Sorting Nexin 5 and Dopamine 1 Receptor Regulate Insulin Signaling and Metablism in Renal Proximal Tubule Cells
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Sorting Nexins in Protein Homeostasis Sara E. Hanley1,And Katrina F
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 6 November 2020 doi:10.20944/preprints202011.0241.v1 Sorting nexins in protein homeostasis Sara E. Hanley1,and Katrina F. Cooper2* 1Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA 1 [email protected] 2 [email protected] * [email protected] Tel: +1 (856)-566-2887 1Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, 08084, USA Abstract: Sorting nexins (SNXs) are a highly conserved membrane-associated protein family that plays a role in regulating protein homeostasis. This family of proteins is unified by their characteristic phox (PX) phosphoinositides binding domain. Along with binding to membranes, this family of SNXs also comprises a diverse array of protein-protein interaction motifs that are required for cellular sorting and protein trafficking. SNXs play a role in maintaining the integrity of the proteome which is essential for regulating multiple fundamental processes such as cell cycle progression, transcription, metabolism, and stress response. To tightly regulate these processes proteins must be expressed and degraded in the correct location and at the correct time. The cell employs several proteolysis mechanisms to ensure that proteins are selectively degraded at the appropriate spatiotemporal conditions. SNXs play a role in ubiquitin-mediated protein homeostasis at multiple levels including cargo localization, recycling, degradation, and function. In this review, we will discuss the role of SNXs in three different protein homeostasis systems: endocytosis lysosomal, the ubiquitin-proteasomal, and the autophagy-lysosomal system. The highly conserved nature of this protein family by beginning with the early research on SNXs and protein trafficking in yeast and lead into their important roles in mammalian systems. -
Diverse Species-Specific Phenotypic Consequences of Loss of Function
www.nature.com/scientificreports OPEN Diverse species‑specifc phenotypic consequences of loss of function sorting nexin 14 mutations Dale Bryant1, Marian Seda1, Emma Peskett1, Constance Maurer1, Gideon Pomeranz1, Marcus Ghosh2, Thomas A. Hawkins2, James Cleak3, Sanchari Datta4, Hanaa Hariri4, Kaitlyn M. Eckert5,6, Daniyal J. Jafree1, Claire Walsh7, Charalambos Demetriou1, Miho Ishida1, Cristina Alemán‑Charlet1, Letizia Vestito1, Rimante Seselgyte1, Jefrey G. McDonald5,6, Maria Bitner‑Glindzicz1, Myriam Hemberger8, Jason Rihel2, Lydia Teboul3, W. Mike Henne4, Dagan Jenkins1, Gudrun E. Moore1 & Philip Stanier1* Mutations in the SNX14 gene cause spinocerebellar ataxia, autosomal recessive 20 (SCAR20) in both humans and dogs. Studies implicating the phenotypic consequences of SNX14 mutations to be consequences of subcellular disruption to autophagy and lipid metabolism have been limited to in vitro investigation of patient‑derived dermal fbroblasts, laboratory engineered cell lines and developmental analysis of zebrafsh morphants. SNX14 homologues Snz (Drosophila) and Mdm1 (yeast) have also been conducted, demonstrated an important biochemical role during lipid biogenesis. In this study we report the efect of loss of SNX14 in mice, which resulted in embryonic lethality around mid‑gestation due to placental pathology that involves severe disruption to syncytiotrophoblast cell diferentiation. In contrast to other vertebrates, zebrafsh carrying a homozygous, maternal zygotic snx14 genetic loss‑of‑function mutation were both viable and anatomically normal. Whilst no obvious behavioural efects were observed, elevated levels of neutral lipids and phospholipids resemble previously reported efects on lipid homeostasis in other species. The biochemical role of SNX14 therefore appears largely conserved through evolution while the consequences of loss of function varies between species. -
Emerging Roles of ARHGAP33 in Intracellular Trafficking of Trkb And
