Chaperoning the Guardian of the Genome. the Two-Faced Role Of
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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. -
Gene Targeting Therapies (Roy Alcalay)
Recent Developments in Gene - Targeted Therapies for Parkinson’s Disease Roy Alcalay, MD, MS Alfred and Minnie Bressler Associate Professor of Neurology Division of Movement Disorders Columbia University Medical Center Disclosures Funding: Dr. Alcalay is funded by the National Institutes of Health, the DOD, the Michael J. Fox Foundation and the Parkinson’s Foundation. Dr. Alcalay receives consultation fees from Genzyme/Sanofi, Restorbio, Janssen, and Roche. Gene Localizations Identified in PD Gene Symbol Protein Transmission Chromosome PARK1 SNCA α-synuclein AD 4q22.1 PARK2 PRKN parkin (ubiquitin ligase) AR 6q26 PARK3 ? ? AD 2p13 PARK4 SNCA triplication α-synuclein AD 4q22.1 PARK5 UCH-L1 ubiquitin C-terminal AD 4p13 hydrolase-L1 PARK6 PINK1 PTEN-induced kinase 1 AR 1p36.12 PARK7 DJ-1 DJ-1 AR 1p36.23 PARK8 LRRK2 leucine rich repeat kinase 2 AD 12q12 PARK9 ATP13A2 lysosomal ATPase AR 1p36.13 PARK10 ? ? (Iceland) AR 1p32 PARK11 GIGYF2 GRB10-interacting GYF protein 2 AD 2q37.1 PARK12 ? ? X-R Xq21-q25 PARK13 HTRA2 serine protease AD 2p13.1 PARK14 PLA2G6 phospholipase A2 (INAD) AR 22q13.1 PARK15 FBXO7 F-box only protein 7 AR 22q12.3 PARK16 ? Discovered by GWAS ? 1q32 PARK17 VPS35 vacuolar protein sorting 35 AD 16q11.2 PARK18 EIF4G1 initiation of protein synth AD 3q27.1 PARK19 DNAJC6 auxilin AR 1p31.3 PARK20 SYNJ1 synaptojanin 1 AR 21q22.11 PARK21 DNAJC13 8/RME-8 AD 3q22.1 PARK22 CHCHD2 AD 7p11.2 PARK23 VPS13C AR 15q22 Gene Localizations Identified in PD Disorder Symbol Protein Transmission Chromosome PD GBA β-glucocerebrosidase AD 1q21 SCA2 -
Structural Basis for High-Affinity Peptide Inhibition of P53 Interactions with MDM2 and MDMX
Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX Marzena Pazgiera,1, Min Liua,b,1, Guozhang Zoua, Weirong Yuana, Changqing Lia, Chong Lia, Jing Lia, Juahdi Monboa, Davide Zellaa, Sergey G. Tarasovc, and Wuyuan Lua,2 aInstitute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201; bThe First Affiliated Hospital, School of Medicine, Xi’an Jiaotong University, Shaanxi Province 710061, China; and cStructural Biophysics Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702 Communicated by Robert C. Gallo, University of Maryland, Baltimore, MD, January 28, 2009 (received for review September 29, 2008) The oncoproteins MDM2 and MDMX negatively regulate the ac- ligase activity (10). Structurally related to MDM2, MDMX of tivity and stability of the tumor suppressor protein p53—a cellular 490-aa residues possesses domain structures arranged similarly process initiated by MDM2 and/or MDMX binding to the N- to MDM2, except that MDMX lacks ubiquitin-ligase function terminal transactivation domain of p53. MDM2 and MDMX in many (11, 12). Growing evidence supports that in unstressed cells tumors confer p53 inactivation and tumor survival, and are impor- MDM2 primarily controls p53 stability through ubiquitylation to tant molecular targets for anticancer therapy. We screened a target the tumor suppressor protein for constitutive degradation duodecimal peptide phage library against site-specifically biotin- by the proteasome (13, 14), whereas MDMX mainly functions as ylated p53-binding domains of human MDM2 and MDMX chemi- a significant p53 transcriptional antagonist independently of cally synthesized via native chemical ligation, and identified sev- MDM2 (15, 16). -
University of Groningen the Human HSP70/HSP40 Chaperone Family
University of Groningen The human HSP70/HSP40 chaperone family Hageman, Jurre IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2008 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Hageman, J. (2008). The human HSP70/HSP40 chaperone family: a study on its capacity to combat proteotoxic stress. s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 30-09-2021 CHAPTER 1 Introduction - Structural and functional diversities between members of the human HSPH, HSPA and DNAJ chaperone families Jurre Hageman and Harm H. -
The Ubiquitin Proteasome System and Its Involvement in Cell Death Pathways
