Syntaxin Binding Mechanism and Disease-Causing Mutations in Munc18-2
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Differential Requirement of NPHP1 for Compartmentalized Protein Localization During
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.20.427412; this version posted January 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Differential requirement of NPHP1 for compartmentalized protein localization during 2 photoreceptor outer segment development and maintenance 3 4 Poppy Dattaa,b,#, J. Thomas Cribbsa,b,#, and Seongjin Seoa,b,* 5 6 aDepartment of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa 7 City, IA 52242, U.S.A. 8 bInstitute for Vision Research, The University of Iowa, Iowa City, IA 52242, U.S.A. 9 10 11 #Equally contributed 12 *To whom correspondence should be addressed: 13 Seongjin Seo, PhD 14 Department of Ophthalmology and Visual Sciences 15 University of Iowa College of Medicine 16 375 Newton Rd 17 3181D MERF 18 Iowa City, IA 52242, U.S.A. 19 Phone: 1-319-353-4477 20 Email: [email protected] 21 22 Running title: Roles of NPHP1 in photoreceptors 23 Keywords: cilia; ciliary gate; compartmentalization; inherited retinal degeneration; nonsense-associated altered 24 splicing; protein confinement; transition zone 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.20.427412; this version posted January 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology
Cancer Research and Treatment 2003;35(4):304-313 New Approaches to Functional Process Discovery in HPV 16-Associated Cervical Cancer Cells by Gene Ontology Yong-Wan Kim, Ph.D.1, Min-Je Suh, M.S.1, Jin-Sik Bae, M.S.1, Su Mi Bae, M.S.1, Joo Hee Yoon, M.D.2, Soo Young Hur, M.D.2, Jae Hoon Kim, M.D.2, Duck Young Ro, M.D.2, Joon Mo Lee, M.D.2, Sung Eun Namkoong, M.D.2, Chong Kook Kim, Ph.D.3 and Woong Shick Ahn, M.D.2 1Catholic Research Institutes of Medical Science, 2Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea, Seoul; 3College of Pharmacy, Seoul National University, Seoul, Korea Purpose: This study utilized both mRNA differential significant genes of unknown function affected by the display and the Gene Ontology (GO) analysis to char- HPV-16-derived pathway. The GO analysis suggested that acterize the multiple interactions of a number of genes the cervical cancer cells underwent repression of the with gene expression profiles involved in the HPV-16- cancer-specific cell adhesive properties. Also, genes induced cervical carcinogenesis. belonging to DNA metabolism, such as DNA repair and Materials and Methods: mRNA differential displays, replication, were strongly down-regulated, whereas sig- with HPV-16 positive cervical cancer cell line (SiHa), and nificant increases were shown in the protein degradation normal human keratinocyte cell line (HaCaT) as a con- and synthesis. trol, were used. Each human gene has several biological Conclusion: The GO analysis can overcome the com- functions in the Gene Ontology; therefore, several func- plexity of the gene expression profile of the HPV-16- tions of each gene were chosen to establish a powerful associated pathway, identify several cancer-specific cel- cervical carcinogenesis pathway. -
The Mouse Organellar Biogenesis Mutant Buff Results from a Mutation in Vps33a, a Homologue of Yeast Vps33 and Drosophila Carnation
The mouse organellar biogenesis mutant buff results from a mutation in Vps33a, a homologue of yeast vps33 and Drosophila carnation Tamio Suzuki*†‡, Naoki Oiso*†, Rashi Gautam†§, Edward K. Novak§, Jean-Jacques Panthier¶, P. G. Suprabhaʈ, Thomas Vida**, Richard T. Swank§, and Richard A. Spritz*†† *Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver, CO 80262; §Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263; ¶Institut National de la Recherche Agronomique, Ecole Nationale Ve´te´ rinaire d’Alfort, 94704 Maisons-Alfort Cedex, France; ʈCenter for Basic Neuroscience, University of Texas Southwestern, Dallas, TX 75390; and **Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, TX 77030 Communicated by Theodore T. Puck, Eleanor Roosevelt Institute for Cancer Research, Denver, CO, December 2, 2002 (received for review July 16, 2002) In the mouse, more than 16 loci are associated with mutant bf-mutant Vps33a does not. These results establish murine bf as