Co-Translational Protein Folding and Sorting in Chloroplasts
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Size Changes in Eukaryotic Ribosomes
Proc. Nat. Acad. Sci. USA Vol. 68, No. 12, pp. 3021-3025, December 1971 Size Changes in Eukaryotic Ribosomes (diffusion constant/sedimentation constant/ribosomal dissociation/chick embryo) JOHN VOURNAKIS AND ALEXANDER RICH Department of Biology, Massachusetts Institute of Technology, Cambridge, Mass. 02139 Contributed by Alexander Rich, September 20, 1971 ABSTRACT Evidence is presented that ribosomes two particles are similar. However, these changes suggest active in protein synthesis and attached to messenger that when the ribosome is attached to messenger RNA it has a RNA on polysomes have a smaller diameter than free cytoplasmic single ribosomes. Measurements have been smaller diameter than is found for the free cytoplastic ribo- made on these two types of ribosomes of differences in some. This more compact form of the ribosome is maintained sedimentation velocity and diffusion constant. Differences even when the nascent polypeptide chain is relased by puro- in these quantities suggest about a 20-A decrease in the mycin. We thus infer that there are substantial differences diameter of the ribosomes from chick embryo muscles in the interactions between the ribosomal subunits when when they are attached to messenger RNA. Similar dif- they ferences are also observed in rabbit reticulocytes and are attached to messenger RNA as compared to the free cyto- mouse ascites tumor cells. These two ribosomal states plasmic single ribosome, which is inactive in protein synthesis. have different sensitivity to Pronase digestion and dis- sociate into ribosomal subunits at different KCI concen- METHODS AND MATERIALS trations. This size difference is not associated with a sig- nificant difference in overall ribosomal mass and appears Preparation of Ribosomes. -
Control of Protein Function
3 Control of Protein Function In the cell, precise regulation of protein function is essential to avoid chaos. This chapter describes the most important molecular mechanisms by which protein function is regulated in cells. These range from control of a protein’s location and lifetime within the cell to the binding of regulatory molecules and covalent modifications such as phosphorylation that rapidly switch protein activity on or off. Also covered here are the nucleotide-driven switches in conformation that underlie the action of motor proteins and that regulate many signal transduction pathways. 3-0 Overview: Mechanisms of Regulation 3-1 Protein Interaction Domains 3-2 Regulation by Location 3-3 Control by pH and Redox Environment 3-4 Effector Ligands: Competitive Binding and Cooperativity 3-5 Effector Ligands: Conformational Change and Allostery 3-6 Protein Switches Based on Nucleotide Hydrolysis 3-7 GTPase Switches: Small Signaling G Proteins 3-8 GTPase Switches: Signal Relay by Heterotrimeric GTPases 3-9 GTPase Switches: Protein Synthesis 3-10 Motor Protein Switches 3-11 Regulation by Degradation 3-12 Control of Protein Function by Phosphorylation 3-13 Regulation of Signaling Protein Kinases: Activation Mechanism 3-14 Regulation of Signaling Protein Kinases: Cdk Activation 3-15 Two-Component Signaling Systems in Bacteria 3-16 Control by Proteolysis: Activation of Precursors 3-17 Protein Splicing: Autoproteolysis by Inteins 3-18 Glycosylation 3-19 Protein Targeting by Lipid Modifications 3-20 Methylation, N-acetylation, Sumoylation and Nitrosylation 3-0 Overview: Mechanisms of Regulation Protein function in living cells is precisely regulated A typical bacterial cell contains a total of about 250,000 protein molecules (comprising different amounts of each of several thousand different gene products), which are packed into a volume so small that it has been estimated that, on average, they are separated from one another by a distance that would contain only a few molecules of water. -
"Hsp70 Chaperones"
