DOCSLIB.ORG

Profiling Protein Prenylation Using a Quantitative Chemical Proteomics Approach

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Profiling Protein Prenylation Using a Quantitative Chemical Proteomics Approach Profiling Protein Prenylation Using a Quantitative Chemical Proteomics Approach A thesis submitted to Imperial College London in candidature for the degree of Doctor of Philosophy of Imperial College Elisabeth Maria Storck Saha Department of Chemistry Imperial College London Exhibition Road London SW7 2AZ September 2016 Declaration of Originality I hereby declare that this thesis is my own work and reports the results of my own original research. Information or results originating from the work of others or in collaboration with others has been acknowledged in the text and references. Elisabeth Storck Saha September 2016 Copyright Declaration The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work. 2 Abstract Prenylation, the attachment of a farnesyl or geranylgeranyl isoprenoid to a C-terminal cysteine, is a post-translational modification which modulates localisation and function of key proteins such as members of the RAS superfamily, nuclear lamins and heterotrimeric G-proteins. In humans, three enzymes catalyse the prenylation reaction: farnesyl transferase, geranylgeranyl transferase type 1 and RAB geranylgeranyl transferase. Substantial effort has gone into developing therapeutics that disrupt prenylation as a means of targeting RAS-driven cancers, yet these approaches have failed to deliver in clinical trials. This is largely due to the fact that the dynamics of prenylation in response to prenyl transferase inhibitors is more complex than originally envisaged and includes changes in prenylation state and altered substrate recognition by the different transferase enzymes. Emerging research shows that prenylation also plays a role in cardiovascular and neurodegenerative diseases, Hutchinson-Gilford progeria syndrome (HGPS), choroideremia and viral infections. Advances in the study of protein prenylation are hampered by the lack of inherent handles that allow for isolation and identification of the prenylated proteome. Novel approaches for profiling the prenylated proteome, its dynamics, and effects of varied inhibitors of the prenyl transferases are imperative for explaining past failures and to direct future studies. This thesis presents a novel set of isoprenoid analogues that can selectively label prenylated proteins in cells. The application of these probes in combination with quantitative proteomic techniques enabled the description of the complex dynamics between different isoprenoid substrates and transferases in response to prenyl transferase inhibitors, and to validate several novel prenylated substrates. We describe attempts to profile prenylation in cells derived from HGPS patients, and explore potential targets of farnesyl transferase inhibition in pulmonary arterial cells. We envisage that the robust methodology presented herein will be widely applicable to the study of prenylation in the context of both health and disease. 3 Dedication This thesis is dedicated to my mother, Karin, and mother-in-law, Chhaya, without whose incredible support this thesis would not have seen the light of day. 4 Acknowledgements First and foremost I would like to thank my supervisors, Professor Ed Tate and Dr Beata Wojciak-Stothard. Ed – thanks for your unrelenting support and enthusiasm throughout the years I have spent in your lab. I will be forever grateful to you for taking me in as a stray back in 2009 and mentoring me though my undergraduate, masters and PhD years. Thanks for continually providing exciting project opportunities and for inspiring great science. Beata – it’s been an absolutely pleasure to work with you and your group. Thanks for teaching me the ropes in the biology lab and for your support and advice throughout this project. Many thanks go to Dr Julia Morales-Sanfrutos and Dr Remi Serwa whose ideas and technical help have been vital in carrying this project forward. Thanks are also due Professor Riki Eggert for her incredible support during the final stages of thesis writing. Thanks to Dr Goska Broncel and Dr Megan Wright for providing capture reagents. Thanks to Dr Andrew Bottrill at Leicester University proteomics facility for processing and analysing proteomics samples during the early stages of this project. Thanks to Dr Lisa Haigh at Imperial College mass spectrometry service for analysing small molecules and proteomics samples. Thanks to Drs Remi Serwa, Goska Broncel, James Clulow and Tom Charlton for running LC-MS/MS samples. Thanks to Drs Will Heal, Victor Goncalves and Jennie Hutton for advice and support in