ARTICLE Received 21 Oct 2015 | Accepted 4 Jan 2016 | Published 3 Feb 2016 DOI: 10.1038/ncomms10594 OPEN Emerging roles of ARHGAP33 in intracellular trafficking of TrkB and pathophysiology of neuropsychiatric disorders Takanobu Nakazawa1,2,3, Ryota Hashimoto4,5, Kazuto Sakoori1, Yuki Sugaya1, Asami Tanimura1, Yuki Hashimotodani1, Kazutaka Ohi4, Hidenaga Yamamori4,6, Yuka Yasuda4, Satomi Umeda-Yano6, Yuji Kiyama7, Kohtarou Konno8, Takeshi Inoue2, Kazumasa Yokoyama2, Takafumi Inoue9, Shusuke Numata10, Tohru Ohnuma11, Nakao Iwata12, Norio Ozaki13, Hitoshi Hashimoto3,5,14, Masahiko Watanabe8, Toshiya Manabe7, Tadashi Yamamoto2,15, Masatoshi Takeda4,5 & Masanobu Kano1 Intracellular trafficking of receptor proteins is essential for neurons to detect various extra- cellular factors during the formation and refinement of neural circuits. However, the precise mechanisms underlying the trafficking of neurotrophin receptors to synapses remain elusive. Here, we demonstrate that a brain-enriched sorting nexin, ARHGAP33, is a new type of regulator for the intracellular trafficking of TrkB, a high-affinity receptor for brain-derived neurotrophic factor. ARHGAP33 knockout (KO) mice exhibit reduced expression of synaptic TrkB, impaired spine development and neuropsychiatric disorder-related behavioural abnormalities. These deficits are rescued by specific pharmacological enhancement of TrkB signalling in ARHGAP33 KO mice. Mechanistically, ARHGAP33 interacts with SORT1 to cooperatively regulate TrkB trafficking. Human ARHGAP33 is associated with brain pheno- types and reduced SORT1 expression is found in patients with schizophrenia. We propose that ARHGAP33/SORT1-mediated TrkB trafficking is essential for synapse development and that the dysfunction of this mechanism may be a new molecular pathology of neuropsychiatric disorders. 1 Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan. -
Spatial and Temporal Aspects of Signalling 6 1
r r r Cell Signalling Biology Michael J. Berridge Module 6 Spatial and Temporal Aspects of Signalling 6 1 Module 6 Spatial and Temporal Aspects of Signalling Synopsis The function and efficiency of cell signalling pathways are very dependent on their organization both in space and time. With regard to spatial organization, signalling components are highly organized with respect to their cellular location and how they transmit information from one region of the cell to another. This spatial organization of signalling pathways depends on the molecular interactions that occur between signalling components that use signal transduction domains to construct signalling pathways. Very often, the components responsible for information transfer mechanisms are held in place by being attached to scaffolding proteins to form macromolecular signalling complexes. Sometimes these macromolecular complexes can be organized further by being localized to specific regions of the cell, as found in lipid rafts and caveolae or in the T-tubule regions of skeletal and cardiac cells. Another feature of the spatial aspects concerns the local Another important temporal aspect is timing and signal and global aspects of signalling. The spatial organization of integration, which relates to the way in which functional signalling molecules mentioned above can lead to highly interactions between signalling pathways are determined localized signalling events, but when the signalling mo- by both the order and the timing of their presentations. lecules are more evenly distributed, signals can spread The organization of signalling systems in both time and more globally throughout the cell. In addition, signals space greatly enhances both their efficiency and versatility. -
The Genetics of Human Skin and Hair Pigmentation
