651
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Verpoorten N, Verhoeven K, Weckx S, Jacobs A, Serneels S, Del Favero J, Ceuterick C, Van Bockstaele DR, Berneman ZN, Van den Bosch L, Robberecht W, Nobbio L, Schenone A, Dessaud E, deLapeyrière O, Huylebroeck D, Zwijsen A, De Jonghe P, Timmerman V. Synaptopodin and 4 novel genes identified in primary sensory neurons. Mol Cell Neurosci 2005; 30:316-25. [PMID: 16139508 DOI: 10.1016/j.mcn.2005.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 06/14/2005] [Accepted: 07/08/2005] [Indexed: 11/20/2022] Open
Abstract
We performed differential gene expression profiling in the peripheral nervous system by comparing the transcriptome of sensory neurons with the transcriptome of lower motor neurons. Using suppression subtractive cDNA hybridization, we identified 5 anonymous transcripts with a predominant expression in sensory neurons. We determined the gene structures and predicted the functional protein domains. The 4930579P15Rik gene encodes for a novel inhibitor of protein phosphatase-1 and 9030217H17Rik was found to be the mouse gene synaptopodin. We performed in situ hybridization for all genes in mouse embryos, and found expression predominantly in the primary class of sensory neurons. Expression of 4930579P15Rik and synaptopodin was restricted to craniospinal sensory ganglia. Neither synaptopodin, nor any known family member of 4930579P15Rik, has ever been described in sensory neurons. The identification of protein domains and expression patterns allows further functional analysis of these novel genes in relation to the development and biology of sensory neurons.
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Affiliation(s)
- Nathalie Verpoorten
- Peripheral Neuropathy Group, Department of Molecular Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, B-2610 Antwerpen, Belgium
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652
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Cioffi DL, Wu S, Alexeyev M, Goodman SR, Zhu MX, Stevens T. Activation of the endothelial store-operated ISOC Ca2+ channel requires interaction of protein 4.1 with TRPC4. Circ Res 2005; 97:1164-72. [PMID: 16254212 DOI: 10.1161/01.res.0000193597.65217.00] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Store-operated calcium (SOC) entry represents the principal Ca2+ entry pathway into nonexcitable cells. Despite intensive investigation, mechanisms underlying activation of SOC entry have remained elusive. The endothelial ISOC channel is a Ca2+-selective SOC entry channel to which the transient receptor potential (TRP) proteins TRPC1 and TRPC4 contribute subunits. Activation of ISOC is specifically regulated by the spectrin-actin membrane skeleton; however, the nature of coupling between the ISOC channel and membrane skeleton is unknown. Here we demonstrate that protein 4.1 is an essential component of the ISOC channel gating mechanism. Protein 4.1 interacts with TRPC4 and the membrane skeleton. Deletion of the protein 4.1 binding domain on TRPC4 or peptide competition to the protein 4.1 binding domain prevents ISOC activation. These findings reveal that interaction of protein 4.1 with TRPC4 is required for activation of the endothelial ISOC channel.
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Affiliation(s)
- Donna L Cioffi
- Center for Lung Biology, Department of Pharmacology, University of South Alabama College of Medicine, Mobile, AL 36688, USA
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653
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Abstract
Ubiquitin regulates cell functions by modifying various proteins, and cytokeratin (CK) is one of the targets of ubiquitilation. Accumulation of modified CK in various cancers has been demonstrated, and the modified CK increases the aggressiveness of the cancer by disrupting the cytoplasmic CK network and allows them to move freely. The phenotype of the cancer cells may be altered in such a way as to facilitate invasion and metastasis. Modified CK also deregulates mechanisms of mitosis and apoptosis, and leads to immortalization. Therapeutic targeting of ubiquitin or ubiquitilated proteins may reduce the malignant potential of cancer cells.
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Affiliation(s)
- Keiichi Iwaya
- Department of Diagnostic Pathology, Tokyo Medical University, Nishi-Shinjuku 6-7-1, Shinjuku-ku, Tokyo 160-0023, Japan
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654
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Deng L, Velikovsky CA, Swaminathan CP, Cho S, Mariuzza RA, Huber R. Structural basis for recognition of the T cell adaptor protein SLP-76 by the SH3 domain of phospholipase Cgamma1. J Mol Biol 2005; 352:1-10. [PMID: 16061254 PMCID: PMC2753203 DOI: 10.1016/j.jmb.2005.06.072] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 06/24/2005] [Accepted: 06/30/2005] [Indexed: 11/29/2022]
Abstract
The enzyme phospholipase Cgamma1 (PLCgamma1) is essential for T cell signaling and activation. Following T cell receptor ligation, PLCgamma1 interacts through its SH2 and SH3 domains with the adaptors LAT and SLP-76, respectively, to form a multiprotein signaling complex that leads to activation of PLCgamma1 by Syk tyrosine kinases. To identify the binding site for PLCgamma1 in SLP-76, we used isothermal titration calorimetry to measure affinities for the interaction of PLCgamma1-SH3 with a set of overlapping peptides spanning the central proline-rich region of SLP-76. PLCgamma1-SH3 bound with high specificity to the SLP-76 motif 186PPVPPQRP193, which represents the minimal binding site. To understand the basis for selective recognition, we determined the crystal structures of PLCgamma1-SH3 in free form, and bound to a 10-mer peptide containing this site, to resolutions of 1.60 A and 1.81 A, respectively. The structures reveal that several key contacting residues of the SH3 shift toward the SLP-76 peptide upon complex formation, optimizing the fit and strengthening hydrophobic interactions. Selectivity results mainly from strict shape complementarity between protein and peptide, rather than sequence-specific hydrogen bonding. In addition, Pro193 of SLP-76 assists in positioning Arg192 into the compass pocket of PLCgamma1-SH3, which coordinates the compass residue through an unusual aspartate. The PLCgamma1-SH3/SLP-76 structure provides insights into ligand binding by SH3 domains related to PLCgamma1-SH3, as well as into recognition by PLCgamma1 of signaling partners other than SLP-76.
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Affiliation(s)
| | | | | | | | - Roy A. Mariuzza
- Corresponding author E-mail address of the corresponding author:
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655
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Wen Y, Shao JZ, Pan XX, Xiang LX. Molecular cloning, characterization and expression analysis of QM gene from grass carp (Ctenopharyngodon idellus) homologous to Wilms' tumor suppressor. Comp Biochem Physiol B Biochem Mol Biol 2005; 141:356-65. [PMID: 15936234 DOI: 10.1016/j.cbpc.2005.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 04/02/2005] [Accepted: 04/20/2005] [Indexed: 12/01/2022]
Abstract
QM, a novel gene that was originally identified as a tumor suppressor, has been cloned from species encompassing members of higher vertebrate, plant and fungal kingdoms, but it is not well documented in fish. In present study, a gene homologous to QM was obtained from grass carp (Ctenopharyngodon idellus) head kidney and spleen cDNA library. The full-length grass carp QM (GcQM) cDNA of 759 bp contains a short 5' UTR of 22 bp, a 3' UTR of 89 bp and an open reading frame of 648 nucleotides that translates into a 215-amino acid peptide with a molecular weight of 24.5 kDa. The predicted GcQM contains a series of functional motifs that belong to the QM family signature conserved among different species. Multiple alignment analysis reveals that GcQM shares an overall identity of 62.4% approximately 97.7% with other members of QM family. The fish QM has a closest genetic relationship to chicken homologue Jif-1. The GcQM expresses constitutively in spleen, heart and brain, and significantly up-regulated by Aeromonas hydrophila and grass carp haemorrhagic virus (GCHV) in head kidney, spleen and liver. The results suggest that grass carp QM homolog is an inflammatory stress inducible gene associated with anti-bacterial and viral defense, and it plays an important role in immune defense.
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Affiliation(s)
- Yi Wen
- College of Life Sciences, Zhejiang University, Hangzhou 310012, People's Republic of China
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656
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Bratt A, Birot O, Sinha I, Veitonmäki N, Aase K, Ernkvist M, Holmgren L. Angiomotin Regulates Endothelial Cell-Cell Junctions and Cell Motility. J Biol Chem 2005; 280:34859-69. [PMID: 16043488 DOI: 10.1074/jbc.m503915200] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have previously identified angiomotin by its ability to bind to and mediate the anti-angiogenic properties of angiostatin. In vivo and in vitro data indicate an essential role of angiomotin in endothelial cell motility. Here we show that angiostatin binds angiomotin on the cell surface and provide evidence for a transmembrane model for the topology of both p80 and p130 angiomotin isoforms. Immunofluorescence analysis shows that angiomotin co-localized with ZO-1 in cell-cell contacts in endothelial cells in vitro and in angiogenic blood vessels of the postnatal mouse retina in vivo. Transfection of p80 as well as p130 angiomotin in Chinese hamster ovary cells resulted in junctional localization of both isoforms. Furthermore, p130 angiomotin could recruit ZO-1 to actin stress fibers. The p130 but not p80 isoform could be coprecipitated with MAGI-1b, a component of endothelial tight junctions. Paracellular permeability, as measured by diffusion of fluorescein isothiocyanate-dextran, was reduced by p80 and p130 angiomotin expression with 70 and 88%, respectively, compared with control. Angiostatin did not have any effect on cell permeability but inhibited the migration of angiomotin-expressing cells in the Boyden chamber assay. We conclude that angiomotin, in addition to controlling cell motility, may play a role in the assembly of endothelial cell-cell junctions.