Hsp70 Chaperones Advanced article Elizabeth A Craig, University of Wisconsin, Madison, Wisconsin, USA Article Contents . Introduction Jaroslaw Marszalek, University of Gdansk, Gdansk, Poland . Hsp70:Client Protein Interaction Cycle . Proliferation of Hsp70 and J-protein Genes . Function and Evolution of Mitochondrial Hsp70 Systems . Conclusions: Versatility of Hsp70 System Allows for Adaptation to New Functions Online posting date: 15th March 2011 Via their interaction with client proteins, Hsp70 molecu- stress. In some cases they also facilitate transfer of client lar chaperone machines function in a variety of cellular proteins to proteolytic systems, particularly when refolding processes, including protein folding, translocation of into the native state is unachievable. See also: Chaperones, proteins across membranes and assembly/disassembly of Chaperonin and Heat-Shock Proteins The ability of Hsp70 chaperones to be involved in such protein complexes. Such machines are composed of a core diverse cellular functions, whereas relying on a single bio- Hsp70, as well as a J-protein and a nucleotide exchange chemical activity, an adenosine triphosphate (ATP)- factor as co-chaperones. These co-factors regulate the dependent client binding and release cycle, is remarkable. cycle of adenosine triphosphate (ATP) hydrolysis and Here, to illustrate the molecular mechanisms and evo- nucleotide exchange, which is critical for Hsp70’s inter- lutionary history behind the specialisation of Hsp70 sys- action with client proteins. Cellular compartments often tems we focus on mitochondrial Hsp70 systems, as they contain multiple Hsp70s, J-proteins and nucleotide exemplify two major strategies of Hsp70 specialisation: exchange factors. The capabilities of Hsp70s to carry out (i) amplification and diversification of HSP70 genes and diverse cellular functions can result from either special- (ii) multiplication and specialisation of genes encoding isation of an Hsp70 or by interaction of a multifunctional their J-proteins co-chaperones (Figure 1). -
Structure of the Molecular Chaperone Prefoldin
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Cell, Vol. 103, 621±632, November 10, 2000, Copyright 2000 by Cell Press Structure of the Molecular Chaperone Prefoldin: Unique Interaction of Multiple Coiled Coil Tentacles with Unfolded Proteins of newly synthesized bacterial %10ف ,Ralf Siegert,² Michel R. Leroux,²³ 1999). In addition Clemens Scheufler, F. Ulrich Hartl,* proteins complete their folding in the sequestered envi- and Ismail Moarefi* ronment provided by GroEL/GroES (Horwich et al., 1993; Max-Planck Institut fuÈ r Biochemie Ewalt et al., 1997; Houry et al., 1999). The eukaryotic Am Klopferspitz 18a Hsp70 chaperone machine also binds nascent chains D82152 Martinsried (Beckmann et al., 1990; Nelson et al., 1992; Eggers et Germany al., 1997; Thulasiraman et al., 1999), and some proteins, including actins and tubulins, depend on the Group II cytosolic chaperonin TRiC (TCP-1 ring Complex; also Summary termed CCT) for folding (Frydman et al., 1992; Gao et al., 1992; Yaffe et al., 1992; Kubota et al., 1995; Siegers Prefoldin (GimC) is a hexameric molecular chaperone et al., 1999). complex built from two related classes of subunits The archaeal Group II chaperonin (thermosome) is and present in all eukaryotes and archaea. Prefoldin closely related to its eukaryotic homologue TRiC (Gutsche et al., 1999). In contrast, Hsp70 proteins and interacts with nascent polypeptide chains and, in vitro, TF are generally missing from the archaeal kingdom can functionally substitute for the Hsp70 chaperone though some archaea have acquired Hsp70, presumably system in stabilizing non-native proteins for subse- by lateral gene transfer (Gribaldo et al., 1999). -
1519038862M28translationand