the synthesis lab. Thanks to Dr Lucie Duluc for providing cell samples. Thanks to Dr Paulina Ciepla for conducting labelling studies in Zebrafish. Thanks to Dr Anna Barnard, Dr Jennie Hutton, Dr Julia Morales-Sanfrutos, Dr Charlotte Sutherell and Scott Lovell for proofreading this thesis. Thanks to the lunch-club crowd who kept me sane during my PhD – Julia, Jenny, Jennie, Gee, Yunyun, Megan, Manue, Goska and Soo Mei. Thanks to all member of the Tate and Wojciak- Stothard lab for making my time in the lab so much fun. Thanks to my husband Suj for his support and encouragement throughout my PhD years and for putting up with my grumpiness during the writing of this thesis. Thanks to my family, especially my mother Karin and mother-in-law Chhaya without whose incredible help with child-minding and cooking this thesis would never have been completed. Finally, no thanks go to my daughter Indira as her arrival in no way facilitated the progress of this PhD! However, she did make it all the more worthwhile, taught me just how much one can achieve with very little sleep and certainly filled my life with more love and fun than I could ever have imagined! 5 Acknowledgement of collaboration Dr Julia Morales-Sanfrutos provided YnMyr-tagged HeLa lysate (Chapter 3), conducted studies to identify YnF-modified peptides in EA.hy926 cells (Chapter 3), prepared Tipifarnib- treated YnF-labelled samples in EA.hy926 cells (Chapter 4) and processed HGPS lysates for proteomics analysis (Chapter 5). Dr Remigiusz Serwa provided prenyl probes (Chapter 2). Dr Lisa Haigh (Imperial College mass spectrometry service) performed mass spectrometry analysis of small molecules and proteomics samples (Chapters 2-5). Dr Megan Wright provided capture reagent AzTB and YnTB (Chapters 2-5) and Dr Goska Broncel provided capture reagent AzRTB (Chapter 3). Dr Andrew Bottrill (University of Leicester, UK) analysed LC-MS/MS samples in initial proteomics studies (Chapter 3). Professor Herbert Waldmann (Max Planck Institute of Molecular Physiology, Dortmund, Germany) provided RABGGTase inhibitor Bon-15 (Chapter 4). Dr Lucie Duluc provided Tipifarnib-treated HPASMC and HPAEC lysates (Chapter 5). Dr Paulina Ciepla conducted labelling studies in zebrafish (Chapter 5). 6 Contents Publications & Presentations Arising From This Thesis ....................................................... 11 Abbreviations ...................................................................................................................... 13 Chapter 1: Introduction .................................................................................................... 16 1.1. Protein Prenylation................................................................................................ 16 1.2. The Prenyl Transferases ....................................................................................... 21 1.2.1. FTase and GGTase-1 .................................................................................... 21 1.2.2. RABGGTase .................................................................................................. 26 1.3. The Role of Prenylation in Disease ....................................................................... 28 1.3.1. Cancer ........................................................................................................... 29 1.3.2. Hutchinson-Gilford Progeria Syndrome .......................................................... 30 1.3.3. Cardiovascular Disease ................................................................................. 32 1.3.4. Choroideremia ............................................................................................... 34 1.3.5. Hepatitis Delta and Hepatitis C Viral Infection ................................................ 34 1.3.6. Other Diseases .............................................................................................. 35 1.4. Chemical Proteomics ............................................................................................ 36 1.4.1. Prenylation Probes ........................................................................................ 37 1.4.2. Mass Spectrometry for Proteomics ................................................................ 42 1.4.3. Quantitative Proteomics ................................................................................. 44 1.5. Project Objectives ................................................................................................. 48 Chapter 2: Novel Probes for Profiling Protein Prenylation ................................................ 50 2.1. Introduction ..........................................................................................................