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Affiliation(s)
- Anders Bratt
- Department of Oncology and Pathology, Cancer Centrum Karolinska, Karolinska Institutet, R8:03 Karolinska University Hospital, 171 76 Stockholm, Sweden
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657
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Lee JS, Kim JH, Jang IH, Kim HS, Han JM, Kazlauskas A, Yagisawa H, Suh PG, Ryu SH. Phosphatidylinositol (3,4,5)-trisphosphate specifically interacts with the phox homology domain of phospholipase D1 and stimulates its activity. J Cell Sci 2005; 118:4405-13. [PMID: 16179605 DOI: 10.1242/jcs.02564] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Phospholipase D (PLD), which catalyzes the hydrolysis of phosphatidylcholine to phosphatidic acid and choline, plays key roles in cellular signal transduction by mediating extracellular stimuli including hormones, growth factors, neurotransmitters, cytokines and extracellular matrix molecules. The molecular mechanisms by which domains regulate the activity of PLD - especially the phox homology (PX) domain - have not been fully elucidated. In this study, we have examined the properties of the PX domains of PLD1 and PLD2 in terms of phosphoinositide binding and PLD activity regulation. Interestingly, the PX domain of PLD1, but not that of PLD2, was found to specifically interact with phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3). We found that mutation of the conserved arginine at position 179 of the PLD1 PX domain to lysine or to alanine (R179A or R179K, respectively) disrupts PtdIns(3,4,5)P3 binding. In NIH-3T3 cells, the EGFP-PLD1 PX wild-type domain, but not the two mutants, localized to the plasma membrane after 5-minute treatment with platelet-derived growth factor (PDGF). The enzymatic activity of PLD1 was stimulated by adding PtdIns(3,4,5)P3 in vitro. Treatment with PDGF resulted in the significant increase of PLD1 activity and phosphorylation of the downstream extracellular signal-regulated kinases (ERKs), which was blocked by pre-treatment of HEK 293 cells with phosphoinositide 3-kinase (PI3K) inhibitor after the endogenous PLD2 had been depleted by siRNA specific for PLD2. Nevertheless, both PLD1 mutants (which cannot interact with PtdIns(3,4,5)P3) did not respond to treatment with PDGF. Moreover, PLD1 was activated in HepG2 cells stably expressing the Y40/51 mutant of PDGF receptor that is required for the binding with PI3K. Our results suggest that the PLD1 PX domain enables PLD1 to mediate signal transduction via ERK1/2 by providing a direct binding site for PtdIns(3,4,5)P3 and by activating PLD1.
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Affiliation(s)
- Jun Sung Lee
- Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea
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658
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Gangenahalli GU, Singh VK, Verma YK, Gupta P, Sharma RK, Chandra R, Gulati S, Luthra PM. Three-Dimensional Structure Prediction of the Interaction of CD34 with the SH3 Domain of Crk-L. Stem Cells Dev 2005; 14:470-7. [PMID: 16305332 DOI: 10.1089/scd.2005.14.470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The monomeric 115-kDa surface protein CD34, which is present on many stem cell populations, has been useful to enumerate the quality and viability of cell suspensions for engraftment. Although these studies assure the validity of CD34 as a stem cell marker, the functional role of this molecule has not been defined. CD34 has been demonstrated to regulate adhesion, differentiation, and proliferation of hematopoietic stem cells and other progenitors. The cytoplasmic domain of CD34 is known to be essential for its function. However, it is not clear how this domain's interactions with other molecules support the functional activity of CD34. Here we show that the cytoplasmic tail of CD34 is structurally similar to the carboxyl terminus of the gap junction protein Connexin 43 (Cx43). Because the activity of CD34 is mediated through its interaction with an SH3 domain of an intracellular protein, we attempted to define the SH3 binding region and amino acids involved in this interaction. We identified Glu325 to Ser334 as potential SH3 binding sites. Our results suggest that the interaction of the cytoplasmic tail of CD34 with the shallow proline-rich motif-binding groove of Crk-L is essential for the function of CD34 in stem cell development.
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Affiliation(s)
- Gurudutta U Gangenahalli
- Stem-Cell Gene Therapy Research Group, Institute of Nuclear Medicine & Allied Sciences, Delhi-110054, India.
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659
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Caro F, Bercovich N, Atorrasagasti C, Levin MJ, Vázquez MP. Protein interactions within the TcZFP zinc finger family members of Trypanosoma cruzi: implications for their functions. Biochem Biophys Res Commun 2005; 333:1017-25. [PMID: 15964555 DOI: 10.1016/j.bbrc.2005.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Accepted: 06/03/2005] [Indexed: 11/15/2022]
Abstract
The small zinc finger proteins tbZFP1 and tbZFP2 have been implicated in the control of Trypanosoma brucei differentiation to the procyclic form. Here, we report that the complete ZFP family in Trypanosoma cruzi is composed by four members, ZFP1A and B, and ZFP2A and B. ZFP1B is a paralog specific gene restricted to T. cruzi, while the ZFP2A and B paralogs diverged prior to the trypanosomatid lineage separation. Moreover, we demonstrate that TcZFP1 and TcZFP2 members interact with each other and that this interaction is mediated by a WW domain in TcZFP2. Also, TcZFP2B strongly homodimerizes by a glycine rich region absent in TcZFP2A. We propose a model to discuss the relevance of these protein-protein interactions in terms of the functions of these proteins.
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Affiliation(s)
- Florence Caro
- Laboratorio de Biología Molecular de la Enfermedad de Chagas-INGEBI-CONICET, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, University of Buenos Aires, Buenos Aires, Argentina
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660
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Bruno LS, Li X, Wang L, Soares RV, Siqueira CC, Oppenheim FG, Troxler RF, Offner GD. Two-hybrid analysis of human salivary mucin MUC7 interactions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1746:65-72. [PMID: 16203048 DOI: 10.1016/j.bbamcr.2005.08.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 08/18/2005] [Accepted: 08/23/2005] [Indexed: 10/25/2022]
Abstract
MUC7 is a low molecular weight monomeric mucin secreted by submandibular, sublingual and minor salivary glands. This mucin has been implicated in the non-immune host defense system in the oral cavity since it binds and agglutinates a variety of oral microbes. To investigate interactions between this mucin and other secretory salivary proteins, a submandibular gland prey library was screened with baits encoding the N- and C-terminal regions of MUC7 in the yeast two-hybrid system. The N-terminal region interacted with several secretory salivary proteins, whereas the C-terminal region did not. Interacting proteins included amylase, acidic proline-rich protein 2, basic proline-rich protein 3, lacrimal proline-rich protein 4, statherin and histatin 1. Formation of complexes between these proteins and the N-terminal region of MUC7 was confirmed in Far Western blotting experiments. Interactions between mucin and non-mucin proteins in saliva could protect complex partners from proteolysis, modulate the biological activity of complexed proteins or serve as a delivery system for distribution of secretory salivary proteins throughout the oral cavity.
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Affiliation(s)
- Lucila S Bruno
- Department of Biochemistry, Boston University Medical Center, Boston, MA 02118, USA
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661
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Gu W, Helms V. Dynamical binding of proline-rich peptides to their recognition domains. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1754:232-8. [PMID: 16203190 DOI: 10.1016/j.bbapap.2005.07.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 07/18/2005] [Accepted: 07/20/2005] [Indexed: 10/25/2022]
Abstract
Recognition of proline-rich sequences plays an important role for the assembly of multi-protein complexes during the course of eukaryotic signal transduction and is mediated by a set of protein folds that share characteristic features. For many complex systems containing proline-rich sequences, multiple binding modes have been found by theoretical and/or experimental studies. In this review, we discuss the different binding modes as well as the correlated dynamics of the peptides and their recognition domains, and some implications to their biological functions. Furthermore, we give an outlook of the systems in the context of systems biology.
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Affiliation(s)
- Wei Gu
- Zentrum für Bioinformatik, Universität des Saarlandes, D-66041 Saarbrücken, Germany
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662
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Reichman C, Singh K, Liu Y, Singh S, Li H, Fajardo JE, Fiser A, Birge RB. Transactivation of Abl by the Crk II adapter protein requires a PNAY sequence in the Crk C-terminal SH3 domain. Oncogene 2005; 24:8187-99. [PMID: 16158059 DOI: 10.1038/sj.onc.1208988] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To gain a better understanding of how Crk II regulates the function of the Abl tyrosine kinase, we explored the function of the C-terminal linker and SH3 domain, a region of Crk II that is still poorly understood. Molecular modeling, tryptophan fluorescence, and covariation sequence alignment indicate that the Crk-SH3-C has a unique binding groove and RT loop not observed in typical SH3 domains. Based on these models, we made a series of mutations in the linker and in residues predicted to destabilize the putative binding pocket and RT loop. In Abl transactivation assays, Y222F and P225A mutations in the linker resulted in strong transactivation of Abl by Crk II. However, mutations predicted to be at the surface of the Crk SH3-C were not activators of Abl. Interestingly, combinations of activating mutations of Crk II with mutations in the highly conserved PNAY sequence in the SH3-C inactivated the activating mutations, suggesting that the SH3-C is necessary for activation. Our data provide insight into the role of highly conserved residues in the Crk-SH3-C, suggesting a mechanism for how the linker and the Crk-SH3-C function in the transactivation of the Abl tyrosine kinase.
