1
|
Carruthers VB, Dou Z. Deciphering protein prenylation in endocytic trafficking in Toxoplasma gondii. mBio 2024; 15:e0028324. [PMID: 38407123 PMCID: PMC11005354 DOI: 10.1128/mbio.00283-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Toxoplasma gondii is a widespread intracellular protozoan pathogen infecting virtually all warm-blooded animals. This parasite acquires host-derived resources to support its replication inside a membrane-bound parasitophorous vacuole within infected host cells. Previous research has discovered that Toxoplasma actively endocytoses host proteins and transports them to a lysosome-equivalent structure for digestion. However, few molecular determinants required for trafficking of host-derived material within the parasite were known. A recent study (Q.-Q. Wang, M. Sun, T. Tang, D.-H. Lai, et al., mBio 14:e01309-23, 2023, https://doi.org/10.1128/mbio.01309-23) identified a critical role for membrane anchoring of proteins via prenylation in the trafficking of endocytosed host proteins by Toxoplasma, including an essential Toxoplasma ortholog of Rab1B. The authors also found that TgRab1 is crucial for protein trafficking of the rhoptry secretory organelles, indicating a dual role in endocytic and exocytic protein trafficking. This study sets the stage for further dissecting endomembrane trafficking in Toxoplasma, along with potentially exploiting protein prenylation as a target for therapeutic development.
Collapse
Affiliation(s)
- Vern B. Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Zhicheng Dou
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| |
Collapse
|
2
|
Pham AC, Holstein SA, Borgstahl GE. Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy. Mol Cancer Ther 2024; 23:14-23. [PMID: 37756579 PMCID: PMC10762340 DOI: 10.1158/1535-7163.mct-23-0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Geranylgeranyl diphosphate synthase (GGDPS), the source of the isoprenoid donor in protein geranylgeranylation reactions, has become an attractive target for anticancer therapy due to the reliance of cancers on geranylgeranylated proteins. Current GGDPS inhibitor development focuses on optimizing the drug-target enzyme interactions of nitrogen-containing bisphosphonate-based drugs. To advance GGDPS inhibitor development, understanding the enzyme structure, active site, and ligand/product interactions is essential. Here we provide a comprehensive structure-focused review of GGDPS. We reviewed available yeast and human GGDPS structures and then used AlphaFold modeling to complete unsolved structural aspects of these models. We delineate the elements of higher-order structure formation, product-substrate binding, the electrostatic surface, and small-molecule inhibitor binding. With the rise of structure-based drug design, the information provided here will serve as a valuable tool for rationally optimizing inhibitor selectivity and effectiveness.
Collapse
Affiliation(s)
- Andrew C. Pham
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sarah A. Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gloria E.O. Borgstahl
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
| |
Collapse
|
3
|
Kim JH, Hildebrandt ER, Sarkar A, Yeung W, Waldon LRA, Kannan N, Schmidt WK. A comprehensive in vivo screen of yeast farnesyltransferase activity reveals broad reactivity across a majority of CXXX sequences. G3 (Bethesda) 2023; 13:jkad094. [PMID: 37119806 PMCID: PMC10320760 DOI: 10.1093/g3journal/jkad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 05/01/2023]
Abstract
The current understanding of farnesyltransferase (FTase) specificity was pioneered through investigations of reporters like Ras and Ras-related proteins that possess a C-terminal CaaX motif that consists of 4 amino acid residues: cysteine-aliphatic1-aliphatic2-variable (X). These studies led to the finding that proteins with the CaaX motif are subject to a 3-step post-translational modification pathway involving farnesylation, proteolysis, and carboxylmethylation. Emerging evidence indicates, however, that FTase can farnesylate sequences outside the CaaX motif and that these sequences do not undergo the canonical 3-step pathway. In this work, we report a comprehensive evaluation of all possible CXXX sequences as FTase targets using the reporter Ydj1, an Hsp40 chaperone that only requires farnesylation for its activity. Our genetic and high-throughput sequencing approach reveals an unprecedented profile of sequences that yeast FTase can recognize in vivo, which effectively expands the potential target space of FTase within the yeast proteome. We also document that yeast FTase specificity is majorly influenced by restrictive amino acids at a2 and X positions as opposed to the resemblance of CaaX motif as previously regarded. This first complete evaluation of CXXX space expands the complexity of protein isoprenylation and marks a key step forward in understanding the potential scope of targets for this isoprenylation pathway.
Collapse
Affiliation(s)
- June H Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily R Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - La Ryel A Waldon
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Walter K Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
4
|
Dey S, Zhou HX. Why Does Synergistic Activation of WASP, but Not N-WASP, by Cdc42 and PIP 2 Require Cdc42 Prenylation? J Mol Biol 2023; 435:168035. [PMID: 36863659 PMCID: PMC10079582 DOI: 10.1016/j.jmb.2023.168035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/16/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
Human WASP and N-WASP are homologous proteins that require the binding of multiple regulators, including the acidic lipid PIP2 and the small GTPase Cdc42, to relieve autoinhibition before they can stimulate the initiation of actin polymerization. Autoinhibition involves intramolecular binding of the C-terminal acidic and central motifs to an upstream basic region and GTPase binding domain. Little is known about how a single intrinsically disordered protein, WASP or N-WASP, binds multiple regulators to achieve full activation. Here we used molecular dynamics simulations to characterize the binding of WASP and N-WASP with PIP2 and Cdc42. In the absence of Cdc42, both WASP and N-WASP strongly associate with PIP2-containing membranes, through their basic region and also possibly through a tail portion of the N-terminal WH1 domain. The basic region also participates in Cdc42 binding, especially for WASP; consequently Cdc42 binding significantly compromises the ability of the basic region in WASP, but not N-WASP, to bind PIP2. PIP2 binding to the WASP basic region is restored only when Cdc42 is prenylated at the C-terminus and tethered to the membrane. This distinction in the activation of WASP and N-WASP may contribute to their different functional roles.
Collapse
Affiliation(s)
- Souvik Dey
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA. https://twitter.com/SouvikDeyUIC
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.
| |
Collapse
|
5
|
Stubbs EB. Isoprenylation of Monomeric GTPases in Human Trabecular Meshwork Cells. Methods Mol Biol 2023; 2625:217-230. [PMID: 36653646 DOI: 10.1007/978-1-0716-2966-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Small monomeric GTPases, including those belonging to the Rho family, regulate a diverse array of intracellular signaling pathways which affect vesicle transport/trafficking, endocytosis, cell cycle progression, cell contractility, and formation of stress fibers or focal adhesions. Functional activation of newly synthesized small monomeric GTPases is facilitated by a multi-step posttranslational process involving transferase-catalyzed addition of farnesyl or geranylgeranyl isoprenoids to conserved cysteine residues within a unique carboxy terminal -CaaX motif. Here, using well-established and widely available contemporary methodologies, detailed protocols by which to semi-quantitatively evaluate the functional consequence of posttranslational isoprenylation in human trabecular meshwork cells are described. We propose the novel concept that posttranslational isoprenylation itself is a key regulator of mammalian Rho GTPase protein expression and turnover.
Collapse
Affiliation(s)
- Evan B Stubbs
- Department of Veterans Affairs, Edward Hines Jr. VA Hospital, Hines, IL, USA.
- Department of Ophthalmology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| |
Collapse
|
6
|
Haney SL, Holstein SA. Targeting the Isoprenoid Biosynthetic Pathway in Multiple Myeloma. Int J Mol Sci 2022; 24:ijms24010111. [PMID: 36613550 PMCID: PMC9820492 DOI: 10.3390/ijms24010111] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Multiple myeloma (MM) is a plasma cell malignancy for which there is currently no cure. While treatment options for MM have expanded over the last two decades, all patients will eventually become resistant to current therapies. Thus, there is an urgent need for novel therapeutic strategies to treat MM. The isoprenoid biosynthetic pathway (IBP) is responsible for the post-translational modification of proteins belonging to the Ras small GTPase superfamily, such as Ras, Rho and Rab family members. Given the important roles these GTPase proteins play in various cellular processes, there is significant interest in the development of inhibitors that disturb their prenylation and consequently their activity in MM cells. Numerous preclinical studies have demonstrated that IBP inhibitors have anti-MM effects, including the induction of apoptosis in MM cells and inhibition of osteoclast activity. Some IBP inhibitors have made their way into the clinic. For instance, nitrogenous bisphosphonates are routinely prescribed for the management MM bone disease. Other IBP inhibitors, including statins and farnesyltransferase inhibitors, have been evaluated in clinical trials for MM, while there is substantial preclinical investigation into geranylgeranyl diphosphate synthase inhibitors. Here we discuss recent advances in the development of IBP inhibitors, assess their mechanism of action and evaluate their potential as anti-MM agents.
Collapse
|
7
|
Morstein J, Bader T, Cardillo AL, Schackmann J, Ashok S, Hougland JL, Hrycyna CA, Trauner DH, Distefano MD. Photoswitchable Isoprenoid Lipids Enable Optical Control of Peptide Lipidation. ACS Chem Biol 2022; 17:2945-2953. [PMID: 36194691 PMCID: PMC9799063 DOI: 10.1021/acschembio.2c00645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Photoswitchable lipids have emerged as attractive tools for the optical control of lipid bioactivity, metabolism, and biophysical properties. Their design is typically based on the incorporation of an azobenzene photoswitch into the hydrophobic lipid tail, which can be switched between its trans- and cis-form using two different wavelengths of light. While glycero- and sphingolipids have been successfully designed to be photoswitchable, isoprenoid lipids have not yet been investigated. Herein, we describe the development of photoswitchable analogs of an isoprenoid lipid and systematically assess their potential for the optical control of various steps in the isoprenylation processing pathway of CaaX proteins in Saccharomyces cerevisiae. One photoswitchable analog of farnesyl diphosphate (AzoFPP-1) allowed effective optical control of substrate prenylation by farnesyltransferase. The subsequent steps of isoprenylation processing (proteolysis by either Ste24 or Rce1 and carboxyl methylation by Ste14) were less affected by photoisomerization of the group introduced into the lipid moiety of the substrate a-factor, a mating pheromone from yeast. We assessed both proteolysis and methylation of the a-factor analogs in vitro and the bioactivity of a fully processed a-factor analog containing the photoswitch, exogenously added to cognate yeast cells. Combined, these data describe the first successful conversion of an isoprenoid lipid into a photolipid and suggest the utility of this approach for the optical control of protein prenylation.
Collapse
Affiliation(s)
- Johannes Morstein
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Taysir Bader
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ariana L. Cardillo
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Julian Schackmann
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Sudhat Ashok
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, USA
| | - James L. Hougland
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, USA
- Department of Biology, Syracuse University, Syracuse, New York 13244, USA
- BioInspired Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, USA
| | | | - Dirk H. Trauner
- Department of Chemistry, New York University, New York, New York 10003, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| |
Collapse
|
8
|
Jeong A, Auger SA, Maity S, Fredriksen K, Zhong R, Li L, Distefano MD. In Vivo Prenylomic Profiling in the Brain of a Transgenic Mouse Model of Alzheimer's Disease Reveals Increased Prenylation of a Key Set of Proteins. ACS Chem Biol 2022; 17:2863-2876. [PMID: 36109170 PMCID: PMC9799064 DOI: 10.1021/acschembio.2c00486] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Dysregulation of protein prenylation has been implicated in many diseases, including Alzheimer's disease (AD). Prenylomic analysis, the combination of metabolic incorporation of an isoprenoid analogue (C15AlkOPP) into prenylated proteins with a bottom-up proteomic analysis, has allowed the identification of prenylated proteins in various cellular models. Here, transgenic AD mice were administered with C15AlkOPP through intracerebroventricular (ICV) infusion over 13 days. Using prenylomic analysis, 36 prenylated proteins were enriched in the brains of AD mice. Importantly, the prenylated forms of 15 proteins were consistently upregulated in AD mice compared to nontransgenic wild-type controls. These results highlight the power of this in vivo metabolic labeling approach to identify multiple post-translationally modified proteins that may serve as potential therapeutic targets for a disease that has proved refractory to treatment thus far. Moreover, this method should be applicable to many other types of protein modifications, significantly broadening its scope.