Load more

Recommended publications
  • A Chemical Proteomic Approach to Investigate Rab Prenylation in Living Systems
    A chemical proteomic approach to investigate Rab prenylation in living systems By Alexandra Fay Helen Berry A thesis submitted to Imperial College London in candidature for the degree of Doctor of Philosophy of Imperial College. Department of Chemistry Imperial College London Exhibition Road London SW7 2AZ August 2012 Declaration of Originality I, Alexandra Fay Helen Berry, hereby declare that this thesis, and all the work presented in it, is my own and that it has been generated by me as the result of my own original research, unless otherwise stated. 2 Abstract Protein prenylation is an important post-translational modification that occurs in all eukaryotes; defects in the prenylation machinery can lead to toxicity or pathogenesis. Prenylation is the modification of a protein with a farnesyl or geranylgeranyl isoprenoid, and it facilitates protein- membrane and protein-protein interactions. Proteins of the Ras superfamily of small GTPases are almost all prenylated and of these the Rab family of proteins forms the largest group. Rab proteins are geranylgeranylated with up to two geranylgeranyl groups by the enzyme Rab geranylgeranyltransferase (RGGT). Prenylation of Rabs allows them to locate to the correct intracellular membranes and carry out their roles in vesicle trafficking. Traditional methods for probing prenylation involve the use of tritiated geranylgeranyl pyrophosphate which is hazardous, has lengthy detection times, and is insufficiently sensitive. The work described in this thesis developed systems for labelling Rabs and other geranylgeranylated proteins using a technique known as tagging-by-substrate, enabling rapid analysis of defective Rab prenylation in cells and tissues. An azide analogue of the geranylgeranyl pyrophosphate substrate of RGGT (AzGGpp) was applied for in vitro prenylation of Rabs by recombinant enzyme.
    [Show full text]
  • C-Terminal Proteolysis of Prenylated Proteins in Trypanosomatids And
    Molecular & Biochemical Parasitology 153 (2007) 115–124 C-terminal proteolysis of prenylated proteins in trypanosomatids and RNA interference of enzymes required for the post-translational processing pathway of farnesylated proteins John R. Gillespie a, Kohei Yokoyama b,∗, Karen Lu a, Richard T. Eastman c, James G. Bollinger b,d, Wesley C. Van Voorhis a,c, Michael H. Gelb b,d, Frederick S. Buckner a,∗∗ a Department of Medicine, University of Washington, 1959 N.E. Pacific St., Seattle, WA 98195, USA b Department of Chemistry, University of Washington, Seattle, WA 98195, USA c Department of Pathobiology, University of Washington, Seattle, Washington 98195, USA d Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA Received 22 December 2006; received in revised form 17 February 2007; accepted 26 February 2007 Available online 1 March 2007 Abstract The C-terminal “CaaX”-motif-containing proteins usually undergo three sequential post-translational processing steps: (1) attachment of a prenyl group to the cysteine residue; (2) proteolytic removal of the last three amino acids “aaX”; (3) methyl esterification of the exposed ␣-carboxyl group of the prenyl-cysteine residue. The Trypanosoma brucei and Leishmania major Ras converting enzyme 1 (RCE1) orthologs of 302 and 285 amino acids-proteins, respectively, have only 13–20% sequence identity to those from other species but contain the critical residues for the activity found in other orthologs. The Trypanosoma brucei a-factor converting enzyme 1 (AFC1) ortholog consists of 427 amino acids with 29–33% sequence identity to those of other species and contains the consensus HExxH zinc-binding motif. The trypanosomatid RCE1 and AFC1 orthologs contain predicted transmembrane regions like other species.