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Affiliation(s)
- Charles Reichman
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
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663
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Balsera M, Arellano JB, Revuelta JL, de las Rivas J, Hermoso JA. The 1.49 A resolution crystal structure of PsbQ from photosystem II of Spinacia oleracea reveals a PPII structure in the N-terminal region. J Mol Biol 2005; 350:1051-60. [PMID: 15982665 DOI: 10.1016/j.jmb.2005.05.044] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 05/13/2005] [Accepted: 05/19/2005] [Indexed: 10/25/2022]
Abstract
We report the high-resolution structure of the spinach PsbQ protein, one of the main extrinsic proteins of higher plant photosystem II (PSII). The crystal structure shows that there are two well-defined regions in PsbQ, the C-terminal region (residues 46-149) folded as a four helix up-down bundle and the N-terminal region (residues 1-45) that is loosely packed. This structure provides, for the first time, insights into the crucial N-terminal region. First, two parallel beta-strands cross spatially, joining the beginning and the end of the N-terminal region of PsbQ. Secondly, the residues Pro9-Pro10-Pro11-Pro12 form a left-handed helix (or a polyproline type II (PPII) structure), which is stabilized by hydrogen bonds between the Pro peptide carbonyl groups and solvent water molecules. Thirdly, residues 14-33 are not visible in the electron density map, suggesting that this loop might be very flexible and presumably extended when PsbQ is free in solution. On the basis of the essential role of the N-terminal region of PsbQ in binding to PSII, we propose that both the PPII structure and the missing loop are key secondary structure elements in the recognition of specific protein-protein interactions between PsbQ and other oxygen-evolving complex extrinsic and/or intrinsic proteins of PSII. In addition, the PsbQ crystal coordinates two zinc ions, one of them is proposed to have a physiological role in higher plants, on the basis of the full conservation of the ligand protein residues in the sequence subfamily.
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Affiliation(s)
- Mónica Balsera
- Instituto de Recursos Naturales y Agrobiología (CSIC), Cordel de Merinas 52, 37008 Salamanca, Spain
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664
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Ignjatovic T, Yang JC, Butler J, Neuhaus D, Nagai K. Structural basis of the interaction between P-element somatic inhibitor and U1-70k essential for the alternative splicing of P-element transposase. J Mol Biol 2005; 351:52-65. [PMID: 15990112 DOI: 10.1016/j.jmb.2005.04.077] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Accepted: 04/28/2005] [Indexed: 11/25/2022]
Abstract
P-element transposition in Drosophila is regulated by tissue-specific alternative splicing of the P-element transposase pre-mRNA. In somatic cells, the P-element somatic inhibitor (PSI) protein binds to exon 3 of the pre-mRNA and recruits U1 small nuclear ribonucleoprotein (snRNP) to the F1 pseudo-splice site. This abrogates binding of U1 snRNP to the genuine 5' splice site, thereby preventing excision of the third intron. Two homologous short sequences, referred to as the A and B boxes, near the C terminus of PSI bind to U1-70k protein within U1 snRNP. We have now mapped the AB box-binding site of U1-70k to a short proline-rich sequence at the C terminus. Our NMR study shows that the B box forms an anti-parallel helical hairpin in which four highly conserved aromatic residues form a cluster on one face of the first helix. This hydrophobic cluster interacts extensively with the proline-rich region of the U1-70k protein.
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Affiliation(s)
- Tijana Ignjatovic
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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665
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Abirami S, Wong CHS, Tsang CW, Ma NL, Goh NK. A theoretical study of potassium cation binding to prolylglycine (PG) and glycylproline (GP) dipeptide. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.05.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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666
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Bhaskar K, Yen SH, Lee G. Disease-related modifications in tau affect the interaction between Fyn and Tau. J Biol Chem 2005; 280:35119-25. [PMID: 16115884 DOI: 10.1074/jbc.m505895200] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Microtubule-associated protein tau is the major component of the neurofibrillary tangles of Alzheimer disease (AD) and is genetically linked to frontotemporal dementias (FTDP-17). We have recently shown that tau interacts with the SH3 domain of Fyn, an Src family non-receptor tyrosine kinase, and is tyrosine-phosphorylated by Fyn on Tyr-18. Also, tyrosine-phosphorylated tau is present in the neuropathology of AD. To determine whether alterations in the tau-Fyn interaction might correlate with disease-related factors in AD and FTDP-17, we have performed real-time surface plasmon resonance studies on a panel of 21 tau constructs with Fyn SH3. We report that the interaction between Fyn SH3 and 3R-tau was 20-fold higher than that with 4R-tau. In addition, the affinity between 4R-tau and Fyn SH3 was increased 25-45-fold by phosphorylation-mimicking mutations or by FTDP-17 mutations. In vitro kinase reactions show that tau, with lower affinity SH3 interactions, exhibited a lower level of Tyr-18 phosphorylation under our reaction conditions. Lastly, we have demonstrated that tau is phosphorylated on Tyr-18 in the tau P301L mouse model for tauopathy (JNPL3). In summary, our results suggest that disease-related phosphorylation and missense mutations of tau increase association of tau with Fyn. Because these effects are mediated through the 4R component of the tau population, these results also have implications for the FTDP-17 diseases caused by increased expression of 4R-tau. Our data support a role for the Fyn-tau interaction in neurodegeneration.
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Affiliation(s)
- Kiran Bhaskar
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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667
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Polo-Parada L, Plattner F, Bose C, Landmesser LT. NCAM 180 acting via a conserved C-terminal domain and MLCK is essential for effective transmission with repetitive stimulation. Neuron 2005; 46:917-31. [PMID: 15953420 DOI: 10.1016/j.neuron.2005.05.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Revised: 04/01/2005] [Accepted: 05/06/2005] [Indexed: 12/31/2022]
Abstract
NCAM 180 isoform null neuromuscular junctions are unable to effectively mobilize and exocytose synaptic vesicles and thus exhibit periods of total transmission failure during high-frequency repetitive stimulation. We have identified a highly conserved C-terminal (KENESKA) domain on NCAM that is required to maintain effective transmission and demonstrate that it acts via a pathway involving MLCK and probably myosin light chain (MLC) and myosin II. By perfecting a method of introducing peptides into adult NMJs, we tested the hypothesized role of proteins in this pathway by competitive disruption of protein-protein interactions. The effects of KENESKA and other peptides on MLCK and MLC activation and on failures in both wild-type and NCAM 180 null junctions supported this pathway, and serine phosphorylation of KENESKA was critical. We propose that this pathway is required to replenish synaptic vesicles utilized during high levels of exocytosis by facilitating myosin-driven delivery of synaptic vesicles to active zones or their subsequent exocytosis.
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Affiliation(s)
- Luis Polo-Parada
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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668
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Duguid EM, Rice PA, He C. The structure of the human AGT protein bound to DNA and its implications for damage detection. J Mol Biol 2005; 350:657-66. [PMID: 15964013 DOI: 10.1016/j.jmb.2005.05.028] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Revised: 05/04/2005] [Accepted: 05/14/2005] [Indexed: 11/23/2022]
Abstract
O6-Alklyguanine-DNA alkyltransferase (AGT) is an important DNA repair protein that protects cells from mutagenesis and toxicity arising from alkylating agents. We present an X-ray crystal structure of the wild-type human protein (hAGT) bound to double-stranded DNA with a chemically modified cytosine base. The protein binds at two different sites: one at the modified base, and the other across a sticky-ended DNA junction. The protein molecule that binds the modified cytosine base flips the base and recognizes it in its active site. The one that binds ends of neighboring DNA molecules partially flips an overhanging thymine base. This base is not inserted into the active-site pocket of the protein. These two different hAGT/DNA interactions observed in the structure suggest that hAGT may not detect DNA lesions by searching for the adduct itself, but rather for weakened and/or distorted base-pairs caused by base damage in the duplex DNA. We propose that hAGT imposes a strain on the DNA duplex and searches for DNA regions where the native structure is destabilized. The structure provides implications for pyrimidine recognition, improved inhibitor design, and a possible protein/protein interaction patch on hAGT.
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Affiliation(s)
- Erica M Duguid
- Department of Chemistry, 5735 South Ellis Avenue, The University of Chicago, Chicago, IL 60637, USA
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669
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Abstract
Critical cellular processes are regulated, in part, by maintaining the appropriate intracellular levels of proteins. Whereas de novo protein synthesis is a comparatively slow process, proteins are rapidly degraded at a rate compatible with the control of cell cycle transitions and cell death induction. A major pathway for protein degradation is initiated by the addition of multiple 76-amino acid ubiquitin monomers via a three-step process of ubiquitin activation and substrate recognition. Polyubiquitination targets proteins for recognition and processing by the 26S proteasome, a cylindrical organelle that recognizes ubiquitinated proteins, degrades the proteins, and recycles ubiquitin. The critical roles played by ubiquitin-mediated protein turnover in cell cycle regulation makes this process a target for oncogenic mutations. Oncogenes of several common malignancies, for example colon and renal cell cancer, code for ubiquitin ligase components. Cervical oncogenesis by human papillomavirus is also mediated by alteration of ubiquitin ligase pathways. Protein degradation pathways are also targets for cancer therapy, as shown by the successful introduction of bortezomib, an inhibitor of the 26S proteasome. Further work in this area holds great promise toward our understanding and treatment of a wide range of cancers.
