Differential Effects of STCH and Stress-Inducible Hsp70 on the Stability and Maturation of NKCC2
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Mea6 Controls VLDL Transport Through the Coordinated Regulation of COPII Assembly
Cell Research (2016) 26:787-804. npg © 2016 IBCB, SIBS, CAS All rights reserved 1001-0602/16 $ 32.00 ORIGINAL ARTICLE www.nature.com/cr Mea6 controls VLDL transport through the coordinated regulation of COPII assembly Yaqing Wang1, *, Liang Liu1, 2, *, Hongsheng Zhang1, 2, Junwan Fan1, 2, Feng Zhang1, 2, Mei Yu3, Lei Shi1, Lin Yang1, Sin Man Lam1, Huimin Wang4, Xiaowei Chen4, Yingchun Wang1, Fei Gao5, Guanghou Shui1, Zhiheng Xu1, 6 1State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; 2University of Chinese Academy of Sciences, Beijing 100101, China; 3School of Life Science, Shandong University, Jinan 250100, China; 4Institute of Molecular Medicine, Peking University, Beijing 100871, China; 5State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; 6Translation- al Medical Center for Stem Cell Therapy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Lipid accumulation, which may be caused by the disturbance in very low density lipoprotein (VLDL) secretion in the liver, can lead to fatty liver disease. VLDL is synthesized in endoplasmic reticulum (ER) and transported to Golgi apparatus for secretion into plasma. However, the underlying molecular mechanism for VLDL transport is still poor- ly understood. Here we show that hepatocyte-specific deletion of meningioma-expressed antigen 6 (Mea6)/cutaneous T cell lymphoma-associated antigen 5C (cTAGE5C) leads to severe fatty liver and hypolipemia in mice. Quantitative lip- idomic and proteomic analyses indicate that Mea6/cTAGE5 deletion impairs the secretion of different types of lipids and proteins, including VLDL, from the liver. -
Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Computational Genome-Wide Identification of Heat Shock Protein Genes in the Bovine Genome [Version 1; Peer Review: 2 Approved, 1 Approved with Reservations]
F1000Research 2018, 7:1504 Last updated: 08 AUG 2021 RESEARCH ARTICLE Computational genome-wide identification of heat shock protein genes in the bovine genome [version 1; peer review: 2 approved, 1 approved with reservations] Oyeyemi O. Ajayi1,2, Sunday O. Peters3, Marcos De Donato2,4, Sunday O. Sowande5, Fidalis D.N. Mujibi6, Olanrewaju B. Morenikeji2,7, Bolaji N. Thomas 8, Matthew A. Adeleke 9, Ikhide G. Imumorin2,10,11 1Department of Animal Breeding and Genetics, Federal University of Agriculture, Abeokuta, Nigeria 2International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA 3Department of Animal Science, Berry College, Mount Berry, GA, 30149, USA 4Departamento Regional de Bioingenierias, Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Queretaro, Mexico 5Department of Animal Production and Health, Federal University of Agriculture, Abeokuta, Nigeria 6Usomi Limited, Nairobi, Kenya 7Department of Animal Production and Health, Federal University of Technology, Akure, Nigeria 8Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, 14623, USA 9School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa 10School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30032, USA 11African Institute of Bioscience Research and Training, Ibadan, Nigeria v1 First published: 20 Sep 2018, 7:1504 Open Peer Review https://doi.org/10.12688/f1000research.16058.1 Latest published: 20 Sep 2018, 7:1504 https://doi.org/10.12688/f1000research.16058.1 Reviewer Status Invited Reviewers Abstract Background: Heat shock proteins (HSPs) are molecular chaperones 1 2 3 known to bind and sequester client proteins under stress. Methods: To identify and better understand some of these proteins, version 1 we carried out a computational genome-wide survey of the bovine 20 Sep 2018 report report report genome. -
UBQLN2 Polyclonal Antibody C-Terminal Ubiquitin-Associated Domain