    [Show full text]
  • Geranylgeranylated Proteins Are Involved in the Regulation of Myeloma Cell Growth
    Vol. 11, 429–439, January 15, 2005 Clinical Cancer Research 429 Geranylgeranylated Proteins are Involved in the Regulation of Myeloma Cell Growth Niels W.C.J. van de Donk,1 Henk M. Lokhorst,3 INTRODUCTION 2 1 Evert H.J. Nijhuis, Marloes M.J. Kamphuis, and Multiple myeloma is characterized by the accumulation Andries C. Bloem1 of slowly proliferating monoclonal plasma cells in the bone Departments of 1Immunology, 2Pulmonary Diseases, and 3Hematology, marrow. Via the production of growth factors, such as University Medical Center Utrecht, Utrecht, the Netherlands interleukin-6 (IL-6) and insulin-like growth factor-I (1–4), and cellular interactions (5, 6), the local bone marrow microenvironment sustains tumor growth and increases the ABSTRACT resistance of tumor cells for apoptosis-inducing signals (7). Purpose: Prenylation is essential for membrane locali- Multiple signaling pathways are involved in the regulation of zation and participation of proteins in various signaling growth and survival of myeloma tumor cells. Activation of the pathways. This study examined the role of farnesylated and Janus-activated kinase-signal transducers and activators of geranylgeranylated proteins in the regulation of myeloma transcription (8), nuclear factor-nB (9–11), and phosphatidy- cell proliferation. linositol 3V-kinase (PI-3K; refs. 4, 12, 13) pathways has been Experimental Design: Antiproliferative and apoptotic implicated in the protection against apoptosis, whereas effects of various modulators of farnesylated and geranyl- activation of the PI-3K (4, 12, 13), nuclear factor-nB (10, 11), geranylated proteins were investigated in myeloma cells. and mitogen-activated protein kinase pathways (14) induces Results: Depletion of geranylgeranylpyrophosphate proliferation in myeloma cell lines.
    [Show full text]
  • The Protein Lipidation and Its Analysis
    Triola, J Glycom Lipidom 2011, S:2 DOI: 10.4172/2153-0637.S2-001 Journal of Glycomics & Lipidomics Research Article Open Access The Protein Lipidation and its Analysis Gemma Triola Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany Abstract Protein Lipidation is essential not only for membrane binding but also for the interaction with effectors and the regulation of signaling processes, thereby playing a key role in controlling protein localization and function. Cholesterylation, the attachment of the glycosylphosphatidylinositol anchor, as well as N-myristoylation, S-prenylation and S-acylation are among the most relevant protein lipidation processes. Little is still known about the significance of the high diversity in lipid modifications as well as the mechanism by which lipidation controls function and activity of the proteins. Although the development of new strategies to uncover these and other unexplored topics is in great demand, important advances have already been achieved during the last years in the analysis of protein lipidation. This review will highlight the most prominent lipid modifications encountered in proteins and will provide an overview of the existing methods for the analysis and identification of lipid modified proteins. Introduction new tools and strategies. As such, this review will highlight the most prominent lipid modifications encountered in proteins and will provide Biological cell membranes are typically formed by mixtures an overview of the existing methods for the analysis and identification of lipids and proteins. Whereas the major lipid components are of lipid modified proteins detailing their advantages and limitations. glycerophospholipids, cholesterol and sphingolipids, proteins located in the membrane can be divided in two main classes, integral proteins Types of Lipidation and associated proteins.
