Modulation of ERQC and ERAD: a Broad-Spectrum Spanner in the Works of Cancer Cells?
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Mir-379 Deletion Ameliorates Features of Diabetic Kidney Disease By
ARTICLE https://doi.org/10.1038/s42003-020-01516-w OPEN miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1 ✉ Mitsuo Kato 1,8 , Maryam Abdollahi 1,8, Ragadeepthi Tunduguru1, Walter Tsark2, Zhuo Chen 1, 1234567890():,; Xiwei Wu3, Jinhui Wang3, Zhen Bouman Chen 1,4, Feng-Mao Lin1, Linda Lanting1, Mei Wang1, Janice Huss5, ✉ Patrick T Fueger 5,6, David Chan7 & Rama Natarajan 1,4 Diabetic kidney disease (DKD) is a major complication of diabetes. Expression of members of the microRNA (miRNA) miR-379 cluster is increased in DKD. miR-379, the most upstream 5′-miRNA in the cluster, functions in endoplasmic reticulum (ER) stress by targeting EDEM3. However, the in vivo functions of miR-379 remain unclear. We created miR-379 knockout (KO) mice using CRISPR-Cas9 nickase and dual guide RNA technique and characterized their phenotype in diabetes. We screened for miR-379 targets in renal mesangial cells from WT vs. miR-379KO mice using AGO2-immunopreciptation and CLASH (cross-linking, ligation, sequencing hybrids) and identified the redox protein thioredoxin and mitochondrial fission-1 protein. miR-379KO mice were protected from features of DKD as well as body weight loss associated with mitochondrial dysfunction, ER- and oxidative stress. These results reveal a role for miR-379 in DKD and metabolic processes via reducing adaptive mitophagy. Strate- gies targeting miR-379 could offer therapeutic options for DKD. 1 Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA. -
Composition and Evolution of the Vertebrate and Mammalian Selenoproteomes
Composition and Evolution of the Vertebrate and Mammalian Selenoproteomes The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Mariotti, Marco, Perry G. Ridge, Yan Zhang, Alexei V. Lobanov, Thomas H. Pringle, Roderic Guigo, Dolph L. Hatfield, and Vadim N. Gladyshev. 2012. Composition and evolution of the vertebrate and mammalian selenoproteomes. PLoS ONE 7(3): e33066. Published Version doi:10.1371/journal.pone.0033066 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10341925 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Composition and Evolution of the Vertebrate and Mammalian Selenoproteomes Marco Mariotti1,2., Perry G. Ridge3., Yan Zhang1,4., Alexei V. Lobanov1, Thomas H. Pringle5, Roderic Guigo2, Dolph L. Hatfield6, Vadim N. Gladyshev1* 1 Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America, 2 Center for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Spain, 3 Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, United States of America, 4 Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China, 5 Sperling Foundation, Eugene, Oregon, United States of America, 6 Laboratory of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America Abstract Background: Selenium is an essential trace element in mammals due to its presence in proteins in the form of selenocysteine (Sec). -
Identification and Characterization of Fep15, a New Selenocysteine-Containing Member of the Sep15 Protein Family
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Vadim Gladyshev Publications Biochemistry, Department of March 2006 Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family Sergey V. Novoselov University of Nebraska-Lincoln Deame Hua University of Nebraska-Lincoln A. V. Lobanov University of Nebraska-Lincoln Vadim N. Gladyshev University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biochemgladyshev Part of the Biochemistry, Biophysics, and Structural Biology Commons Novoselov, Sergey V.; Hua, Deame; Lobanov, A. V.; and Gladyshev, Vadim N., "Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family" (2006). Vadim Gladyshev Publications. 62. https://digitalcommons.unl.edu/biochemgladyshev/62 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Vadim Gladyshev Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Biochemical Journal 394:3 (March 15, 2006), pp. 575–579. doi: 10.1042/BJ20051569. Copyright © 2005 The Biochemical Society, London. Used by permission. Submitted September 22, 2005; revised October 18, 2005; accepted and prepublished online October 20, 2005; published online February 24, 2006. Identifi cation and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family Sergey V. Novoselov, Deame Hua, Alexey V. Lobanov, and Vadim N. Gladyshev* Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE 68588 *Corresponding author; email: [email protected] Abstract: Sec (selenocysteine) is a rare amino acid in proteins. -
Focus on the Small Heat Shock Protein HSPB1 Autofagie in De Erfelij
