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Auger SA, Venkatachalapathy S, Suazo KFG, Wang Y, Sarkis AW, Bernhagen K, Justyna K, Schaefer JV, Wollack JW, Plückthun A, Li L, Distefano MD. Broadening the Utility of Farnesyltransferase-Catalyzed Protein Labeling Using Norbornene-Tetrazine Click Chemistry. Bioconjug Chem 2024; 35:922-933. [PMID: 38654427 DOI: 10.1021/acs.bioconjchem.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Bioorthogonal chemistry has gained widespread use in the study of many biological systems of interest, including protein prenylation. Prenylation is a post-translational modification, in which one or two 15- or 20-carbon isoprenoid chains are transferred onto cysteine residues near the C-terminus of a target protein. The three main enzymes─protein farnesyltransferase (FTase), geranylgeranyl transferase I (GGTase I), and geranylgeranyl transferase II (GGTase II)─that catalyze this process have been shown to tolerate numerous structural modifications in the isoprenoid substrate. This feature has previously been exploited to transfer an array of farnesyl diphosphate analogues with a range of functionalities, including an alkyne-containing analogue for copper-catalyzed bioconjugation reactions. Reported here is the synthesis of an analogue of the isoprenoid substrate embedded with norbornene functionality (C10NorOPP) that can be used for an array of applications, ranging from metabolic labeling to selective protein modification. The probe was synthesized in seven steps with an overall yield of 7% and underwent an inverse electron demand Diels-Alder (IEDDA) reaction with tetrazine-containing tags, allowing for copper-free labeling of proteins. The use of C10NorOPP for the study of prenylation was explored in the metabolic labeling of prenylated proteins in HeLa, COS-7, and astrocyte cells. Furthermore, in HeLa cells, these modified prenylated proteins were identified and quantified using label-free quantification (LFQ) proteomics with 25 enriched prenylated proteins. Additionally, the unique chemistry of C10NorOPP was utilized for the construction of a multiprotein-polymer conjugate for the targeted labeling of cancer cells. That construct was prepared using a combination of norbornene-tetrazine conjugation and azide-alkyne cycloaddition, highlighting the utility of the additional degree of orthogonality for the facile assembly of new protein conjugates with novel structures and functions.
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Affiliation(s)
- Shelby A Auger
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Sneha Venkatachalapathy
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Kiall Francis G Suazo
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Yiao Wang
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Alexander W Sarkis
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Kaitlyn Bernhagen
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - James W Wollack
- Department of Chemistry and Biochemistry, St. Catherine University, 2004 Randolph Avenue, St. Paul, Minnesota 55105, United States
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich CH-8057, Switzerland
| | - Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota─Twin Cities, 2001 6th Street SE, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota─Twin Cities, 207 Pleasant Street, Minneapolis, Minnesota 55455, United States
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2
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Hildebrandt ER, Hussain SA, Sieburg MA, Ravishankar R, Asad N, Gore S, Ito T, Hougland JL, Dore TM, Schmidt WK. Targeted genetic and small molecule disruption of N-Ras CaaX cleavage alters its localization and oncogenic potential. Bioorg Chem 2024; 147:107316. [PMID: 38583246 PMCID: PMC11098683 DOI: 10.1016/j.bioorg.2024.107316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/16/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024]
Abstract
Ras GTPases and other CaaX proteins undergo multiple post-translational modifications at their carboxyl-terminus. These events initiate with prenylation of a cysteine and are followed by endoproteolytic removal of the 'aaX' tripeptide and carboxylmethylation. Some CaaX proteins are only subject to prenylation, however, due to the presence of an uncleavable sequence. In this study, uncleavable sequences were used to stage Ras isoforms in a farnesylated and uncleaved state to address the impact of CaaX proteolysis on protein localization and function. This targeted strategy is more specific than those that chemically inhibit the Rce1 CaaX protease or delete the RCE1 gene because global abrogation of CaaX proteolysis impacts the entire CaaX protein proteome and effects cannot be attributed to any specific CaaX protein of the many concurrently affected. With this targeted strategy, clear mislocalization and reduced activity of farnesylated and uncleaved Ras isoforms was observed. In addition, new peptidomimetics based on cleavable Ras CaaX sequences and the uncleavable CAHQ sequence were synthesized and tested as Rce1 inhibitors using in vitro and cell-based assays. Consistently, these non-hydrolyzable peptidomimetic Rce1 inhibitors recapitulate Ras mislocalization effects when modeled on cleavable but not uncleavable CaaX sequences. These findings indicate that a prenylated and uncleavable CaaX sequence, which can be easily applied to a wide range of mammalian CaaX proteins, can be used to probe the specific impact of CaaX proteolysis on CaaX protein properties under conditions of an otherwise normally processed CaaX protein proteome.