UBQLN2 polyclonal antibody C-terminal ubiquitin-associated domain. They physically associate with both proteasomes and ubiquitin ligases, Catalog Number: PAB1699 and thus thought to functionally link the ubiquitination machinery to the proteasome to affect in vivo protein Regulatory Status: For research use only (RUO) degradation. This ubiquilin has also been shown to bind the ATPase domain of the Hsp70-like Stch protein. Product Description: Rabbit polyclonal antibody raised [provided by RefSeq] against synthetic peptide of UBQLN2. References: Immunogen: A synthetic peptide (conjugated with KLH) 1. Structural studies of the interaction between ubiquitin corresponding to C-terminus of human UBQLN2. family proteins and proteasome subunit S5a. Walters KJ, Kleijnen MF, Goh AM, Wagner G, Howley PM. Host: Rabbit Biochemistry. 2002 Feb 12;41(6):1767-77. 2. The hPLIC proteins may provide a link between the Reactivity: Human ubiquitination machinery and the proteasome. Kleijnen Applications: WB-Ce MF, Shih AH, Zhou P, Kumar S, Soccio RE, Kedersha (See our web site product page for detailed applications NL, Gill G, Howley PM. Mol Cell. 2000 Aug;6(2):409-19. information) 3. Selection system for genes encoding nuclear-targeted proteins. Ueki N, Oda T, Kondo M, Yano K, Noguchi T, Protocols: See our web site at Muramatsu M. Nat Biotechnol. 1998 http://www.abnova.com/support/protocols.asp or product Dec;16(13):1338-42. page for detailed protocols Form: Liquid Purification: Protein G purification Recommend Usage: Western Blot (1:1000) The optimal working dilution should be determined by the end user. Storage Buffer: In PBS (0.09% sodium azide) Storage Instruction: Store at 4°C. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Essential Genes and Their Role in Autism Spectrum Disorder
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Essential Genes And Their Role In Autism Spectrum Disorder Xiao Ji University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, and the Genetics Commons Recommended Citation Ji, Xiao, "Essential Genes And Their Role In Autism Spectrum Disorder" (2017). Publicly Accessible Penn Dissertations. 2369. https://repository.upenn.edu/edissertations/2369 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2369 For more information, please contact [email protected]. Essential Genes And Their Role In Autism Spectrum Disorder Abstract Essential genes (EGs) play central roles in fundamental cellular processes and are required for the survival of an organism. EGs are enriched for human disease genes and are under strong purifying selection. This intolerance to deleterious mutations, commonly observed haploinsufficiency and the importance of EGs in pre- and postnatal development suggests a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication and repetitive behavior. More and more genetic evidence points to a polygenic model of ASD and it is estimated that hundreds of genes contribute to ASD. The central question addressed in this dissertation is whether genes with a strong effect on survival and fitness (i.e. EGs) play a specific oler in ASD risk. I compiled a comprehensive catalog of 3,915 mammalian EGs by combining human orthologs of lethal genes in knockout mice and genes responsible for cell-based essentiality. -
Murine SEC24D Can Substitute Functionally for SEC24C in Vivo
bioRxiv preprint doi: https://doi.org/10.1101/284398; this version posted March 22, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Functional Overlap Between Mouse SEC24C and SEC24D Murine SEC24D Can Substitute Functionally for SEC24C in vivo Elizabeth J. Adams1,2, Rami Khoriaty2,3, Anna Kiseleva1, Audrey C. A. Cleuren1,7, Kärt Tomberg1,4, Martijn A. van der Ent3, Peter Gergics4, K. Sue O’Shea5, Thomas L. Saunders3, David Ginsburg1-4,6,7 1From the Life Sciences Institute, 2Program in Cellular and Molecular Biology, 3Department of Internal Medicine, 4Departement of Human Genetics, 5Department of Cell and Developmental Biology, 6Department of Pediatrics and the 7Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109 ABSTRACT The COPII component SEC24 mediates the recruitment of transmembrane cargoes or cargo adaptors into newly forming COPII vesicles on the ER membrane. Mammalian genomes encode four Sec24 paralogs (Sec24a-d), with two subfamilies based on sequence homology (SEC24A/B and C/D), though little is known about their comparative functions and cargo-specificities. Complete deficiency for Sec24d results in very early embryonic lethality in mice (before the 8 cell stage), with later embryonic lethality (E 7.5) observed in Sec24c null mice. To test the potential overlap in function between SEC24C/D, we employed dual recombinase mediated cassette exchange to generate a Sec24cc-d allele, in which the C-terminal 90% of SEC24C has been replaced by SEC24D coding sequence. In contrast to the embryonic lethality at E7.5 of SEC24C-deficiency, Sec24cc-d/c-d pups survive to term, though dying shortly after birth. -
