Effects of Oxidative Stress on Protein Translation
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Structure of the Mammalian 80S Initiation Complex with Initiation Factor 5B on HCV-IRES RNA
ARTICLES Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA Hiroshi Yamamoto1,3, Anett Unbehaun1,3, Justus Loerke1, Elmar Behrmann1, Marianne Collier1, Jörg Bürger1,2, Thorsten Mielke1,2 & Christian M T Spahn1 The universally conserved eukaryotic initiation factor (eIF) 5B, a translational GTPase, is essential for canonical translation initiation. It is also required for initiation facilitated by the internal ribosomal entry site (IRES) of hepatitis C virus (HCV) RNA. Met eIF5B promotes joining of 60S ribosomal subunits to 40S ribosomal subunits bound by initiator tRNA (Met-tRNAi ). However, the exact molecular mechanism by which eIF5B acts has not been established. Here we present cryo-EM reconstructions of the Met mammalian 80S–HCV-IRES–Met-tRNAi –eIF5B–GMPPNP complex. We obtained two substates distinguished by the rotational state of the ribosomal subunits and the configuration of initiator tRNA in the peptidyl (P) site. Accordingly, a combination of Met conformational changes in the 80S ribosome and in initiator tRNA facilitates binding of the Met-tRNAi to the 60S P site and redefines the role of eIF5B as a tRNA-reorientation factor. Met Eukaryotic translation initiation is a highly regulated process within stable ribosomal binding of Met-tRNAi and elongation competence the translation cycle that proceeds via 48S and 80S initiation-complex in vivo11–13. However, the molecular mechanism linking eIF5B–GTP Met Met intermediates. At least 12 eIFs facilitate recruitment of Met-tRNAi hydrolysis and proper placement of Met-tRNAi in the ribosomal and mRNA to the ribosomal 40S subunit and regulate the interaction of P site is not known. -
Evolution of Translation EF-Tu: Trna
University of Illinois at Urbana-Champaign Luthey-Schulten Group NIH Resource for Macromolecular Modeling and Bioinformatics Computational Biophysics Workshop Evolution of Translation EF-Tu: tRNA VMD Developer: John Stone MultiSeq Developers Tutorial Authors Elijah Roberts Ke Chen John Eargle John Eargle Dan Wright Zhaleh Ghaemi Jonathan Lai Zan Luthey-Schulten August 2014 A current version of this tutorial is available at http://www.scs.illinois.edu/~schulten/tutorials/ef-tu CONTENTS 2 Contents 1 Introduction 3 1.1 The Elongation Factor Tu . 3 1.2 Getting Started . 4 1.2.1 Requirements . 4 1.2.2 Copying the tutorial files . 4 1.2.3 Working directory . 4 1.2.4 Preferences . 4 1.3 Configuring BLAST for MultiSeq . 5 2 Comparative Analysis of EF-Tu 5 2.1 Finding archaeal EF1A sequences . 6 2.2 Aligning archaeal sequences and removing redundancy . 8 2.3 Finding bacteria EF-Tu sequences . 11 2.4 Performing ClustalW Multiple Sequence and Profile-Profile Align- ments . 12 2.5 Creating Multiple Sequence with MAFFT . 16 2.6 Conservation of EF-Tu among the Bacteria . 16 2.7 Finding conserved residues across the bacterial and archaeal do- mains . 20 2.8 EF-Tu Interface with the Ribosome . 21 3 Computing a Maximum Likelihood Phylogenetic Tree with RAxML 23 3.1 Load the Phylogenetic Tree into MultiSeq . 25 3.2 Reroot and Manipulate the Phylogenetic Tree . 25 4 MultiSeq TCL Scripting: Genomic Context 27 5 Appendix A 30 5.1 Building a BLAST Database . 30 6 Appendix B 31 6.1 Saving QR subset of alignments in PHYLIP and FASTA format 31 6.2 Calculating Maximum Likelihood Trees with RAxML . -
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. -
Proteomics Provides Insights Into the Inhibition of Chinese Hamster V79
www.nature.com/scientificreports OPEN Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment Jifeng Liu1,2, Tengfei Ma1,2, Mingzhong Gao3, Yilin Liu4, Jun Liu1, Shichao Wang2, Yike Xie2, Ling Wang2, Juan Cheng2, Shixi Liu1*, Jian Zou1,2*, Jiang Wu2, Weimin Li2 & Heping Xie2,3,5 As resources in the shallow depths of the earth exhausted, people will spend extended periods of time in the deep underground space. However, little is known about the deep underground environment afecting the health of organisms. Hence, we established both deep underground laboratory (DUGL) and above ground laboratory (AGL) to investigate the efect of environmental factors on organisms. Six environmental parameters were monitored in the DUGL and AGL. Growth curves were recorded and tandem mass tag (TMT) proteomics analysis were performed to explore the proliferative ability and diferentially abundant proteins (DAPs) in V79 cells (a cell line widely used in biological study in DUGLs) cultured in the DUGL and AGL. Parallel Reaction Monitoring was conducted to verify the TMT results. γ ray dose rate showed the most detectable diference between the two laboratories, whereby γ ray dose rate was signifcantly lower in the DUGL compared to the AGL. V79 cell proliferation was slower in the DUGL. Quantitative proteomics detected 980 DAPs (absolute fold change ≥ 1.2, p < 0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. KEGG pathway analysis revealed that seven pathways (e.g. -
Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6
Research Collection Doctoral Thesis Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6 Author(s): Voigts-Hoffmann, Felix Publication Date: 2012 Permanent Link: https://doi.org/10.3929/ethz-a-007303759 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library ETH Zurich Dissertation No. 20189 Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6 A dissertation submitted to ETH ZÜRICH for the degree of Doctor of Sciences (Dr. sc. ETH Zurich) presented by Felix Voigts-Hoffmann MSc Molecular Biotechnology, Universität Heidelberg born April 11, 1981 citizen of Göttingen, Germany accepted on recommendation of Prof. Dr. Nenad Ban (Examiner) Prof. Dr. Raimund Dutzler (Co-examiner) Prof. Dr. Rudolf Glockshuber (Co-examiner) 2012 blank page ii Summary Ribosomes are large complexes of several ribosomal RNAs and dozens of proteins, which catalyze the synthesis of proteins according to the sequence encoded in messenger RNA. Over the last decade, prokaryotic ribosome structures have provided the basis for a mechanistic understanding of protein synthesis. While the core functional centers are conserved in all kingdoms, eukaryotic ribosomes are much larger than archaeal or bacterial ribosomes. Eukaryotic ribosomal rRNA and proteins contain extensions or insertions to the prokaryotic core, and many eukaryotic proteins do not have prokaryotic counterparts. Furthermore, translation regulation and ribosome biogenesis is much more complex in eukaryotes, and defects in components of the translation machinery are associated with human diseases and cancer. -
Ef-G:Trna Dynamics During the Elongation Cycle of Protein Synthesis
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2015 Ef-G:trna Dynamics During the Elongation Cycle of Protein Synthesis Rong Shen University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons Recommended Citation Shen, Rong, "Ef-G:trna Dynamics During the Elongation Cycle of Protein Synthesis" (2015). Publicly Accessible Penn Dissertations. 1131. https://repository.upenn.edu/edissertations/1131 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1131 For more information, please contact [email protected]. Ef-G:trna Dynamics During the Elongation Cycle of Protein Synthesis Abstract During polypeptide elongation cycle, prokaryotic elongation factor G (EF-G) catalyzes the coupled translocations on the ribosome of mRNA and A- and P-site bound tRNAs. Continued progress has been achieved in understanding this key process, including results of structural, ensemble kinetic and single- molecule studies. However, most of work has been focused on the pre-equilibrium states of this fast process, leaving the real time dynamics, especially how EF-G interacts with the A-site tRNA in the pretranslocation complex, not fully elucidated. In this thesis, the kinetics of EF-G catalyzed translocation is investigated by both ensemble and single molecule fluorescence resonance energy transfer studies to further explore the underlying mechanism. In the ensemble work, EF-G mutants were designed and expressed successfully. The labeled EF-G mutants show good translocation activity in two different assays. In the smFRET work, by attachment of a fluorescent probe at position 693 on EF-G permits monitoring of FRET efficiencies to sites in both ribosomal protein L11 and A-site tRNA. -
The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition
Critical Reviews in Biochemistry and Molecular Biology, 40:285–311, 2005 Copyright c Taylor & Francis Inc. ! ISSN: 1040-9238 print / 1549-7798 online DOI: 10.1080/10409230500326334 The Ribosomal Peptidyl Transferase Center: Structure, Function, Evolution, Inhibition Norbert Polacek Innsbruck Biocenter, Division of ABSTRACT The ribosomal peptidyl transferase center (PTC) resides in the Genomics and RNomics, large ribosomal subunit and catalyzes the two principal chemical reactions of Innsbruck Medical University, protein synthesis: peptide bond formation and peptide release. The catalytic Innsbruck, Austria mechanisms employed and their inhibition by antibiotics have been in the Alexander S. Mankin focus of molecular and structural biologists for decades. With the elucidation Center for Pharmaceutical of atomic structures of the large ribosomal subunit at the dawn of the new Biotechnology, University of millennium, these questions gained a new level of molecular significance. The Illinois at Chicago, Chicago, crystallographic structures compellingly confirmed that peptidyl transferase is IL 60607, USA an RNA enzyme. This places the ribosome on the list of naturally occurring riboyzmes that outlived the transition from the pre-biotic RNA World to con- temporary biology. Biochemical, genetic and structural evidence highlight the role of the ribosome as an entropic catalyst that accelerates peptide bond for- mation primarily by substrate positioning. At the same time, peptide release should more strongly depend on chemical catalysis likely involving an rRNA group of the PTC. The PTC is characterized by the most pronounced accu- mulation of universally conserved rRNA nucleotides in the entire ribosome. Thus, it came as a surprise that recent findings revealed an unexpected high level of variation in the mode of antibiotic binding to the PTC of ribosomes from different organisms. -
Mitochondrial Translation and Its Impact on Protein Homeostasis And
Mitochondrial translation and its impact on protein homeostasis and aging Tamara Suhm Academic dissertation for the Degree of Doctor of Philosophy in Biochemistry at Stockholm University to be publicly defended on Friday 15 February 2019 at 09.00 in Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B. Abstract Besides their famous role as powerhouse of the cell, mitochondria are also involved in many signaling processes and metabolism. Therefore, it is unsurprising that mitochondria are no isolated organelles but are in constant crosstalk with other parts of the cell. Due to the endosymbiotic origin of mitochondria, they still contain their own genome and gene expression machinery. The mitochondrial genome of yeast encodes eight proteins whereof seven are core subunits of the respiratory chain and ATP synthase. These subunits need to be assembled with subunits imported from the cytosol to ensure energy supply of the cell. Hence, coordination, timing and accuracy of mitochondrial gene expression is crucial for cellular energy production and homeostasis. Despite the central role of mitochondrial translation surprisingly little is known about the molecular mechanisms. In this work, I used baker’s yeast Saccharomyces cerevisiae to study different aspects of mitochondrial translation. Exploiting the unique possibility to make directed modifications in the mitochondrial genome of yeast, I established a mitochondrial encoded GFP reporter. This reporter allows monitoring of mitochondrial translation with different detection methods and enables more detailed studies focusing on timing and regulation of mitochondrial translation. Furthermore, employing insights gained from bacterial translation, we showed that mitochondrial translation efficiency directly impacts on protein homeostasis of the cytoplasm and lifespan by affecting stress handling. -
Peptidyl-Transferase Ribozymes: Trans Reactions, Structural Characterization and Ribosomal RNA-Like Features Wang Zhang* and Thomas R Cech
Research Paper 539 Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features Wang Zhang* and Thomas R Cech Background: One of the most significant questions in understanding the origin Address: Howard Hughes Medical Institute, of life concerns the order of appearance of DNA, RNA and protein during early Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, biological evolution. If an ‘RNA world’ was a precursor to extant life, RNA must USA. be able not only to catalyze RNA replication but also to direct peptide synthesis. Iterative RNA selection previously identified catalytic RNAs (ribozymes) that form *Present address: Program in Molecular Medicine, amide bonds between RNA and an amino acid or between two amino acids. University of Massachusetts Medical Center, 373 Plantation Street, Worcester, MA 01605, USA. Results: We