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Affiliation(s)
- Emily R Hildebrandt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Shaneela A Hussain
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | | | - Rajani Ravishankar
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Nadeem Asad
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | - Sangram Gore
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE
| | - Takahiro Ito
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - James L Hougland
- Department of Chemistry, Syracuse University, Syracuse, NY, USA; Department of Biology, Syracuse University, Syracuse, NY, USA; BioInspired Syracuse, Syracuse University, Syracuse, NY, USA
| | - Timothy M Dore
- New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, UAE; Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Walter K Schmidt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
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3
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Suazo KF, Mishra V, Maity S, Auger SA, Justyna K, Petre AM, Ottoboni L, Ongaro J, Corti SP, Lotti F, Przedborski S, Distefano MD. Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors. Bioorg Chem 2024; 147:107365. [PMID: 38636436 DOI: 10.1016/j.bioorg.2024.107365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Protein prenylation is one example of a broad class of post-translational modifications where proteins are covalently linked to various hydrophobic moieties. To globally identify and monitor levels of all prenylated proteins in a cell simultaneously, our laboratory and others have developed chemical proteomic approaches that rely on the metabolic incorporation of isoprenoid analogues bearing bio-orthogonal functionality followed by enrichment and subsequent quantitative proteomic analysis. Here, several improvements in the synthesis of the alkyne-containing isoprenoid analogue C15AlkOPP are reported to improve synthetic efficiency. Next, metabolic labeling with C15AlkOPP was optimized to obtain useful levels of metabolic incorporation of the probe in several types of primary cells. Those conditions were then used to study the prenylomes of motor neurons (ES-MNs), astrocytes (ES-As), and their embryonic stem cell progenitors (ESCs), which allowed for the identification of 54 prenylated proteins from ESCs, 50 from ES-MNs, and 84 from ES-As, representing all types of prenylation. Bioinformatic analysis revealed specific enriched pathways, including nervous system development, chemokine signaling, Rho GTPase signaling, and adhesion. Hierarchical clustering showed that most enriched pathways in all three cell types are related to GTPase activity and vesicular transport. In contrast, STRING analysis showed significant interactions in two populations that appear to be cell type dependent. The data provided herein demonstrates that robust incorporation of C15AlkOPP can be obtained in ES-MNs and related primary cells purified via magnetic-activated cell sorting allowing the identification and quantification of numerous prenylated proteins. These results suggest that metabolic labeling with C15AlkOPP should be an effective approach for investigating the role of prenylated proteins in primary cells in both normal cells and disease pathologies, including ALS.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Vartika Mishra
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA.
| | - Sanjay Maity
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shelby A Auger
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alexandru M Petre
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Jessica Ongaro
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania P Corti
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA.
| | - Serge Przedborski
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Neuroscience, Pathology, and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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4
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Suazo KF, Mishra V, Maity S, Auger SA, Justyna K, Petre A, Ottoboni L, Ongaro J, Corti SP, Lotti F, Przedborski S, Distefano MD. Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583211. [PMID: 38496415 PMCID: PMC10942399 DOI: 10.1101/2024.03.03.583211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Protein prenylation is one example of a broad class of post-translational modifications where proteins are covalently linked to various hydrophobic moieties. To globally identify and monitor levels of all prenylated proteins in a cell simultaneously, our laboratory and others have developed chemical proteomic approaches that rely on the metabolic incorporation of isoprenoid analogues bearing bio-orthogonal functionality followed by enrichment and subsequent quantitative proteomic analysis. Here, several improvements in the synthesis of the alkyne-containing isoprenoid analogue C15AlkOPP are reported to improve synthetic efficiency. Next, metabolic labeling with C15AlkOPP was optimized to obtain useful levels of metabolic incorporation of the probe in several types of primary cells. Those conditions were then used to study the prenylomes of motor neurons (ES-MNs), astrocytes (ES-As), and their embryonic stem cell progenitors (ESCs), which allowed for the identification of 54 prenylated proteins from ESCs, 50 from ES-MNs and 84 from ES-As, representing all types of prenylation. Bioinformatic analysis revealed specific enriched pathways, including nervous system development, chemokine signaling, Rho GTPase signaling, and adhesion. Hierarchical clustering showed that most enriched pathways in all three cell types are related to GTPase activity and vesicular transport. In contrast, STRING analysis showed significant interactions in two populations that appear to be cell type dependent. The data provided herein demonstrates that robust incorporation of C15AlkOPP can be obtained in ES-MNs and related primary cells purified via magnetic-activated cell sorting allowing the identification and quantification of numerous prenylated proteins. These results suggest that metabolic labeling with C15AlkOPP should be an effective approach for investigating the role of prenylated proteins in primary cells in both normal cells and disease pathologies, including ALS.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Vartika Mishra