Collapse
Affiliation(s)
- Angela Jeong
- University of Minnesota, Minneapolis, MN, 55455 USA
| | | | - Sanjay Maity
- University of Minnesota, Minneapolis, MN, 55455 USA
| | | | - Rui Zhong
- University of Minnesota, Minneapolis, MN, 55455 USA
| | - Ling Li
- University of Minnesota, Minneapolis, MN, 55455 USA
| | | |
Collapse
|
9
|
Maxwell ZA, Suazo KF, Brown HM, Distefano MD, Arriaga EA. Combining Isoprenoid Probes with Antibody Markers for Mass Cytometric Analysis of Prenylation in Single Cells. Anal Chem 2022; 94:11521-11528. [PMID: 35952372 PMCID: PMC9441216 DOI: 10.1021/acs.analchem.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein prenylation is an essential post-translational modification that plays a key role in facilitating protein localization. Aberrations in protein prenylation have been indicated in multiple disease pathologies including progeria, some forms of cancer, and Alzheimer's disease. While there are single-cell methods to study prenylation, these methods cannot simultaneously assess prenylation and other cellular changes in the complex cell environment. Here, we report a novel method to monitor, at the single-cell level, prenylation and expression of autophagy markers. An isoprenoid analogue containing a terminal alkyne, substrate of prenylation enzymes, was metabolically incorporated into cells in culture. Treatment with a terbium reporter containing an azide functional group, followed by copper-catalyzed azide-alkyne cycloaddition, covalently attached terbium ions to prenylated proteins within cells. In addition, simultaneous treatment with a holmium-containing analogue of the reporter, without an azide functional group, was used to correct for non-specific retention at the single-cell level. This procedure was compatible with other mass cytometric sample preparation steps that use metal-tagged antibodies. We demonstrate that this method reports changes in levels of prenylation in competitive and inhibitor assays, while tracking autophagy molecular markers with metal-tagged antibodies. The method reported here makes it possible to track prenylation along with other molecular pathways in single cells of complex systems, which is essential to elucidate the role of this post-translational modification in disease, cell response to pharmacological treatments, and aging.
Collapse
|
10
|
Berger BM, Yeung W, Goyal A, Zhou Z, Hildebrandt ER, Kannan N, Schmidt WK. Functional classification and validation of yeast prenylation motifs using machine learning and genetic reporters. PLoS One 2022; 17:e0270128. [PMID: 35749383 PMCID: PMC9231725 DOI: 10.1371/journal.pone.0270128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/05/2022] [Indexed: 11/19/2022] Open
Abstract
Protein prenylation by farnesyltransferase (FTase) is often described as the targeting of a cysteine-containing motif (CaaX) that is enriched for aliphatic amino acids at the a1 and a2 positions, while quite flexible at the X position. Prenylation prediction methods often rely on these features despite emerging evidence that FTase has broader target specificity than previously considered. Using a machine learning approach and training sets based on canonical (prenylated, proteolyzed, and carboxymethylated) and recently identified shunted motifs (prenylation only), this study aims to improve prenylation predictions with the goal of determining the full scope of prenylation potential among the 8000 possible Cxxx sequence combinations. Further, this study aims to subdivide the prenylated sequences as either shunted (i.e., uncleaved) or cleaved (i.e., canonical). Predictions were determined for Saccharomyces cerevisiae FTase and compared to results derived using currently available prenylation prediction methods. In silico predictions were further evaluated using in vivo methods coupled to two yeast reporters, the yeast mating pheromone a-factor and Hsp40 Ydj1p, that represent proteins with canonical and shunted CaaX motifs, respectively. Our machine learning-based approach expands the repertoire of predicted FTase targets and provides a framework for functional classification.
Collapse
Affiliation(s)
- Brittany M. Berger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Wayland Yeung
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Arnav Goyal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Zhongliang Zhou
- Department of Computer Science, University of Georgia, Athens, Georgia, United States of America
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| |
Collapse
|
11
|
Hossain MS, Zhang Z, Ashok S, Jenks AR, Lynch CJ, Hougland JL, Mozhdehi D. Temperature-Responsive Nano-Biomaterials from Genetically Encoded Farnesylated Disordered Proteins. ACS Appl Bio Mater 2022; 5:1846-1856. [PMID: 35044146 PMCID: PMC9115796 DOI: 10.1021/acsabm.1c01162] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
Despite broad interest in understanding the biological implications of protein farnesylation in regulating different facets of cell biology, the use of this post-translational modification to develop protein-based materials and therapies remains underexplored. The progress has been slow due to the lack of accessible methodologies to generate farnesylated proteins with broad physicochemical diversities rapidly. This limitation, in turn, has hindered the empirical elucidation of farnesylated proteins' sequence-structure-function rules. To address this gap, we genetically engineered prokaryotes to develop operationally simple, high-yield biosynthetic routes to produce farnesylated proteins and revealed determinants of their emergent material properties (nano-aggregation and phase-behavior) using scattering, calorimetry, and microscopy. These outcomes foster the development of farnesylated proteins as recombinant therapeutics or biomaterials with molecularly programmable assembly.
Collapse
Affiliation(s)
- Md. Shahadat Hossain
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Zhe Zhang
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Sudhat Ashok
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Ashley R. Jenks
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Christopher J. Lynch
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| |
Collapse
|
12
|
Marchwicka A, Kamińska D, Monirialamdari M, Błażewska KM, Gendaszewska-Darmach E. Protein Prenyltransferases and Their Inhibitors: Structural and Functional Characterization. Int J Mol Sci 2022; 23:ijms23105424. [PMID: 35628237 PMCID: PMC9141697 DOI: 10.3390/ijms23105424] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Protein prenylation is a post-translational modification controlling the localization, activity, and protein–protein interactions of small GTPases, including the Ras superfamily. This covalent attachment of either a farnesyl (15 carbon) or a geranylgeranyl (20 carbon) isoprenoid group is catalyzed by four prenyltransferases, namely farnesyltransferase (FTase), geranylgeranyltransferase type I (GGTase-I), Rab geranylgeranyltransferase (GGTase-II), and recently discovered geranylgeranyltransferase type III (GGTase-III). Blocking small GTPase activity, namely inhibiting prenyltransferases, has been proposed as a potential disease treatment method. Inhibitors of prenyltransferase have resulted in substantial therapeutic benefits in various diseases, such as cancer, neurological disorders, and viral and parasitic infections. In this review, we overview the structure of FTase, GGTase-I, GGTase-II, and GGTase-III and summarize the current status of research on their inhibitors.
Collapse
Affiliation(s)
- Aleksandra Marchwicka
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
| | - Daria Kamińska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
| | - Mohsen Monirialamdari
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (M.M.); (K.M.B.)
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (M.M.); (K.M.B.)
| | - Edyta Gendaszewska-Darmach
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
- Correspondence:
| |
Collapse
|
13
|
Ribeiro I, Ducos E, Giglioli-Guivarc'h N, Dutilleul C. Tagging and Capture of Prenylated CaaX-Proteins from Plant Cell Cultures. Methods Mol Biol 2022; 2505:241-248. [PMID: 35732949 DOI: 10.1007/978-1-0716-2349-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The tagging-via-substrate strategy allows the probing of in vivo post-translationally modified proteins thanks to a labeled substrate. This method has been used for the detection and proteomic analysis of prenylated proteins in mammals and more recently in plants. It consists of the labeling of prenylated proteins by supplying azido-prenyl to cells. The azido-prenylated proteins are then selectively linked to biotin alkyne, which allows their capture using streptavidin beads, and their subsequent identification by mass spectrometry. In this chapter, we describe this procedure on Arabidopsis cell suspension and how it can be applied for Catharanthus roseus cells.
Collapse
Affiliation(s)
- Iliana Ribeiro
- EA2106 "Biomolécules et Biotechnologies Végétales", Faculté des Sciences Pharmaceutiques, Université de Tours, Parc de Grandmont, Tours, France
| | - Eric Ducos
- EA2106 "Biomolécules et Biotechnologies Végétales", Faculté des Sciences Pharmaceutiques, Université de Tours, Parc de Grandmont, Tours, France
| | - Nathalie Giglioli-Guivarc'h
- EA2106 "Biomolécules et Biotechnologies Végétales", Faculté des Sciences Pharmaceutiques, Université de Tours, Parc de Grandmont, Tours, France
| | - Christelle Dutilleul
- EA2106 "Biomolécules et Biotechnologies Végétales", Faculté des Sciences Pharmaceutiques, Université de Tours, Parc de Grandmont, Tours, France.
| |
Collapse
|
14
|
Gutkowska M, Kaus‐Drobek M, Hoffman‐Sommer M, Małgorzata Pamuła M, Daria Leja A, Perycz M, Lichocka M, Witek A, Wojtas M, Dadlez M, Swiezewska E, Surmacz L. Impact of C-terminal truncations in the Arabidopsis Rab escort protein (REP) on REP-Rab interaction and plant fertility. Plant J 2021; 108:1400-1421. [PMID: 34592024 PMCID: PMC9293207 DOI: 10.1111/tpj.15519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Lipid anchors are common post-translational modifications for proteins engaged in signaling and vesicular transport in eukaryotic cells. Rab proteins are geranylgeranylated at their C-termini, a modification which is important for their stable binding to lipid bilayers. The Rab escort protein (REP) is an accessory protein of the Rab geranylgeranyl transferase (RGT) complex and it is obligatory for Rab prenylation. While REP-Rab interactions have been studied by biochemical, structural, and genetic methods in animals and yeast, data on the plant RGT complex are still limited. Here we use hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the structural basis of plant REP-Rab binding. The obtained results show that the interaction of REP with Rabs is highly dynamic and involves specific structural changes in both partners. In some cases the Rab and REP regions involved in the interaction are molecule-specific, and in other cases they are common for a subset of Rabs. In particular, the C-terminus of REP is not involved in binding of unprenylated Rab proteins in plants, in contrast to mammalian REP. In line with this, a C-terminal REP truncation does not have pronounced phenotypic effects in planta. On the contrary, a complete lack of functional REP leads to male sterility in Arabidopsis: pollen grains develop in the anthers, but they do not germinate efficiently and hence are unable to transmit the mutated allele. The presented data show that the mechanism of action of REP in the process of Rab geranylgeranylation is different in plants than in animals or yeast.