phenotypes that include defective pigmentation, aberrant target- a murine homologue to the yeast vps33 mutant and suggest ing of lysosomal enzymes, prolonged bleeding, and immunodefi- VPS33A as a candidate gene for some cases of human HPS. ciency, the result of defective biogenesis of cytoplasmic organelles: melanosomes, lysosomes, and various storage granules. Many of Materials and Methods these mouse mutants are homologous to the human Hermansky– Mice and Backcross. Mice carrying the spontaneous mutation bf on Pudlak syndrome (HPS), Chediak–Higashi syndrome, and Griscelli the C57BL͞6J strain were obtained from The Jackson Labora- syndrome. We have mapped and positionally cloned one of these tory and were subsequently bred at Roswell Park Cancer Insti- mouse loci, buff (bf), which has a mutant phenotype similar to that tute. -
Defining the Kv2.1–Syntaxin Molecular Interaction Identifies a First-In-Class Small Molecule Neuroprotectant
Defining the Kv2.1–syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant Chung-Yang Yeha,b,1, Zhaofeng Yec,d,1, Aubin Moutale, Shivani Gaura,b, Amanda M. Hentonf,g, Stylianos Kouvarosf,g, Jami L. Salomana, Karen A. Hartnett-Scotta,b, Thanos Tzounopoulosa,f,g, Rajesh Khannae, Elias Aizenmana,b,g,2, and Carlos J. Camachoc,2 aDepartment of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261; bPittsburgh Institute for Neurodegenerative Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261; cDepartment of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261; dSchool of Medicine, Tsinghua University, Beijing 100871, China; eDepartment of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ 85724; fDepartment of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261; and gPittsburgh Hearing Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261 Edited by Lily Yeh Jan, University of California, San Francisco, CA, and approved June 19, 2019 (received for review February 27, 2019) + The neuronal cell death-promoting loss of cytoplasmic K follow- (13). The Kv2.1-dependent cell death pathway is normally initiated ing injury is mediated by an increase in Kv2.1 potassium channels in by the oxidative liberation of zinc from intracellular metal-binding the plasma membrane. This phenomenon relies on Kv2.1 binding to proteins (14), leading to the sequential phosphorylation of syntaxin 1A via 9 amino acids within the channel intrinsically disor- Kv2.1 residues Y124 and S800 by Src and p38 kinases, respectively dered C terminus. Preventing this interaction with a cell and blood- (15–17). -
RNA-Seq Transcriptome Reveals Different Molecular Responses
Zhao et al. BMC Genomics (2020) 21:475 https://doi.org/10.1186/s12864-020-06885-4 RESEARCH ARTICLE Open Access RNA-Seq transcriptome reveals different molecular responses during human and mouse oocyte maturation and fertilization Zheng-Hui Zhao1,2, Tie-Gang Meng1,3, Ang Li1, Heide Schatten4, Zhen-Bo Wang1,2* and Qing-Yuan Sun1,3* Abstract Background: Female infertility is a worldwide concern and the etiology of infertility has not been thoroughly demonstrated. Although the mouse is a good model system to perform functional studies, the differences between mouse and human also need to be considered. The objective of this study is to elucidate the different molecular mechanisms underlying oocyte maturation and fertilization between human and mouse. Results: A comparative transcriptome analysis was performed to identify the differentially expressed genes and associated biological processes between human and mouse oocytes. In total, 8513 common genes, as well as 15, 165 and 6126 uniquely expressed genes were detected in human and mouse MII oocytes, respectively. Additionally, the ratios of non-homologous genes in human and mouse MII oocytes were 37 and 8%, respectively. Functional categorization analysis of the human MII non-homologous genes revealed that cAMP-mediated signaling, sister chromatid cohesin, and cell recognition were the major enriched biological processes. Interestingly, we couldn’t detect any GO categories in mouse non-homologous genes. Conclusions: This study demonstrates that human and mouse oocytes exhibit significant differences in gene expression profiles during oocyte maturation, which probably deciphers the differential molecular responses to oocyte maturation and fertilization. The significant differences between human and mouse oocytes limit the generalizations from mouse to human oocyte maturation. -