    [Show full text]
  • Glycosylphosphatidylinositol-Anchored Proteins As Chaperones and Co-Receptors for FERONIA Receptor Kinase Signaling in Arabidops
    RESEARCH ARTICLE elifesciences.org Glycosylphosphatidylinositol-anchored proteins as chaperones and co-receptors for FERONIA receptor kinase signaling in Arabidopsis Chao Li1, Fang-Ling Yeh1†, Alice Y Cheung1,2,3*, Qiaohong Duan1, Daniel Kita1,2‡, Ming-Che Liu1,4, Jacob Maman1, Emily J Luu1, Brendan W Wu1§, Laura Gates1¶, Methun Jalal1, Amy Kwong1, Hunter Carpenter1, Hen-Ming Wu1,2* 1Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, United States; 2Molecular and Cell Biology Program, University of 3 *For correspondence: acheung@ Massachusetts, Amherst, United States; Plant Biology Graduate Program, University 4 biochem.umass.edu (AYC); of Massachusetts, Amherst, United States; Graduate Institute of Biotechnology, [email protected] National Chung Hsing University, Tai Chung, Taiwan (HMW) Present address: †Clinical Research Center, Chung Shan Medical University Hospital, Abstract The Arabidopsis receptor kinase FERONIA (FER) is a multifunctional regulator for Taichung, Taiwan; ‡Department plant growth and reproduction. Here we report that the female gametophyte-expressed of Vascular Biology, University of glycosylphosphatidylinositol-anchored protein (GPI-AP) LORELEI and the seedling-expressed Connecticut Health Center, LRE-like GPI-AP1 (LLG1) bind to the extracellular juxtamembrane region of FER and show that this Farmington, United States; interaction is pivotal for FER function. LLG1 interacts with FER in the endoplasmic reticulum and on § Department of Immunology, the cell surface, and loss
    [Show full text]
  • Protein Prenylation in Plant Stress Responses
    molecules Review Protein Prenylation in Plant Stress Responses Michal Hála * and Viktor Žárský Department of Experimental Plant Biology, Faculty of Science, Charles University, Viniˇcná 5, 128 44 Prague, Czech Republic; [email protected] * Correspondence: [email protected]; Tel.: +420-221951686 Academic Editors: Ewa Swiezewska and Liliana Surmacz Received: 30 September 2019; Accepted: 25 October 2019; Published: 30 October 2019 Abstract: Protein prenylation is one of the most important posttranslational modifications of proteins. Prenylated proteins play important roles in different developmental processes as well as stress responses in plants as the addition of hydrophobic prenyl chains (mostly farnesyl or geranyl) allow otherwise hydrophilic proteins to operate as peripheral lipid membrane proteins. This review focuses on selected aspects connecting protein prenylation with plant responses to both abiotic and biotic stresses. It summarizes how changes in protein prenylation impact plant growth, deals with several families of proteins involved in stress response and highlights prominent regulatory importance of prenylated small GTPases and chaperons. Potential possibilities of these proteins to be applicable for biotechnologies are discussed. Keywords: plants; stress; protein prenyl transferases; prenylated proteins 1. Introduction to Protein Prenylation in Plants Protein prenylation (i.e., addition of one or more isoprenoid side chains) is one of the key post-translational protein modifications which contributes significantly to the regulation of life processes at the lipid membrane-protein interface in most organisms. Such hydrophobic modifications permit otherwise hydrophilic proteins to operate as peripheral membrane proteins (for a general overview, see [1–3]). Despite our focus on intensely studied protein prenylation in eukaryotes, it seems to be important for prokaryotic cells as well.
    [Show full text]
  • Lack of the Consensus Sequence Necessary for Tryptophan Prenylation in the Comx Pheromone Precursor
    Biosci. Biotechnol. Biochem., 76 (8), 1492–1496, 2012 Lack of the Consensus Sequence Necessary for Tryptophan Prenylation in the ComX Pheromone Precursor y Fumitada TSUJI,1; Ayako ISHIHARA,1 Aya NAKAGAWA,1 Masahiro OKADA,2 Shigeyuki KITAMURA,1 Kyoko KANAMARU,1 Yuichi MASUDA,3 Kazuma MURAKAMI,3 Kazuhiro IRIE,3 and Youji SAKAGAMI1 1Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601, Japan 2Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan 3Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan Received March 19, 2012; Accepted May 7, 2012; Online Publication, August 7, 2012 [doi:10.1271/bbb.120206] ComX, an oligopeptide pheromone that stimulates the pheromones from other strains also contain either natural genetic competence controlled by quorum geranyl- or farnesyl-modified tryptophan residues. sensing in Bacillus subtilis and related bacilli, contains Prenyl post-translational modification is essential for a prenyl-modified tryptophan residue. Since ComX is the biological activity of the ComX pheromone.5–8) the only protein known to contain prenylated trypto- Apart from ComX, however, no other proteins contain- phan, the universality of this unique posttranslational ing prenylated tryptophan residues have so far been modification has yet to be determined. Recently, we identified. developed a cell-free assay system in which the trypto- Prenylation (farnesylation and geranylgeranylation) phan residue in the ComXRO-E-2 pheromone precursor of proteins on cysteine residues is a well-known post- derived from B. subtilis strain RO-E-2 can be gerany- translational modification. Prenyl modification of cys- lated by the ComQRO-E-2 enzyme.