characterized peptidyl-transferase reactions catalyzed by two Correspondence: Thomas R Cech different families of ribozymes that use substrates that mimic A site and P site E-mail: [email protected] tRNAs. The family II ribozyme secondary structure was modeled using chemical Key words: metal ions, peptidyl transferase, modification, enzymatic digestion and mutational analysis. Two regions ribosomal RNA structure, RNA catalysis, RNA resemble the peptidyl-transferase region of 23s ribosomal RNA in sequence structure and structural context; these regions are important for peptide-bond formation. A shortened form of this ribozyme was engineered to catalyze intermolecular Received: 3 August 1998 (‘trans’) peptide-bond formation, with the two amino-acid substrates binding Revisions requested: 18 August 1998 Revisions received: 26 August 1998 through an attached AMP or oligonucleotide moiety. -
ANA-1 Murine Macrophages Ribosomal Peptidyl Transferase Activity in Cleavage Is Associated with Inhibition of Nitric Oxide-Depen
Nitric Oxide-Dependent Ribosomal RNA Cleavage Is Associated with Inhibition of Ribosomal Peptidyl Transferase Activity in ANA-1 Murine Macrophages This information is current as of October 2, 2021. Charles Q. Cai, Hongtao Guo, Rebecca A. Schroeder, Cecile Punzalan and Paul C. Kuo J Immunol 2000; 165:3978-3984; ; doi: 10.4049/jimmunol.165.7.3978 http://www.jimmunol.org/content/165/7/3978 Downloaded from References This article cites 13 articles, 5 of which you can access for free at: http://www.jimmunol.org/content/165/7/3978.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on October 2, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2000 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Nitric Oxide-Dependent Ribosomal RNA Cleavage Is Associated with Inhibition of Ribosomal Peptidyl Transferase Activity in ANA-1 Murine Macrophages1 Charles Q. Cai,* Hongtao Guo,* Rebecca A. Schroeder,† Cecile Punzalan,* Paul C. Kuo2* NO can regulate specific cellular functions by altering transcriptional programs and protein reactivity. -
A Master Autoantigen-Ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 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. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases Julia Y. Wang1*, Michael W. Roehrl1, Victor B. Roehrl1, and Michael H. Roehrl2* 1 Curandis, New York, USA 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA * Correspondence: [email protected] or [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 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. Abstract Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. -
Proteomic Analysis of Mtor Inhibition-Mediated Phosphorylation
Protein Cell DOI 10.1007/s13238-016-0279-0 Protein & Cell LETTER Proteomic analysis of mTOR inhibition- mediated phosphorylation changes in ribosomal proteins and eukaryotic translation initiation factors Dear Editor, analysis based on the SILAC (stable isotope labeling by amino acids in cell culture) method was carried out to analyze affinity The mammalian target of rapamycin (mTOR), as a critical enriched phosphoproteins from the untreated and rapamycin- Cell energy sensor and cell-growth regulator, controls protein treated 293T cells. The experimental workflow was displayed & 12 14 synthesis, autophagy and many important cellular processes in Fig. 1A. Briefly, cells grown in light medium ( C6 N2-Lysine 12 0 0 through forming functional distinct complexes, mTORC1 and and C6-Arginine, K R ) were treated with 200 nmol/L rapa- 13 15 mTORC2. mTORC1 that is sensitive to rapamycin, regulates mycin for 2 h, while cells grown in heavy medium ( C6 N2- 13 8 6 cell growth and protein synthesis, while mTORC2 that is Lysine and C6-Arginine, K R ) were untreated. Sucrose insensitive to rapamycin, regulates cellular metabolism and cushion centrifugation was used to isolate ribosomes. Pro- Protein the cytoskeletal organization (Gingras et al., 2001; Hay and teins extracted from the whole cell lysate or the isolated ribo- Sonenberg, 2004). Translation initiation is the rate-limiting some fraction of the untreated and rapamycin-treated cells step in protein synthesis, which proceeds through a multi- were mixed and trypsin digested. Then phosphopeptides step process that can be divided into three major steps. First, were enriched with TiO2 beads and analyzed by nano-LC-MS/ eukaryotic translation initiation factor 2 (eIF2) binds with GTP MS.