GG20CH03_Pavan ARjats.cls July 31, 2019 17:4 Annual Review of Genomics and Human Genetics The Genetics of Human Skin and Hair Pigmentation William J. Pavan1 and Richard A. Sturm2 1Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA; email: [email protected] 2Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4102, Australia; email: [email protected] Annu. Rev. Genom. Hum. Genet. 2019. 20:41–72 Keywords First published as a Review in Advance on melanocyte, melanogenesis, melanin pigmentation, skin color, hair color, May 17, 2019 genome-wide association study, GWAS The Annual Review of Genomics and Human Genetics is online at genom.annualreviews.org Abstract https://doi.org/10.1146/annurev-genom-083118- Human skin and hair color are visible traits that can vary dramatically Access provided by University of Washington on 09/02/19. For personal use only. 015230 within and across ethnic populations. The genetic makeup of these traits— Annu. Rev. Genom. Hum. Genet. 2019.20:41-72. Downloaded from www.annualreviews.org Copyright © 2019 by Annual Reviews. including polymorphisms in the enzymes and signaling proteins involved in All rights reserved melanogenesis, and the vital role of ion transport mechanisms operating dur- ing the maturation and distribution of the melanosome—has provided new insights into the regulation of pigmentation. A large number of novel loci involved in the process have been recently discovered through four large- scale genome-wide association studies in Europeans, two large genetic stud- ies of skin color in Africans, one study in Latin Americans, and functional testing in animal models. -
Snp Associations with Tuberculosis Susceptibility in a Ugandan
SNP ASSOCIATIONS WITH TUBERCULOSIS SUSCEPTIBILITY IN A UGANDAN HOUSEHOLD CONTACT STUDY by ALLISON REES BAKER Submitted in partial fulfillment of the requirements For the degree of Master of Science Thesis Advisor: Dr. Catherine M. Stein Department of Epidemiology and Biostatistics CASE WESTERN RESERVE UNIVERSITY August, 2010 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of ______________________________________________________ candidate for the ________________________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. Table of Contents Table of Contents...............................................................................................................iii List of Tables ..................................................................................................................... iv Acknowledgements............................................................................................................. v List of Commonly Used Abbreviations ............................................................................. vi Chapter 1: Literature -
Temporal Epigenomic Profiling Identifies AHR As a Dynamic Super-Enhancer Controlled Regulator of Mesenchymal Multipotency
bioRxiv preprint doi: https://doi.org/10.1101/183988; this version posted November 17, 2017. 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. Gerard et al.: Time-series epigenomic profiles of mesenchymal differentiation 1 Temporal epigenomic profiling identifies AHR as a 2 dynamic super-enhancer controlled regulator of 3 mesenchymal multipotency 4 Deborah Gérard1, Florian Schmidt2,3, Aurélien Ginolhac1, Martine Schmitz1, 5 Rashi Halder4, Peter Ebert3, Marcel H. Schulz2,3, Thomas Sauter1 and Lasse 6 Sinkkonen1* 7 1Life Sciences Research Unit, University of Luxembourg, L-4367 Belvaux, 8 Luxembourg 9 2Excellence Cluster for Multimodal Computing and Interaction, Saarland Informatics 10 Campus, Germany 11 3Computational Biology & Applied Algorithmics, Max Planck Institute for 12 Informatics, Saarland Informatics Campus, Germany 13 4Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur- 14 Alzette, L-4362, Luxembourg 15 16 [email protected]; [email protected]; [email protected]; 17 [email protected]; [email protected]; [email protected]; 18 [email protected]; [email protected]; [email protected] 19 20 *Corresponding author: Dr. Lasse Sinkkonen 21 Life Sciences Research Unit, University of Luxembourg 22 6, Avenue du Swing, L-4367 Belvaux, Luxembourg 23 Tel.: +352-4666446839 24 E-mail: [email protected] 25 1 bioRxiv preprint doi: https://doi.org/10.1101/183988; this version posted November 17, 2017. -
SNX13 Reduction Mediates Heart Failure Through Degradative Sorting of Apoptosis Repressor with Caspase Recruitment Domain