Collapse
Affiliation(s)
- Małgorzata Gutkowska
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Magdalena Kaus‐Drobek
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
- Mossakowski Medical Research CentrePolish Academy of Sciencesul. Pawinskiego 5, 02‐106WarsawPoland
| | - Marta Hoffman‐Sommer
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | | | - Anna Daria Leja
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Małgorzata Perycz
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
- Institute of Computer SciencePolish Academy of Sciencesul. Jana Kazimierza 501‐248WarsawPoland
| | - Małgorzata Lichocka
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Agnieszka Witek
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Magdalena Wojtas
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Michał Dadlez
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Ewa Swiezewska
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Liliana Surmacz
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| |
Collapse
|
15
|
Schey GL, Buttery PH, Hildebrandt ER, Novak SX, Schmidt WK, Hougland JL, Distefano MD. MALDI-MS Analysis of Peptide Libraries Expands the Scope of Substrates for Farnesyltransferase. Int J Mol Sci 2021; 22:ijms222112042. [PMID: 34769472 PMCID: PMC8584866 DOI: 10.3390/ijms222112042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022] Open
Abstract
Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This modification typically causes proteins to associate with the membrane and allows them to participate in signaling pathways. In the canonical understanding of FTase, the isoprenoids are attached to the cysteine residue of a four-amino-acid CaaX box sequence. However, recent work has shown that five-amino-acid sequences can be recognized, including the pentapeptide CMIIM. This paper describes a new systematic approach to discover novel peptide substrates for FTase by combining the combinatorial power of solid-phase peptide synthesis (SPPS) with the ease of matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). The workflow consists of synthesizing focused libraries containing 10-20 sequences obtained by randomizing a synthetic peptide at a single position. Incubation of the library with FTase and farnesyl pyrophosphate (FPP) followed by mass spectrometric analysis allows the enzymatic products to be clearly resolved from starting peptides due to the increase in mass that occurs upon farnesylation. Using this method, 30 hits were obtained from a series of libraries containing a total of 80 members. Eight of the above peptides were selected for further evaluation, reflecting a mixture that represented a sampling of diverse substrate space. Six of these sequences were found to be bona fide substrates for FTase, with several meeting or surpassing the in vitro efficiency of the benchmark sequence CMIIM. Experiments in yeast demonstrated that proteins bearing these sequences can be efficiently farnesylated within live cells. Additionally, a bioinformatics search showed that a variety of pentapeptide CaaaX sequences can be found in the mammalian genome, and several of these sequences display excellent farnesylation in vitro and in yeast cells, suggesting that the number of farnesylated proteins within mammalian cells may be larger than previously thought.
Collapse
Affiliation(s)
- Garrett L. Schey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Peter H. Buttery
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (W.K.S.)
| | - Sadie X. Novak
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (S.X.N.); (J.L.H.)
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (W.K.S.)
| | - James L. Hougland
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (S.X.N.); (J.L.H.)
- BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - Mark D. Distefano
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence:
| |
Collapse
|
16
|
Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, Wilson SJ. A prenylated dsRNA sensor protects against severe COVID-19. Science 2021; 374:eabj3624. [PMID: 34581622 PMCID: PMC7612834 DOI: 10.1126/science.abj3624] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that 2′-5′-oligoadenylate synthetase 1 (OAS1), through ribonuclease L, potently inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We show that a common splice-acceptor single-nucleotide polymorphism (Rs10774671) governs whether patients express prenylated OAS1 isoforms that are membrane-associated and sense-specific regions of SARS-CoV-2 RNAs or if they only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. In hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting that this antiviral defense is a major component of a protective antiviral response.
Collapse
Affiliation(s)
- Arthur Wickenhagen
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Elena Sugrue
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Spyros Lytras
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Srikeerthana Kuchi
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Marko Noerenberg
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Matthew L. Turnbull
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Colin Loney
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Vanessa Herder
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jay Allan
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Innes Jarmson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Natalia Cameron-Ruiz
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Margus Varjak
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Rute M. Pinto
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Jeffrey Y. Lee
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Louisa Iselin
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natasha Palmalux
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Douglas G. Stewart
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Simon Swingler
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Edward J. D. Greenwood
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Thomas W. M. Crozier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Quan Gu
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Emma L. Davies
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Fabio Trindade Maranhão Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
| | - Monique Freire Santana
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
| | - Luiz Carlos de Lima Ferreira
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Graeme Grimes
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - ISARIC4C Investigators
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paolo, Brazil
- Department of Education and Research, Oncology Control Centre of Amazonas State (FCECON), Manaus, Amazonas, Brazil
- Postgraduate Program in Tropical Medicine, Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Edinburgh Clinical Research Facility, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Joao Luiz Da Silva Filho
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Matthias Marti
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Joseph Hughes
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Eddie C. Y. Wang
- Division of Infection & Immunity, Cardiff University, Cardiff, UK
| | - Antonia Ho
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ruth F. Jarrett
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Alfredo Castello
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - David L. Robertson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Malcolm G. Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children’s Hospital, Liverpool, UK
| | - Peter J. M. Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare, National Health Service Trust London, London, UK
| | - Massimo Palmarini
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Paul J. Lehner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - J. Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Suzannah J. Rihn
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | - Sam J. Wilson
- Medical Research Council–University of Glasgow Centre for Virus Research (CVR), Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| |
Collapse
|
17
|
Chamberlain SG, Gohlke A, Shafiq A, Squires IJ, Owen D, Mott HR. Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs. Proc Natl Acad Sci U S A 2021; 118:e2104219118. [PMID: 34480001 PMCID: PMC8433508 DOI: 10.1073/pnas.2104219118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022] Open
Abstract
RalA is a small GTPase and a member of the Ras family. This molecular switch is activated downstream of Ras and is widely implicated in tumor formation and growth. Previous work has shown that the ubiquitous Ca2+-sensor calmodulin (CaM) binds to small GTPases such as RalA and K-Ras4B, but a lack of structural information has obscured the functional consequences of these interactions. Here, we have investigated the binding of CaM to RalA and found that CaM interacts exclusively with the C terminus of RalA, which is lipidated with a prenyl group in vivo to aid membrane attachment. Biophysical and structural analyses show that the two RalA membrane-targeting motifs (the prenyl anchor and the polybasic motif) are engaged by distinct lobes of CaM and that CaM binding leads to removal of RalA from its membrane environment. The structure of this complex, along with a biophysical investigation into membrane removal, provides a framework with which to understand how CaM regulates the function of RalA and sheds light on the interaction of CaM with other small GTPases, including K-Ras4B.
Collapse
Affiliation(s)
- Samuel G Chamberlain
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Andrea Gohlke
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Arooj Shafiq
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Iolo J Squires
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
| |
Collapse
|
18
|
Wang X, Zhang R, Huang Z, Zang S, Wu Q, Xia L. Inhibition of the miR-155 and protein prenylation feedback loop alleviated acute graft-versus-host disease through regulating the balance between T helper 17 and Treg cells. Transpl Immunol 2021; 69:101461. [PMID: 34487810 DOI: 10.1016/j.trim.2021.101461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/19/2022]
Abstract
MicroRNA-155(miR-155) and protein prenylation have been reported to participate in acute graft-versus-host disease (aGVHD) through modulating T lymphocyte differentiation, however the mechanism remains elusive. In this study, we found that the expression of miR-155 and protein prenyltransferases in peripheral blood T lymphocytes of aGVHD mice was significantly increased. Suppression of miR-155 by antagomir-155 could remarkably reduce prenyltransferases mRNA and protein expression in T lymphocytes of aGVHD mice. Conversely, prenyltransferase inhibitors significantly reduced the level of miR-155. Inhibition of this feedback loop of miR-155 and protein prenylation in aGVHD mice led to improved survival and lower aGVHD histopathology scores and significantly induced T cell deficient differentiation towards T helper 17 (Th17) cells and titled differentiation towards CD4+CD25hi regulatory T (Treg) cells. Furthermore, the immunoregulatory effects and protection from aGVHD of prenyltransferase inhibitors could be reversed by the addition of miR-155. The dual treatment of prenylation inhibitors and antagomir-155 showed synergistic effects on T polarization and protection from aGVHD. Consistent with the in vivo changes, inhibition of this feedback loop of miR-155 and protein prenylation affected Th17 and Treg cell polarization in vitro. Our data suggest that miR-155 and protein prenylation may constitute a feedback loop that amplifies immune and inflammatory responses in subjects with aGVHD, and they may serve as potential targets for aGVHD prophylaxis and treatment.
Collapse
Affiliation(s)
- Xiaoxiao Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue,Wuhan 430022, China; Department of Geriatrics,Union Hospital,Tongji Medical College, Huazhong University of Science and Technology,1277 JieFang Avenue,Wuhan 430022,China; Institute of Gerontology,Union Hospital,Tongji Medical College, Huazhong University of Science and Technology,1277 JieFang Avenue,Wuhan 430022,China
| | - Ran Zhang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Zhenli Huang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue,Wuhan 430022, China
| | - Sibin Zang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue,Wuhan 430022, China
| | - Qiuling Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue,Wuhan 430022, China.
| | - Linghui Xia
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue,Wuhan 430022, China.
| |
Collapse
|
19
|
Tennakoon M, Senarath K, Kankanamge D, Chadee DN, Karunarathne A. A short C-terminal peptide in Gγ regulates Gβγ signaling efficacy. Mol Biol Cell 2021; 32:1446-1458. [PMID: 34106735 PMCID: PMC8351738 DOI: 10.1091/mbc.e20-11-0750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/03/2021] [Accepted: 06/04/2021] [Indexed: 01/03/2023] Open
Abstract
G protein beta-gamma (Gβγ) subunits anchor to the plasma membrane (PM) through the carboxy-terminal (CT) prenyl group in Gγ. This interaction is crucial for the PM localization and functioning of Gβγ, allowing GPCR-G protein signaling to proceed. The diverse Gγ family has 12 members, and we have recently shown that the signaling efficacies of major Gβγ effectors are Gγ-type dependent. This dependency is due to the distinct series of membrane-interacting abilities of Gγ. However, the molecular process allowing for Gβγ subunits to exhibit a discrete and diverse range of Gγ-type-dependent membrane affinities is unclear and cannot be explained using only the type of prenylation. The present work explores the unique designs of membrane-interacting CT residues in Gγ as a major source for this Gγ-type-dependent Gβγ signaling. Despite the type of prenylation, the results show signaling efficacy at the PM, and associated cell behaviors of Gβγ are governed by crucially located specific amino acids in the five to six residue preprenylation region of Gγ. The provided molecular picture of Gγ-membrane interactions may explain how cells gain Gγ-type-dependent G protein-GPCR signaling as well as how Gβγ elicits selective signaling at various subcellular compartments.
Collapse
Affiliation(s)
- Mithila Tennakoon
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| | - Kanishka Senarath
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| | - Dinesh Kankanamge
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| | - Deborah N. Chadee
- Department of Biological Sciences, The University of Toledo, Toledo, OH 43606
| | - Ajith Karunarathne
- Department of Chemistry and Biochemistry, The University of Toledo, Toledo, OH 43606
| |
Collapse
|
20
|
Feng Z, Shi H, Lv M, Ma Y, Li J. Protein farnesylation negatively regulates brassinosteroid signaling via reducing BES1 stability in Arabidopsis thaliana. J Integr Plant Biol 2021; 63:1353-1366. [PMID: 33764637 PMCID: PMC8360029 DOI: 10.1111/jipb.13093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Brassinosteroids (BRs) are a group of steroidal phytohormones, playing critical roles in almost all physiological aspects during the life span of a plant. In Arabidopsis, BRs are perceived at the cell surface, triggering a reversible phosphorylation-based signaling cascade that leads to the activation and nuclear accumulation of a family of transcription factors, represented by BES1 and BZR1. Protein farnesylation is a type of post-translational modification, functioning in many important cellular processes. Previous studies demonstrated a role of farnesylation in BR biosynthesis via regulating the endoplasmic reticulum localization of a key bassinolide (BL) biosynthetic enzyme BR6ox2. Whether such a process is also involved in BR signaling is not understood. Here, we demonstrate that protein farnesylation is involved in mediating BR signaling in Arabidopsis. A loss-of-function mutant of ENHANCED RESPONSE TO ABA 1 (ERA1), encoding a β subunit of the protein farnesyl transferase holoenzyme, can alter the BL sensitivity of bak1-4 from a reduced to a hypersensitive level. era1 can partially rescue the BR defective phenotype of a heterozygous mutant of bin2-1, a gain-of-function mutant of BIN2 which encodes a negative regulator in the BR signaling. Our genetic and biochemical analyses revealed that ERA1 plays a significant role in regulating the protein stability of BES1.