Fluorescence Lifetime Imaging Microscopy Reveals Rerouting Of
RESEARCH ARTICLE Fluorescence Lifetime Imaging Microscopy reveals rerouting of SNARE trafficking driving dendritic cell activation Danie¨ lle Rianne Jose´ Verboogen, Natalia Gonza´ lez Mancha, Martin ter Beest, Geert van den Bogaart* Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands Abstract SNARE proteins play a crucial role in intracellular trafficking by catalyzing membrane fusion, but assigning SNAREs to specific intracellular transport routes is challenging with current techniques. We developed a novel Fo¨ rster resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM)-based technique allowing visualization of real-time local interactions of fluorescently tagged SNARE proteins in live cells. We used FRET-FLIM to delineate the trafficking steps underlying the release of the inflammatory cytokine interleukin-6 (IL-6) from human blood- derived dendritic cells. We found that activation of dendritic cells by bacterial lipopolysaccharide leads to increased FRET of fluorescently labeled syntaxin 4 with VAMP3 specifically at the plasma membrane, indicating increased SNARE complex formation, whereas FRET with other tested SNAREs was unaltered. Our results revealed that SNARE complexing is a key regulatory step for cytokine production by immune cells and prove the applicability of FRET-FLIM for visualizing SNARE complexes in live cells with subcellular spatial resolution. DOI: 10.7554/eLife.23525.001 *For correspondence: geert. [email protected] Introduction Competing interests: The One of the central paradigms in cell biology is that all intracellular membrane fusion, except for authors declare that no mitochondrial fusion, is catalyzed by soluble NSF (N-ethylmaleimide-sensitive fusion protein) attach- competing interests exist. ment protein receptor (SNARE) proteins (Hong, 2005; Jahn and Scheller, 2006). -
The Genetics of Bipolar Disorder
Molecular Psychiatry (2008) 13, 742–771 & 2008 Nature Publishing Group All rights reserved 1359-4184/08 $30.00 www.nature.com/mp FEATURE REVIEW The genetics of bipolar disorder: genome ‘hot regions,’ genes, new potential candidates and future directions A Serretti and L Mandelli Institute of Psychiatry, University of Bologna, Bologna, Italy Bipolar disorder (BP) is a complex disorder caused by a number of liability genes interacting with the environment. In recent years, a large number of linkage and association studies have been conducted producing an extremely large number of findings often not replicated or partially replicated. Further, results from linkage and association studies are not always easily comparable. Unfortunately, at present a comprehensive coverage of available evidence is still lacking. In the present paper, we summarized results obtained from both linkage and association studies in BP. Further, we indicated new potential interesting genes, located in genome ‘hot regions’ for BP and being expressed in the brain. We reviewed published studies on the subject till December 2007. We precisely localized regions where positive linkage has been found, by the NCBI Map viewer (http://www.ncbi.nlm.nih.gov/mapview/); further, we identified genes located in interesting areas and expressed in the brain, by the Entrez gene, Unigene databases (http://www.ncbi.nlm.nih.gov/entrez/) and Human Protein Reference Database (http://www.hprd.org); these genes could be of interest in future investigations. The review of association studies gave interesting results, as a number of genes seem to be definitively involved in BP, such as SLC6A4, TPH2, DRD4, SLC6A3, DAOA, DTNBP1, NRG1, DISC1 and BDNF. -
CORVET, CHEVI and HOPS – Multisubunit Tethers of the Endo