ARTICLE Received 2 May 2014 | Accepted 8 Sep 2014 | Published 8 Oct 2014 DOI: 10.1038/ncomms6177 SNX13 reduction mediates heart failure through degradative sorting of apoptosis repressor with caspase recruitment domain Jun Li1,2,*, Changming Li1,3,*, Dasheng Zhang1,2, Dan Shi1,2, Man Qi1,3, Jing Feng1,3, Tianyou Yuan1,2, Xinran Xu1,2, Dandan Liang1,2, Liang Xu1,2, Hong Zhang1,2, Yi Liu1,2, Jinjin Chen1,3, Jiangchuan Ye1,3, Weifang Jiang4, Yingyu Cui1,5, Yangyang Zhang6, Luying Peng1,2,5, Zhaonian Zhou1,7 & Yi-Han Chen1,2,3,5 Heart failure (HF) is associated with complicated molecular remodelling within cardio- myocytes; however, the mechanisms underlying this process remain unclear. Here we show that sorting nexin-13 (SNX13), a member of both the sorting nexin and the regulator of G protein signalling (RGS) protein families, is a potent mediator of HF. Decreased levels of SNX13 are observed in failing hearts of humans and of experimental animals. SNX13-deficient zebrafish recapitulate HF with striking cardiomyocyte apoptosis. Mechanistically, a reduction in SNX13 expression facilitates the degradative sorting of apoptosis repressor with caspase recruitment domain (ARC), which is a multifunctional inhibitor of apoptosis. Consequently, the apoptotic pathway is activated, resulting in the loss of cardiac cells and the dampening of cardiac function. The N-terminal PXA structure of SNX13 is responsible for mediating the endosomal trafficking of ARC. Thus, this study reveals that SNX13 profoundly affects cardiac performance through the SNX13-PXA-ARC-caspase signalling pathway. 1 Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai 200120, China. -
(PX) Domains Based on Their Phosphoinositide Binding Specificities
ARTICLE https://doi.org/10.1038/s41467-019-09355-y OPEN Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities Mintu Chandra1, Yanni K.-Y. Chin1, Caroline Mas1,6, J. Ryan Feathers2, Blessy Paul1, Sanchari Datta2, Kai-En Chen 1, Xinying Jia 3, Zhe Yang4, Suzanne J. Norwood1, Biswaranjan Mohanty5, Andrea Bugarcic1, Rohan D. Teasdale1,4, W. Mike Henne2, Mehdi Mobli 3 & Brett M. Collins1 1234567890():,; Phox homology (PX) domains are membrane interacting domains that bind to phosphati- dylinositol phospholipids or phosphoinositides, markers of organelle identity in the endocytic system. Although many PX domains bind the canonical endosome-enriched lipid PtdIns3P, others interact with alternative phosphoinositides, and a precise understanding of how these specificities arise has remained elusive. Here we systematically screen all human PX domains for their phospholipid preferences using liposome binding assays, biolayer interferometry and isothermal titration calorimetry. These analyses define four distinct classes of human PX domains that either bind specifically to PtdIns3P, non-specifically to various di- and tri- phosphorylated phosphoinositides, bind both PtdIns3P and other phosphoinositides, or associate with none of the lipids tested. A comprehensive evaluation of PX domain structures reveals two distinct binding sites that explain these specificities, providing a basis for defining and predicting the functional membrane interactions of the entire PX domain protein family. 1 Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia. 2 Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 3 Centre for Advanced Imaging and School of Chemistry and Molecular Biology, The University of Queensland, St. -
Identification of Genomic Alterations in Castration Resistant Prostate Cancer Using Next Generation Sequencing