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032
| | - Sanjay Maity
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Shelby A Auger
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Alex Petre
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Jessica Ongaro
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania P Corti
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032
| | - Serge Przedborski
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032
- Department of Neuroscience, Pathology, and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN USA 55455
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5
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Suazo KF, Bělíček J, Schey GL, Auger SA, Petre AM, Li L, Błażewska KM, Kopečný D, Distefano MD. Thinking outside the CaaX-box: an unusual reversible prenylation on ALDH9A1. RSC Chem Biol 2023; 4:913-925. [PMID: 37920391 PMCID: PMC10619140 DOI: 10.1039/d3cb00089c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/15/2023] [Indexed: 11/04/2023] Open
Abstract
Protein lipidation is a post-translational modification that confers hydrophobicity on protein substrates to control their cellular localization, mediate protein trafficking, and regulate protein function. In particular, protein prenylation is a C-terminal modification on proteins bearing canonical motifs catalyzed by prenyltransferases. Prenylated proteins have been of interest due to their numerous associations with various diseases. Chemical proteomic approaches have been pursued over the last decade to define prenylated proteomes (prenylome) and probe their responses to perturbations in various cellular systems. Here, we describe the discovery of prenylation of a non-canonical prenylated protein, ALDH9A1, which lacks any apparent prenylation motif. This enzyme was initially identified through chemical proteomic profiling of prenylomes in various cell lines. Metabolic labeling with an isoprenoid probe using overexpressed ALDH9A1 revealed that this enzyme can be prenylated inside cells but does not respond to inhibition by prenyltransferase inhibitors. Site-directed mutagenesis of the key residues involved in ALDH9A1 activity indicates that the catalytic C288 bears the isoprenoid modification likely through an NAD+-dependent mechanism. Furthermore, the isoprenoid modification is also susceptible to hydrolysis, indicating a reversible modification. We hypothesize that this modification originates from endogenous farnesal or geranygeranial, the established degradation products of prenylated proteins and results in a thioester form that accumulates. This novel reversible prenoyl modification on ALDH9A1 expands the current paradigm of protein prenylation by illustrating a potentially new type of protein-lipid modification that may also serve as a novel mechanism for controlling enzyme function.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota Minneapolis MN 55455 USA
| | - Jakub Bělíček
- Department of Experimental Biology, Faculty of Science, Palacký University CZ-78371 Czech Republic
| | - Garrett L Schey
- Department of Medicinal Chemistry, University of Minnesota Minneapolis MN 55455 USA
| | - Shelby A Auger
- Department of Chemistry, University of Minnesota Minneapolis MN 55455 USA
| | - Alexandru M Petre
- Department of Chemistry, University of Minnesota Minneapolis MN 55455 USA
| | - Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota Minneapolis MN 55455 USA
| | - Katarzyna M Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology Łódź Poland
| | - David Kopečný
- Department of Experimental Biology, Faculty of Science, Palacký University CZ-78371 Czech Republic
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota Minneapolis MN 55455 USA
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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] [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.
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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
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Murali M, Murali VP, Joseph MM, Rajan S, Maiti KK. Elucidating cell surface glycan imbalance through SERS guided metabolic glycan labelling: An appraisal of metastatic potential in cancer cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 234:112506. [PMID: 35785648 DOI: 10.1016/j.jphotobiol.2022.112506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/14/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
The intrinsic complexities of cell-surface glycans impede tracking the metabolic changes in cells. By coupling metabolic glycan labelling (MGL) and surface-enhanced Raman scattering (SERS), we employed the MGL-SERS strategy to elucidate the differential glycosylation pattern in cancer cell lines. Herein, for the first time, we are reporting an N-alkyl derivative of glucosamine (GlcNPhAlk) as a glycan labelling precursor. The extent of labelling was assessed by utilizing Raman imaging and verified by complementary fluorescence and Western blot analysis. MGL-SERS technique was implemented for a comparative evaluation of cell surface glycan imbalance in different cancer cells wherein a linear relationship between glycan expression and metastatic potential was established. Further, the effect of sialyltransferase inhibitor, P-3Fax-Neu5Ac, on metabolic labelling of GlcNPhAlk proved the incorporation of GlcNPhAlk to the terminal glycans through the sialic acid biosynthetic pathway. Hence, this methodology unveils the phenomenon of metastatic progression in cancer cells with inherent glycosylation-related dysplasia.