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs189134. doi:10.1242/jcs.189134 REVIEW SUBJECT COLLECTION: CELL BIOLOGY AND DISEASE CORVET, CHEVI and HOPS – multisubunit tethers of the endo-lysosomal system in health and disease Jan van der Beek‡, Caspar Jonker*,‡, Reini van der Welle, Nalan Liv and Judith Klumperman§ ABSTRACT contact between two opposing membranes and pull them close Multisubunit tethering complexes (MTCs) are multitasking hubs that together to allow interactions between SNARE proteins (Murray form a link between membrane fusion, organelle motility and signaling. et al., 2016). SNARE assembly then provides additional fusion CORVET, CHEVI and HOPS are MTCs of the endo-lysosomal system. specificity and drives the actual fusion process (Ohya et al., 2009; They regulate the major membrane flows required for endocytosis, Stroupe et al., 2009). In this Review, we focus on the role of tethering lysosome biogenesis, autophagy and phagocytosis. In addition, proteins in endo-lysosomal fusion events. individual subunits control complex-independent transport of specific Tethering proteins can be divided into two main groups: long cargoes and exert functions beyond tethering, such as attachment to coiled-coil proteins (Gillingham and Munro, 2003) and microtubules and SNARE activation. Mutations in CHEVI subunits multisubunit tethering complexes (MTCs). MTCs form a lead to arthrogryposis, renal dysfunction and cholestasis (ARC) heterogenic group of protein complexes that consist of up to ten ∼ syndrome, while defects in CORVET and, particularly, HOPS are subunits resulting in a general length of 50 nm (Brocker et al., associated with neurodegeneration, pigmentation disorders, liver 2012; Chou et al., 2016; Hsu et al., 1998; Lürick et al., 2018; Ren malfunction and various forms of cancer. -
S41467-019-09800-Y.Pdf
ARTICLE https://doi.org/10.1038/s41467-019-09800-y OPEN Vps11 and Vps18 of Vps-C membrane traffic complexes are E3 ubiquitin ligases and fine-tune signalling Gregory Segala 1, Marcela A. Bennesch1, Nastaran Mohammadi Ghahhari1, Deo Prakash Pandey1,3, Pablo C. Echeverria 1, François Karch 2, Robert K. Maeda2 & Didier Picard 1 1234567890():,; In response to extracellular signals, many signalling proteins associated with the plasma membrane are sorted into endosomes. This involves endosomal fusion, which depends on the complexes HOPS and CORVET. Whether and how their subunits themselves modulate signal transduction is unknown. We show that Vps11 and Vps18 (Vps11/18), two common subunits of the HOPS/CORVET complexes, are E3 ubiquitin ligases. Upon overexpression of Vps11/ Vps18, we find perturbations of ubiquitination in signal transduction pathways. We specifi- cally demonstrate that Vps11/18 regulate several signalling factors and pathways, including Wnt, estrogen receptor α (ERα), and NFκB. For ERα, we demonstrate that the Vps11/18- mediated ubiquitination of the scaffold protein PELP1 impairs the activation of ERα by c-Src. Thus, proteins involved in membrane traffic, in addition to performing their well-described role in endosomal fusion, fine-tune signalling in several different ways, including through ubiquitination. 1 Département de Biologie Cellulaire, Université de Genève, Sciences III, 30 quai Ernest-Ansermet, 1211 Genève, Switzerland. 2 Département de Génétique et Évolution, Université de Genève, Sciences III, 30 quai Ernest-Ansermet, -
The Impact of Transcription Factor Prospero Homeobox 1 on the Regulation of Thyroid Cancer Malignancy
International Journal of Molecular Sciences Review The Impact of Transcription Factor Prospero Homeobox 1 on the Regulation of Thyroid Cancer Malignancy Magdalena Rudzi ´nska 1,2 and Barbara Czarnocka 1,* 1 Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland; [email protected] 2 Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia * Correspondence: [email protected]; Tel.: +48-225693812; Fax: +48-225693712 Received: 7 April 2020; Accepted: 30 April 2020; Published: 2 May 2020 Abstract: Transcription factor Prospero homeobox 1 (PROX1) is continuously expressed in the lymphatic endothelial cells, playing an essential role in their differentiation. Many reports have shown that PROX1 is implicated in cancer development and acts as an oncoprotein or suppressor in a tissue-dependent manner. Additionally, the PROX1 expression in many types of tumors has prognostic significance and is associated with patient outcomes. In our previous experimental studies, we showed that PROX1 is present in the thyroid cancer (THC) cells of different origins and has a high impact on follicular thyroid cancer (FTC) phenotypes, regulating migration, invasion, focal adhesion, cytoskeleton reorganization, and angiogenesis. Herein, we discuss the PROX1 transcript and protein structures, the expression pattern of PROX1 in THC specimens, and its epigenetic regulation. Next, we emphasize the biological processes and genes regulated by PROX1 in CGTH-W-1 cells, derived from squamous cell carcinoma of the thyroid gland. Finally, we discuss the interaction of PROX1 with other lymphatic factors. In our review, we aimed to highlight the importance of vascular molecules in cancer development and provide an update on the functionality of PROX1 in THC biology regulation. -
