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Deletion Constructs (deletion + construct)
Selected AbstractsBlocking Dishevelled signaling in the noncanonical Wnt pathway in sea urchins disrupts endoderm formation and spiculogenesis, but not secondary mesoderm formationDEVELOPMENTAL DYNAMICS, Issue 7 2009Christine A. Byrum Abstract Dishevelled (Dsh) is a phosphoprotein key to beta-catenin dependent (canonical) and beta-catenin independent (noncanonical) Wnt signaling. Whereas canonical Wnt signaling has been intensively studied in sea urchin development, little is known about other Wnt pathways. To examine roles of these beta-catenin independent pathways in embryogenesis, we used Dsh-DEP, a deletion construct blocking planar cell polarity (PCP) and Wnt/Ca2+ signaling. Embryos overexpressing Dsh-DEP failed to gastrulate or undergo skeletogenesis, but produced pigment cells. Although early mesodermal gene expression was largely unperturbed, embryos exhibited reduced expression of genes regulating endoderm specification and differentiation. Overexpressing activated beta-catenin failed to rescue Dsh-DEP embryos, indicating that Dsh-DEP blocks endoderm formation downstream of initial canonical Wnt signaling. Because Dsh-DEP-like constructs block PCP signaling in other metazoans, and disrupting RhoA or Fz 5/8 in echinoids blocks subsets of the Dsh-DEP phenotypes, our data suggest that noncanonical Wnt signaling is crucial for sea urchin endoderm formation and skeletogenesis. Developmental Dynamics 238:1649,1665, 2009. © 2009 Wiley-Liss, Inc. [source] Overproduction, crystallization and preliminary crystallographic analysis of a novel human DNA-repair enzyme that recognizes oxidative DNA damageACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2004Viswanath Bandaru DNA glycosylases repair oxidative DNA damage caused by free radicals. Recently, NEIL1, a human homolog of Escherichia coli DNA glycosylase endonuclease VIII, has been identified and shown to exhibit broad substrate specificity for a variety of types of pyrimidine-base damage. An active C-terminal deletion construct of NEIL1 was overexpressed in E. coli and crystallized. The unliganded NEIL1 crystallizes in space group R3, with unit-cell parameters a = b = 132.2, c = 51.1,Å. Complete data sets were collected from native, selenomethionyl and iodinated NEIL1 to 2.1, 2.3 and 2.4,Å, respectively. [source] Characterization of epitopes recognized by anti- Streptococcus mutans P1 monoclonal antibodiesFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 3 2007William P. McArthur Abstract Sequences contributing to epitopes recognized by a panel of monoclonal antibodies (mAbs) against the Streptococcus mutans surface protein P1 were delineated by Western blot and enzyme-linked immunosorbent assay using a battery of deletion constructs and recombinant polypeptides. mAbs that recognize complex discontinuous epitopes reconstituted by combining the alanine-rich and proline-rich repeat domains and varying degrees of flanking sequence were identified as well as mAbs that bound epitopes contained within contiguous segments of P1. Cross-reactivity with SspA and SspB from Streptococcus gordonii is also reported. This information enables insight into the structure and function of a streptococcal adhesin and its correlates of protection and furthers our understanding of the immunomodulatory and bacterial-adherence inhibition activities of anti-P1 mAbs. [source] Caenorhabditis elegans DYF-11, an orthologue of mammalian Traf3ip1/MIP-T3, is required for sensory cilia formationGENES TO CELLS, Issue 1 2008Hirofumi Kunitomo Cilia and flagella play critical roles in cell motility, development and sensory perception in animals. Formation and maintenance of cilia require a conserved protein transport system called intraflagellar transport (IFT). Here, we show that Caenorhabditis elegans dyf-11 encodes an evolutionarily conserved protein required for cilium biogenesis. dyf-11 is expressed in most of the ciliated neurons and is regulated by DAF-19, a crucial transcription factor for ciliary genes in C. elegans. dyf-11 mutants exhibit stunted cilia, fluorescent dye-filling defects (Dyf) of sensory neurons, and abnormal chemotaxis (Che). Cell- and stage-specific rescue experiments indicated that DYF-11 is required for formation and maintenance of sensory cilia in cell-autonomous manner. Fluorescent protein-tagged DYF-11 localizes to cilia and moves antero- and retrogradely via IFT. Analysis of DYF-11 movement in bbs mutants further suggested that DYF-11 is likely associated with IFT complex B. Domain analysis using DYF-11 deletion constructs revealed that the