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Affiliation(s)
- Madhukrishnan Murali
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishnu Priya Murali
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India
| | - Manu M Joseph
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India
| | - Soumya Rajan
- Government College, Kasargod 671123, Kerala, India
| | - Kaustabh Kumar Maiti
- Chemical Sciences & Technology Division (CSTD), Organic Chemistry Section, CSIR- National Institute for Interdisciplinary Science & Technology (CSIR-NIIST), Industrial Estate, Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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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] [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.
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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [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.
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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:
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Elsabrouty R, Jo Y, Hwang S, Jun DJ, DeBose-Boyd RA. Type 1 polyisoprenoid diphosphate phosphatase modulates geranylgeranyl-mediated control of HMG CoA reductase and UBIAD1. eLife 2021; 10:64688. [PMID: 34842525 PMCID: PMC8641950 DOI: 10.7554/elife.64688] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 11/28/2021] [Indexed: 11/18/2022] Open
Abstract
UbiA prenyltransferase domain-containing protein-1 (UBIAD1) utilizes geranylgeranyl pyrophosphate (GGpp) to synthesize the vitamin K2 subtype menaquinone-4. The prenyltransferase has emerged as a key regulator of sterol-accelerated, endoplasmic reticulum (ER)-associated degradation (ERAD) of HMG CoA reductase, the rate-limiting enzyme in synthesis of cholesterol and nonsterol isoprenoids including GGpp. Sterols induce binding of UBIAD1 to reductase, inhibiting its ERAD. Geranylgeraniol (GGOH), the alcohol derivative of GGpp, disrupts this binding and thereby stimulates ERAD of reductase and translocation of UBIAD1 to Golgi. We now show that overexpression of Type 1 polyisoprenoid diphosphate phosphatase (PDP1), which dephosphorylates GGpp and other isoprenyl pyrophosphates to corresponding isoprenols, abolishes protein geranylgeranylation as well as GGOH-induced ERAD of reductase and Golgi transport of UBIAD1. Conversely, these reactions are enhanced in the absence of PDP1. Our findings indicate PDP1-mediated hydrolysis of GGpp significantly contributes to a feedback mechanism that maintains optimal intracellular levels of the nonsterol isoprenoid.
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Affiliation(s)
- Rania Elsabrouty
- Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Youngah Jo
- Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Seonghwan Hwang
- Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Dong-Jae Jun
- Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
| | - Russell A DeBose-Boyd
- Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, United States
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11
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 PMCID: PMC8820976 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F. Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
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12
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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] [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.
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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.
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13
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Losada de la Lastra A, Hassan S, Tate EW. Deconvoluting the biology and druggability of protein lipidation using chemical proteomics. Curr Opin Chem Biol 2021; 60:97-112. [PMID: 33221680 DOI: 10.1016/j.cbpa.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 01/13/2023]
Abstract
Lipids are indispensable cellular building blocks, and their post-translational attachment to proteins makes them important regulators of many biological processes. Dysfunction of protein lipidation is also implicated in many pathological states, yet its systematic analysis presents significant challenges. Thanks to innovations in chemical proteomics, lipidation can now be readily studied by metabolic tagging using functionalized lipid analogs, enabling global profiling of lipidated substrates using mass spectrometry. This has spearheaded the first deconvolution of their full scope in a range of contexts, from cells to pathogens and multicellular organisms. Protein N-myristoylation, S-acylation, and S-prenylation are the most well-studied lipid post-translational modifications because of their extensive contribution to the regulation of diverse cellular processes. In this review, we focus on recent advances in the study of these post-translational modifications, with an emphasis on how novel mass spectrometry methods have elucidated their roles in fundamental biological processes.
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Affiliation(s)
- Ana Losada de la Lastra
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Sarah Hassan
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK.