    [Show full text]
  • Characterization of Prenylated C-Terminal Peptides Using a Novel Capture Technique
    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.15.908152; this version posted January 15, 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. TITLE: Characterization of Prenylated C-terminal Peptides Using a Novel Capture Technique Coupled with LCMS Running Title: Characterization of prenylated peptides from mouse brain James A. Wilkins*, Krista Kaasik, Robert J. Chalkley and Al L. Burlingame From the Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, Rm N472, San Francisco, CA 94158 * Corresponding author; email address: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.15.908152; this version posted January 15, 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. Characterization of prenylated peptides from mouse brain 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.15.908152; this version posted January 15, 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. Characterization of prenylated peptides from mouse brain ABSTRACT Post-translational modifications play a critical and diverse role in regulating cellular activities.
    [Show full text]
  • A User's Guide to Cell-Free Protein Synthesis
    Review A User’s Guide to Cell-Free Protein Synthesis Nicole E. Gregorio 1,2 , Max Z. Levine 1,3 and Javin P. Oza 1,2,* 1 Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA; [email protected] (N.E.G.); [email protected] (M.Z.L.) 2 Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA 93407, USA 3 Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA * Correspondence: [email protected]; Tel.: +1-805-756-2265 Received: 15 February 2019; Accepted: 6 March 2019; Published: 12 March 2019 Abstract: Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities for protein expression, metabolic engineering, therapeutic development, education, and more. The advantages of CFPS over in vivo protein expression include its open system, the elimination of reliance on living cells, and the ability to focus all system energy on production of the protein of interest. Over the last 60 years, the CFPS platform has grown and diversified greatly, and it continues to evolve today. Both new applications and new types of extracts based on a variety of organisms are current areas of development. However, new users interested in CFPS may find it challenging to implement a cell-free platform in their laboratory due to the technical and functional considerations involved in choosing and executing a platform that best suits their needs. Here we hope to reduce this barrier to implementing CFPS by clarifying the similarities and differences amongst cell-free platforms, highlighting the various applications that have been accomplished in each of them, and detailing the main methodological and instrumental requirement for their preparation.
    [Show full text]
  • Role for Protein Prenylation and "CAAX" Processing in Photoreceptor Neurons
    Graduate Theses, Dissertations, and Problem Reports 2016 Role for protein prenylation and "CAAX" processing in photoreceptor neurons Nachiket D. Pendse Follow this and additional works at: https://researchrepository.wvu.edu/etd Recommended Citation Pendse, Nachiket D., "Role for protein prenylation and "CAAX" processing in photoreceptor neurons" (2016). Graduate Theses, Dissertations, and Problem Reports. 6397. https://researchrepository.wvu.edu/etd/6397 This Dissertation is protected by copyright and/or related rights. It has been brought to you by the The Research Repository @ WVU with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you must obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. This Dissertation has been accepted for inclusion in WVU Graduate Theses, Dissertations, and Problem Reports collection by an authorized administrator of The Research Repository @ WVU. For more information, please contact [email protected]. Role for protein prenylation and “CAAX” processing in photoreceptor neurons Nachiket D. Pendse Dissertation submitted to the Department of Biology at West Virginia University in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Visvanathan Ramamurthy, Ph.D., Chair Maxim Sokolov, Ph.D. Peter Mathers, Ph.D. Andrew Dacks, Ph.D. Shuo Wei, Ph.D. Graduate Program in Biology West Virginia University School of Medicine Morgantown, West Virginia 2016 Key Words: Prenylation, photoreceptor neurons, retina, phototransduction and vision Copyright 2016 Nachiket Pendse ABSTRACT Role for protein prenylation and “CAAX” processing in photoreceptor neurons Nachiket D.