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Affiliation(s)
- Aparna Mani
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3800 Reservoir Rd NW, Washington, DC 20007-2197, USA
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670
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Choi WS, Khurana A, Mathur R, Viswanathan V, Steele DF, Fedida D. Kv1.5 surface expression is modulated by retrograde trafficking of newly endocytosed channels by the dynein motor. Circ Res 2005; 97:363-71. [PMID: 16051887 DOI: 10.1161/01.res.0000179535.06458.f8] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this article we have investigated the mechanisms by which retrograde trafficking regulates the surface expression of the voltage-gated potassium channel, Kv1.5. Overexpression of p50/dynamitin, known to disrupt the dynein-dynactin complex responsible for carrying vesicle cargo, substantially increased outward K+ currents in HEK293 cells stably expressing Kv1.5 (0.57+/-0.07 nA/pF, n=12; to 1.18+/-0.2 nA/pF, n=12, P<0.01), as did treatment of the cells with a dynamin inhibitory peptide, which blocks endocytosis. Nocodazole pretreatment, which depolymerizes the microtubule cytoskeleton along which dynein tracks, also doubled Kv1.5 currents in HEK cells and sustained K+ currents in isolated rat atrial myocytes. These increased currents were blocked by 1 mmol/L 4-aminopyridine, and the specific Kv1.5 antagonist, DMM (100 nM). Confocal imaging of both HEK cells and myocytes, as well as experiments testing the sensitivity of the channel in living cells to external Proteinase K, showed that this increase of K+ current density was caused by a redistribution of channels toward the plasma membrane. Coimmunoprecipitation experiments demonstrated a direct interaction between Kv1.5 and the dynein motor complex in both heterologous cells and rat cardiac myocytes, supporting the role of this complex in Kv1.5 trafficking, which required an intact SH3-binding domain in the Kv1.5 N terminus to occur. These experiments highlight a pathway for Kv1.5 internalization from the cell surface involving early endosomes, followed by later trafficking by the dynein motor along microtubules. This work has significant implications for understanding the way Kv channel surface expression is regulated.
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Affiliation(s)
- Woo Sung Choi
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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671
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Pérez-Gómez E, Eleno N, López-Novoa JM, Ramirez JR, Velasco B, Letarte M, Bernabéu C, Quintanilla M. Characterization of murine S-endoglin isoform and its effects on tumor development. Oncogene 2005; 24:4450-61. [PMID: 15806144 DOI: 10.1038/sj.onc.1208644] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Endoglin is a transmembrane glycoprotein that acts as an auxiliary receptor for transforming growth factor-beta (TGF-beta) and modulates cellular responses to this pleiotropic cytokine. Endoglin is strongly expressed in endothelial cells, where it appears to exert a crucial role in vascular development and angiogenesis. Two endoglin isoforms (L and S), differing in their cytoplasmic domains, have been previously characterized in human tissues. We now demonstrate the existence of similar L- and S-endoglin variants in murine tissues with 47 and 35 amino acids, respectively, in their cytoplasmic tail. RT-PCR analysis showed that L is the predominant endoglin isoform expressed in mouse tissues, although S-endoglin mRNA is significantly expressed in liver and lung, as well as in endothelial cell lines. Furthermore, a protein of size equivalent to recombinant S-endoglin expressed in mammalian cells was detected in mouse endothelial cells by Western blot analysis. L- and S-endoglin isoforms can form disulfide-linked heterodimers, as demonstrated by cotransfection of L- and S-endoglin constructs. To address the role of S-endoglin in vivo, an S-Eng(+) transgenic mouse model that targets S-endoglin expression to the endothelium was generated. The lethal phenotype of endoglin-null (Eng(-/-)) mice was not rescued by breeding S-Eng(+) transgenic mice into the endoglin-null background. S-Eng(+) mice exhibited reduced tumor growth and neovascularization after transplantation of Lewis lung carcinoma cells. In addition, S-Eng(+) mice showed a drastic inhibition of benign papilloma formation when subjected to two-stage chemical skin carcinogenesis. These results point to S-endoglin as an antiangiogenic molecule, in contrast to L-endoglin which is proangiogenic. Oncogene (2005) 24, 4450-4461. doi:10.1038/sj.onc.1208644 Published online 4 April 2005.
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Affiliation(s)
- Eduardo Pérez-Gómez
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Arturo Duperier 4, 28029 Madrid, Spain
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672
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Cabanes D, Sousa S, Cebriá A, Lecuit M, García-del Portillo F, Cossart P. Gp96 is a receptor for a novel Listeria monocytogenes virulence factor, Vip, a surface protein. EMBO J 2005; 24:2827-38. [PMID: 16015374 PMCID: PMC1182245 DOI: 10.1038/sj.emboj.7600750] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Accepted: 06/27/2005] [Indexed: 11/09/2022] Open
Abstract
By comparative genomics, we have identified a gene of the intracellular pathogen Listeria monocytogenes that encodes an LPXTG surface protein absent from nonpathogenic Listeria species. This gene, vip, is positively regulated by PrfA, the transcriptional activator of the major Listeria virulence factors. Vip is anchored to the Listeria cell wall by sortase A and is required for entry into some mammalian cells. Using a ligand overlay approach, we identified a cellular receptor for Vip, the endoplasmic reticulum (ER) resident chaperone Gp96 recently shown to interact with TLRs. The Vip-Gp96 interaction is critical for bacterial entry into some cells. Comparative infection studies using oral and intravenous inoculation of nontransgenic and transgenic mice expressing human E-cadherin demonstrated a role for Vip in Listeria virulence, not only at the intestine level but also in late stages of the infectious process. Vip thus appears as a new virulence factor exploiting Gp96 as a receptor for cell invasion and/or signalling events that may interfere with the host immune response in the course of the infection.
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Affiliation(s)
- Didier Cabanes
- Unité des Interactions Bactéries Cellules Institut Pasteur, INSERM U604, INRA USC 2020, Paris, France
| | - Sandra Sousa
- Unité des Interactions Bactéries Cellules Institut Pasteur, INSERM U604, INRA USC 2020, Paris, France
| | - Antonio Cebriá
- Departamento de Biotecnologia Microbiana, Centro National de Biotecnologia-CSIC Darwin 3, Madrid, Spain
| | - Marc Lecuit
- Unité des Interactions Bactéries Cellules Institut Pasteur, INSERM U604, INRA USC 2020, Paris, France
| | | | - Pascale Cossart
- Unité des Interactions Bactéries Cellules Institut Pasteur, INSERM U604, INRA USC 2020, Paris, France
- Unité des Interactions Bactéries Cellules Institut Pasteur, INSERM U604, INRA USC 2020, 28 rue du Dr Roux, 75015 Paris, France. Tel.: +33 1 4568 8841; Fax: +33 1 4568 8706; E-mail:
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673
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Davison EM, Harrison MM, Walhout AJM, Vidal M, Horvitz HR. lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein. Genetics 2005; 171:1017-31. [PMID: 16020796 PMCID: PMC1456809 DOI: 10.1534/genetics.104.034173] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ras-mediated vulval development in C. elegans is inhibited by the functionally redundant sets of class A, B, and C synthetic Multivulva (synMuv) genes. Three of the class B synMuv genes encode an Rb/DP/E2F complex that, by analogy with its mammalian and Drosophila counterparts, has been proposed to silence genes required for vulval specification through chromatin modification and remodeling. Two class A synMuv genes, lin-15A and lin-56, encode novel nuclear proteins that appear to function as a complex. We show that a third class A synMuv gene, lin-8, is the defining member of a novel C. elegans gene family. The LIN-8 protein is nuclear and can interact physically with the product of the class B synMuv gene lin-35, the C. elegans homolog of mammalian Rb. LIN-8 likely acts with the synMuv A proteins LIN-15A and LIN-56 in the nucleus, possibly in a protein complex with the synMuv B protein LIN-35 Rb. Other LIN-8 family members may function in similar complexes in different cells or at different stages. The nuclear localization of LIN-15A, LIN-56, and LIN-8, as well as our observation of a direct physical interaction between class A and class B synMuv proteins, supports the hypothesis that the class A synMuv genes control vulval induction through the transcriptional regulation of gene expression.
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Affiliation(s)
- Ewa M Davison
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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674
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Shimokawa N, Dikic I, Sugama S, Koibuchi N. Molecular responses to acidosis of central chemosensitive neurons in brain. Cell Signal 2005; 17:799-808. [PMID: 15763422 DOI: 10.1016/j.cellsig.2005.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 12/24/2004] [Accepted: 01/07/2005] [Indexed: 11/22/2022]
Abstract
Significant advances have been made in understanding how neurons sense and respond to acidosis at the cellular level. Decrease in pH of the cerebrospinal fluid followed by hypercapnia (increased arterial CO2) is monitored by the chemosensory neurons of the medulla oblongata. Then the intracellular signalling pathways are activated to regulate specific gene expression, which leads to a hyperventilatory response. However, little is known about molecular details of such cellular responses. Recent studies have identified several transcription factors such as c-Jun, Fos and small Maf proteins that may play critical roles in the brain adaptation to hypercapnia. Hypercapnic stimulation also activates c-Jun NH2-terminal kinase (JNK) cascade via influx of extracellular Ca2+ through voltage-gated Ca2+ channels. In addition, several transmembrane proteins including Rhombex-29 (rhombencephalic expression protein-29 kDa) and Past-A (proton-associated sugar transporter-A) have been implicated in regulation of H+ sensitivity and brain acidosis-mediated energy metabolism, respectively. This review discusses current knowledge on the signalling mechanisms and molecular basis of neuronal adaptation during acidosis.
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Affiliation(s)
- Noriaki Shimokawa
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi-shi 371-8511, Japan.
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675
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Kofler M, Motzny K, Beyermann M, Freund C. Novel interaction partners of the CD2BP2-GYF domain. J Biol Chem 2005; 280:33397-402. [PMID: 16000308 DOI: 10.1074/jbc.m503989200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The GYF domain of CD2BP2 serves as an adapter that recognizes proline-rich sequences in intracellular proteins. Although the T cell adhesion molecule CD2 and the core splicing protein SmB/B' were previously shown to interact with CD2BP2-GYF, we are now using a general approach to identify putative GYF domain target sites within the human proteome. The phage display-derived recognition motif for CD2BP2-GYF is PPG(W/F/Y/M/L). SPOT analysis confirmed that the GYF domain interacts with peptides from human proteins containing the consensus site. Epitope mapping by NMR spectroscopy performed for several peptides revealed a conserved binding surface. A direct interaction of the CD2BP2-GYF domain with the novel protein interaction partners PI31 and NPWBP was verified by yeast two-hybrid analysis.