Cell Death and Differentiation (2010) 17, 1–3 & 2010 Macmillan Publishers Limited All rights reserved 1350-9047/10 $32.00 www.nature.com/cdd Editorial The ubiquitin proteasome system and its involvement in cell death pathways F Bernassola1, A Ciechanover2 and G Melino1,3 Cell Death and Differentiation (2010) 17, 1–3; doi:10.1038/cdd.2009.189 Following the awarding of the 2004 Nobel Prize in Chemistry Inactivation of the proteasome following caspase-mediated to Aaron Ciechanover, Avram Hershko, and Irwin A Rose cleavage may disable the proteasome, interfering with its for the discovery of ubiquitin (Ub)-mediated degradation, role in the regulation of key cellular processes and thereby Cell Death and Differentiation has drawn the attention of facilitating induction of apoptosis. The noted recent develop- its readers to the Ub Proteasome System (UPS) and its ments show how understanding of these functions is just involvement in regulating cell death pathways.1–4 The current starting to emerge. For example, why does dIAP1 associate set of reviews is an update on this theme.5–16 with multiple E2s via its RING finger? Does dIAP1 also interact From previous review articles published in Cell Death and with the E3 – the F-box protein Morgue, which is a part of an Differentiation, it was apparent that the UPS has a major SCF E3 complex? Why does dIAP1, which is an E3, have to mechanistic role in regulating cell death via modification and interact with other ligases such as the N-end rule UBR1 and degradation of key regulatory proteins involved in -
Mitochondrial Quality Control in Neurodegenerative Diseases: Focus on Parkinson’S Disease and Huntington’S Disease
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Mitochondrial quality control in neurodegenerative diseases: focus on Parkinson’s disease and Huntington’s disease TESI DOCTORAL 2018 Programa de Doctorat en Neurociències Institut de Neurociències Tesi realitzada al laboratori de Malalties Neurodegeenratives de l’Institut de Recerca de la Vall d’Hebron (VHIR) Doctorand Director Tutor Sandra Franco Iborra Miquel Vila Bover José Rodríguez Álvarez Co-directora Co-directora Celine Perier Marta Martínez Vicente i AGRAÏMENTS En primer lloc vull agraïr al Miquel Vila per l’oportunitat que em va donar de començar a fer la tesi doctoral al seu lab. Gràcies per tenir sempre la porta oberta del teu despatx, per la confiança dipositada en mi i per tot el que m’has ensenyat durant tots aquests anys. A més, he tingut la sort de tenir no només un director de tesis sinó tres! Celine muchas gracias por estar siempre ahí, por ensenyarme tu manera de hacer ciencia (que me encanta!) y por ser siempre tan positiva. En mi manera de trabajar hay un poquito de ti y espero ir pasando este conocimiento a los demás porque en todo laboratorio debería ser obligatorio que hubiera alguien como tu. -
Global Analysis of Chaperone Effects Using a Reconstituted Cell-Free Translation System
Global analysis of chaperone effects using a reconstituted cell-free translation system Tatsuya Niwaa, Takashi Kanamorib,1, Takuya Uedab,2, and Hideki Taguchia,2 aDepartment of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan; and bDepartment of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan Edited by George H. Lorimer, University of Maryland, College Park, MD, and approved April 19, 2012 (received for review January 25, 2012) Protein folding is often hampered by protein aggregation, which can three chaperone systems are known to act cooperatively: TF and be prevented by a variety of chaperones in the cell. A dataset that DnaK exhibit overlapping cotranslational roles in vivo (13–15). evaluates which chaperones are effective for aggregation-prone Overexpression of DnaK/DnaJ and GroEL/GroES in E. coli proteins would provide an invaluable resource not only for un- rpoH mutant cells, which are deficient in heat-shock proteins, derstanding the roles of chaperones, but also for broader applications prevents aggregation of newly translated proteins (16). GroEL is in protein science and engineering. Therefore, we comprehensively believed to be involved in folding after the polypeptides are re- evaluated the effects of the major Escherichia coli chaperones, trigger leased from the ribosome, although the possible cotranslational factor, DnaK/DnaJ/GrpE, and GroEL/GroES, on ∼800 aggregation- involvement of GroEL has also been reported (17–20). prone cytosolic E. coli proteins, using a reconstituted chaperone-free Over the past two decades many efforts have been focused on translation system. -
XIAO-DISSERTATION-2015.Pdf