    [Show full text]
  • Isoprenylcysteine Carboxylmethyltransferase Regulates Mitochondrial Respiration and Cancer Cell Metabolism
    Oncogene (2015) 34, 3296–3304 © 2015 Macmillan Publishers Limited All rights reserved 0950-9232/15 www.nature.com/onc ORIGINAL ARTICLE Isoprenylcysteine carboxylmethyltransferase regulates mitochondrial respiration and cancer cell metabolism JT Teh1,5, WL Zhu1,2,5, OR Ilkayeva3,YLi4, J Gooding3, PJ Casey1, SA Summers4, CB Newgard3 and M Wang1,2 Isoprenylcysteine carboxylmethyltransferase (Icmt) catalyzes the last of the three-step posttranslational protein prenylation process for the so-called CaaX proteins, which includes many signaling proteins, such as most small GTPases. Despite extensive studies on Icmt and its regulation of cell functions, the mechanisms of much of the impact of Icmt on cellular functions remain unclear. Our recent studies demonstrated that suppression of Icmt results in induction of autophagy, inhibition of cell growth and inhibition of proliferation in various cancer cell types, prompting this investigation of potential metabolic regulation by Icmt. We report here the findings that Icmt inhibition reduces the function of mitochondrial oxidative phosphorylation in multiple cancer cell lines. In-depth oximetry analysis demonstrated that functions of mitochondrial complex I, II and III are subject to Icmt regulation. Consistently, Icmt inhibition decreased cellular ATP and depleted critical tricarboxylic acid cycle metabolites, leading to suppression of cell anabolism and growth, and marked autophagy. Several different approaches demonstrated that the impact of Icmt inhibition on cell proliferation and viability was
    [Show full text]
  • Not So Slim Anymore—Evidence for the Role of SUMO in the Regulation of Lipid Metabolism
    biomolecules Review Not So Slim Anymore—Evidence for the Role of SUMO in the Regulation of Lipid Metabolism Amir Sapir Department of Biology and the Environment, Faculty of Natural Sciences, University of Haifa–Oranim, Tivon 36006, Israel; [email protected]; Tel.: +972-495-396-15 Received: 2 June 2020; Accepted: 3 August 2020; Published: 6 August 2020 Abstract: One of the basic building blocks of all life forms are lipids—biomolecules that dissolve in nonpolar organic solvents but not in water. Lipids have numerous structural, metabolic, and regulative functions in health and disease; thus, complex networks of enzymes coordinate the different compositions and functions of lipids with the physiology of the organism. One type of control on the activity of those enzymes is the conjugation of the Small Ubiquitin-like Modifier (SUMO) that in recent years has been identified as a critical regulator of many biological processes. In this review, I summarize the current knowledge about the role of SUMO in the regulation of lipid metabolism. In particular, I discuss (i) the role of SUMO in lipid metabolism of fungi and invertebrates; (ii) the function of SUMO as a regulator of lipid metabolism in mammals with emphasis on the two most well-characterized cases of SUMO regulation of lipid homeostasis. These include the effect of SUMO on the activity of two groups of master regulators of lipid metabolism—the Sterol Regulatory Element Binding Protein (SERBP) proteins and the family of nuclear receptors—and (iii) the role of SUMO as a regulator of lipid metabolism in arteriosclerosis, nonalcoholic fatty liver, cholestasis, and other lipid-related human diseases.
    [Show full text]