Identification of Genomic Alterations in Castration Resistant Prostate Cancer using Next Generation Sequencing Thesis Submitted for a Doctoral Degree in Natural Sciences (Dr. rer. nat) Faculty of Mathematics and Natural Sciences Rheinische Friedrich-Wilhelms- Submitted by Roopika Menon from Chandigarh, India Bonn 2013 Prepared with the consent of the Faculty of Mathematics and Natural Sciences at the Rheinische Friedrich-Wilhelms- 1. Reviewer: Prof. Dr. Sven Perner 2. Reviewer: Prof. Dr. Hubert Schorle Date of examination: 19 November 2013 Year of Publication: 2014 Declaration I solemnly declare that the work submitted here is the result of my own investigation, except where otherwise stated. This work has not been submitted to any other University or Institute towards the partial fulfillment of any degree. ____________________________________________________________________ Roopika Menon; Author Acknowledgements This thesis would not have been possible without the help and support of many people. I would like to dedicate this thesis to all the people who have helped make this dream a reality. This thesis would have not been possible without the patience, support and guidance of my supervisor, Prof. Dr. Sven Perner. It has truly been an honor to be his first PhD student. He has both consciously and unconsciously made me into the researcher that I am today. My PhD experience has truly been the ‘best’ because of his time, ideas, funding and most importantly his incredible sense of humor. He encouraged and gave me the opportunity to travel around the world to develop as a scientist. I cannot thank him enough for this immense opportunity, which stands as a stepping-stone to my career in science. -
556 Positive Significant Genes Computed Quantities Input
Significant Genes List Input Parameters Imputation Engine Data Type Data in log scale? Number of Permutations Blocked Permutation? RNG Seed (Delta, Fold Change) (Upper Cutoff, Lower Cutoff) Computed Quantities Computed Exchangeability Factor S0 S0 percentile False Significant Number (Median, 90 percentile) False Discovery Rate (Median, 90 percentile) Pi0Hat 556 Positive Significant Genes Row Gene Name 5288 AGI_HUM1_OLIGO_A_23_P170096 6496 AGI_HUM1_OLIGO_A_23_P210021 9658 AGI_HUM1_OLIGO_A_23_P43444 9730 AGI_HUM1_OLIGO_A_23_P44466 12489 AGI_HUM1_OLIGO_A_23_P81507 666 AGI_HUM1_OLIGO_A_23_P108599 2085 AGI_HUM1_OLIGO_A_23_P127727 8831 AGI_HUM1_OLIGO_A_23_P32499 2483 AGI_HUM1_OLIGO_A_23_P132736 5424 AGI_HUM1_OLIGO_A_23_P17808 11383 AGI_HUM1_OLIGO_A_23_P66543 8456 AGI_HUM1_OLIGO_A_23_P2762 5455 AGI_HUM1_OLIGO_A_23_P1823 11724 AGI_HUM1_OLIGO_A_23_P71067 692 AGI_HUM1_OLIGO_A_23_P108932 4216 AGI_HUM1_OLIGO_A_23_P155504 13553 AGI_HUM1_OLIGO_A_23_P96529 5370 AGI_HUM1_OLIGO_A_23_P171284 10443 AGI_HUM1_OLIGO_A_23_P53946 5573 AGI_HUM1_OLIGO_A_23_P1981 3624 AGI_HUM1_OLIGO_A_23_P147869 9215 AGI_HUM1_OLIGO_A_23_P3766 10396 AGI_HUM1_OLIGO_A_23_P53257 9179 AGI_HUM1_OLIGO_A_23_P37251 8146 AGI_HUM1_OLIGO_A_23_P257762 6728 AGI_HUM1_OLIGO_A_23_P212720 6322 AGI_HUM1_OLIGO_A_23_P208059 6707 AGI_HUM1_OLIGO_A_23_P212499 12483 AGI_HUM1_OLIGO_A_23_P8142 7995 AGI_HUM1_OLIGO_A_23_P255925 6898 AGI_HUM1_OLIGO_A_23_P214681 8593 AGI_HUM1_OLIGO_A_23_P29472 8259 AGI_HUM1_OLIGO_A_23_P259192 13318 AGI_HUM1_OLIGO_A_23_P93015 10290 AGI_HUM1_OLIGO_A_23_P51861 9965 AGI_HUM1_OLIGO_A_23_P47709 -
Snazarus and Its Human Ortholog SNX25 Regulate Autophagic Flux By
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.08.439013; this version posted April 8, 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-ND 4.0 International license. 1 Snazarus and its human ortholog SNX25 regulate autophagic flux 2 by affecting VAMP8 endocytosis 3 4 Annie Lauzier1, Marie-France Bossanyi1, Rupali Ugrankar2, W. Mike Henne2 and Steve Jean1* 5 6 *Corresponding author: 7 Email: [email protected] 8 Telephone: 819-821-8000 Ext: 70450 9 Fax: 819-820-6831 10 11 1Faculté de Médecine et des Sciences de la Santé 12 DéparteMent d’iMMunologie et de biologie cellulaire 13 Université de Sherbrooke 14 3201, Rue Jean Mignault 15 Sherbrooke, Québec, Canada, J1E 4K8 16 17 2DepartMent of Cell Biology, UT Southwestern Medical Center 18 6000 Hary Lines Boulevard 19 Dallas, TX, USA, 75390 20 21 Running title: Snazarus is required for autophagy 22 Keywords: Snazarus, Sorting nexin 25, Autophagy, VAMP8, Endocytosis 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.08.439013; this version posted April 8, 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-ND 4.0 International license. 24 Abstract 25 Autophagy, the degradation and recycling of cytosolic components in the lysosome, is an essential 26 cellular MechanisM.