Paper No. : 15 Molecular Cell Biology Module : 28 Translation and Post-translation Modifications in Eukaryotes Development Team Principal Investigator : Prof. Neeta Sehgal Department of Zoology, University of Delhi Co-Principal Investigator : Prof. D.K. Singh Department of Zoology, University of Delhi Paper Coordinator : Prof. Kuldeep K. Sharma Department of Zoology, University of Jammu Content Writer : Dr. Renu Solanki, Deen Dayal Upadhyaya College Dr. Sudhida Gautam, Hansraj College, University of Delhi Mr. Kiran K. Salam, Hindu College, University of Delhi Content Reviewer : Prof. Rup Lal Department of Zoology, University of Delhi 1 Molecular Genetics ZOOLOGY Translation and Post-translation Modifications in Eukaryotes Description of Module Subject Name ZOOLOGY Paper Name Molecular Cell Biology; Zool 015 Module Name/Title Cell regulatory mechanisms Module Id M28: Translation and Post-translation Modifications in Eukaryotes Keywords Genome, Proteome diversity, post-translational modifications, glycosylation, phosphorylation, methylation Contents 1. Learning Objectives 2. Introduction 3. Purpose of post translational modifications 4. Post translational modifications 4.1. Phosphorylation, the addition of a phosphate group 4.2. Methylation, the addition of a methyl group 4.3. Glycosylation, the addition of sugar groups 4.4. Disulfide bonds, the formation of covalent bonds between 2 cysteine amino acids 4.5. Proteolysis/ Proteolytic Cleavage 4.6. Subunit binding to form a multisubunit protein 4.7. S-nitrosylation 4.8. Lipidation 4.9. Acetylation 4.10. Ubiquitylation 4.11. SUMOlytion 4.12. Vitamin C-Dependent Modifications 4.13. Vitamin K-Dependent Modifications 4.14. Selenoproteins 4.15. Myristoylation 5. Chaperones: Role in PTM and mechanism 6. Role of PTMs in diseases 7. Detecting and Quantifying Post-Translational Modifications 8. -
Protein Targeting Or Protein Sorting
Protein targeting or Protein sorting Refer Page 1068 to 1074 Principles of Biochemistry by Lehninger & Page 663 Baltimore Mol Cell Biology • Protein targeting or Protein sorting is the process of delivery of newly synthesized proteins to their proper cellular destinations • Proteins are sorted to the endoplasmic reticulum (ER), mitochondria, chloroplasts, lysosomes, peroxisomes, and the nucleus by different mechanisms • The process can occur either during protein synthesis or soon after synthesis of proteins by translation at the ribosome. • Most of the integral membrane proteins, secretory proteins and lysosomal proteins are sorted to ER lumen from where these proteins are modified for further sorting • For membrane proteins, targeting leads to insertion of the protein into the lipid bilayer • For secretory/water-soluble proteins, targeting leads to translocation of the entire protein across the membrane into the aqueous interior of the organelle. • Protein destined for cytosol simply remain where they are synthesized • Mitochondrial and chloroplast proteins are first completely synthesized and released from ribosomes. These are then bound by cytosolic chaperone proteins and delivered to receptor on target organelle. • Nuclear proteins such as DNA and RNA polymerases, histones, topoisomerases and proteins that regulate gene expression contain Nuclear localization signal (NLS) which is not removed after the protein is translocated. Unlike ER localization signal sequence which is at N terminal, NLS ca be located almost anywhere along the -
Chaperonin Function: Folding by Forced Unfolding
R EPORTS (1985); N. Romani et al., ibid. 169, 1169 (1989); C. migrated was measured with the clonotypic antibody 26. J. G. Cyster, J. Exp. Med. 189, 447 (1999). Heufler et al., ibid. 176, 1221 (1992). to TCR KJ1-26 (28). Overnight incubation of day 2 27. G. G. MacPherson, C. D. Jenkins, M. J. Stein, C. Ed- 23. R. Bonecchi et al., ibid. 187, 129 (1998). draining lymph node cells (at 107 cells/ml) in medium wards, J. Immunol. 154, 1317 (1995). 24. Anti-OVA (DO11.10) T cell receptor (TCR) transgenic containing interleukin-2 (IL-2) (4 ng/ml) increased 28. K. Haskins et al., J. Exp. Med. 157, 1149 (1983). 1 lymph node cells (5 3 106 cells) were transferred to the sensitivity of activated KJ1-26 cells to MDC 29. We thank R. Locksley, S. Luther, K. Reif, and A. Weiss for comments on the manuscript; M. Ansel for help BALB/c mice that were immunized 1 day later with (14). Therefore, IL-2–cultured cells were used in ex- with the in vivo transfer experiments; and C. 100-mg OVA in Freund’s complete adjuvant (25). periments to detect chemokine production by puri- McArthur for cell sorting. Supported in part by NIH fied lymph node DCs and stromal cells. Draining (pool of brachial, axillary, and inguinal) and grant AI-40098, the Pew Foundation (J.G.C.), and the nondraining (mesenteric) lymph node cells were iso- 25. E. R. Kearney, K. A. Pape, D. Y. Loh, M. K. Jenkins, American Lung Association (H.L.T.). lated 1 to 5 days later and used in MDC chemotaxis Immunity 1, 327 (1994); K. -