Collapse
Affiliation(s)
- Zengxiu Feng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Hongyong Shi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Minghui Lv
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yuang Ma
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| |
Collapse
|
21
|
Mathews ES, Jezewski AJ, Odom John AR. Protein Prenylation and Hsp40 in Thermotolerance of Plasmodium falciparum Malaria Parasites. mBio 2021; 12:e0076021. [PMID: 34182772 PMCID: PMC8262983 DOI: 10.1128/mbio.00760-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/01/2021] [Indexed: 12/31/2022] Open
Abstract
During its complex life cycle, the malaria parasite survives dramatic environmental stresses, including large temperature shifts. Protein prenylation is required during asexual replication of Plasmodium falciparum, and the canonical heat shock protein 40 protein (HSP40; PF3D7_1437900) is posttranslationally modified with a 15-carbon farnesyl isoprenyl group. In other organisms, farnesylation of Hsp40 orthologs controls their localization and function in resisting environmental stress. In this work, we find that plastidial isopentenyl pyrophosphate (IPP) synthesis and protein farnesylation are required for malaria parasite survival after cold and heat shock. Furthermore, loss of HSP40 farnesylation alters its membrane attachment and interaction with proteins in essential pathways in the parasite. Together, this work reveals that farnesylation is essential for parasite survival during temperature stress. Farnesylation of HSP40 may promote thermotolerance by guiding distinct chaperone-client protein interactions.
Collapse
Affiliation(s)
- Emily S. Mathews
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew J. Jezewski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Audrey R. Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Disease, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
22
|
Suazo KF, Jeong A, Ahmadi M, Brown C, Qu W, Li L, Distefano MD. Metabolic labeling with an alkyne probe reveals similarities and differences in the prenylomes of several brain-derived cell lines and primary cells. Sci Rep 2021; 11:4367. [PMID: 33623102 PMCID: PMC7902609 DOI: 10.1038/s41598-021-83666-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Protein prenylation involves the attachment of one or two isoprenoid group(s) onto cysteine residues positioned near the C-terminus. This modification is essential for many signal transduction processes. In this work, the use of the probe C15AlkOPP for metabolic labeling and identification of prenylated proteins in a variety of cell lines and primary cells is explored. Using a single isoprenoid analogue, 78 prenylated protein groups from the three classes of prenylation substrates were identified including three novel prenylation substrates in a single experiment. Applying this method to three brain-related cell lines including neurons, microglia, and astrocytes showed substantial overlap (25%) in the prenylated proteins identified. In addition, some unique prenylated proteins were identified in each type. Eight proteins were observed exclusively in neurons, five were observed exclusively in astrocytes and three were observed exclusively in microglia, suggesting their unique roles in these cells. Furthermore, inhibition of farnesylation in primary astrocytes revealed the differential responses of farnesylated proteins to an FTI. Importantly, these results provide a list of 19 prenylated proteins common to all the cell lines studied here that can be monitored using the C15AlkOPP probe as well as a number of proteins that were observed in only certain cell lines. Taken together, these results suggest that this chemical proteomic approach should be useful in monitoring the levels and exploring the underlying role(s) of prenylated proteins in various diseases.
Collapse
Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Angela Jeong
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mina Ahmadi
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Caroline Brown
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wenhui Qu
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
23
|
Ogura M, Endo K, Suzuki T, Homma Y. Prenylated quinolinecarboxylic acid compound-18 prevents sensory nerve fiber outgrowth through inhibition of the interleukin-31 pathway. PLoS One 2021; 16:e0246630. [PMID: 33539470 PMCID: PMC7861556 DOI: 10.1371/journal.pone.0246630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 01/25/2021] [Indexed: 11/24/2022] Open
Abstract
Interleukin-31 (IL-31) is involved in excessive development of cutaneous sensory nerves in atopic dermatitis (AD), leading to severe pruritus. We previously reported that PQA-18, a prenylated quinolinecarboxylic acid (PQA) derivative, is an immunosuppressant with inhibition of p21-activated kinase 2 (PAK2) and improves skin lesions in Nc/Nga mice as an AD model. In the present study, we investigate the effect of PQA-18 on sensory nerves in lesional skin. PQA-18 alleviates cutaneous nerve fiber density in the skin of Nc/Nga mice. PQA-18 also inhibits IL-31-induced sensory nerve fiber outgrowth in dorsal root ganglion cultures. Signaling analysis reveals that PQA-18 suppresses phosphorylation of PAK2, Janus kinase 2, and signal transducer and activator of transcription 3 (STAT3), activated by IL-31 receptor (IL-31R), resulting in inhibition of neurite outgrowth in Neuro2A cells. Gene silencing analysis for PAK2 confirms the requirement for STAT3 phosphorylation and neurite outgrowth elicited by IL-31R activation. LC/MS/MS analysis reveals that PQA-18 prevents the formation of PAK2 activation complexes induced by IL-31R activation. These results suggest that PQA-18 inhibits the IL-31 pathway through suppressing PAK2 activity, which suppresses sensory nerve outgrowth. PQA-18 may be a valuable lead for the development of a novel drug for pruritus of AD.
Collapse
Affiliation(s)
- Masato Ogura
- Fukushima Medical University School of Medicine, Fukushima, Japan
- * E-mail:
| | - Kumiko Endo
- Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Toshiyuki Suzuki
- Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yoshimi Homma
- Fukushima Medical University School of Medicine, Fukushima, Japan
| |
Collapse
|
24
|
Ötzkan S, Muller WE, Gibson Wood W, Eckert GP. Effects of 7,8-Dihydroxyflavone on Lipid Isoprenoid and Rho Protein Levels in Brains of Aged C57BL/6 Mice. Neuromolecular Med 2020; 23:130-139. [PMID: 33377988 PMCID: PMC7929957 DOI: 10.1007/s12017-020-08640-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022]
Abstract
Synaptic impairment may be the main cause of cognitive dysfunction in brain aging that is probably due to a reduction in synaptic contact between the axonal buttons and dendritic spines. Rho proteins including the small GTPase Rac1 have become key regulators of neuronal morphogenesis that supports synaptic plasticity. Small Rho- and Ras-GTPases are post-translationally modified by the isoprenoids geranylgeranyl pyrophosphate (GGPP) and farnesyl pyrophosphate (FPP), respectively. For all GTPases, anchoring in the plasma membrane is essential for their activation by guanine nucleotide exchange factors (GEFs). Rac1-specific GEFs include the protein T lymphoma invasion and metastasis 1 (Tiam1). Tiam1 interacts with the TrkB receptor to mediate the brain-derived neurotrophic factor (BDNF)-induced activation of Rac1, resulting in cytoskeletal rearrangement and changes in cellular morphology. The flavonoid 7,8-dihydroxyflavone (7,8-DHF) acts as a highly affine-selective TrkB receptor agonist and causes the dimerization and autophosphorylation of the TrkB receptor and thus the activation of downstream signaling pathways. In the current study, we investigated the effects of 7,8-DHF on cerebral lipid isoprenoid and Rho protein levels in male C57BL/6 mice aged 3 and 23 months. Aged mice were daily treated with 100 mg/kg b.w. 7,8-DHF by oral gavage for 21 days. FPP, GGPP, and cholesterol levels were determined in brain tissue. In the same tissue, the protein content of Tiam1 and TrkB in was measured. The cellular localization of the small Rho-GTPase Rac1 and small Rab-GTPase Rab3A was studied in total brain homogenates and membrane preparations. We report the novel finding that 7,8-DHF restored levels of the Rho proteins Rac1 and Rab3A in membrane preparations isolated from brains of treated aged mice. The selective TrkB agonist 7,8-DHF did not affect BDNF and TrkB levels, but restored Tiam1 levels that were found to be reduced in brains of aged mice. FPP, GGPP, and cholesterol levels were significantly elevated in brains of aged mice but not changed by 7,8-DHF treatment. Hence, 7,8-DHF may be useful as pharmacological tool to treat age-related cognitive dysfunction although the underlying mechanisms need to be elucidated in detail.
Collapse
Affiliation(s)
- Sarah Ötzkan
- Department of Pharmacology, Biocenter Niederursel, University of Frankfurt, Goethe-University, Max-von-Laue-St. 9, 60438, Frankfurt, Germany
| | - Walter E Muller
- Department of Pharmacology, Biocenter Niederursel, University of Frankfurt, Goethe-University, Max-von-Laue-St. 9, 60438, Frankfurt, Germany
| | - W Gibson Wood
- Department of Pharmacology, Geriatric Research, Education and Clinical Center, University of Minnesota School of Medicine, VAMC, Minneapolis, MN, 55417, USA
| | - Gunter P Eckert
- Department of Pharmacology, Biocenter Niederursel, University of Frankfurt, Goethe-University, Max-von-Laue-St. 9, 60438, Frankfurt, Germany.
- Institute of Nutritional Sciences, Laboratory for Nutrition in Prevention and Therapy, Justus-Liebig-University of Giessen, Biomedical Research Center Seltersberg (BFS), Schubertstr. 81, 35392, Giessen, Germany.
| |
Collapse
|
25
|
Rogers MJ, Mönkkönen J, Munoz MA. Molecular mechanisms of action of bisphosphonates and new insights into their effects outside the skeleton. Bone 2020; 139:115493. [PMID: 32569873 DOI: 10.1016/j.bone.2020.115493] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/09/2020] [Accepted: 06/11/2020] [Indexed: 12/27/2022]
Abstract
Bisphosphonates (BP) are a class of calcium-binding drug used to prevent bone resorption in skeletal disorders such as osteoporosis and metastatic bone disease. They act by selectively targeting bone-resorbing osteoclasts and can be grouped into two classes depending on their intracellular mechanisms of action. Simple BPs cause osteoclast apoptosis after cytoplasmic conversion into toxic ATP analogues. In contrast, nitrogen-containing BPs potently inhibit FPP synthase, an enzyme of the mevalonate (cholesterol biosynthesis) pathway. This results in production of a toxic metabolite (ApppI) and the loss of long-chain isoprenoid lipids required for protein prenylation, a process necessary for the function of small GTPase proteins essential for the survival and activity of osteoclasts. In this review we provide a state-of-the-art overview of these mechanisms of action and a historical perspective of how they were discovered. Finally, we challenge the long-held dogma that BPs act only in the skeleton and highlight recent studies that reveal insights into hitherto unknown effects on tumour-associated and tissue-resident macrophages.