coiled-coil region is required for proper localization and ciliogenesis. We further show that Traf3ip1/MIP-T3, the mammalian orthologue of DYF-11, localizes to cilia in the MDCK renal epithelial cells. [source] ELKS, a protein structurally related to the active zone protein CAST, is involved in Ca2+ -dependent exocytosis from PC12 cellsGENES TO CELLS, Issue 6 2006Eiji Inoue The active zone protein CAST binds directly to the other active zone proteins RIM, Bassoon and Piccolo, and it has been suggested that these protein,protein interactions play an important role in neurotransmitter release. To further elucidate the molecular mechanism, we attempted to examine the function of CAST using PC12 cells as a model system. Although PC12 cells do not express CAST, they do express ELKS, a protein structurally related to CAST. Endogenous and exogenously expressed ELKS, RIM2 and Bassoon were colocalized in punctate signals in PC12 cells. Over-expression of full-length ELKS resulted in a significant increase in stimulated exocytosis of human growth hormone (hGH) from PC12 cells, similar to the effect of full-length RIM2. This increase was not observed following over-expression of deletion constructs of ELKS that lacked either the last three amino acids (IWA) required for binding to RIM2 or a central region necessary for binding to Bassoon. Moreover, over-expression of the NH2 -terminal RIM2-binding domain of Munc13-1, which is known to inhibit the binding between RIM and Munc13-1, inhibited the stimulated increase in hGH secretion by full-length RIM2. Furthermore, this construct also inhibited the stimulated increase in hGH secretion induced by full-length ELKS. These results suggest that ELKS is involved in Ca2+ -dependent exocytosis from PC12 cells at least partly via the RIM2-Munc13-1 pathway. [source] Role of the Latent Transforming Growth Factor ,,Binding Protein 1 in Fibrillin-Containing Microfibrils in Bone Cells In Vitro and In VivoJOURNAL OF BONE AND MINERAL RESEARCH, Issue 1 2000Sarah L. Dallas Abstract Latent transforming growth factor ,,binding proteins (LTBPs) are extracellular matrix (ECM) proteins that bind latent transforming growth factor , (TGF-,) and influence its availability in bone and other connective tissues. LTBPs have homology with fibrillins and may have related functions as microfibrillar proteins. However, at present little is known about their structural arrangement in the ECM. By using antibodies against purified LTBP1, against a short peptide in LTBP1, and against epitope-tagged LTBP1 constructs, we have shown colocalization of LTBP1 and fibrillin 1 in microfibrillar structures in the ECM of cultured primary osteoblasts. Immunoelectron microscopy confirmed localization of LTBP1 to 10- to 12-nm microfibrils and suggested an ordered aggregation of LTBP1 into these structures. Early colocalization of LTBP1 with fibronectin suggested a role for fibronectin in the initial assembly of LTBP1 into the matrix; however, in more differentiated osteoblast cultures, LTBP1 and fibronectin 1 were found in distinct fibrillar networks. Overexpression of LTBP1 deletion constructs in osteoblast-like cells showed that N-terminal amino acids 67,467 were sufficient for incorporation into fibrillin-containing microfibrils and suggested that LTBP1 can be produced by cells distant from the site of fibril formation. In embryonic long bones in vivo, LTBP1 and fibrillin 1 colocalized at the surface of newly forming osteoid and bone. However, LTBP1-positive fibrils, which did not contain fibrillin 1, were present in cartilage matrix. These studies show that in addition to regulating TGF,1, LTBP1 may function as a structural component of connective tissue microfibrils. LTBP1 may therefore be a candidate gene for Marfan-related connective tissue disorders in which linkage to fibrillins has been excluded. [source] Transcriptional regulation of aquaporin 3 by insulinJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2007Shota Higuchi Abstract In the current study, we identified a regulatory factor for the transcription of aquaporin 3 (AQP3) whose expression is repressed by insulin. We constructed a luciferase reporter vector containing bp ,1382 to ,12 of the 5,-flanking region of the AQP3 gene for a reporter gene assay and observed that luciferase activity in transfectants with the plasmid decreased on treatment with insulin. Serial deletion constructs revealed two regions responsible for the insulin-mediated repression, one between bps ,1382 and ,780, and the other between bps ,404 and ,82. mRNA expression of forkhead box a2 (Foxa2), the binding site of which was located between bps ,1382 and ,780, was found to decrease on treatment with insulin. A mutant reporter plasmid with an altered Foxa2-binding site and siRNA for the Foxa2 sequence counteracted the insulin-mediated repression of AQP3 transcription. These results suggest that Foxa2 is one of the transcriptional regulators for AQP3 gene expression regulated by insulin. J. Cell. Biochem. 