Functional and Physical Interaction Between Yeast Hsp90 and Hsp70
Functional and physical interaction between yeast PNAS PLUS Hsp90 and Hsp70 Andrea N. Kravatsa, Joel R. Hoskinsa, Michael Reidyb, Jill L. Johnsonc, Shannon M. Doylea, Olivier Genesta,1, Daniel C. Masisonb, and Sue Wicknera,2 aLaboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; bLaboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; and cDepartment of Biological Sciences, University of Idaho, Moscow, ID 83844 Contributed by Sue Wickner, January 25, 2018 (sent for review November 17, 2017; reviewed by Daniel N. A. Bolon and Jeffrey L. Brodsky) Heat shock protein 90 (Hsp90) is a highly conserved ATP-dependent changes in response to ATP binding, hydrolysis, and ADP release molecular chaperone that is essential in eukaryotes. It is required for (1,3,6,14–16). In the absence of ATP, the Hsp90 dimer acquires the activation and stabilization of more than 200 client proteins, an open, V-shaped structure such that the protomers interact via including many kinases and steroid hormone receptors involved in the C-terminal dimerization domain (16). When ATP is bound, the cell-signaling pathways. Hsp90 chaperone activity requires collabo- protein takes on a closed conformation with the two N-domains of ration with a subset of the many Hsp90 cochaperones, including the the dimer interacting and a portion of the N-domain, the “lid,” Hsp70 chaperone. In higher eukaryotes, the collaboration between closing over the nucleotide in each protomer (16, 17). Additional Hsp90 and Hsp70 is indirect and involves Hop, a cochaperone that conformational changes occur upon ATP hydrolysis, resulting in a interacts with both Hsp90 and Hsp70. -
Chaperonin-Assisted Protein Folding: a Chronologue
Quarterly Reviews of Chaperonin-assisted protein folding: Biophysics a chronologue cambridge.org/qrb Arthur L. Horwich1,2 and Wayne A. Fenton2 1Howard Hughes Medical Institute, Yale School of Medicine, Boyer Center, 295 Congress Avenue, New Haven, CT 06510, USA and 2Department of Genetics, Yale School of Medicine, Boyer Center, 295 Congress Avenue, New Invited Review Haven, CT 06510, USA Cite this article: Horwich AL, Fenton WA (2020). Chaperonin-assisted protein folding: a Abstract chronologue. Quarterly Reviews of Biophysics This chronologue seeks to document the discovery and development of an understanding of – 53, e4, 1 127. https://doi.org/10.1017/ oligomeric ring protein assemblies known as chaperonins that assist protein folding in the cell. S0033583519000143 It provides detail regarding genetic, physiologic, biochemical, and biophysical studies of these Received: 16 August 2019 ATP-utilizing machines from both in vivo and in vitro observations. The chronologue is orga- Revised: 21 November 2019 nized into various topics of physiology and mechanism, for each of which a chronologic order Accepted: 26 November 2019 is generally followed. The text is liberally illustrated to provide firsthand inspection of the key Key words: pieces of experimental data that propelled this field. Because of the length and depth of this Chaperonin; GroEL; GroES; Hsp60; protein piece, the use of the outline as a guide for selected reading is encouraged, but it should also be folding of help in pursuing the text in direct order. Author for correspondence: Arthur L. Horwich, E-mail: [email protected] Table of contents I. Foundational discovery of Anfinsen and coworkers – the amino acid sequence of a polypeptide contains all of the information required for folding to the native state 7 II. -