Collapse
Affiliation(s)
- Michael J Rogers
- Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, UNSW Sydney, Australia.
| | - Jukka Mönkkönen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Finland.
| | - Marcia A Munoz
- Garvan Institute of Medical Research, Sydney, Australia; St Vincent's Clinical School, UNSW Sydney, Australia.
| |
Collapse
|
26
|
Assi M, Pirlot B, Stroobant V, Thissen JP, Jacquemin P. A Novel KRAS Antibody Highlights a Regulation Mechanism of Post-Translational Modifications of KRAS during Tumorigenesis. Int J Mol Sci 2020; 21:ijms21176361. [PMID: 32887255 PMCID: PMC7504708 DOI: 10.3390/ijms21176361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
KRAS is a powerful oncogene responsible for the development of many cancers. Despite the great progress in understanding its function during the last decade, the study of KRAS expression, subcellular localization, and post-translational modifications remains technically challenging. Accordingly, many facets of KRAS biology are still unknown. Antibodies could be an effective and easy-to-use tool for in vitro and in vivo research on KRAS. Here, we generated a novel rabbit polyclonal antibody that allows immunolabeling of cells and tissues overexpressing KRAS. Cell transfection experiments with expression vectors for the members of the RAS family revealed a preferential specificity of this antibody for KRAS. In addition, KRAS was sensitively detected in a mouse tissue electroporated with an expression vector. Interestingly, our antibody was able to detect endogenous forms of unprenylated (immature) and prenylated (mature) KRAS in mouse organs. We found that KRAS prenylation was increased ex vivo and in vivo in a model of KRASG12D-driven tumorigenesis, which was concomitant with an induction of expression of essential KRAS prenylation enzymes. Therefore, our tool helped us to put the light on new regulations of KRAS activation during cancer initiation. The use of this tool by the RAS community could contribute to discovering novel aspects of KRAS biology.
Collapse
Affiliation(s)
- Mohamad Assi
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
- Correspondence: (M.A.); (P.J.); Tel.: +32-2764-75-31 (M.A. & P.J.)
| | - Boris Pirlot
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, 1200 Brussels, Belgium; (B.P.); (J.-P.T.)
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-Paul Thissen
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, 1200 Brussels, Belgium; (B.P.); (J.-P.T.)
| | - Patrick Jacquemin
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
- Correspondence: (M.A.); (P.J.); Tel.: +32-2764-75-31 (M.A. & P.J.)
| |
Collapse
|
27
|
Wilkins JA, Kaasik K, Chalkley RJ, Burlingame AL. Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS. Mol Cell Proteomics 2020; 19:1005-1016. [PMID: 32284353 PMCID: PMC7261820 DOI: 10.1074/mcp.ra120.001944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/19/2020] [Indexed: 01/16/2023] Open
Abstract
Posttranslational modifications play a critical and diverse role in regulating cellular activities. Despite their fundamentally important role in cellular function, there has been no report to date of an effective generalized approach to the targeting, extraction, and characterization of the critical c-terminal regions of natively prenylated proteins. Various chemical modification and metabolic labeling strategies in cell culture have been reported. However, their applicability is limited to cell culture systems and does not allow for analysis of tissue samples. The chemical characteristics (hydrophobicity, low abundance, highly basic charge) of many of the c-terminal regions of prenylated proteins have impaired the use of standard proteomic workflows. In this context, we sought a direct approach to the problem in order to examine these proteins in tissue without the use of labeling. Here we demonstrate that prenylated proteins can be captured on chromatographic resins functionalized with mixed disulfide functions. Protease treatment of resin-bound proteins using chymotryptic digestion revealed peptides from many known prenylated proteins. Exposure of the protease-treated resin to reducing agents and hydro organic mixtures released c-terminal peptides with intact prenyl groups along with other enzymatic modifications expected in this protein family. Database and search parameters were selected to allow for c-terminal modifications unique to these molecules such as CAAX box processing and c-terminal methylation. In summary, we present a direct approach to enrich and obtain information at a molecular level of detail about prenylation of proteins from tissue and cell extracts using high-performance LC-MS without the need for metabolic labeling and derivatization.
Collapse
Affiliation(s)
- James A Wilkins
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158.
| | - Krista Kaasik
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158
| | - Robert J Chalkley
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158
| | - Alma L Burlingame
- Mass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158
| |
Collapse
|
28
|
Abstract
The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell.
Collapse
Affiliation(s)
- Urban Bezeljak
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Hrushikesh Loya
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Beata Kaczmarek
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Timothy E Saunders
- Mechanobiology Institute, National University of Singapore, Singapore 119077;
- Department of Biological Sciences, National University of Singapore, Singapore 119077
| | - Martin Loose
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria;
| |
Collapse
|
29
|
Wu JR, Wang TY, Weng CP, Duong NKT, Wu SJ. AtJ3, a specific HSP40 protein, mediates protein farnesylation-dependent response to heat stress in Arabidopsis. Planta 2019; 250:1449-1460. [PMID: 31309322 DOI: 10.1007/s00425-019-03239-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Despite AtJ3 and AtJ2 sharing a high protein-sequence identity and both being substrates of protein farnesyltransferase (PFT), AtJ3 but not AtJ2 mediates in Arabidopsis the heat-dependent phenotypes derived from farnesylation modification. Arabidopsis HEAT-INTOERANT 5 (HIT5)/ENHANCED RESPONSE TO ABA 1 (ERA1) encodes the β-subunit of the protein farnesyltransferase (PFT), and the hit5/era1 mutant is better able to tolerate heat-shock stress than the wild type. Given that Arabidopsis AtJ2 (J2) and AtJ3 (J3) are heat-shock protein 40 (HSP40) homologs, sharing 90% protein-sequence identity, and each contains a CaaX box for farnesylation; atj2 (j2) and atj3 (j3) mutants were subjected to heat-shock treatment. Results showed that j3 but not j2 manifested the heat-shock tolerant phenotype. In addition, transgenic j3 plants that expressed a CaaX- abolishing J3C417S construct maintained the same capacity to tolerate heat shock as j3. The basal transcript levels of HEAT-SHOCK PROTEIN 101 (HSP101) in hit5/era1 and j3 were higher than those in the wild type. Although the capacities of j3/hsp101 and hit5/hsp101 double mutants to tolerate heat-shock stress declined compared to those of j3 and hit5/era1, they were still greater than that of the wild type. These results show that a lack of farnesylated J3 contributes to the heat-dependent phenotypes of hit5/era1, in part by the modulation of HSP101 activity, and also indicates that (a) mediator(s) other than J3 is (are) involved in the PFT-regulated heat-stress response. In addition, because HSP40s are known to function in dimer formation, bimolecular fluorescence complementation experiments were performed, and results show that J3 could dimerize regardless of farnesylation. In sum, in this study, a specific PFT substrate was identified, and its roles in the farnesylation-regulated heat-stress responses were clarified, which could be of use in future agricultural applications.
Collapse
Affiliation(s)
- Jia-Rong Wu
- Department of Life Sciences, National Central University, 300 Jhong-Da Road, Jhong-Li District, Taoyuan City, 32001, Taiwan
| | - Tzu-Yun Wang
- Department of Life Sciences, National Central University, 300 Jhong-Da Road, Jhong-Li District, Taoyuan City, 32001, Taiwan
| | - Chi-Pei Weng
- Department of Life Sciences, National Central University, 300 Jhong-Da Road, Jhong-Li District, Taoyuan City, 32001, Taiwan
| | - Ngoc Kieu Thi Duong
- Department of Life Sciences, National Central University, 300 Jhong-Da Road, Jhong-Li District, Taoyuan City, 32001, Taiwan
| | - Shaw-Jye Wu
- Department of Life Sciences, National Central University, 300 Jhong-Da Road, Jhong-Li District, Taoyuan City, 32001, Taiwan.
| |
Collapse
|
30
|
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.
Collapse
Affiliation(s)
- Michal Hála
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic.
| | - Viktor Žárský
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic.
| |
Collapse
|
31
|
Khan IU, Rono JK, Zhang BQ, Liu XS, Wang MQ, Wang LL, Wu XC, Chen X, Cao HW, Yang ZM. Identification of novel rice (Oryza sativa) HPP and HIPP genes tolerant to heavy metal toxicity. Ecotoxicol Environ Saf 2019; 175:8-18. [PMID: 30878662 DOI: 10.1016/j.ecoenv.2019.03.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/06/2019] [Accepted: 03/10/2019] [Indexed: 05/27/2023]
Abstract
HPP (heavy metal associated plant protein) and HIPP (heavy metal associated isoprenylated plant protein) are a group of metal-binding metallochaperones playing crucial roles in metal homeostasis and detoxification. Up to now, only few of them have been functionally identified in plants. Here, we identified 54 HPP and HIPP genes in rice genome. Analysis of the transcriptome datasets of the rice genome exposed to cadmium (Cd) revealed 17 HPP/HIPP genes differentially expressed, with 11 being upregulated (>2 fold change, p < 0.05). Comprehensive analysis of transcripts by qRT-PCR showed that both types of genes displayed diverse expression pattern in rice under excess manganese (Mn), copper (Cu) and Cd stress. Multiple genomic analyses of HPPs/HIPPs including phylogenesis, conserved domains and motifs, genomic arrangement and genomic and tandem duplication were performed. To identify the role of the genes, OsHIPP16, OsHIPP34 and OsHIPP60 were randomly selected to express in yeast (Saccharomyces cerevisiae) mutants pmrl, cup2, ycf1 and zrc1, exhibiting sensitivity to Mn, Cu, Cd and Zn toxicity, respectively. Complementation test showed that the transformed cells accumulated more metals in the cells, but their growth status was improved. To confirm the functional role, two mutant oshipp42 lines defective in OsHIPP42 expression were identified under metal stress. Under normal condition, no difference of growth between the oshipp42 mutant and wild-type plants was observed. Upon excess Cu, Zn, Cd and Mn, the oshipp42 lines grew weaker than the wild-type. Our work provided a novel source of heavy metal-binding genes in rice that can be potentially used to develop engineered plants for phytoremediation in heavy metal-contaminated soils.
Collapse
Affiliation(s)
- Irfan Ullah Khan
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Justice Kipkoir Rono
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Bai Qing Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xue Song Liu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Meng Qi Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Lei Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xue Chun Wu
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Chen
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Wei Cao
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi Min Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
32
|
Kuchay S, Wang H, Marzio A, Jain K, Homer H, Fehrenbacher N, Philips MR, Zheng N, Pagano M. GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase. Nat Struct Mol Biol 2019; 26:628-636. [PMID: 31209342 PMCID: PMC6609460 DOI: 10.1038/s41594-019-0249-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022]
Abstract
Protein prenylation is believed to be catalyzed by three heterodimeric enzymes: FTase, GGTase1 and GGTase2. Here we report the identification of a previously unknown human prenyltransferase complex consisting of an orphan prenyltransferase α-subunit, PTAR1, and the catalytic β-subunit of GGTase2, RabGGTB. This enzyme, which we named GGTase3, geranylgeranylates FBXL2 to allow its localization at cell membranes, where this ubiquitin ligase mediates the polyubiquitylation of membrane-anchored proteins. In cells, FBXL2 is specifically recognized by GGTase3 despite having a typical carboxy-terminal CaaX prenylation motif that is predicted to be recognized by GGTase1. Our crystal structure analysis of the full-length GGTase3-FBXL2-SKP1 complex reveals an extensive multivalent interface specifically formed between the leucine-rich repeat domain of FBXL2 and PTAR1, which unmasks the structural basis of the substrate-enzyme specificity. By uncovering a missing prenyltransferase and its unique mode of substrate recognition, our findings call for a revision of the 'prenylation code'.