CELLULAR AND PROCESS ENGINEERING TO IMPROVE MAMMALIAN MEMBRANE PROTEIN EXPRESSION By Su Xiao A dissertation is submitted to Johns Hopkins University in conformity with the requirements for degree of Doctor of Philosophy Baltimore, Maryland May 2015 © 2015 Su Xiao All Rights Reserved Abstract Improving the expression level of recombinant mammalian proteins has been pursued for production of commercial biotherapeutics in industry, as well as for biomedical studies in academia, as an adequate supply of correctly folded proteins is a prerequisite for all structure and function studies. Presented in this dissertation are different strategies to improve protein functional expression level, especially for membrane proteins. The model protein is neurotensin receptor 1 (NTSR1), a hard-to- express G protein-coupled receptor (GPCR). GPCRs are integral membrane proteins playing a central role in cell signaling and are targets for most of the medicines sold worldwide. Obtaining adequate functional GPCRs has been a bottleneck in their structure studies because the expression of these proteins from mammalian cells is very low. The first strategy is the adoption of mammalian inducible expression system. A stable and inducible T-REx-293 cell line overexpressing an engineered rat NTSR1 was constructed. 2.5 million Functional copies of NTSR1 per cell were detected on plasma membrane, which is 167 fold improvement comparing to NTSR1 constitutive expression. The second strategy is production process development including suspension culture adaptation and induction parameter optimization. A further 3.5 fold improvement was achieved and approximately 1 milligram of purified functional NTSR1 per liter suspension culture was obtained. This was comparable yield to the transient baculovirus- insect cell system. -
Roles of Extracellular Hsps As Biomarkers in Immune Surveillance and Immune Evasion
International Journal of Molecular Sciences Review Roles of Extracellular HSPs as Biomarkers in Immune Surveillance and Immune Evasion 1,2,3, 4, 1,5, , Eman A. Taha y, Kisho Ono y and Takanori Eguchi * y 1 Department of Dental Pharmacology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan; [email protected] 2 Department of Medical Bioengineering, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan 3 Department of Biochemistry, Ain Shams University Faculty of Science, Cairo 11566, Egypt 4 Department of Oral and Maxillofacial Surgery, Okayama University Hospital, Okayama 700-0914, Japan; [email protected] 5 Advanced Research Center for Oral and Craniofacial Sciences, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8525, Japan * Correspondence: [email protected]; Tel.: +81-86-235-6662 These authors contributed equally to this work. y Received: 16 August 2019; Accepted: 14 September 2019; Published: 17 September 2019 Abstract: Extracellular heat shock proteins (ex-HSPs) have been found in exosomes, oncosomes, membrane surfaces, as well as free HSP in cancer and various pathological conditions, also known as alarmins. Such ex-HSPs include HSP90 (α, β, Gp96, Trap1), HSP70, and large and small HSPs. Production of HSPs is coordinately induced by heat shock factor 1 (HSF1) and hypoxia-inducible factor 1 (HIF-1), while matrix metalloproteinase 3 (MMP-3) and heterochromatin protein 1 are novel inducers of HSPs. Oncosomes released by tumor cells are a major aspect of the resistance-associated secretory phenotype (RASP) by which immune evasion can be established. -
Mitochondrial Protein Quality Control Mechanisms
G C A T T A C G G C A T genes Review Mitochondrial Protein Quality Control Mechanisms Pooja Jadiya * and Dhanendra Tomar * Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA * Correspondence: [email protected] (P.J.); [email protected] (D.T.); Tel.: +1-215-707-9144 (D.T.) Received: 29 April 2020; Accepted: 15 May 2020; Published: 18 May 2020 Abstract: Mitochondria serve as a hub for many cellular processes, including bioenergetics, metabolism, cellular signaling, redox balance, calcium homeostasis, and cell death. The mitochondrial proteome includes over a thousand proteins, encoded by both the mitochondrial and nuclear genomes. The majority (~99%) of proteins are nuclear encoded that are synthesized in the cytosol and subsequently imported into the mitochondria. Within the mitochondria, polypeptides fold and assemble into their native functional form. Mitochondria health and integrity depend on correct protein import, folding, and regulated turnover termed as mitochondrial protein quality