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14
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Juarez D, Fruman DA. Targeting the Mevalonate Pathway in Cancer. Trends Cancer 2021; 7:525-540. [PMID: 33358111 DOI: 10.1016/j.trecan.2020.11.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023]
Abstract
The mevalonate synthesis inhibitors, statins, are mainstay therapeutics for cholesterol management and cardiovascular health. Thirty years of research have uncovered supportive roles for the mevalonate pathway in numerous cellular processes that support oncogenesis, most recently macropinocytosis. Central to the diverse mechanisms of statin sensitivity is an acquired dependence on one mevalonate pathway output, protein geranylgeranylation. New chemical prenylation probes and the discovery of a novel geranylgeranyl transferase hold promise to deepen our understanding of statin mechanisms of action. Further, insights into statin selection and the counterproductive role of dietary geranylgeraniol highlight how we should assess statins in the clinic. Lastly, rational combination strategies preview how statins will enter the oncology toolbox.
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Affiliation(s)
- Dennis Juarez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - David A Fruman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
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15
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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: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [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.
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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.
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16
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Wang X, Zeng X, Lin Q, Li M, Walsh PJ, Chruma JJ. Palladium‐Catalysed Decarboxylative Generation and Regiodivergent Prenylation of 2‐Azaallyl Anions. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900491] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xiaoqian Wang
- Key Laboratory of Green Chemistry & Technology (MOE), College of Chemistry and Sino-British Materials Research Institute, College of Physical Science & Technology Sichuan University No. 29, Wangjiang Road, Chengdu Sichuan 610064 People's Republic of China
| | - Xi Zeng
- Key Laboratory of Green Chemistry & Technology (MOE), College of Chemistry and Sino-British Materials Research Institute, College of Physical Science & Technology Sichuan University No. 29, Wangjiang Road, Chengdu Sichuan 610064 People's Republic of China
| | - Qiao Lin
- Key Laboratory of Green Chemistry & Technology (MOE), College of Chemistry and Sino-British Materials Research Institute, College of Physical Science & Technology Sichuan University No. 29, Wangjiang Road, Chengdu Sichuan 610064 People's Republic of China
| | - Minyan Li
- Roy and Diana Vagelos Laboratories, Penn/Merck Laboratory for High-Throughput Experimentation, Department of Chemistry University of Pennsylvania 231 South 34th Street, Philadelphia Pennsylvania 19104-6323 United States
| | - Patrick J. Walsh
- Roy and Diana Vagelos Laboratories, Penn/Merck Laboratory for High-Throughput Experimentation, Department of Chemistry University of Pennsylvania 231 South 34th Street, Philadelphia Pennsylvania 19104-6323 United States
| | - Jason J. Chruma
- Key Laboratory of Green Chemistry & Technology (MOE), College of Chemistry and Sino-British Materials Research Institute, College of Physical Science & Technology Sichuan University No. 29, Wangjiang Road, Chengdu Sichuan 610064 People's Republic of China
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17
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Storck EM, Morales-Sanfrutos J, Serwa RA, Panyain N, Lanyon-Hogg T, Tolmachova T, Ventimiglia LN, Martin-Serrano J, Seabra MC, Wojciak-Stothard B, Tate EW. Dual chemical probes enable quantitative system-wide analysis of protein prenylation and prenylation dynamics. Nat Chem 2019; 11:552-561. [PMID: 30936521 PMCID: PMC6544531 DOI: 10.1038/s41557-019-0237-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 02/27/2019] [Indexed: 12/14/2022]
Abstract
Post-translational farnesylation or geranylgeranylation at a C-terminal cysteine residue regulates the localization and function of over 100 proteins, including the Ras isoforms, and is a therapeutic target in diseases including cancer and infection. Here, we report global and selective profiling of prenylated proteins in living cells enabled by the development of isoprenoid analogues YnF and YnGG in combination with quantitative chemical proteomics. Eighty prenylated proteins were identified in a single human cell line, 64 for the first time at endogenous abundance without metabolic perturbation. We further demonstrate that YnF and YnGG enable direct identification of post-translationally processed prenylated peptides, proteome-wide quantitative analysis of prenylation dynamics and alternative prenylation in response to four different prenyltransferase inhibitors, and quantification of defective Rab prenylation in a model of the retinal degenerative disease choroideremia.
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Affiliation(s)
- Elisabeth M Storck
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Julia Morales-Sanfrutos
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Remigiusz A Serwa
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Nattawadee Panyain
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Tanya Tolmachova
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Leandro N Ventimiglia
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Juan Martin-Serrano
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Miguel C Seabra
- Molecular Medicine Section, National Heart and Lung Institute, Imperial College London, London, UK
- CEDOC, NOVA Medical School, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Beata Wojciak-Stothard
- Centre for Pharmacology and Therapeutics, Department of Medicine, Imperial College London, London, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK.