Faculteit Faculteit Farmaceutische, Biomedische en Diergeneeskundige wetenschappen Biochemie en Biotechnologie Autophagy in inherited peripheral neuropathies: Focus on the small heat shock protein HSPB1 Autofagie in de erfelijke perifere neuropathieën: Focus op de kleine heat shock proteïne HSPB1 Proefschrift voorgelegd tot het behalen van de graad van Doctor in de Wetenschappen: Biochemie en Biotechnologie aan de Universiteit Antwerpen. te verdedigen door Mansour HAIDAR Promotor Prof. Dr. Vincent Timmerman Antwerpen, 2018 1 2 “Haud igitur redit ad Nihilum res ulla, sed omnes Discidio redeunt in corpora materiai” Lucretius, De Rerum Natura, Book I. 250 3 4 Members of the jury Chair Prof. Dr. Wim Vanden Berghe, PhD (UA, Antwerp, Belgium) Promotor Prof. Dr. Vincent Timmerman, PhD (UA, Antwerp, Belgium) Internal jury member Prof. Dr. Wim Martinet, PhD (UA, Antwerp, Belgium) External jury members Prof. Dr. Joy Irobi (UHasselt, Hasselt, Belgium) Prof. Dr. Maurizio D’Antonio (San Raffaele Institute, Milan, Italy) Prof. Dr. Ir. Winnok De Vos (UA, Antwerp, Belgium) 5 6 Table of Contents Summary/Samenvatting 9 Rationale and Aims 13 Introduction Chapter 1 Autophagy as an emerging common pathomechanism in inherited 15 peripheral neuropathies Chapter 2 Small heat shock proteins: Their role in proteostasis 79 and neurodegeneration Results Chapter 3 HSPB1 is required for Autophagy: Insights from CMT-causing mutations 103 Chapter 4 An interactomics study of HSPB1 wild-type and mutant links it to the 129 autophagy receptor P62 Discussion 179 List of abbreviations 195 Curriculum Vitae 199 Acknowledgements 203 7 8 Summary Inherited peripheral neuropathies (IPNs) are genetically heterogeneous disorders affecting mainly the peripheral nervous system and with over 1500 mutations in more than 80 affected genes discovered so far. -
Deficiency in the 15-Kda Selenoprotein Inhibits Tumorigenicity and Metastasis of Colon Cancer Cells
Published OnlineFirst April 13, 2010; DOI: 10.1158/1940-6207.CAPR-10-0003 Published Online First on April 13, 2010 as 10.1158/1940-6207.CAPR-10-0003 Research Article Cancer Prevention Research Deficiency in the 15-kDa Selenoprotein Inhibits Tumorigenicity and Metastasis of Colon Cancer Cells Robert Irons1,3,4, Petra A. Tsuji1,2,3, Bradley A. Carlson3, Ping Ouyang1,3, Min-Hyuk Yoo3, Xue-Ming Xu3, Dolph L. Hatfield3, Vadim N. Gladyshev5, and Cindy D. Davis1 Abstract Selenium has cancer-preventive activity that is mediated, in part, through selenoproteins. The role of the 15-kDa selenoprotein (Sep15) in colon cancer was assessed by preparing and using mouse colon CT26 cells stably transfected with short hairpin RNA constructs targeting Sep15. Metabolic 75Se labeling and Northern and Western blot analyses revealed that >90% of Sep15 was downregulated. Growth of the resulting Sep15-deficient CT26 cells was reduced (P < 0.01), and cells formed significantly (P < 0.001) fewer colonies in soft agar compared with control CT26 cells. Whereas most (14 of 15) BALB/c mice injected with control cells developed tumors, few (3 of 30) mice injected with Sep15-deficient cells developed tumors (P < 0.0001). The ability to form pulmonary metastases had similar results. Mice injected with the plasmid-transfected control cells had >250 lung metastases per mouse; however, mice injected with cells with downregulation of Sep15 only had 7.8 ± 5.4 metastases. To investigate molecular targets affected by Sep15 status, gene expression patterns between control and knockdown CT26 cells were compared. Ingenuity Pathways Analysis was used to analyze the 1,045 genes that were significantly (P < 0.001) affected by Sep15 deficiency. -
A Large Prospective Study of SEP15 Genetic Variation, Interaction with Plasma Selenium Levels, and Prostate Cancer Risk and Survival
A large prospective study of SEP15 genetic variation, interaction with plasma selenium levels, and prostate cancer risk and survival The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Penney, K. L., F. R. Schumacher, H. Li, P. Kraft, J. S. Morris, T. Kurth, L. A. Mucci, et al. 2010. “A Large Prospective Study of SEP15 Genetic Variation, Interaction with Plasma Selenium Levels, and Prostate Cancer Risk and Survival.” Cancer Prevention Research 3 (5): 604– 10. https://doi.org/10.1158/1940-6207.capr-09-0216. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:41292599 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Cancer Prev Res (Phila). Author manuscript; available in PMC 2011 May 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Cancer Prev Res (Phila). 2010 May ; 3(5): 604±610. doi:10.1158/1940-6207.CAPR-09-0216. A large prospective study of SEP15 genetic variation, interaction with plasma selenium levels, and prostate cancer risk and survival Kathryn L. Penney1,2, Fredrick R. Schumacher3, Haojie Li4, Peter Kraft1, J. Steven Morris5, Tobias Kurth1,6, Lorelei A. Mucci1,2, David J. Hunter1,2, Philip W. Kantoff7, Meir J. Stampfer1,2, and Jing -