Collapse
Affiliation(s)
- Shafi Kuchay
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hui Wang
- Department of Pharmacology, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Antonio Marzio
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Kunj Jain
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Harrison Homer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Nicole Fehrenbacher
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Mark R Philips
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
- Perlmutter NYU Cancer Center, New York University School of Medicine, New York, NY, USA.
| |
Collapse
|
33
|
Fisch D, Bando H, Clough B, Hornung V, Yamamoto M, Shenoy AR, Frickel E. Human GBP1 is a microbe-specific gatekeeper of macrophage apoptosis and pyroptosis. EMBO J 2019; 38:e100926. [PMID: 31268602 PMCID: PMC6600649 DOI: 10.15252/embj.2018100926] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/31/2022] Open
Abstract
The guanylate binding protein (GBP) family of interferon-inducible GTPases promotes antimicrobial immunity and cell death. During bacterial infection, multiple mouse Gbps, human GBP2, and GBP5 support the activation of caspase-1-containing inflammasome complexes or caspase-4 which trigger pyroptosis. Whether GBPs regulate other forms of cell death is not known. The apicomplexan parasite Toxoplasma gondii causes macrophage death through unidentified mechanisms. Here we report that Toxoplasma-induced death of human macrophages requires GBP1 and its ability to target Toxoplasma parasitophorous vacuoles through its GTPase activity and prenylation. Mechanistically, GBP1 promoted Toxoplasma detection by AIM2, which induced GSDMD-independent, ASC-, and caspase-8-dependent apoptosis. Identical molecular determinants targeted GBP1 to Salmonella-containing vacuoles. GBP1 facilitated caspase-4 recruitment to Salmonella leading to its enhanced activation and pyroptosis. Notably, GBP1 could be bypassed by the delivery of Toxoplasma DNA or bacterial LPS into the cytosol, pointing to its role in liberating microbial molecules. GBP1 thus acts as a gatekeeper of cell death pathways, which respond specifically to infecting microbes. Our findings expand the immune roles of human GBPs in regulating not only pyroptosis, but also apoptosis.
Collapse
Affiliation(s)
- Daniel Fisch
- Host‐Toxoplasma Interaction LaboratoryThe Francis Crick InstituteLondonUK
- MRC Centre for Molecular Bacteriology & InfectionImperial CollegeLondonUK
| | - Hironori Bando
- Department of ImmunoparasitologyResearch Institute for Microbial DiseasesOsaka UniversityOsakaJapan
- Laboratory of ImmunoparasitologyWPI Immunology Frontier Research CenterOsaka UniversityOsakaJapan
| | - Barbara Clough
- Host‐Toxoplasma Interaction LaboratoryThe Francis Crick InstituteLondonUK
| | - Veit Hornung
- Gene Center and Department of Biochemistry & Center for Integrated Protein Science (CIPSM)Ludwig‐Maximilians‐Universität MünchenMunichGermany
| | - Masahiro Yamamoto
- Department of ImmunoparasitologyResearch Institute for Microbial DiseasesOsaka UniversityOsakaJapan
- Laboratory of ImmunoparasitologyWPI Immunology Frontier Research CenterOsaka UniversityOsakaJapan
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology & InfectionImperial CollegeLondonUK
- The Francis Crick InstituteLondonUK
| | - Eva‐Maria Frickel
- Host‐Toxoplasma Interaction LaboratoryThe Francis Crick InstituteLondonUK
| |
Collapse
|
34
|
Agamasu C, Ghirlando R, Taylor T, Messing S, Tran TH, Bindu L, Tonelli M, Nissley DV, McCormick F, Stephen AG. KRAS Prenylation Is Required for Bivalent Binding with Calmodulin in a Nucleotide-Independent Manner. Biophys J 2019; 116:1049-1063. [PMID: 30846362 PMCID: PMC6428923 DOI: 10.1016/j.bpj.2019.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/30/2019] [Accepted: 02/04/2019] [Indexed: 12/11/2022] Open
Abstract
Deregulation of KRAS4b signaling pathway has been implicated in 30% of all cancers. Membrane localization of KRAS4b is an essential step for the initiation of the downstream signaling cascades that guide various cellular mechanisms. KRAS4b plasma membrane (PM) binding is mediated by the insertion of a prenylated moiety that is attached to the terminal carboxy-methylated cysteine, in addition to electrostatic interactions of its positively charged hypervariable region with anionic lipids. Calmodulin (CaM) has been suggested to selectively bind KRAS4b to act as a negative regulator of the RAS/mitogen-activated protein kinase (MAPK) signaling pathway by displacing KRAS4b from the membrane. However, the mechanism by which CaM can recognize and displace KRAS4b from the membrane is not well understood. In this study, we employed biophysical and structural techniques to characterize this mechanism in detail. We show that KRAS4b prenylation is required for binding to CaM and that the hydrophobic pockets of CaM can accommodate the prenylated region of KRAS4b, which might represent a novel CaM-binding motif. Remarkably, prenylated KRAS4b forms a 2:1 stoichiometric complex with CaM in a nucleotide-independent manner. The interaction between prenylated KRAS4b and CaM is enthalpically driven, and electrostatic interactions also contribute to the formation of the complex. The prenylated KRAS4b terminal KSKTKC-farnesylation and carboxy-methylation is sufficient for binding and defines the minimal CaM-binding motif. This is the same region implicated in membrane and phosphodiesterase6-δ binding. Finally, we provide a structure-based docking model by which CaM binds to prenylated KRAS4b. Our data provide new insights into the KRAS4b-CaM interaction and suggest a possible mechanism whereby CaM can regulate KRAS4b membrane localization.
Collapse
Affiliation(s)
- Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Lakshman Bindu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Marco Tonelli
- National Magnetic Resource Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Frank McCormick
- Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland.
| |
Collapse
|
35
|
Shang XY, Chen JJ, Song XY, Wang W, Chen Y, Yao GD, Song SJ. Daphnegiravone D from Daphne giraldii Nitsche induces p38-dependent apoptosis via oxidative and nitrosative stress in hepatocellular carcinoma cells. Biomed Pharmacother 2018; 107:1426-1433. [PMID: 30257359 DOI: 10.1016/j.biopha.2018.08.141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/14/2018] [Accepted: 08/25/2018] [Indexed: 01/27/2023] Open
Abstract
Daphnegiravone D (DGD), a prenylated flavonoid from Daphne giraldii Nitsche, significantly inhibited cell growth of several cancer cell lines without cytotoxicity on human normal cells. Our previous study showed that DGD could induce apoptosis in hepatocellular carcinoma Hep3B and HepG2 cells, but the detailed mechanism was still unclear. The present study provides that DGD-induced oxidative and nitrosative stress contribute to apoptotic cell death in Hep3B and HepG2 cells. Furthermore, there is a positive loop between oxidative stress and p38 activation, similar result is observed between nitrosative stress and p38. N-Acetylcysteine (NAC), a reactive oxygen species scavenger, could relieve DGD-induced oxidative stress, but exerts little effect on nitrosative stress. In addition, carboxy-PTIO (PTIO, a well-known scavenger of reactive nitrogen species) down-regulates the induction of nitrosative stress without obvious effect on oxidative stress in DGD-treated cells. In conclusion, the induction of oxidative and nitrosative stress could enhance p38-mediated apoptosis in DGD-treated Hep3B and HepG2 cells. Moreover, we speculated that OS and NS could not ultimately affect each other in DGD-treated HCC cells. This study gives a new insight on the mechanism of DGD-induced apoptotic cell death via oxidative and nitrosative stress in HCC cells.
Collapse
Affiliation(s)
- Xin-Yue Shang
- School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Jing-Jie Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Xiao-Yu Song
- School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Wei Wang
- School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Yao Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China
| | - Guo-Dong Yao
- School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| | - Shao-Jiang Song
- School of Traditional Chinese Materia Medica, Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, People's Republic of China.
| |
Collapse
|
36
|
Kulakowski G, Bousquet H, Manneville J, Bassereau P, Goud B, Oesterlin LK. Lipid packing defects and membrane charge control RAB GTPase recruitment. Traffic 2018; 19:536-545. [PMID: 29573133 PMCID: PMC6032855 DOI: 10.1111/tra.12568] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/21/2022]
Abstract
Specific intracellular localization of RAB GTPases has been reported to be dependent on protein factors, but the contribution of the membrane physicochemical properties to this process has been poorly described. Here, we show that three RAB proteins (RAB1/RAB5/RAB6) preferentially bind in vitro to disordered and curved membranes, and that this feature is uniquely dependent on their prenyl group. Our results imply that the addition of a prenyl group confers to RAB proteins, and most probably also to other prenylated proteins, the ability to sense lipid packing defects induced by unsaturated conical-shaped lipids and curvature. Consistently, RAB recruitment increases with the amount of lipid packing defects, further indicating that these defects drive RAB membrane targeting. Membrane binding of RAB35 is also modulated by lipid packing defects but primarily dependent on negatively charged lipids. Our results suggest that a balance between hydrophobic insertion of the prenyl group into lipid packing defects and electrostatic interactions of the RAB C-terminal region with charged membranes tunes the specific intracellular localization of RAB proteins.
Collapse
Affiliation(s)
- Guillaume Kulakowski
- Institut CurieParis Sciences et Lettres Research University, Sorbonne Université, CNRS UMR144ParisFrance
| | - Hugo Bousquet
- Institut CurieParis Sciences et Lettres Research University, Sorbonne Université, CNRS UMR144ParisFrance
| | - Jean‐Baptiste Manneville
- Institut CurieParis Sciences et Lettres Research University, Sorbonne Université, CNRS UMR144ParisFrance
| | - Patricia Bassereau
- Laboratoire Physico Chimie, Institut CurieParis Sciences et Lettres Research University, Sorbonne Université, CNRS UMR168ParisFrance
| | - Bruno Goud
- Institut CurieParis Sciences et Lettres Research University, Sorbonne Université, CNRS UMR144ParisFrance
| | - Lena K. Oesterlin
- Institut CurieParis Sciences et Lettres Research University, Sorbonne Université, CNRS UMR144ParisFrance
| |
Collapse
|
37
|
Procter L, Grose C, Esposito D. Production of authentic geranylgeranylated KRAS4b using an engineered baculovirus system. Protein Expr Purif 2018; 151:99-105. [PMID: 29936133 DOI: 10.1016/j.pep.2018.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022]
Abstract
Protein prenylation is a vital eukaryotic post-translational modification which permits interaction of proteins with cellular membranes. Prenylated proteins are involved in a number of human diseases, and play a major role in cancers driven by the oncogene KRAS, which is normally farnesylated. In cases where the farnesylation machinery is inhibited, however, KRAS eludes inactivation by using an alternative prenylation pathway in which the protein is geranylgeranylated. In order to study this alternative prenylation, large quantities of accurately processed protein are required. We have developed a system to permit high-yield production of geranylgeranylated KRAS which utilizes an engineered baculovirus system. The development of this system helped to elucidate a potential metabolic bottleneck in insect cell production that should enable better production of any geranylgeranylated proteins using this system.