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Affiliation(s)
- Michael Kofler
- Protein Engineering Group, Forschungsinstitut für Molekulare Pharmakologie and Freie Universität Berlin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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676
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Rath A, Davidson AR, Deber CM. The structure of "unstructured" regions in peptides and proteins: role of the polyproline II helix in protein folding and recognition. Biopolymers 2005; 80:179-85. [PMID: 15700296 DOI: 10.1002/bip.20227] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Classical descriptions of the three-dimensional shapes of proteins usually invoke three main structures: alpha-helix, beta-sheet, and beta-turn. More recently, the polyproline II (PPII) structure has been implicated in diverse biological activities including signal transduction, transcription, cell motility, and immune response. Concurrently, evidence is accumulating that PPII structure has a significant role in the unfolded states of proteins. In this article, we connect the structural properties of PPII helices to their roles in protein recognition and protein unfolded states. The properties unique to the PPII conformation are linked to the exploitation of this structure for the molecular recognition of proteins, using peptide ligands of the Src homology 3 (SH3) domain as an example. The evidence supporting a role for PPII conformation in protein-unfolded states is also presented in the context of the forces that may stabilize the PPII conformation in unfolded polypeptides.
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Affiliation(s)
- Arianna Rath
- Division of Structural Biology & Biochemistry, Research Institute, Hospital for Sick Children, Toronto M5G 1X8, Ontario, Canada
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677
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Choe SS, Dodd DA, Kirkegaard K. Inhibition of cellular protein secretion by picornaviral 3A proteins. Virology 2005; 337:18-29. [PMID: 15914217 DOI: 10.1016/j.virol.2005.03.036] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Revised: 02/10/2005] [Accepted: 03/30/2005] [Indexed: 10/25/2022]
Abstract
During poliovirus infection, anterograde traffic between the endoplasmic reticulum and the Golgi is inhibited due to the action of 3A, an 87 amino acid viral protein. The ability of poliovirus protein 3A to inhibit ER-to-Golgi traffic is not required for virus growth. Instead, we have suggested that the inhibition of host protein secretion, shown to reduce the secretion of interferon-beta, IL-6, and IL-8 and the expression of both newly synthesized MHC class I and TNF receptor in the plasma membrane of infected cells, affects growth in host organisms. To determine whether the ability of poliovirus 3A to inhibit ER-to-Golgi traffic is conserved, the ability of 3A proteins from several picornaviruses, including human rhinovirus 14, foot-and-mouth disease virus, enterovirus 71, hepatitis A, and Theiler's virus, was tested. Only the 3A proteins from another poliovirus, Sabin 3, and closely related coxsackievirus B3 inhibited ER-to-Golgi traffic as effectively as the 3A protein from poliovirus Mahoney type 1. Site-directed mutagenesis based on these findings and the three-dimensional structure of the amino-terminal domain of poliovirus 3A protein revealed that residues in the unstructured amino terminus of 3A are critical for the inhibition of host protein secretion.
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Affiliation(s)
- Sunny S Choe
- Department of Microbiology and Immunology, Stanford University School of Medicine, CA 94305-5127, USA
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678
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Abstract
BACKGROUND Tooth staining is a common feature of chlorhexidine treatment for periodontal disease and there is a large variation between patients as to the degree of their tooth staining. Although the mechanism of tooth staining is uncertain, diet, smoking and oral hygiene appear probable factors. OBJECTIVES This study investigated the role of saliva in chlorhexidine-induced tooth staining and used tea as the staining agent in an in vitro model with hydroxyapatite mimicking teeth. METHODS Saliva has been used to create an acquired pellicle and in solution to mimic its effects in vivo. Using different combinations of tea, chlorhexidine and parotid saliva, substances binding to hydroxyapatite were analysed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using this system, tea, chlorhexidine and salivary proteins were clearly identifiable following staining by Coomassie Brilliant Blue. RESULTS The results indicated that tea interacted with many salivary proteins, in particular proline-rich proteins and histatins. Chlorhexidine did not appear to complex with or precipitate salivary proteins nor prevent the formation of an acquired pellicle on the hydroxyapatite. In isolation, tea and chlorhexidine bound in small amounts to hydroxyapatite, but when added in combination, binding of both to hydroxyapatite was greatly increased. The acquired pellicle reduced chlorhexidine and tea binding, but conversely increased the binding of either tea or chlorhexidine alone to hydroxyapatite. CONCLUSION In conclusion, salivary proteins play an important role in the staining process and the combination of tea and chlorhexidine appears to be a very potent staining factor.
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Affiliation(s)
- G H Carpenter
- Salivary Research Unit, GKT Dental School, Guys Hospital, London, UK.
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679
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Solomaha E, Szeto FL, Yousef MA, Palfrey HC. Kinetics of Src Homology 3 Domain Association with the Proline-rich Domain of Dynamins. J Biol Chem 2005; 280:23147-56. [PMID: 15834155 DOI: 10.1074/jbc.m501745200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dynamin function is mediated in part through association of its proline-rich domain (PRD) with the Src homology 3 (SH3) domains of several putative binding proteins. To assess the specificity and kinetics of this process, we undertook surface plasmon resonance studies of the interaction between isolated PRDs of dynamin-1 and -2 and several purified SH3 domains. Glutathione S-transferase-linked SH3 domains bound with high affinity (K(D) approximately 10 nm to 1 microm) to both dynamin-1 and -2. The simplest interaction appeared to take place with the amphiphysin-SH3 domain; this bound to a single high affinity site (K(D) approximately 10 nm) in the C terminus of dynamin-1 PRD, as predicted by previous studies. Binding to the dynamin-2 PRD was also monophasic but with a slightly lower affinity (K(D) approximately 25 nm). Endophilin-SH3 binding to both dynamin-1 and -2 PRDs was biphasic, with one high affinity site (K(D) approximately 14 nm) in the N terminus of the PRD and another lower affinity site (K(D) approximately 60 nm) in the C terminus of dynamin-1. The N-terminal site in dynamin-2 PRD had a 10-fold lower affinity for endophilin-SH3. Preloading of dynamin-1 PRD with the amphiphysin-SH3 domain partially occluded binding of the endophilin-SH3 domain, indicating overlap between the binding sites in the C terminus, but endophilin was still able to interact with the high affinity N-terminal site. This shows that more than one SH3 domain can simultaneously bind to the PRD and suggests that competition probably occurs in vivo between different SH3-containing proteins for the limited number of PXXP motifs. Endophilin-SH3 binding to the high affinity site was disrupted when dynamin-1 PRD was phosphorylated with Cdk5, indicating that this site overlaps the phosphorylation sites, but amphiphysin-SH3 binding was unaffected. Other SH3 domains showed similarly complex binding characteristics, and substantial differences were noted between the PRDs from dynamin-1 and -2. For example, SH3 domains from c-Src, Grb2, and intersectin bound only to the C-terminal half of dynamin-2 PRD but to both the N- and C-terminal portions of dynamin-1 PRD. Thus, differential binding of SH3 domain-containing proteins to dynamin-1 and -2 may contribute to the distinct functions performed by these isoforms.
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Affiliation(s)
- Elena Solomaha
- Department of Neurobiology, Pharamacology, and Physiology, University of Chicago, IL 60637, USA
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680
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Thomas KM, Naduthambi D, Tririya G, Zondlo NJ. Proline Editing: A Divergent Strategy for the Synthesis of Conformationally Diverse Peptides. Org Lett 2005; 7:2397-400. [PMID: 15932207 DOI: 10.1021/ol0506720] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Strong conformational biases in peptides and proteins can be achieved with 4-substituted proline residues (cis-, trans-, or disubstituted fluoroproline or hydroxyproline). The practical, divergent synthesis of peptides containing these residues, via postsynthetic modification of a peptide containing an internal trans-hydroxyproline residue, is described. Significant differences in the conformations of the peptides Ac-TYXN-NH2 were observed, including K(trans/cis) values, which varied from 1.5 (X = cis-fluoroproline) to 7.0 (X = trans-fluoroproline).
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Affiliation(s)
- Krista M Thomas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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681
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Wessels E, Duijsings D, Notebaart RA, Melchers WJG, van Kuppeveld FJM. A proline-rich region in the coxsackievirus 3A protein is required for the protein to inhibit endoplasmic reticulum-to-golgi transport. J Virol 2005; 79:5163-73. [PMID: 15795300 PMCID: PMC1069528 DOI: 10.1128/jvi.79.8.5163-5173.2005] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of the 3A protein of coxsackievirus B (CVB) to inhibit protein secretion was investigated for this study. Here we show that the ectopic expression of CVB 3A blocked the transport of both the glycoprotein of vesicular stomatitis virus, a membrane-bound secretory marker, and the alpha-1 protease inhibitor, a luminal secretory protein, at a step between the endoplasmic reticulum (ER) and the Golgi complex. CVB 3A contains a conserved proline-rich region in its N terminus. The importance of this proline-rich region was investigated by introducing Pro-to-Ala substitutions. The mutation of Pro19 completely abolished the ability of 3A to inhibit ER-to-Golgi transport. The mutation of Pro14, Pro17, or Pro20 also impaired this ability, but to a lesser extent. The mutation of Pro18 had no effect. We also investigated the possible importance of this proline-rich region for the function of 3A in viral RNA replication. To this end, we introduced the Pro-to-Ala mutations into an infectious cDNA clone of CVB3. The transfection of cells with in vitro-transcribed RNAs of these clones gave rise to mutant viruses that replicated with wild-type characteristics. We concluded that the proline-rich region in CVB 3A is required for its ability to inhibit ER-to-Golgi transport, but not for its function in viral RNA replication. The functional relevance of the proline-rich region is discussed in light of the proposed structural model of 3A.