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18
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Bader TK, Rappe TM, Veglia G, Distefano MD. Synthesis and NMR Characterization of the Prenylated Peptide, a-Factor. Methods Enzymol 2019; 614:207-238. [PMID: 30611425 DOI: 10.1016/bs.mie.2018.09.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Protein and peptide prenylation is an essential biological process involved in many signal transduction pathways. Hence, it plays a critical role in establishing many major human ailments, including Alzheimer's disease, amyotrophic lateral sclerosis (ALS), malaria, and Ras-related cancers. Yeast mating pheromone a-factor is a small dodecameric peptide that undergoes prenylation and subsequent processing in a manner identical to larger proteins. Due to its small size in addition to its well-characterized behavior in yeast, a-factor is an attractive model system to study the prenylation pathway. Traditionally, chemical synthesis and characterization of a-factor have been challenging, which has limited its use in prenylation studies. In this chapter, a robust method for the synthesis of a-factor is presented along with a description of the characterization of the peptide using MALDI and NMR. Finally, complete assignments of resonances from the isoprenoid moiety and a-factor from COSY, TOCSY, HSQC, and long-range HMBC NMR spectra are presented. This methodology should be useful for the synthesis and characterization of other mature prenylated peptides and proteins.
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Affiliation(s)
- Taysir K Bader
- University of Minnesota, Twin Cities, Minneapolis, MN, United States
| | - Todd M Rappe
- University of Minnesota, Twin Cities, Minneapolis, MN, United States
| | - Gianlugi Veglia
- University of Minnesota, Twin Cities, Minneapolis, MN, United States
| | - Mark D Distefano
- University of Minnesota, Twin Cities, Minneapolis, MN, United States.
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19
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Ahmadi M, Suazo KF, Distefano MD. Optimization of Metabolic Labeling with Alkyne-Containing Isoprenoid Probes. Methods Mol Biol 2019; 2009:35-43. [PMID: 31152393 DOI: 10.1007/978-1-4939-9532-5_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein prenylation, found in eukaryotes, is a posttranslational modification in which one or two isoprenoid groups are added to the C terminus of selected proteins using either a farnesyl group or a geranylgeranyl group. Prenylation facilitates protein localization mainly to the plasma membrane where the prenylated proteins, including small GTPases, mediate signal transduction pathways. Changes in the level of prenylated proteins may serve a critical function in a variety of diseases. Metabolic labeling using modified isoprenoid probes followed by enrichment and proteomic analysis allows the identities and levels of prenylated proteins to be investigated. In this protocol, we illustrate how the conditions for metabolic labeling are optimized to maximize probe incorporation in HeLa cells through a combination of in-gel fluorescence and densitometric analysis.
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Affiliation(s)
- Mina Ahmadi
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
| | | | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
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20
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Suazo KF, Hurben AK, Liu K, Xu F, Thao P, Sudheer C, Li L, Distefano MD. Metabolic Labeling of Prenylated Proteins Using Alkyne-Modified Isoprenoid Analogues. ACTA ACUST UNITED AC 2018; 10:e46. [PMID: 30058775 DOI: 10.1002/cpch.46] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein prenylation involves the attachment of a farnesyl or geranylgeranyl group onto a cysteine residue located near the C-terminus of a protein, recognized via a specific prenylation motif, and results in the formation of a thioether bond. To identify putative prenylated proteins and investigate changes in their levels of expression, metabolic labeling and subsequent bioorthogonal labeling has become one of the methods of choice. In that strategy, synthetic analogues of biosynthetic precursors for post-translational modification bearing bioorthogonal functionality are added to the growth medium from which they enter cells and become incorporated into proteins. Subsequently, the cells are lysed and proteins bearing the analogues are then covalently modified using selective chemical reagents that react via bioorthogonal processes, allowing a variety of probes for visualization or enrichment to be attached for subsequent analysis. Here, we describe protocols for synthesizing several different isoprenoid analogues and describe how they are metabolically incorporated into mammalian cells, and the incorporation into prenylated proteins visualized via in-gel fluorescence analysis. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Alexander K Hurben
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Kevin Liu
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Feng Xu
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Pa Thao
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Ch Sudheer
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
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21
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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: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [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.