control (MPQC). Failure to maintain these processes can cause mitochondrial dysfunction that leads to various pathophysiological outcomes and the commencement of diseases. Here, we summarize the current knowledge about the role of different MPQC regulatory systems such as mitochondrial chaperones, proteases, the ubiquitin-proteasome system, mitochondrial unfolded protein response, mitophagy, and mitochondria-derived vesicles in the maintenance of mitochondrial proteome and health. The proper understanding of mitochondrial protein quality control mechanisms will provide relevant insights to treat multiple human diseases. Keywords: mitochondria; proteome; ubiquitin; proteasome; chaperones; protease; mitophagy; mitochondrial protein quality control; mitochondria-associated degradation; mitochondrial unfolded protein response 1. Introduction Mitochondria are double membrane, dynamic, and semiautonomous organelles which have several critical cellular functions. -
This Is the Accepted Version of the Author's Manuscript. Reis SD, Pinho BR, Oliveira JMA "Modulation of Molecular Chapero
This is the Accepted Version of the Author’s Manuscript. Reis SD, Pinho BR, Oliveira JMA "Modulation of molecular chaperones in Huntington’s disease and other polyglutamine disorders". Molecular Neurobiology. September 2016 DOI: 10.1007/s12035-016-0120-z Link to Publisher: https://link.springer.com/article/10.1007%2Fs12035-016-0120-z Links to Full Text (RedCube, shared via Springer Nature) – View Only http://rdcu.be/kwjE 1 ! Title page Modulation of molecular chaperones in Huntington’s disease and other polyglutamine disorders Sara D. Reis, Brígida R. Pinho, Jorge M. A. Oliveira* REQUIMTE/LAQV, Department of Drug Sciences, Pharmacology Lab, Faculty of Pharmacy, University of Porto, Porto, Portugal *Corresponding author: Jorge M. Ascenção Oliveira Tel. +351 220428610 Email: [email protected] Acknowledgements This work was supported by Fundação para a Ciência e a Tecnologia (FCT): Strategic award UID/QUI/50006/2013, and by the research grant PTDC/NEU-NMC/0412/2014 (PI: JMAO), co- financed by the European Union (FEDER, QREN, COMPETE) – POCI-01-0145-FEDER- 016577. SDR acknowledges FCT for her PhD Grant (PD/BD/113567/2015). BRP acknowledges FCT for her PostDoc Grant (SFRH/BPD/102259/2014). We thank Ana Isabel Duarte (PhD, U. Coimbra) and Maria Clara Quintas (PhD, U. Porto) for reading and commenting the initial manuscript draft. 2 ! Abstract Polyglutamine expansion mutations in specific proteins underlie the pathogenesis of a group of progressive neurodegenerative disorders, including Huntington’s disease, spinal and bulbar muscular atrophy, dentatorubral-pallidoluysian atrophy, and several spinocerebellar ataxias. The different mutant proteins share ubiquitous expression and abnormal proteostasis, with misfolding and aggregation, but nevertheless evoke distinct patterns of neurodegeneration. -
Genomic Identification, Evolution and Sequence Analysis of the Heat
G C A T T A C G G C A T genes Article Genomic Identification, Evolution and Sequence Analysis of the Heat-Shock Protein Gene Family in Buffalo 1, 2, 3 4 1 Saif ur Rehman y, Asif Nadeem y , Maryam Javed , Faiz-ul Hassan , Xier Luo , Ruqayya Bint Khalid 3 and Qingyou Liu 1,* 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; [email protected] (S.u.R.); [email protected] (X.L.) 2 Department of Biotechnology, Virtual University of Pakistan, Lahore-54000, Pakistan; [email protected] 3 Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore-54000, Pakistan; [email protected] (M.J.); [email protected] (R.B.K.) 4 Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad-38040, Pakistan; [email protected] * Correspondence: [email protected]; Tel.: +86-138-7880-5296 These authors contributed equally to this manuscript. y Received: 26 October 2020; Accepted: 18 November 2020; Published: 23 November 2020 Abstract: Heat-shock proteins (HSP) are conserved chaperones crucial for protein degradation, maturation, and refolding. These adenosine triphosphate dependent chaperones were classified based on their molecular mass that ranges between 10–100 kDA, including; HSP10, HSP40, HSP70, HSP90, HSPB1, HSPD, and HSPH1 family. HSPs are essential for cellular responses and imperative for protein homeostasis and survival under stress conditions. This study performed a computational analysis of the HSP protein family to better understand these proteins at the molecular level.