The Microrna-29 Family Dictates the Balance Between Homeostatic and Pathological Glucose Handling in Diabetes and Obesity
Diabetes Volume 65, January 2016 53 James Dooley,1,2 Josselyn E. Garcia-Perez,1,2 Jayasree Sreenivasan,1,2,3 Susan M. Schlenner,1,2 Roman Vangoitsenhoven,4 Aikaterini S. Papadopoulou,1,5 Lei Tian,1,2 Susann Schonefeldt,1,2 Lutgarde Serneels,1,5 Christophe Deroose,6 Kim A. Staats,1,2 Bart Van der Schueren,4 Bart De Strooper,1,5 Owen P. McGuinness,7 Chantal Mathieu,4 and Adrian Liston1,2 The microRNA-29 Family Dictates the Balance Between Homeostatic and Pathological Glucose Handling in Diabetes and Obesity Diabetes 2016;65:53–61 | DOI: 10.2337/db15-0770 The microRNA-29 (miR-29) family is among the most glucose levels are subject to large environmental chal- abundantly expressed microRNA in the pancreas and lenges due to dietary consumption. miRNA can act to liver. Here, we investigated the function of miR-29 in stabilize stochastic perturbations, acting as a buffer glucose regulation using miR-29a/b-1 (miR-29a)-deficient fl against uctuation in basal transcription and making it METABOLISM mice and newly generated miR-29b-2/c (miR-29c)- attractive to speculate that miRNA may have important fi de cient mice. We observed multiple independent functions in regulating glucose handling (1). Indeed, mu- functions of the miR-29 family, which can be segregated tations in the miRNA-splicing enzyme Dicer have been into a hierarchical physiologic regulation of glucose associated with a number of endocrine disturbances (2), handling. miR-29a, and not miR-29c, was observed to with severe effects of Dicer-deficiency on pancreatic be a positive regulator of insulin secretion in vivo, with b-cells (3–5) and hepatocytes (6,7). -
Cholesterol Regulates Syntaxin 6 Trafficking at Trans-Golgi Network
Cell Reports Article Cholesterol Regulates Syntaxin 6 Trafficking at trans-Golgi Network Endosomal Boundaries Meritxell Reverter,1,11 Carles Rentero,1,11 Ana Garcia-Melero,1 Monira Hoque,2 Sandra Vila` de Muga,1 Anna A´ lvarez-Guaita,1 James R.W. Conway,3 Peta Wood,2 Rose Cairns,2 Lilia Lykopoulou,4 Daniel Grinberg,5 Lluı¨saVilageliu,5 Marta Bosch,6 Joerg Heeren,7 Juan Blasi,8 Paul Timpson,3 Albert Pol,1,6,9 Francesc Tebar,1,6 Rachael Z. Murray,10 Thomas Grewal,2,* and Carlos Enrich1,6,* 1Departament de Biologia Cel$lular, Immunologia i Neurocie` ncies, Facultat de Medicina, Universitat de Barcelona, 08036 Barcelona, Spain 2Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia 3Garvan Institute of Medical Research and Kinghorn Cancer Centre, Cancer Research Program, St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010, Australia 4First Department of Pediatrics, University of Athens, Aghia Sofia Children’s Hospital, 11527 Athens, Greece 5Departament de Gene` tica, Facultat de Biologia, Universitat de Barcelona, CIBERER, IBUB, 08028 Barcelona, Spain 6Centre de Recerca Biome` dica CELLEX, Institut d’Investigacions Biome` diques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain 7Department of Biochemistry and Molecular Biology II. Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany 8Department of Pathology and Experimental Therapeutics, IDIBELL-University of Barcelona, L’Hospitalet de Llobregat, 08907 Barcelona, Spain 9Institucio´ Catalana de Recerca i Estudis Avac¸ ats (ICREA), 08010 Barcelona, Spain 10Tissue Repair and Regeneration Program, Institute of Health and Biomedical, Innovation, Queensland University of Technology, Brisbane, QLD 4095, Australia 11Co-first author *Correspondence: [email protected] (T.G.), [email protected] (C.E.) http://dx.doi.org/10.1016/j.celrep.2014.03.043 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).