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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
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22
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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23
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Pickens CJ, Johnson SN, Pressnall MM, Leon MA, Berkland CJ. Practical Considerations, Challenges, and Limitations of Bioconjugation via Azide-Alkyne Cycloaddition. Bioconjug Chem 2018; 29:686-701. [PMID: 29287474 PMCID: PMC6310217 DOI: 10.1021/acs.bioconjchem.7b00633] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interrogating biological systems is often limited by access to biological probes. The emergence of "click chemistry" has revolutionized bioconjugate chemistry by providing facile reaction conditions amenable to both biologic molecules and small molecule probes such as fluorophores, toxins, or therapeutics. One particularly popular version is the copper-catalyzed azide-alkyne cycloaddition (AAC) reaction, which has spawned new alternatives such as the strain-promoted azide-alkyne cycloaddition reaction, among others. This focused review highlights practical approaches to AAC reactions for the synthesis of peptide or protein bioconjugates and contrasts current challenges and limitations in light of recent advances in the field. The conical success of antibody drug conjugates has expanded the toolbox of linkers and payloads to facilitate practical applications of bioconjugation to create novel therapeutics and biologic probes. The AAC reaction in particular is poised to enable a large set of functionalized molecules as a combinatorial approach to high-throughput bioconjugate generation, screening, and honing of lead compounds.
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Affiliation(s)
- Chad J Pickens
- Department of Pharmaceutical Chemistry , University of Kansas , 2095 Constant Avenue , Lawrence , Kansas 66047 , United States
| | - Stephanie N Johnson
- Department of Pharmaceutical Chemistry , University of Kansas , 2095 Constant Avenue , Lawrence , Kansas 66047 , United States
| | - Melissa M Pressnall
- Department of Pharmaceutical Chemistry , University of Kansas , 2095 Constant Avenue , Lawrence , Kansas 66047 , United States
| | - Martin A Leon
- Department of Chemistry , University of Kansas , 1251 Wescoe Hall Drive , Lawrence , Kansas 66047 , United States
| | - Cory J Berkland
- Department of Pharmaceutical Chemistry , University of Kansas , 2095 Constant Avenue , Lawrence , Kansas 66047 , United States
- Department of Chemistry , University of Kansas , 1251 Wescoe Hall Drive , Lawrence , Kansas 66047 , United States
- Department of Chemical and Petroleum Engineering , University of Kansas , , 4132 Learned Hall, 1530 W. 15th , Lawrence , Kansas 66045 , United States
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24
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Hottman D, Cheng S, Gram A, LeBlanc K, Yuan LL, Li L. Systemic or Forebrain Neuron-Specific Deficiency of Geranylgeranyltransferase-1 Impairs Synaptic Plasticity and Reduces Dendritic Spine Density. Neuroscience 2018; 373:207-217. [PMID: 29406266 DOI: 10.1016/j.neuroscience.2018.01.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 01/03/2018] [Accepted: 01/13/2018] [Indexed: 01/23/2023]
Abstract
Isoprenoids and prenylated proteins regulate a variety of cellular functions, including neurite growth and synaptic plasticity. Importantly, they are implicated in the pathogenesis of several diseases, including Alzheimer's disease (AD). Recently, we have shown that two protein prenyltransferases, farnesyltransferase (FT) and geranylgeranyltransferase-1 (GGT), have differential effects in a mouse model of AD. Haplodeficiency of either FT or GGT attenuates amyloid-β deposition and neuroinflammation but only reduction in FT rescues cognitive function. The current study aimed to elucidate the potential mechanisms that may account for the lack of cognitive benefit in GGT-haplodeficient mice, despite attenuated neuropathology. The results showed that the magnitude of long-term potentiation (LTP) was markedly suppressed in hippocampal slices from GGT-haplodeficient mice. Consistent with the synaptic dysfunction, there was a significant decrease in cortical spine density and cognitive function in GGT-haplodeficient mice. To further study the neuron-specific effects of GGT deficiency, we generated conditional forebrain neuron-specific GGT-knockout (GGTf/fCre+) mice using a Cre/LoxP system under the CAMKIIα promoter. We found that both the magnitude of hippocampal LTP and the dendritic spine density of cortical neurons were decreased in GGTf/fCre+ mice compared with GGTf/fCre- mice. Immunoblot analyses of cerebral lysate showed a significant reduction in cell membrane-associated (geranylgeranylated) Rac1 and RhoA but not (farnesylated) H-Ras, in GGTf/fCre+ mice, suggesting that insufficient geranylgeranylation of the Rho family of small GTPases may underlie the detrimental effects of GGT deficiency. These findings reinforce the critical role of GGT in maintaining spine structure and synaptic/cognitive function in development and in the mature brain.