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Affiliation(s)
- Els Wessels
- Department of Medical Microbiology, Nijmegen Center for Molecular Life Sciences, University Medical Center Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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682
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Kurihara Y, Watanabe H, Kawaguchi A, Hori T, Mishiro K, Ono M, Sawada H, Uesugi S. Dynamic changes in intranuclear and subcellular localizations of mouse Prrp/DAZAP1 during spermatogenesis: the necessity of the C-terminal proline-rich region for nuclear import and localization. ACTA ACUST UNITED AC 2005; 67:325-33. [PMID: 15700540 DOI: 10.1679/aohc.67.325] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Mouse Prrp (mPrrp)/DAZAP1 is a mouse ortholog of Xenopus Prrp, which is involved in vegetal pole localization of Vg1 mRNA in oocytes and is highly expressed in the testis. The mouse protein has been reported to be a shuttling protein which localizes in the nucleus of pre-meiotic spermatogenic cells and round spermatids, and shifts its location into the cytoplasm in elongating spermatids, suggesting that mPrrp may be involved in mRNA transport as well as that of the Xenopus ortholog. We reexamined immunohistochemical analyses of mPrrp/DAZAP1 during spermatogenesis utilizing a newly established monoclonal antibody and reconfirmed it to be a shuttling protein. We also carried out new observations that included remarkable intranuclear movement during spermatogenesis. In addition, we found that a long amino acid stretch which spanned over the C-terminal half of the protein was required for the nuclear import. These observations demonstrated dynamic changes in subnuclear and subcellular localization which might reflect specific functions during spermatogenesis.
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Affiliation(s)
- Yasuyuki Kurihara
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Hodogaya, Yokohama, Japan.
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683
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Kapp K, Knobloch J, Schüssler P, Sroka S, Lammers R, Kunz W, Grevelding CG. The Schistosoma mansoni Src kinase TK3 is expressed in the gonads and likely involved in cytoskeletal organization. Mol Biochem Parasitol 2005; 138:171-82. [PMID: 15555729 DOI: 10.1016/j.molbiopara.2004.07.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 07/23/2004] [Accepted: 07/31/2004] [Indexed: 10/26/2022]
Abstract
Cytoplasmic protein tyrosine kinases of the Src family play a pivotal role in the regulation of cellular processes including proliferation and differentiation. Among other functions, Src kinases are involved in regulating the cell architecture. In an approach to identify protein tyrosine kinases from the medically important parasite Schistosoma mansoni, we isolated the TK3 gene by degenerate primer PCR and cDNA library screening. Sequencing of the complete cDNA and data-base analyses indicated that TK3 is a Src family kinase. Its predicted size of 71 kDa was confirmed by Western blot analysis. Southern blot analysis showed that TK3 is a single-copy gene, and Northern blot and RT-PCR experiments indicated its expression in both sexes and throughout development. Localization studies by in situ hybridization and immunolocalization revealed that TK3 is predominantly expressed in the reproductive organs such as the testes of the male and the ovary as well as the vitellarium of the female. Its enzymatic activity was confirmed by functional analyses. In transient transfection experiments with HEK293 cells, TK3 phosphorylated the well-known Src-kinase substrate p130 Cas, an intracellular scaffolding protein. Yeast two-hybrid screenings in a heterologous invertebrate system identified dAbi, vinculin and tubulin as binding partners, representing molecules that fulfill functions in the cell architecture of many organisms. These findings suggest that TK3 may play a role in signal transduction pathways organizing the cytoskeleton in the gonads of schistosomes.
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Affiliation(s)
- Katja Kapp
- Institut für Genetik, Genetische Parasitologie und Biologisch-Medizinisches-Forschungszentrum, Universitätsstr. 1, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
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684
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Ball LJ, Kühne R, Schneider-Mergener J, Oschkinat H. Recognition of Proline-Rich Motifs by Protein-Protein-Interaction Domains. Angew Chem Int Ed Engl 2005; 44:2852-69. [PMID: 15880548 DOI: 10.1002/anie.200400618] [Citation(s) in RCA: 211] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Protein-protein interactions are essential in every aspect of cellular activity. Multiprotein complexes form and dissociate constantly in a specifically tuned manner, often by conserved mechanisms. Protein domains that bind proline-rich motifs (PRMs) are frequently involved in signaling events. The unique properties of proline provide a mechanism for highly discriminatory recognition without requiring high affinities. We present herein a detailed, quantitative assessment of the structural features that define the interfaces between PRM-binding domains and their target PRMs, and investigate the specificity of PRM recognition. Together with the analysis of peptide-library screens, this approach has allowed the identification of several highly conserved key interactions found in all complexes of PRM-binding domains. The inhibition of protein-protein interactions by using small-molecule agents is very challenging. Therefore, it is important to first pinpoint the critical interactions that must be considered in the design of inhibitors of PRM-binding domains.
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Affiliation(s)
- Linda J Ball
- Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
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685
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Ball LJ, Kühne R, Schneider-Mergener J, Oschkinat H. Erkennung Prolin-reicher Motive (PRMs) durch Protein-Protein-Wechselwirkungsdomänen. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200400618] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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686
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Menendez A, Scott JK. The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies. Anal Biochem 2005; 336:145-57. [PMID: 15620878 DOI: 10.1016/j.ab.2004.09.048] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Indexed: 10/26/2022]
Affiliation(s)
- Alfredo Menendez
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6.
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687
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Jaronczyk K, Carmichael J, Hobman T. Exploring the functions of RNA interference pathway proteins: some functions are more RISCy than others? Biochem J 2005; 387:561-71. [PMID: 15845026 PMCID: PMC1134985 DOI: 10.1042/bj20041822] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Revised: 12/23/2004] [Accepted: 02/22/2005] [Indexed: 01/21/2023]
Abstract
PPD (PAZ Piwi domain) proteins and the Dicer family have been the subjects of intense study over the last 6 years. These proteins have well-established roles in RNAi (RNA interference), a process that relies on siRNAs (small interfering RNAs) or miRNAs (microRNAs) to mediate specificity. The development of techniques for applying RNAi as a laboratory tool and a molecular therapeutic technique has rapidly outpaced our understanding of the biology of this process. However, over the last 2 years, great strides have been made towards elucidating how PPD proteins and Dicer regulate gene-silencing at the pre- and post-transcriptional levels. In addition, evidence is beginning to emerge that suggests that these proteins have additional siRNA-independent roles as cell-cycle regulators. In the present review, we summarize the well-known roles of these two classes of proteins in gene-silencing pathways, as well as explore the evidence for novel roles of PPD and Dicer proteins.
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Key Words
- dicer
- gene expression
- gene silencing
- paz piwi domain protein (ppd protein)
- rna-induced silencing complex (risc)
- rna interference (rnai)
- ds, double-stranded
- fxr, fragile x mental retardation protein
- gfp, green fluorescent protein
- mirna, microrna
- mirnp, mirna-containing ribonucleoprotein
- mvh, mammalian vasa homologue
- ppd, paz piwi domain
- risc, rna-induced silencing complex
- rits, rna-induced initiation of transcriptional gene silencing
- rnai, rna interference
- sirna, small interfering rna
- ss, single-stranded
- utr, untranslated region
- vig, vasa intronic gene protein
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Affiliation(s)
- Katarzyna Jaronczyk
- *Department of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Jon B. Carmichael
- *Department of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Tom C. Hobman
- *Department of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7
- †Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada T6G 2H7
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688
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Bour G, Plassat JL, Bauer A, Lalevée S, Rochette-Egly C. Vinexin beta interacts with the non-phosphorylated AF-1 domain of retinoid receptor gamma (RARgamma) and represses RARgamma-mediated transcription. J Biol Chem 2005; 280:17027-37. [PMID: 15734736 DOI: 10.1074/jbc.m501344200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear retinoic acid receptors (RARs) are ligand-dependent transcription factors that regulate the expression of retinoic acid target genes. Although the importance of RAR phosphorylation in their N-terminal domain is clearly established, the underlying mechanism for the phosphorylation-dependent transcriptional activity of the receptors had not been elucidated yet. Here, using a yeast two-hybrid system, we report the isolation of vinexin beta as a new cofactor that interacts with the N-terminal A/B domain of the RARgamma isotype. Vinexin beta is a multiple SH3 motif-containing protein associated with the cytoskeleton and also present in the nucleus. We demonstrate that vinexin beta colocalizes with RARgamma in the nucleus and interacts with the non-phosphorylated form of the AF-1 domain of RARgamma. We also show that this interaction is prevented upon phosphorylation of the AF-1 domain. Using F9 cells stably overexpressing vinexin beta or vinexin knockdown by RNA interference, we demonstrate that vinexin beta is an inhibitor of RARgamma-mediated transcription. We propose a model in which phosphorylation of the AF-1 domain controls RARgamma-mediated transcription through triggering the dissociation of vinexin beta.
