as probe, two positive BAC clones were identified. The P2B8 BAC clone, of about 135 kbp and containing the complete BBI family, was chosen and partially sequenced. Our results confirm that a small multigene family codes for three double-headed inhibitors named: tc-BBI-1, tc-BBI-2 and et-BBI. They contain the binding loop trypsin/chymotrypsin (tc-BBI-1 and tc-BBI-2) and the elastase/trypsin one (et-BBI), respectively. Genes coding for tc-BBI-1 and et-BBI, were found to be very close to each other and arranged in a head to head fashion. Southern blot hybridisation on genomic DNA digested with PstI enzyme suggests that all three genes are present in a fragment of 19 kbp. Northern blot analyses on RNA isolated from various common bean organs showed that the expression of tc-BBI-1 and et-BBI was restricted to the developing cotyledons. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

<Emphasis Type="Italic">Apis mellifera</Emphasis> and <Emphasis Type="Italic">Osmia cornuta</Emphasis> as carriers for the secondary spread of <Emphasis Type="Italic">Bacillus subtilis</Emphasis> on apple flowers

The efficiency of two pollinators, Apis mellifera L. (Hymenoptera: Apidae) and the mason bee Osmia cornuta (Latreille) (Hymenoptera: Megachilidae), as carriers of biocontrol agents (BCA) from flower to flower (secondary colonisation) was investigated on apple cv ‘Golden Delicious’. The BCA tested was Bacillus subtilis, strain BD170 (Biopro®) developed for the control of the ‘fire blight’ caused by Erwinia amylovora (Burril) Winslow et al. The two insect species were studied as secondary BCA carriers on apple plants in pots under net screened tunnels. Their behaviour and capacity to deposit the BCA in the most receptive flower parts were compared both by washing, diluting and plating the flower organs on a recovery medium and by means of PCR analyses based on a molecular marker. O. cornuta showed better performances with respect to A. mellifera. For the field trials, pollinators were introduced in four apple orchards. During apple’s flowering, the BD170 (100 g hl^?l) was sprayed once in two fields, and twice in the others. The pollinators’ efficacy in carrying the BCA from sprayed flowers to the stigmas of newly opened ones at different times after the spray treatment was evaluated. The detection of the BCA was performed by PCR analysis. The percentages of positive PCR flower samples were higher in the internal treated areas of the fields with respect to the external untreated ones, but the high colonisation level found in the latter and in the flowers opened in both areas several days after the treatment(s) demonstrated that pollinators can play an important role as secondary carriers.