Evaluation of the Role of Human Dnajas in the Response to Cytotoxic Chemotherapeutic Agents in a Yeast Model System
Hindawi BioMed Research International Volume 2020, Article ID 9097638, 14 pages https://doi.org/10.1155/2020/9097638 Research Article Evaluation of the Role of Human DNAJAs in the Response to Cytotoxic Chemotherapeutic Agents in a Yeast Model System AurelliaWhitmore,DevonFreeny,SamanthaJ.Sojourner,JanaS.Miles,WillieM.Graham, and Hernan Flores-Rozas College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, USA Correspondence should be addressed to Hernan Flores-Rozas; hernan.fl[email protected] Received 25 September 2019; Revised 3 January 2020; Accepted 9 January 2020; Published 14 February 2020 Guest Editor: Chengsheng Wu Copyright © 2020 Aurellia Whitmore et al. -is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Heat-shock proteins (HSPs) play a crucial role in maintaining protein stability for cell survival during stress-induced insults. Overexpression of HSPs in cancer cells results in antiapoptotic activity contributing to cancer cell survival and restricting the efficacy of cytotoxic chemotherapy, which continues to play an important role in the treatment of many cancers, including triple- negative breast cancer (TNBC). First-line therapy for TNBC includes anthracycline antibiotics, which are associated with serious dose-dependent side effects and the development of resistance. We previously identified YDJ1, which encodes a heat-shock protein 40 (HSP40), as an important factor in the cellular response to anthracyclines in yeast, with mutants displaying over 100- fold increased sensitivity to doxorubicin. In humans, the DNAJA HSP40s are homologues of YDJ1. To determine the role of DNAJAs in the cellular response to cytotoxic drugs, we investigated their ability to rescue ydj1Δ mutants from exposure to chemotherapeutic agents. -
Consequences of Mutations in the Genes of the ER Export Machinery COPII in Vertebrates
Biomedical Sciences Publications Biomedical Sciences 1-22-2020 Consequences of mutations in the genes of the ER export machinery COPII in vertebrates Chung-Ling Lu Iowa State University, [email protected] Jinoh Kim Iowa State University, [email protected] Follow this and additional works at: https://lib.dr.iastate.edu/bms_pubs Part of the Cellular and Molecular Physiology Commons, Molecular Biology Commons, and the Molecular Genetics Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ bms_pubs/81. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Biomedical Sciences at Iowa State University Digital Repository. It has been accepted for inclusion in Biomedical Sciences Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Consequences of mutations in the genes of the ER export machinery COPII in vertebrates Abstract Coat protein complex II (COPII) plays an essential role in the export of cargo molecules such as secretory proteins, membrane proteins, and lipids from the endoplasmic reticulum (ER). In yeast, the COPII machinery is critical for cell viability as most COPII knockout mutants fail to survive. In mice and fish, homozygous knockout mutants of most COPII genes are embryonic lethal, reflecting the essentiality of the COPII machinery in the early stages of vertebrate development. In humans, COPII mutations, which are often hypomorphic, cause diseases having distinct clinical features. This is interesting as the fundamental cellular defect of these diseases, that is, failure of ER export, is similar. -
ER-To-Golgi Trafficking and Its Implication in Neurological Diseases
cells Review ER-to-Golgi Trafficking and Its Implication in Neurological Diseases 1,2, 1,2 1,2, Bo Wang y, Katherine R. Stanford and Mondira Kundu * 1 Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; [email protected] (B.W.); [email protected] (K.R.S.) 2 Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA * Correspondence: [email protected]; Tel.: +1-901-595-6048 Present address: School of Life Sciences, Xiamen University, Xiamen 361102, China. y Received: 21 November 2019; Accepted: 7 February 2020; Published: 11 February 2020 Abstract: Membrane and secretory proteins are essential for almost every aspect of cellular function. These proteins are incorporated into ER-derived carriers and transported to the Golgi before being sorted for delivery to their final destination. Although ER-to-Golgi trafficking is highly conserved among eukaryotes, several layers of complexity