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MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Motifs
- Amino Acid Sequence
- Animals
- COS Cells
- Cell Nucleus/metabolism
- Chloramphenicol O-Acetyltransferase/metabolism
- Cloning, Molecular
- DNA, Complementary/metabolism
- Glutathione Transferase/metabolism
- Humans
- Immunoprecipitation
- Mice
- Microscopy, Fluorescence
- Molecular Sequence Data
- Muscle Proteins/chemistry
- Muscle Proteins/metabolism
- Phosphorylation
- Plasmids/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA/metabolism
- RNA Interference
- RNA, Small Interfering/metabolism
- Receptors, Retinoic Acid/chemistry
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Time Factors
- Transcription, Genetic
- Transcriptional Activation
- Transfection
- Tretinoin/metabolism
- Two-Hybrid System Techniques
- beta-Galactosidase/metabolism
- src Homology Domains
- Retinoic Acid Receptor gamma
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Affiliation(s)
- Gaétan Bour
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université Louis Pasteur, Unité Mixte de Recherche 7104, 67404 Illkirch Cedex, France
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689
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Winters MJ, Pryciak PM. Interaction with the SH3 domain protein Bem1 regulates signaling by the Saccharomyces cerevisiae p21-activated kinase Ste20. Mol Cell Biol 2005; 25:2177-90. [PMID: 15743816 PMCID: PMC1061602 DOI: 10.1128/mcb.25.6.2177-2190.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Saccharomyces cerevisiae PAK (p21-activated kinase) family kinase Ste20 functions in several signal transduction pathways, including pheromone response, filamentous growth, and hyperosmotic resistance. The GTPase Cdc42 localizes and activates Ste20 by binding to an autoinhibitory motif within Ste20 called the CRIB domain. Another factor that functions with Ste20 and Cdc42 is the protein Bem1. Bem1 has two SH3 domains, but target ligands for these domains have not been described. Here we identify an evolutionarily conserved binding site for Bem1 between the CRIB and kinase domains of Ste20. Mutation of tandem proline-rich (PxxP) motifs in this region disrupts Bem1 binding, suggesting that it serves as a ligand for a Bem1 SH3 domain. These PxxP motif mutations affect signaling additively with CRIB domain mutations, indicating that Bem1 and Cdc42 make separable contributions to Ste20 function, which cooperate to promote optimal signaling. This PxxP region also binds another SH3 domain protein, Nbp2, but analysis of bem1Delta versus nbp2Delta strains shows that the signaling defects of PxxP mutants result from impaired binding to Bem1 rather than from impaired binding to Nbp2. Finally, the PxxP mutations also reduce signaling by constitutively active Ste20, suggesting that postactivation functions of PAKs can be promoted by SH3 domain proteins, possibly by colocalizing PAKs with their substrates. The overall results also illustrate how the final signaling function of a protein can be governed by combinatorial addition of multiple, independent protein-protein interaction modules.
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Affiliation(s)
- Matthew J Winters
- Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 377 Plantation St., Four Biotech, Rm. 330, Worcester, MA 01605, USA
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690
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Lua BL, Low BC. Cortactin phosphorylation as a switch for actin cytoskeletal network and cell dynamics control. FEBS Lett 2005; 579:577-85. [PMID: 15670811 DOI: 10.1016/j.febslet.2004.12.055] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Revised: 12/01/2004] [Accepted: 12/06/2004] [Indexed: 12/27/2022]
Abstract
Cortactin is an important molecular scaffold for actin assembly and organization. Novel mechanistic functions of cortactin have emerged with more interacting partners identified, revealing its multifaceted roles in regulating actin cytoskeletal networks that are necessary for endocytosis, cell migration and invasion, adhesion, synaptic organization and cell morphogenesis. These processes are mediated by its multi-domains binding to F-actin and Arp2/3 complex and various SH3 targets. Furthermore, its role in actin remodeling is subjected to regulation by tyrosine and serine/threonine kinases. Elucidating the mechanisms underlying cortactin phosphorylation and its functional consequences would provide new insights to various aspects of cell dynamics control.
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Affiliation(s)
- Bee Leng Lua
- Cell Signaling and Developmental Biology Laboratory, Department of Biological Sciences, The National University of Singapore, 14 Science Drive 4, Singapore 117543, The Republic of Singapore
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691
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Zhang H, Christoforou A, Aravind L, Emmons SW, van den Heuvel S, Haber DA. The C. elegans Polycomb gene SOP-2 encodes an RNA binding protein. Mol Cell 2005; 14:841-7. [PMID: 15200961 DOI: 10.1016/j.molcel.2004.06.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Revised: 04/23/2004] [Accepted: 04/27/2004] [Indexed: 10/26/2022]
Abstract
Epigenetic silencing of Hox cluster genes by Polycomb group (PcG) proteins is thought to involve the formation of a stably inherited repressive chromatin structure. Here we show that the C. elegans-specific PcG protein SOP-2 directly binds to RNA through three nonoverlapping regions, each of which is essential for its localization to characteristic nuclear bodies and for its in vivo function in the repression of Hox genes. Functional studies indicate that the RNA involved in SOP-2 binding is distinct from either siRNA or microRNA. Remarkably, the vertebrate PcG protein Rae28, which is functionally and structurally related to SOP-2, also binds to RNA through an FCS finger domain. Substitution of the Rae28 FCS finger for the essential RNA binding region of SOP-2 partially restores localization to nuclear bodies. These observations suggest that direct binding to RNA is an evolutionarily conserved and potentially important property of PcG proteins.
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Affiliation(s)
- Hong Zhang
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
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692
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Wang ML, Yao H, Xu WB. Prediction by support vector machines and analysis by Z-score of poly-l-proline type II conformation based on local sequence. Comput Biol Chem 2005; 29:95-100. [PMID: 15833437 DOI: 10.1016/j.compbiolchem.2005.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2004] [Revised: 01/08/2005] [Accepted: 02/18/2005] [Indexed: 11/25/2022]
Abstract
In recent years, the poly-L-proline type II (PPII) conformation has gained more and more importance. This structure plays vital roles in many biological processes. But few studies have been made to predict PPII secondary structures computationally. The support vector machine (SVM) represents a new approach to supervised pattern classification and has been successfully applied to a wide range of pattern recognition problems. In this paper, we present a SVM prediction method of PPII conformation based on local sequence. The overall accuracy for both the independent testing set and estimate of jackknife testing reached approximately 70%. Matthew's correlation coefficient (MCC) could reach 0.4. By comparing the results of training and testing datasets with different sequence identities, we suggest that the performance of this method correlates with the sequence identity of dataset. The parameter of SVM kernel function was an important factor to the performance of this method. The propensities of residues located at different positions were also analyzed. By computing Z-scores, we found that P and G were the two most important residues to PPII structure conformation.
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Affiliation(s)
- Ming-Lei Wang
- Laboratory of Bioinformatics, The Key Laboratory of Industrial Biotechnology, Ministry of Education, Southern Yangtze University, Wuxi 214036, China.
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693
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Akbarali HI. Signal-transduction pathways that regulate smooth muscle function. II. Receptor-ion channel coupling mechanisms in gastrointestinal smooth muscle. Am J Physiol Gastrointest Liver Physiol 2005; 288:G598-602. [PMID: 15764809 DOI: 10.1152/ajpgi.00402.2004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Regulation of membrane ion channels by second messengers is an important mechanism by which gastrointestinal smooth muscle excitability is controlled. Receptor-mediated phosphorylation of Ca(2+) channels has been known for some time; however, recent findings indicate that these channels may also modulate intracellular signaling. The plasmalemma ion channels may also function as a point of convergence between different receptor types. In this review, the molecular mechanisms that link channel function and signal transduction are discussed. Emerging evidence also indicates altered second-messenger modulation of the Ca(2+) channel in the pathophysiology of smooth muscle dysmotility.
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Affiliation(s)
- Hamid I Akbarali
- Dept. of Physiology, Univ. of Oklahoma Health Sciences Center, 940 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA.
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694
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Ferreon JC, Ferreon ACM, Li K, Lemon SM. Molecular determinants of TRIF proteolysis mediated by the hepatitis C virus NS3/4A protease. J Biol Chem 2005; 280:20483-92. [PMID: 15767257 DOI: 10.1074/jbc.m500422200] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Persistent infections with hepatitis C virus (HCV) are a major cause of liver disease and reflect its ability to disrupt virus-induced signaling pathways activating cellular antiviral defenses. HCV evasion of double-stranded RNA signaling through Toll-like receptor 3 is mediated by the viral protease NS3/4A, which directs proteolysis of its proline-rich adaptor protein, Toll-IL-1 receptor domain containing adaptor-inducing interferon-beta (TRIF). The TRIF cleavage site has remarkable homology with the viral NS4B/5A substrate, although an 8-residue polyproline track extends upstream from the P(6) position in lieu of the acidic residue present in viral substrates. Circular dichroism (CD) spectroscopy confirmed that a substantial fraction of TRIF exists as polyproline II helices, and inclusion of the polyproline track increased affinity of P side TRIF peptides for the HCV-BK protease. A polyproline II peptide representing an SH3 binding motif (PPPVPPRRR, Sos) bound NS3 with moderate affinity, resulting in inhibition of proteolytic activity. Chemical shift perturbations in NMR spectra indicated that Sos binds a 3(10) helix close to the protease active site. Thus, a polyproline II interaction with the 3(10) helix likely facilitates NS3/4A recognition of TRIF, indicating a significant difference from NS3/4A recognition of viral substrates. Because SH3 binding motifs are also present in NS5A, a viral protein that interacts with NS3, we speculate that the NS3 3(10) helix may be a site of interaction with other viral proteins.