A Global Analysis of Enzyme Compartmentalization to Glycosomes
pathogens Article A Global Analysis of Enzyme Compartmentalization to Glycosomes Hina Durrani 1, Marshall Hampton 2 , Jon N. Rumbley 3 and Sara L. Zimmer 1,* 1 Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA; [email protected] 2 Mathematics & Statistics Department, University of Minnesota Duluth, Duluth, MN 55812, USA; [email protected] 3 College of Pharmacy, University of Minnesota, Duluth Campus, Duluth, MN 55812, USA; [email protected] * Correspondence: [email protected] Received: 25 March 2020; Accepted: 9 April 2020; Published: 12 April 2020 Abstract: In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. -
Cilia and Flagella: from Discovery to Disease Dylan J
Dartmouth Undergraduate Journal of Science Volume 20 Article 2 Number 1 Assembly 2017 Cilia and Flagella: From Discovery to Disease Dylan J. Cahill Dylan Cahill, [email protected] Follow this and additional works at: https://digitalcommons.dartmouth.edu/dujs Part of the Engineering Commons, Life Sciences Commons, Medicine and Health Sciences Commons, Physical Sciences and Mathematics Commons, and the Social and Behavioral Sciences Commons Recommended Citation Cahill, Dylan J. (2017) "Cilia and Flagella: From Discovery to Disease," Dartmouth Undergraduate Journal of Science: Vol. 20 : No. 1 , Article 2. Available at: https://digitalcommons.dartmouth.edu/dujs/vol20/iss1/2 This Research Article is brought to you for free and open access by the Student-led Journals and Magazines at Dartmouth Digital Commons. It has been accepted for inclusion in Dartmouth Undergraduate Journal of Science by an authorized editor of Dartmouth Digital Commons. For more information, please contact [email protected]. BIOLOGY Cilia and Flagella: FromCilia and Discovery Flagella: to Disease From Discovery to Disease BY DYLAN CAHILL ‘18 Introduction certain insect sperm fagella (3, 5, 6). A unique Figure 1: Chlamydomonas intracellular transport mechanism known as reinhardtii, a single-celled, bi- In 1674, peering through the lens of a crude flagellate green alga, viewed intrafagellar transport is responsible for the light microscope, Antoni van Leeuwenhoek with a scanning electron assembly and maintenance of these organelles Chlamydomonas observed individual living cells for the frst time microscope. is (3, 6). Cilia and fagella are primarily composed a model organism in flagellar in history (1). He noted long, thin appendages of the protein tubulin, which polymerizes into dynamics and motility studies. -
Structural and Functional Dissection of Reovirus Capsid Folding and Assembly by the Prefoldin-Tric/CCT Chaperone Network
Structural and functional dissection of reovirus capsid folding and assembly by the prefoldin-TRiC/CCT chaperone network Jonathan J. Knowltona,b,1, Daniel Gestautc,1, Boxue Mad,e,f,2, Gwen Taylora,g,2, Alpay Burak Sevenh,i, Alexander Leitnerj, Gregory J. Wilsonk, Sreejesh Shankerl, Nathan A. Yatesm, B. V. Venkataram Prasadl, Ruedi Aebersoldj,n, Wah Chiud,e,f, Judith Frydmanc,3, and Terence S. Dermodya,g,o,3 aDepartment of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224; bDepartment of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232; cDepartment of Biology, Stanford University, Stanford, CA 94305; dDepartment of Bioengineering, Stanford University, Stanford, CA 94305; eDepartment of Microbiology and Immunology, Stanford University, Stanford, CA 94305; fDepartment of Photon Science, Stanford University, Stanford, CA 94305; gCenter for Microbial Pathogenesis, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224; hDepartment of Structural Biology, Stanford University, Stanford, CA 94305; iDepartment of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA 94305; jDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; kDepartment of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232; lVerna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030; mDepartment of Cell Biology, University of Pittsburgh School of Medicine,