have been added to meet the increased demands of complex cell types in metazoans. The specialized morphology of neurons and the necessity for precise spatiotemporal control over membrane and secretory protein localization and function make them particularly vulnerable to defects in trafficking. This review summarizes the general mechanisms involved in ER-to-Golgi trafficking and highlights mutations in genes affecting this process, which are associated with neurological diseases in humans. Keywords: COPII trafficking; endoplasmic reticulum; Golgi apparatus; neurological disease 1. Overview Approximately one-third of all proteins encoded by the mammalian genome are exported from the endoplasmic reticulum (ER) and transported to the Golgi apparatus, where they are sorted for delivery to their final destination in membrane compartments or secretory vesicles [1]. -
Machine Learning Models for Predicting Protein Condensate Formation from Sequence Determinants and Embeddings
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.26.354753; this version posted October 26, 2020. 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-NC-ND 4.0 International license. Machine learning models for predicting protein condensate formation from sequence determinants and embeddings Kadi L. Saar,1;2;† Alexey S. Morgunov,1;3;† Runzhang Qi,1 William E. Arter,1 Georg Krainer,1 Alpha A. Lee2 & Tuomas P. J. Knowles1;2;∗ 1 Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK 2 Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK 3 Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge CB1 8DH, UK † These authors contributed equally ∗ To whom correspondence should be addressed: [email protected] Abstract Intracellular phase separation of proteins into biomolecular condensates is increasingly recognised as an important phenomenon for cellular compartmentalisation and regulation of biological function. Different hypotheses about the parameters that determine the ten- dency of proteins to form condensates have been proposed with some of them probed ex- perimentally through the use of constructs generated by sequence alterations. To broaden the scope of these observations, here, we established an in silico strategy for understanding on a global level the associations between protein sequence and condensate formation, and used this information to construct machine learning classifiers for predicting liquid–liquid phase separation (LLPS) from protein sequence. -
(Stch) Gene Reduces Prion Disease Incubation Time in Mice
Overexpression of the Hspa13 (Stch) gene reduces prion disease incubation time in mice Julia Grizenkovaa,b, Shaheen Akhtara,b, Holger Hummericha,b, Andrew Tomlinsona,b, Emmanuel A. Asantea,b, Adam Wenborna,b, Jérémie Fizeta,b, Mark Poultera,b, Frances K. Wisemanb, Elizabeth M. C. Fisherb, Victor L. J. Tybulewiczc, Sebastian Brandnerb, John Collingea,b, and Sarah E. Lloyda,b,1 aMedical Research Council (MRC) Prion Unit and bDepartment of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London WC1N 3BG, United Kingdom; and cDivision of Immune Cell Biology, MRC National Institute for Medical Research, London NW7 1AA, United Kingdom Edited by Reed B. Wickner, National Institutes of Health, Bethesda, MD, and approved July 10, 2012 (received for review May 28, 2012) Prion diseases are fatal neurodegenerative disorders that include way crosses and a heterogeneous cross (12–14). In these studies, bovine spongiform encephalopathy (BSE) and scrapie in animals the underlying functional polymorphism is unknown but could be and Creutzfeldt-Jakob disease (CJD) in humans. They are character- an amino acid change within the coding region of a protein or ized by long incubation periods, variation in which is determined by splicing variant or may occur within noncoding sequences such as many factors including genetic background. In some cases it is pos- untranslated regions, promoters, or other regulatory regions sible that incubation time may be directly correlated to the level of thereby influencing the pattern or level of expression. Although gene expression. To test this hypothesis, we combined incubation incubation time is a polygenic trait, it is possible that in some cases, time data from five different inbred lines of mice with quantitative there may be a direct correlation between incubation time and gene expression profiling in normal brains and identified five genes individual gene expression level.