A Regulatory Role for Sec Trna in Selenoprotein Synthesis
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press A regulatory role for Sec tRNA[Ser]Sec in selenoprotein synthesis RUTH R. JAMESON and ALAN M. DIAMOND Department of Human Nutrition, University of Illinois at Chicago, Chicago, Illinois 60612, USA ABSTRACT Selenium is biologically active through the functions of selenoproteins that contain the amino acid selenocysteine. This amino acid is translated in response to in-frame UGA codons in mRNAs that include a SECIS element in its 3 untranslated region, and this process requires a unique tRNA, referred to as tRNA[Ser]Sec. The translation of UGA as selenocysteine, rather than its use as a termination signal, is a candidate restriction point for the regulation of selenoprotein synthesis by selenium. A specialized reporter construct was used that permits the evaluation of SECIS-directed UGA translation to examine mechanisms of the regulation of selenoprotein translation. Using SECIS elements from five different selenoprotein mRNAs, UGA translation was quantified in response to selenium supplementation and alterations in tRNA[Ser]Sec levels and isoform distributions. Although each of the evaluated SECIS elements exhibited differences in their baseline activities, each was stimulated to a similar extent by increased selenium or tRNA[Ser]Sec levels and was inhibited by diminished levels of the methylated isoform of tRNA[Ser]Sec achieved using a dominant-negative acting mutant tRNA[Ser]Sec. tRNA[Ser]Sec was found to be limiting for UGA translation under conditions of high selenoprotein mRNA in both a transient reporter assay and in cells with elevated GPx-1 mRNA. -
<I>AUREOCOCCUS ANOPHAGEFFERENS</I>
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2016 MOLECULAR AND ECOLOGICAL ASPECTS OF THE INTERACTIONS BETWEEN AUREOCOCCUS ANOPHAGEFFERENS AND ITS GIANT VIRUS Mohammad Moniruzzaman University of Tennessee, Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Moniruzzaman, Mohammad, "MOLECULAR AND ECOLOGICAL ASPECTS OF THE INTERACTIONS BETWEEN AUREOCOCCUS ANOPHAGEFFERENS AND ITS GIANT VIRUS. " PhD diss., University of Tennessee, 2016. https://trace.tennessee.edu/utk_graddiss/4152 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Mohammad Moniruzzaman entitled "MOLECULAR AND ECOLOGICAL ASPECTS OF THE INTERACTIONS BETWEEN AUREOCOCCUS ANOPHAGEFFERENS AND ITS GIANT VIRUS." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Microbiology. Steven W. Wilhelm, Major Professor We have read this dissertation -
On the Road to Selenocysteine
COMMENTARY On the road to selenocysteine Alan M. Diamond* Department of Human Nutrition, University of Illinois, Chicago, IL 60612 ecades ago, a mammalian purified PSTK established the substrate enzymes with antioxidant capabilities tRNA that exclusively bound specificity of this enzyme exclusively for (glutathione peroxidases) and those the UGA stop codon was both seryl-tRNA[Ser]Sec isoforms, which involved with the maintenance of the identified by using the triplet differ by only a single modified base (5). reduced cellular environment (thiore- Dbinding assay that was instrumental in It is highly significant that the initial doxin reductases) and the maturation deciphering the genetic code (1). The method of detection, a computer- of thyroxin (thyroid hormone deiodi- possibility of a naturally occurring sup- assisted analysis of genomes that were nases). Other mammalian selenopro- pressor tRNA presented the dilemma known either to contain or to be miss- teins of known function include SelP, of explaining the biological function of ing the selenoprotein synthesis machin- which is involved with selenium trans- such a molecule. In the same year, an ery, was successful at all. The presence port; SPS2, which is required for Sec equally perplexing report indicated the of PSTK in archaeal and eukaryote ge- synthesis; and SelR, a methionine sul- existence of tRNA from either rooster nomes that were known to translation- foxide reductase (reviewed in ref. 12). or rat liver that was aminoacylated ally synthesize selenoproteins, but its Although the biochemical properties with phosphoserine (2). That observa- absence in the genomes of organisms (i.e., cellular location and binding part- tion was verified several years later that do not, is consistent with the role ners) are known for several other sel- when phosphoseryl tRNA was also of PSTK indicated by Carlson et al. -