102: 1051,1058, 2007. © 2007 Wiley-Liss, Inc. [source] Identification of a 251-bp Fragment of the PAI-1 Gene Promoter That Mediates the Ethanol-Induced Suppression of PAI-1 ExpressionALCOHOLISM, Issue 5 2001Hernan E. Grenett Background: Moderate alcohol consumption reduces the risk for coronary heart disease. This cardioprotection may be due to ethanol enhancement of fibrinolysis. Fibrinolysis involves the interaction of plasminogen activators (PAs) and the plasminogen activator inhibitor type-1 (PAI-1). Factor(s) that decrease endothelial cell (EC) PAI-1 expression increase fibrinolysis and may decrease the risk for cardiovascular disease. Methods: Five promoter deletion fragments were generated from a 1.1-kb PAI-1 promoter fragment and ligated to a luciferase reporter gene. Cultured human umbilical vein endothelial cells (HUVECs) were transiently transfected with these PAI-1 deletion constructs. A 251-base pair (bp) fragment of the PAI-1 promoter, positions ,800 to ,549, was cloned upstream of a heterologous promoter/enhancer. ECs luciferase activity was measured in the absence/presence of 20 mM ethanol. Electrophoresis mobility shift assays were performed with nuclear extracts from untreated and ethanol-treated ECs using this 251-bp fragment. Results: Deletion analysis showed a region between position ,800 and ,549 mediated ethanol repression of luciferase activity. This 251-bp promoter fragment also repressed the activity of a heterologous promoter/enhancer in the presence of ethanol. Using the labeled 251-bp fragment, nuclear extracts from ethanol-treated ECs contained two inducible bands and one enhanced band. Non-ethanol treated nuclear extracts also contained a band that was not observed in ethanol-treated samples. Competition using 100-fold molar excess of unlabeled probe abolished these four bands. Conclusions: Repression of PAI-I gene transcription in cultured HUVECs exposed to ethanol may involve the interaction of several transcription factors with binding sites localized between positions ,800 and ,549 of the PAI-1 gene promoter. [source] Functional characterization of transcription factor binding sites for HNF1-alpha, HNF3-beta (FOXA2), HNF4-alpha, Sp1 and Sp3 in the human prothrombin gene enhancerJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 8 2003H. Ceelie Summary.,Background:,Prothrombin is a key component in blood coagulation. Overexpression of prothrombin leads to an increased risk of venous thrombosis. Therefore, the study of the transcriptional regulation of the prothrombin gene may help to identify mechanisms of overexpression. Objectives:,The aim of our study was to localize the regions within the prothrombin enhancer responsible for its activity, to identify the proteins binding to these regions, and to establish their functional importance. Methods:,We constructed a set of prothrombin promoter 5, deletion constructs containing the firefly luciferase reporter gene, which were transiently transfected in HepG2, HuH7 and HeLa cells. Putative transcription factor (TF) binding sites were evaluated by electrophoretic mobility shift assays. The functional importance of each TF binding site was evaluated by site directed mutagenesis and transient transfection of the mutant constructs. Results:,We confirmed the major contribution of the enhancer region to the transcriptional activity of the prothrombin promoter. Analysis of this region revealed putative binding sites for hepatocyte nuclear factor HNF4, HNF3-beta and specificity protein(Sp)1. We identified six different TFs binding to three evolutionary conserved sites in the enhancer: HNF4-alpha (site 1), HNF1-alpha, HNF3-beta and an as yet unidentified TF (site 2) and the ubiquitously expressed TFs Sp1 and Sp3 (site 3). Mutagenesis studies showed that loss of binding of HNF3-beta resulted in a considerable decrease of enhancer activity, whereas loss of HNF4-alpha or Sp1/Sp3 resulted in milder reductions. Conclusions:,The prothrombin enhancer plays a major role in regulation of prothrombin expression. Six different TFs are able to bind to this region. At least three of these TFs, HNF4-alpha, HNF3-beta and Sp1/Sp3, are important in regulation of prothrombin expression. [source] The hydroxyproline-rich glycoprotein domain of the Arabidopsis LRX1 requires Tyr for function