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Affiliation(s)
- Josephine C Ferreon
- Department of Microbiology and Immunology, Center for Hepatitis Research, Institute for Human Infections and Immunity, University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1019, USA
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695
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Brondani V, Schefer Q, Hamy F, Klimkait T. The peptidyl-prolyl isomerase Pin1 regulates phospho-Ser77 retinoic acid receptor alpha stability. Biochem Biophys Res Commun 2005; 328:6-13. [PMID: 15670742 DOI: 10.1016/j.bbrc.2004.12.130] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Indexed: 11/25/2022]
Abstract
Peptidyl-prolyl isomerases (PPIase) facilitate the cis-trans interconversion of the peptidyl-prolyl bond and in such way affect protein folding. Pin1 is a PPIase, which specifically recognizes phosphorylated S/T-P bonds. The transcription factor TFIIH mediates phosphorylation of the retinoic acid receptor alpha (RARalpha) at position Ser77. In the presence of retinoic acid ligand (RA), the Ser77 non-phosphorylated receptor is suggested to undergo degradation through the proteasome pathway. Here we provide evidence that Pin1 is able to selectively destabilize RARalpha in a ligand independent-manner. We show that this is caused by RARalpha ubiquitination, which in turn is phosphorylation dependent. The single mutation Ser77>A completely abolishes RARalpha degradation whereas the mutation Ser77>E rescues this effect. In addition, we correlate RARalpha stability to Ser77 phosphorylation required for the ligand independent transcriptional activity on fgf8 promoter. Finally, we show that the ligand-independent Ser77 phosphorylation requires the genuine ligand-binding domain.
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Affiliation(s)
- Vincent Brondani
- Institute of Medical Microbiology, University of Basel, Peterplatz 10, CH-4003, Basel, Switzerland.
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696
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Dupré S, Urban-Grimal D, Haguenauer-Tsapis R. Ubiquitin and endocytic internalization in yeast and animal cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1695:89-111. [PMID: 15571811 DOI: 10.1016/j.bbamcr.2004.09.024] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Endocytosis is involved in a wide variety of cellular processes, and the internalization step of endocytosis has been extensively studied in both lower and higher eukaryotic cells. Studies in mammalian cells have described several endocytic pathways, with the main emphasis on clathrin-dependent endocytosis. Genetic studies in yeast have underlined the critical role of actin and actin-binding proteins, lipid modification, and the ubiquitin conjugation system. The combined results of studies of endocytosis in higher and lower eukaryotic cells reveal an interesting interplay in the two systems, including a crucial role for ubiquitin-associated events. The ubiquitylation of yeast cell-surface proteins clearly acts as a signal triggering their internalization. Mammalian cells display variations on the common theme of ubiquitin-linked endocytosis, according to the cell-surface protein considered. Many plasma membrane channels, transporters and receptors undergo cell-surface ubiquitylation, required for the internalization or later endocytic steps of some cell-surface proteins, whereas for others, internalization involves interaction with the ubiquitin conjugation system or with ancillary proteins, which are themselves ubiquitylated. Epsins and Eps15 (or Eps15 homologs), are commonly involved in the process of endocytosis in all eukaryotes, their critical role in this process stemming from their capacity to bind ubiquitin, and to undergo ubiquitylation.
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Affiliation(s)
- S Dupré
- Institut Jacques Monod-CNRS Universités Paris VI and Paris VII, 2 place Jussieu 75005 Paris, France
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697
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Zhu G, Fujii K, Belkina N, Liu Y, James M, Herrero J, Shaw S. Exceptional Disfavor for Proline at the P+1 Position among AGC and CAMK Kinases Establishes Reciprocal Specificity between Them and the Proline-directed Kinases. J Biol Chem 2005; 280:10743-8. [PMID: 15647260 DOI: 10.1074/jbc.m413159200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To precisely regulate critical signaling pathways, two kinases that phosphorylate distinct sites on the same protein substrate must have mutually exclusive specificity. Evolution could assure this by designing families of kinase such as basophilic kinases and proline-directed kinase with distinct peptide specificity; their reciprocal peptide specificity would have to be very complete, since recruitment of substrate allows phosphorylation of even rather poor phosphorylation sites in a protein. Here we report a powerful evolutionary strategy that assures distinct substrates for basophilic kinases (PKA, PKG and PKC (AGC) and calmodulin-dependent protein kinase (CAMK)) and proline-directed kinase, namely by the presence or absence of proline at the P + 1 position in substrates. Analysis of degenerate and non-degenerate peptides by in vitro kinase assays reveals that proline at the P + 1 position in substrates functions as a "veto" residue in substrate recognition by AGC and CAMK kinases. Furthermore, analysis of reported substrates of two typical basophilic kinases, protein kinase C and protein kinase A, shows the lowest occurrence of proline at the P + 1 position. Analysis of crystal structures and sequence conservation provides a molecular basis for this disfavor and illustrate its generality.
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Affiliation(s)
- Guozhi Zhu
- Experimental Immunology Branch, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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698
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Schleinkofer K, Wiedemann U, Otte L, Wang T, Krause G, Oschkinat H, Wade RC. Comparative structural and energetic analysis of WW domain-peptide interactions. J Mol Biol 2005; 344:865-81. [PMID: 15533451 DOI: 10.1016/j.jmb.2004.09.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Revised: 08/02/2004] [Accepted: 09/22/2004] [Indexed: 10/26/2022]
Abstract
WW domains are small globular protein interaction modules found in a wide spectrum of proteins. They recognize their target proteins by binding specifically to short linear peptide motifs that are often proline-rich. To infer the determinants of the ligand binding propensities of WW domains, we analyzed 42 WW domains. We built models of the 3D structures of the WW domains and their peptide complexes by comparative modeling supplemented with experimental data from peptide library screens. The models provide new insights into the orientation and position of the peptide in structures of WW domain-peptide complexes that have not yet been determined experimentally. From a protein interaction property similarity analysis (PIPSA) of the WW domain structures, we show that electrostatic potential is a distinguishing feature of WW domains and we propose a structure-based classification of WW domains that expands the existent ligand-based classification scheme. Application of the comparative molecular field analysis (CoMFA), GRID/GOLPE and comparative binding energy (COMBINE) analysis methods permitted the derivation of quantitative structure-activity relationships (QSARs) that aid in identifying the specificity-determining residues within WW domains and their ligand-recognition motifs. Using these QSARs, a new group-specific sequence feature of WW domains that target arginine-containing peptides was identified. Finally, the QSAR models were applied to the design of a peptide to bind with greater affinity than the known binding peptide sequences of the yRSP5-1 WW domain. The prediction was verified experimentally, providing validation of the QSAR models and demonstrating the possibility of rationally improving peptide affinity for WW domains. The QSAR models may also be applied to the prediction of the specificity of WW domains with uncharacterized ligand-binding properties.
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Affiliation(s)
- Karin Schleinkofer
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69012 Heidelberg, Germany
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699
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Shiokawa D, Matsushita T, Kobayashi T, Matsumoto Y, Tanuma SI. Characterization of the human DNAS1L2 gene and the molecular mechanism for its transcriptional activation induced by inflammatory cytokines. Genomics 2005; 84:95-105. [PMID: 15203207 DOI: 10.1016/j.ygeno.2004.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Accepted: 02/02/2004] [Indexed: 11/27/2022]
Abstract
DNAS1L2, a member of the DNase I-like endonuclease family, is the only divalent cation-dependent acid DNase so far identified in mammals. The presence of a proline-rich domain (PRD) is its unique feature among family members. We found that a novel transcript encoding a short product, DNAS1L2-S, is expressed in peripheral blood leukocytes. Although DNAS1L2-S lacks the PRD, its enzymatic properties are apparently the same as those of the previously identified long form, DNAS1L2-L. Sequence analysis reveals that DNAS1L2 consists of seven exons. The exon/intron boundaries agree with the GT/AG rule with one exception: GC replaces GT at the 5' splice site in the sixth intron. TNF-alpha and IL-1beta are found to be potent inducers of DNAS1L2 expression in keratinocytes. They induce DNAS1L2 activation via the NF-kappaB pathway, and an NF-kappaB binding site located within the 5' flanking region is identified as the cis-responsive element.
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Affiliation(s)
- Daisuke Shiokawa
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Watanabe N, Lam E. Two Arabidopsis metacaspases AtMCP1b and AtMCP2b are arginine/lysine-specific cysteine proteases and activate apoptosis-like cell death in yeast. J Biol Chem 2005; 280:14691-9. [PMID: 15691845 DOI: 10.1074/jbc.m413527200] [Citation(s) in RCA: 192] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Metacaspases in plants, fungi, and protozoa constitute new members of a conserved superfamily of caspase-related proteases. A yeast caspase-1 protein (Yca1p), which is the single metacaspase in Saccharomyces cerevisiae, was shown to mediate apoptosis triggered by oxidative stress or aging in yeast. To examine whether plant metacaspase genes are functionally related to YCA1, we carried out analyses of AtMCP1b and AtMCP2b, representing the two subtypes of the Arabidopsis metacaspase family, utilizing yeast strains with wild-type and the disrupted YCA1 gene (yca1Delta). Inducible expression of AtMCP1b and AtMCP2b significantly promoted yeast apoptosis-like cell death of both the wild-type and yca1Delta strains, relative to the vector controls, during oxidative stress and early aging process. Mutational analysis of the two AtMCPs revealed that their cell-death-inducing activities depend on their catalytic center cysteine residues as well as caspase-like processing. In addition, the phenotype induced by the expression of two AtMCPs was effectively prevented when the cells were pretreated with a broad-spectrum caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl-ketone. These results suggest that the two subtypes of Arabidopsis metacaspases are functionally related to Yca1p with caspase-like characteristics. However, we found that bacterial and yeast extracts containing AtMCP1b, AtMCP2b, or Yca1p exhibit arginine/lysine-specific endopeptidase activities but cannot cleave caspase-specific substrates. Together, the results strongly implicate that expression of metacaspases could result in the activation of downstream protease(s) with caspase-like activities that are required to mediate cell death activation via oxidative stress in yeast. Metacaspases from higher plants may serve similar functions.
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Affiliation(s)
- Naohide Watanabe
- Biotechnology Center for Agriculture and the Environment, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901-8520, USA
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