Thyroxine Binding to Type III Iodothyronine Deiodinase Craig A
www.nature.com/scientificreports OPEN Thyroxine binding to type III iodothyronine deiodinase Craig A. Bayse*, Eric S. Marsan, Jenna R. Garcia & Alexis T. Tran‑Thompson Iodothyronine deiodinases (Dios) are important selenoproteins that control the concentration of the active thyroid hormone (TH) triiodothyronine through regioselective deiodination. The X‑ray structure of a truncated monomer of Type III Dio (Dio3), which deiodinates TH inner rings through a selenocysteine (Sec) residue, revealed a thioredoxin-fold catalytic domain supplemented with an unstructured Ω-loop. Loop dynamics are driven by interactions of the conserved Trp207 with solvent in multi-microsecond molecular dynamics simulations of the Dio3 thioredoxin(Trx)-fold domain. Hydrogen bonding interactions of Glu200 with residues conserved across the Dio family anchor the loop’s n‑terminus to the active site Ser‑cys-Thr‑Sec sequence. A key long‑lived loop conformation coincides with the opening of a cryptic pocket that accommodates thyroxine (T4) through an I⋯Se halogen bond to Sec170 and the amino acid group with a polar cleft. The Dio3-T4 complex is stabilized by an I⋯O halogen bond between an outer ring iodine and Asp211, consistent with Dio3 selectivity for inner ring deiodination. Non-conservation of residues, such as Asp211, in other Dio types in the fexible portion of the loop sequence suggests a mechanism for regioselectivity through Dio type- specifc loop conformations. Cys168 is proposed to attack the selenenyl iodide intermediate to regenerate Dio3 based upon structural comparison with related Trx-fold proteins. Iodothyronine deiodinase (Dio) membrane selenoproteins regulate thyroid hormone (TH) activity through regioselective deiodination (Fig. 1a)1–10. -
NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer
Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-7-2018 Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer Jairo Ramos [email protected] Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Clinical Epidemiology Commons Recommended Citation Ramos, Jairo, "Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer" (2018). FIU Electronic Theses and Dissertations. 3872. https://digitalcommons.fiu.edu/etd/3872 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida DECIPHER MECHANISMS BY WHICH NUCLEAR RESPIRATORY FACTOR ONE (NRF1) COORDINATES CHANGES IN THE TRANSCRIPTIONAL AND CHROMATIN LANDSCAPE AFFECTING DEVELOPMENT AND PROGRESSION OF INVASIVE BREAST CANCER A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in PUBLIC HEALTH by Jairo Ramos 2018 To: Dean Tomás R. Guilarte Robert Stempel College of Public Health and Social Work This dissertation, Written by Jairo Ramos, and entitled Decipher Mechanisms by Which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer, having been approved in respect to style and intellectual content, is referred to you for judgment. -
Downloaded Per Proteome Cohort Via the Web- Site Links of Table 1, Also Providing Information on the Deposited Spectral Datasets
www.nature.com/scientificreports OPEN Assessment of a complete and classifed platelet proteome from genome‑wide transcripts of human platelets and megakaryocytes covering platelet functions Jingnan Huang1,2*, Frauke Swieringa1,2,9, Fiorella A. Solari2,9, Isabella Provenzale1, Luigi Grassi3, Ilaria De Simone1, Constance C. F. M. J. Baaten1,4, Rachel Cavill5, Albert Sickmann2,6,7,9, Mattia Frontini3,8,9 & Johan W. M. Heemskerk1,9* Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome‑wide transcriptomes (57.8 k mRNAs). For 14.8 k protein‑coding transcripts, we assigned the proteins to 21 UniProt‑based classes, based on their preferential intracellular localization and presumed function. This classifed transcriptome‑proteome profle of platelets revealed: (i) Absence of 37.2 k genome‑ wide transcripts. (ii) High quantitative similarity of platelet and megakaryocyte transcriptomes (R = 0.75) for 14.8 k protein‑coding genes, but not for 3.8 k RNA genes or 1.9 k pseudogenes (R = 0.43–0.54), suggesting redistribution of mRNAs upon platelet shedding from megakaryocytes. (iii) Copy numbers of 3.5 k proteins that were restricted in size by the corresponding transcript levels (iv) Near complete coverage of identifed proteins in the relevant transcriptome (log2fpkm > 0.20) except for plasma‑derived secretory proteins, pointing to adhesion and uptake of such proteins. (v) Underrepresentation in the identifed proteome of nuclear‑related, membrane and signaling proteins, as well proteins with low‑level transcripts.