but not for insolubilization in the cell wallTHE PLANT JOURNAL, Issue 4 2010Christoph Ringli Summary Extensins, hydroxyproline-rich repetitive glycoproteins with Ser,Hyp4 motifs, are structural proteins in plant cell walls. The leucine-rich repeat extensin 1 (LRX1) of Arabidopsis thaliana is an extracellular protein with both a leucine-rich repeat and an extensin domain, and has been demonstrated to be important for cell-wall formation in root hairs. lrx1 mutants develop defective cell walls, resulting in a strong root hair phenotype. The extensin domain is essential for protein function and is thought to confer insolubilization of LRX1 in the cell wall. Here, in vivo characterization of the LRX1 extensin domain is described. First, a series of LRX1 extensin deletion constructs was produced that led to identification of a much shorter, functional extensin domain. Tyr residues can induce intra- and inter-molecular cross-links in extensins, and substitution of Tyr in the extensin domain by Phe led to reduced activity of the corresponding LRX1 protein. An additional function of Tyr (or Phe) is provided by the aromatic nature of the side chain. This suggests that these residues might be involved in hydrophobic stacking, possibly as a mechanism of protein assembly. Finally, modified LRX1 proteins lacking Tyr in the extensin domain are still insolubilized in the cell wall, indicating strong interactions of extensins within the cell wall in addition to the well-described Tyr cross-links. [source] Identification of polymorphisms in the ovine Shadow of prion protein (SPRN) gene and assessment of their effect on promoter activity and susceptibility for classical scrapieANIMAL GENETICS, Issue 2 2010E. Lampo Summary Shadow of prion protein (SPRN) is an interesting candidate gene thought to be involved in prion pathogenesis. In humans, an association has already been discovered between mutations in SPRN and the incidence of variant and sporadic Creutzfeldt-Jakob disease. However, in sheep, the effect of mutations in SPRN is largely unknown. Therefore, we analysed the presence of mutations in the entire ovine SPRN gene, their association with scrapie susceptibility and their effect on SPRN promoter activity. In total, 26 mutations were found: seven in the promoter region, four in intron 1, seven in the coding sequence and eight in the 3, untranslated region. The mutations detected in the coding sequence and the promoter region were subsequently analysed in more detail. In the coding sequence, a polymorphism causing a deletion of two alanines was found to be associated with susceptibility for classical scrapie in sheep. Furthermore, a functional analysis of deletion constructs of the ovine SPRN promoter revealed that the region 464 to 230 bp upstream of exon 1 (containing a putative AP-2 and putative Sp1 binding sites) is of functional importance for SPRN transcription. Six mutations in the SPRN promoter were also found to alter the promoter activity in vitro. However, no association between any of these promoter mutations and susceptibility for classical scrapie was found. [source] Attachment of Neisseria gonorrhoeae to the cellular pilus receptor CD46: identification of domains important for bacterial adherenceCELLULAR MICROBIOLOGY, Issue 3 2001Helena Källström Pili of Neisseria gonorrhoeae mediate binding of the bacteria to human host cells. Membrane cofactor protein (MCP or CD46), a human cell-surface protein involved in regulation of complement activation, acts as a cellular pilus receptor. In this work, we examined which domains of CD46 mediate bacterial adherence. The CD46 expression was quantified and characterized in human epithelial cell lines. N. gonorrhoeae showed the highest adherence to ME180 cells, which have BC1 as the dominant phenotype. The BC isoforms of CD46 were expressed in all cell lines tested. The adherence was not enhanced by high expression of other isoforms, showing that the BC domain of CD46 is important in adherence of N. gonorrhoeae to human cells. To characterize the pilus-binding site within the CD46 molecule, a set of CD46,BC1 deletion constructs were transfected into COS-7 cells. Piliated N. gonorrhoeae attached well to CD46,BC1-expressing COS-7 cells. We show that the complement control protein repeat 3 (CCP-3) and the serine,threonine,proline (STP)-rich domain of CD46 are important for efficient adherence to host cells. Further, partial deletion of the cytoplasmic tail of CD46 results in low bacterial binding, indicating that the cytoplasmic tail takes part in the process of establishing a stable interaction between N. gonorrhoeae and host cells. [source] | |||||||||||||