Collapse
Affiliation(s)
- Lauren Procter
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD, 21702, USA
| | - Carissa Grose
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD, 21702, USA
| | - Dominic Esposito
- Protein Expression Laboratory, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. PO Box B, Frederick, MD, 21702, USA.
| |
Collapse
|
38
|
Jeong A, Suazo KF, Wood WG, Distefano MD, Li L. Isoprenoids and protein prenylation: implications in the pathogenesis and therapeutic intervention of Alzheimer's disease. Crit Rev Biochem Mol Biol 2018; 53:279-310. [PMID: 29718780 PMCID: PMC6101676 DOI: 10.1080/10409238.2018.1458070] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mevalonate-isoprenoid-cholesterol biosynthesis pathway plays a key role in human health and disease. The importance of this pathway is underscored by the discovery that two major isoprenoids, farnesyl and geranylgeranyl pyrophosphate, are required to modify an array of proteins through a process known as protein prenylation, catalyzed by prenyltransferases. The lipophilic prenyl group facilitates the anchoring of proteins in cell membranes, mediating protein-protein interactions and signal transduction. Numerous essential intracellular proteins undergo prenylation, including most members of the small GTPase superfamily as well as heterotrimeric G proteins and nuclear lamins, and are involved in regulating a plethora of cellular processes and functions. Dysregulation of isoprenoids and protein prenylation is implicated in various disorders, including cardiovascular and cerebrovascular diseases, cancers, bone diseases, infectious diseases, progeria, and neurodegenerative diseases including Alzheimer's disease (AD). Therefore, isoprenoids and/or prenyltransferases have emerged as attractive targets for developing therapeutic agents. Here, we provide a general overview of isoprenoid synthesis, the process of protein prenylation and the complexity of prenylated proteins, and pharmacological agents that regulate isoprenoids and protein prenylation. Recent findings that connect isoprenoids/protein prenylation with AD are summarized and potential applications of new prenylomic technologies for uncovering the role of prenylated proteins in the pathogenesis of AD are discussed.
Collapse
Affiliation(s)
- Angela Jeong
- Departments of Experimental and Clinical Pharmacolog,University of Minnesota, Minneapolis, MN 55455
| | | | - W. Gibson Wood
- Departments of Pharmacology, University of Minnesota, Minneapolis, MN 55455
| | - Mark D. Distefano
- Departments of Chemistry,University of Minnesota, Minneapolis, MN 55455
| | - Ling Li
- Departments of Experimental and Clinical Pharmacolog,University of Minnesota, Minneapolis, MN 55455
- Departments of Pharmacology, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
39
|
Pelleieux S, Picard C, Lamarre-Théroux L, Dea D, Leduc V, Tsantrizos YS, Poirier J. Isoprenoids and tau pathology in sporadic Alzheimer's disease. Neurobiol Aging 2018; 65:132-139. [PMID: 29476987 DOI: 10.1016/j.neurobiolaging.2018.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/07/2017] [Accepted: 01/21/2018] [Indexed: 12/12/2022]
Abstract
The mevalonate pathway has been described to play a key role in Alzheimer's disease (AD) physiopathology. Farnesyl pyrophosphate (FPP) and geranylgeranyl pyrophosphate (GGPP) are nonsterol isoprenoids derived from mevalonate, which serve as precursors to numerous human metabolites. They facilitate protein prenylation; hFPP and hGGPP synthases act as gateway enzymes to the prenylation of the small guanosine triphosphate (GTP)ase proteins such as RhoA and cdc42 that have been shown to facilitate phospho-tau (p-Tau, i.e., protein tau phosphorylated) production in the brain. In this study, a significant positive correlation was observed between the synthases mRNA prevalence and disease status (FPPS, p < 0.001, n = 123; GGPPS, p < 0.001, n = 122). The levels of mRNA for hFPPS and hGGPPS were found to significantly correlate with the amount of p-Tau protein levels (p < 0.05, n = 34) and neurofibrillary tangle density (p < 0.05, n = 39) in the frontal cortex. Interestingly, high levels of hFPPS and hGGPPS mRNA prevalence are associated with earlier age of onset in AD (p < 0.05, n = 58). Together, these results suggest that accumulation of p-Tau in the AD brain is related, at least in part, to increased levels of neuronal isoprenoids.
Collapse
Affiliation(s)
- Sandra Pelleieux
- Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Cynthia Picard
- Douglas Mental Health University Institute, McGill University, Montreal, Canada; Center for Studies on the Prevention of Alzheimer's Disease, McGill University, Montreal, Canada
| | | | - Doris Dea
- Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Valérie Leduc
- Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Youla S Tsantrizos
- Department of Chemistry, McGill University, Montreal, Canada; Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Judes Poirier
- Douglas Mental Health University Institute, McGill University, Montreal, Canada; Center for Studies on the Prevention of Alzheimer's Disease, McGill University, Montreal, Canada.
| |
Collapse
|
40
|
Abstract
Glucose-stimulated insulin secretion (GSIS) involves interplay between metabolic and cationic events. Seminal contributions from multiple laboratories affirm essential roles for small G-proteins (Rac1, Cdc42, Arf6, Rab27A) in GSIS. Activation of these signalling proteins promotes cytoskeletal remodeling, transport and docking of insulin granules on the plasma membrane for exocytotic secretion of insulin. Evidence in rodent and human islets suggests key roles for lipidation (farnesylation and geranylgeranylation) of these G-proteins for their targeting to appropriate cellular compartments for optimal regulation of effectors leading to GSIS. Interestingly, however, inhibition of prenylation appears to cause mislocalization of non-prenylated, but (paradoxically) activated G-proteins, in "inappropriate" compartments leading to activation of stress kinases and onset of mitochondrial defects, loss in GSIS and apoptosis of the islet β-cell. This review highlights our current understanding of roles of G-proteins and their post-translational lipidation (prenylation) signalling networks in islet function in normal health, metabolic stress (glucolipotoxicity and ER stress) and diabetes. Critical knowledge gaps that need to be addressed for the development of therapeutics to halt defects in these signalling steps in β-cells in models of impaired insulin secretion and diabetes are also highlighted and discussed.
Collapse
Affiliation(s)
- Anjaneyulu Kowluru
- β-Cell Biochemistry Laboratory, John D. Dingell VA Medical Center, and Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan
| |
Collapse
|
41
|
Shimizu H, Toma-Fukai S, Saijo S, Shimizu N, Kontani K, Katada T, Shimizu T. Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding. J Biol Chem 2017; 292:13441-13448. [PMID: 28630045 PMCID: PMC5555202 DOI: 10.1074/jbc.m117.792556] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/14/2017] [Indexed: 01/15/2023] Open
Abstract
Small GTPases are molecular switches that have critical biological roles and are controlled by GTPase-activating proteins and guanine nucleotide exchange factors (GEFs). The smg GDP dissociation stimulator (SmgGDS) protein functions as a GEF for the RhoA and RhoC small GTPases. SmgGDS has various regulatory roles, including small GTPase trafficking and localization and as a molecular chaperone, and interacts with many small GTPases possessing polybasic regions. Two SmgGDS splice variants, SmgGDS-558 and SmgGDS-607, differ in GEF activity and binding affinity for RhoA depending on the lipidation state, but the reasons for these differences are unclear. Here we determined the crystal structure of SmgGDS-558, revealing a fold containing tandem copies of armadillo repeats not present in other GEFs. We also observed that SmgGDS harbors distinct positively and negatively charged regions, both of which play critical roles in binding to RhoA and GEF activity. This is the first report demonstrating a relationship between the molecular function and atomic structure of SmgGDS. Our findings indicate that the two SmgGDS isoforms differ in GTPase binding and GEF activity, depending on the lipidation state, thus providing useful information about the cellular functions of SmgGDS in cells.
Collapse
Affiliation(s)
- Hikaru Shimizu
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sachiko Toma-Fukai
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinya Saijo
- the Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan, and
| | - Nobutaka Shimizu
- the Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan, and
| | - Kenji Kontani
- the Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose-shi, Tokyo 204-8588, Japan
| | - Toshiaki Katada
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiyuki Shimizu
- From the Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan,
| |
Collapse
|
42
|
Abstract
Small monomeric GTPases, including those belonging to the Rho family, regulate a diverse array of intracellular signaling pathways which affect vesicle transport/trafficking, endocytosis, cell cycle progression, cell contractility, and formation of stress fibers or focal adhesions. Functional activation of newly synthesized small monomeric GTPases is facilitated by a multistep post-translational process involving transferase-catalyzed addition of farnesyl or geranylgeranyl isoprenoids to conserved cysteine residues within a unique carboxy terminal CaaX motif. Here, using well-established and widely available contemporary methodologies, detailed protocols by which to semi-quantitatively evaluate the functional consequence of post-translational isoprenylation in human trabecular meshwork cells are described. We introduce the concept that isoprenylation alone is itself a key regulator of mammalian Rho GTPase expression and turnover.
Collapse
Affiliation(s)
- Evan B Stubbs
- Research Service, Department of Veterans Affairs, Edward Hines Jr. VA Hospital, Hines, IL, 60141, USA.
- Department of Ophthalmology, Stritch School of Medicine, Loyola University Chicago, 2160 South First Ave., LUH-North Entrance, Suite 2601, Maywood, IL, 60153, USA.
| |
Collapse
|
43
|
Gopalakrishna KN, Boyd K, Artemyev NO. Mechanisms of mutant PDE6 proteins underlying retinal diseases. Cell Signal 2017; 37:74-80. [PMID: 28583373 DOI: 10.1016/j.cellsig.2017.06.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
Mutations in PDE6 genes encoding the effector enzymes in rods and cones underlie severe retinal diseases including retinitis pigmentosa (RP), autosomal dominant congenital stationary night blindness (adCSNB), and achromatopsia (ACHM). Here we examined a spectrum of pathogenic missense mutations in PDE6 using the system based on co-expression of cone PDE6C with its specialized chaperone AIPL1 and the regulatory Pγ subunit as a potent co-chaperone. We uncovered two mechanisms of PDE6C mutations underlying ACHM: (a) folding defects leading to expression of catalytically inactive proteins and (b) markedly diminished ability of Pγ to co-chaperone mutant PDE6C proteins thereby dramatically reducing the levels of functional enzyme. The mechanism of the Rambusch adCSNB associated with the H258N substitution in PDE6B was probed through the analysis of the model mutant PDE6C-H262N. We identified two interrelated deficits of PDE6C-H262N: disruption of the inhibitory interaction of Pγ with mutant PDE6C that markedly reduced the ability of Pγ to augment the enzyme folding. Thus, we conclude that the Rambusch adCSNB is triggered by low levels of the constitutively active PDE6. Finally, we examined PDE6C-L858V, which models PDE6B-L854V, an RP-linked mutation that alters the protein isoprenyl modification. This analysis suggests that the type of prenyl modifications does not impact the folding of PDE6, but it modulates the enzyme affinity for its trafficking partner PDE6D. Hence, the pathogenicity of PDE6B-L854V likely arises from its trafficking deficiency. Taken together, our results demonstrate the effectiveness of the PDE6C expression system to evaluate pathogenicity and elucidate the mechanisms of PDE6 mutations in retinal diseases.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Color Vision Defects/genetics
- Color Vision Defects/metabolism
- Cyclic Nucleotide Phosphodiesterases, Type 6/analysis
- Cyclic Nucleotide Phosphodiesterases, Type 6/genetics
- Cyclic Nucleotide Phosphodiesterases, Type 6/metabolism
- Eye Diseases, Hereditary/genetics
- Eye Diseases, Hereditary/metabolism
- Eye Proteins/analysis
- Eye Proteins/genetics
- Eye Proteins/metabolism
- Gene Expression
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/metabolism
- HEK293 Cells
- Humans
- Mice
- Models, Molecular
- Mutation, Missense
- Myopia/genetics
- Myopia/metabolism
- Night Blindness/genetics
- Night Blindness/metabolism
- Protein Folding
- Protein Prenylation
- Retinal Diseases/genetics
- Retinal Diseases/metabolism
Collapse
Affiliation(s)
- Kota N Gopalakrishna
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Kimberly Boyd
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, United States.
| |
Collapse
|
44
|
Mehmood S, Marcoux J, Gault J, Quigley A, Michaelis S, Young SG, Carpenter EP, Robinson CV. Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24. Nat Chem 2016; 8:1152-1158. [PMID: 27874871 PMCID: PMC5123592 DOI: 10.1038/nchem.2591] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 07/05/2016] [Indexed: 12/25/2022]
Abstract
Off-target binding of hydrophobic drugs can lead to unwanted side effects, either through specific or non-specific binding to unintended membrane protein targets. However, distinguishing the binding of drugs to membrane proteins from that of detergents, lipids and cofactors is challenging. Here, we use high-resolution mass spectrometry to study the effects of HIV protease inhibitors on the human zinc metalloprotease ZMPSTE24. This intramembrane protease plays a major role in converting prelamin A to mature lamin A. We monitored the proteolysis of farnesylated prelamin A peptide by ZMPSTE24 and unexpectedly found retention of the C-terminal peptide product with the enzyme. We also resolved binding of zinc, lipids and HIV protease inhibitors and showed that drug binding blocked prelamin A peptide cleavage and conferred stability to ZMPSTE24. Our results not only have relevance for the progeria-like side effects of certain HIV protease inhibitor drugs, but also highlight new approaches for documenting off-target drug binding.
Collapse
Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Julien Marcoux
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Andrew Quigley
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Stephen G Young
- Departments of Medicine and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| |
Collapse
|
45
|
Fansa EK, Kösling SK, Zent E, Wittinghofer A, Ismail S. PDE6δ-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity. Nat Commun 2016; 7:11366. [PMID: 27063844 PMCID: PMC5512577 DOI: 10.1038/ncomms11366] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 03/18/2016] [Indexed: 01/06/2023] Open
Abstract
The phosphodiesterase 6 delta subunit (PDE6δ) shuttles several farnesylated cargos between membranes. The cargo sorting mechanism between cilia and other compartments is not understood. Here we show using the inositol polyphosphate 5'-phosphatase E (INPP5E) and the GTP-binding protein (Rheb) that cargo sorting depends on the affinity towards PDE6δ and the specificity of cargo release. High-affinity cargo is exclusively released by the ciliary transport regulator Arl3, while low-affinity cargo is released by Arl3 and its non-ciliary homologue Arl2. Structures of PDE6δ/cargo complexes reveal the molecular basis of the sorting signal which depends on the residues at the -1 and -3 positions relative to farnesylated cysteine. Structure-guided mutation allows the generation of a low-affinity INPP5E mutant which loses exclusive ciliary localization. We postulate that the affinity to PDE6δ and the release by Arl2/3 in addition to a retention signal are the determinants for cargo sorting and enrichment at its destination.
Collapse
Affiliation(s)
- Eyad Kalawy Fansa
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | | | - Eldar Zent
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Alfred Wittinghofer
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Shehab Ismail
- CR-UK Beatson Institute, Garscube Estate Switchback Road, Glasgow G61 1BD, UK
| |
Collapse
|
46
|
Jennings BC, Danowitz AM, Wang YC, Gibbs RA, Distefano MD, Fierke CA. Analogs of farnesyl diphosphate alter CaaX substrate specificity and reactions rates of protein farnesyltransferase. Bioorg Med Chem Lett 2016; 26:1333-6. [PMID: 26803203 PMCID: PMC4747817 DOI: 10.1016/j.bmcl.2015.12.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 12/18/2015] [Accepted: 12/22/2015] [Indexed: 11/26/2022]
Abstract
Attempts to identify the prenyl-proteome of cells or changes in prenylation following drug treatment have used 'clickable' alkyne-modified analogs of the lipid substrates farnesyl- and geranylgeranyl-diphosphate (FPP and GGPP). We characterized the reactivity of four alkyne-containing analogs of FPP with purified protein farnesyltransferase and a small library of dansylated peptides using an in vitro continuous spectrofluorimetric assay. These analogs alter prenylation specificity and reactivity suggesting that in vivo results obtained using these FPP analogs should be interpreted cautiously.
Collapse
Affiliation(s)
| | - Amy M Danowitz
- Department of Chemistry and Biochemistry, Mercyhurst University, Erie, PA 16546, USA
| | - Yen-Chih Wang
- Department of Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Richard A Gibbs
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA
| | - Mark D Distefano
- Department of Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
47
|
Wang YC, Distefano MD. Synthetic isoprenoid analogues for the study of prenylated proteins: Fluorescent imaging and proteomic applications. Bioorg Chem 2016; 64:59-65. [PMID: 26709869 PMCID: PMC4731301 DOI: 10.1016/j.bioorg.2015.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/01/2015] [Accepted: 12/10/2015] [Indexed: 01/09/2023]
Abstract
Protein prenylation is a posttranslational modification catalyzed by prenyltransferases involving the attachment of farnesyl or geranylgeranyl groups to residues near the C-termini of proteins. This irreversible covalent modification is important for membrane localization and proper signal transduction. Here, the use of isoprenoid analogues for studying prenylated proteins is reviewed. First, experiments with analogues containing small fluorophores that are alternative substrates for prenyltransferases are described. Those analogues have been useful for quantifying binding affinity and for the production of fluorescently labeled proteins. Next, the use of analogues that incorporate biotin, bioorthogonal groups or antigenic moieties is described. Such probes have been particularly useful for identifying proteins that are naturally prenylated within mammalian cells. Overall, the use of isoprenoid analogues has contributed significantly to the understanding of protein prenlation.
Collapse
Affiliation(s)
- Yen-Chih Wang
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark D Distefano
- Departments of Chemistry and Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| |
Collapse
|
48
|
Abstract
Today, Fmoc SPPS is the method of choice for peptide synthesis. Very-high-quality Fmoc building blocks are available at low cost because of the economies of scale arising from current multiton production of therapeutic peptides by Fmoc SPPS. Many modified derivatives are commercially available as Fmoc building blocks, making synthetic access to a broad range of peptide derivatives straightforward. The number of synthetic peptides entering clinical trials has grown continuously over the last decade, and recent advances in the Fmoc SPPS technology are a response to the growing demand from medicinal chemistry and pharmacology. Improvements are being continually reported for peptide quality, synthesis time and novel synthetic targets. Topical peptide research has contributed to a continuous improvement and expansion of Fmoc SPPS applications.
Collapse
Affiliation(s)
- Raymond Behrendt
- Novabiochem, Merck & CieIm Laternenacker 58200SchaffhausenSwitzerland
| | - Peter White
- Novabiochem, Merck Chemicals LtdPadge RoadBeestonNG9 2JRUK
| | - John Offer
- The Francis Crick Institute215 Euston RoadLondonNW1 2BEUK
| |
Collapse
|
49
|
Dutilleul C, Ribeiro I, Blanc N, Nezames CD, Deng XW, Zglobicki P, Palacio Barrera AM, Atehortùa L, Courtois M, Labas V, Giglioli-Guivarc'h N, Ducos E. ASG2 is a farnesylated DWD protein that acts as ABA negative regulator in Arabidopsis. Plant Cell Environ 2016; 39:185-98. [PMID: 26147561 DOI: 10.1111/pce.12605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 05/12/2023]
Abstract
The tagging-via-substrate approach designed for the capture of mammal prenylated proteins was adapted to Arabidopsis cell culture. In this way, proteins are in vivo tagged with an azide-modified farnesyl moiety and captured thanks to biotin alkyne Click-iT® chemistry with further streptavidin-affinity chromatography. Mass spectrometry analyses identified four small GTPases and ASG2 (ALTERED SEED GERMINATION 2), a protein previously associated to the seed germination gene network. ASG2 is a conserved protein in plants and displays a unique feature that associates WD40 domains and tetratricopeptide repeats. Additionally, we show that ASG2 has a C-terminal CaaX-box that is farnesylated in vitro. Protoplast transfections using CaaX prenyltransferase mutants show that farnesylation provokes ASG2 nucleus exclusion. Moreover, ASG2 interacts with DDB1 (DAMAGE DNA BINDING protein 1), and the subcellular localization of this complex depends on ASG2 farnesylation status. Finally, germination and root elongation experiments reveal that asg2 and the farnesyltransferase mutant era1 (ENHANCED RESPONSE TO ABSCISIC ACID (ABA) 1) behave in similar manners when exposed to ABA or salt stress. To our knowledge, ASG2 is the first farnesylated DWD (DDB1 binding WD40) protein related to ABA response in Arabidopsis that may be linked to era1 phenotypes.
Collapse
Affiliation(s)
- Christelle Dutilleul
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Iliana Ribeiro
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Nathalie Blanc
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Cynthia D Nezames
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Xing Wang Deng
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520-8104, USA
| | - Piotr Zglobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Ana María Palacio Barrera
- Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia
| | - Lucia Atehortùa
- Universidad de Antioquia, Laboratorio de Biotecnología, Sede de Investigación Universitaria, Medellín, Colombia
| | - Martine Courtois
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Valérie Labas
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, UMR CNRS 7247, UFR, IFC, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, Nouzilly, F-37380, France
| | - Nathalie Giglioli-Guivarc'h
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| | - Eric Ducos
- EA2106 'Biomolécules et Biotechnologies Végétales', UFR des Sciences et Techniques, Université François Rabelais de Tours, Tours, F-37200, France
| |
Collapse
|
50
|
Zhang Y, Blanden MJ, Sudheer C, Gangopadhyay SA, Rashidian M, Hougland JL, Distefano MD. Simultaneous Site-Specific Dual Protein Labeling Using Protein Prenyltransferases. Bioconjug Chem 2015; 26:2542-53. [PMID: 26561785 PMCID: PMC4769283 DOI: 10.1021/acs.bioconjchem.5b00553] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Site-specific protein labeling is an important technique in protein chemistry and is used for diverse applications ranging from creating protein conjugates to protein immobilization. Enzymatic reactions, including protein prenylation, have been widely exploited as methods to accomplish site-specific labeling. Enzymatic prenylation is catalyzed by prenyltransferases, including protein farnesyltransferase (PFTase) and geranylgeranyltransferase type I (GGTase-I), both of which recognize C-terminal CaaX motifs with different specificities and transfer prenyl groups from isoprenoid diphosphates to their respective target proteins. A number of isoprenoid analogues containing bioorthogonal functional groups have been used to label proteins of interest via PFTase-catalyzed reaction. In this study, we sought to expand the scope of prenyltransferase-mediated protein labeling by exploring the utility of rat GGTase-I (rGGTase-I). First, the isoprenoid specificity of rGGTase-I was evaluated by screening eight different analogues and it was found that those with bulky moieties and longer backbone length were recognized by rGGTase-I more efficiently. Taking advantage of the different substrate specificities of rat PFTase (rPFTase) and rGGTase-I, we then developed a simultaneous dual labeling method to selectively label two different proteins by using isoprenoid analogue and CaaX substrate pairs that were specific to only one of the prenyltransferases. Using two model proteins, green fluorescent protein with a C-terminal CVLL sequence (GFP-CVLL) and red fluorescent protein with a C-terminal CVIA sequence (RFP-CVIA), we demonstrated that when incubated together with both prenyltransferases and the selected isoprenoid analogues, GFP-CVLL was specifically modified with a ketone-functionalized analogue by rGGTase-I and RFP-CVIA was selectively labeled with an alkyne-containing analogue by rPFTase. By switching the ketone-containing analogue to an azide-containing analogue, it was possible to create protein tail-to-tail dimers in a one-pot procedure through the copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction. Overall, with the flexibility of using different isoprenoid analogues, this system greatly extends the utility of protein labeling using prenyltransferases.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Ch. Sudheer
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | | | - Mohammad Rashidian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - James L. Hougland
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| |
Collapse
|