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Affiliation(s)
- David Hottman
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Shaowu Cheng
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, United States; College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Yuelu District, Changsha, Hunan 410208, China
| | - Andrea Gram
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Kyle LeBlanc
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Li-Lian Yuan
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, United States; Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA 50312, United States
| | - Ling Li
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455, United States; Department of Pharmacology and Graduate Programs in Neuroscience, University of Minnesota, Minneapolis, MN 55455, United States.
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25
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Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
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Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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26
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Blanden MJ, Suazo KF, Hildebrandt ER, Hardgrove DS, Patel M, Saunders WP, Distefano MD, Schmidt WK, Hougland JL. Efficient farnesylation of an extended C-terminal C( x) 3X sequence motif expands the scope of the prenylated proteome. J Biol Chem 2017; 293:2770-2785. [PMID: 29282289 DOI: 10.1074/jbc.m117.805770] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/24/2017] [Indexed: 12/25/2022] Open
Abstract
Protein prenylation is a post-translational modification that has been most commonly associated with enabling protein trafficking to and interaction with cellular membranes. In this process, an isoprenoid group is attached to a cysteine near the C terminus of a substrate protein by protein farnesyltransferase (FTase) or protein geranylgeranyltransferase type I or II (GGTase-I and GGTase-II). FTase and GGTase-I have long been proposed to specifically recognize a four-amino acid CAAX C-terminal sequence within their substrates. Surprisingly, genetic screening reveals that yeast FTase can modify sequences longer than the canonical CAAX sequence, specifically C(x)3X sequences with four amino acids downstream of the cysteine. Biochemical and cell-based studies using both peptide and protein substrates reveal that mammalian FTase orthologs can also prenylate C(x)3X sequences. As the search to identify physiologically relevant C(x)3X proteins begins, this new prenylation motif nearly doubles the number of proteins within the yeast and human proteomes that can be explored as potential FTase substrates. This work expands our understanding of prenylation's impact within the proteome, establishes the biologically relevant reactivity possible with this new motif, and opens new frontiers in determining the impact of non-canonically prenylated proteins on cell function.
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Affiliation(s)
- Melanie J Blanden
- Department of Chemistry, Syracuse University, Syracuse, New York 13244
| | - Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emily R Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Daniel S Hardgrove
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Meet Patel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - William P Saunders
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Walter K Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - James L Hougland
- Department of Chemistry, Syracuse University, Syracuse, New York 13244.
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27
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Sinclair WR, Shrimp JH, Zengeya TT, Kulkarni RA, Garlick JM, Luecke H, Worth AJ, Blair IA, Snyder NW, Meier JL. Bioorthogonal pro-metabolites for profiling short chain fatty acylation. Chem Sci 2017; 9:1236-1241. [PMID: 29675169 PMCID: PMC5885804 DOI: 10.1039/c7sc00247e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 12/07/2017] [Indexed: 12/18/2022] Open
Abstract
A systematically designed panel of biorthogonal pro-metabolites was synthesized and evaluated as agents for tracing cellular short chain fatty acylation.
Short chain fatty acids (SCFAs) play a central role in health and disease. One function of these signaling molecules is to serve as precursors for short chain fatty acylation, a class of metabolically-derived posttranslational modifications (PTMs) that are established by lysine acetyltransferases (KATs) and lysine deacetylases (KDACs). Via this mechanism, short chain fatty acylation serves as an integrated reporter of metabolism as well as KAT and KDAC activity, and has the potential to illuminate the role of these processes in disease. However, few methods to study short chain fatty acylation exist. Here we report a bioorthogonal pro-metabolite strategy for profiling short chain fatty acylation in living cells. Inspired by the dietary component tributyrin, we synthesized a panel of ester-caged bioorthogonal short chain fatty acids. Cellular evaluation of these agents led to the discovery of an azido-ester that is metabolized to its cognate acyl-coenzyme A (CoA) and affords robust protein labeling profiles. We comprehensively characterize the metabolic dependence, toxicity, and histone deacetylase (HDAC) inhibitor sensitivity of these bioorthogonal pro-metabolites, and apply an optimized probe to identify novel candidate protein targets of short chain fatty acids in cells. Our studies showcase the utility of bioorthogonal pro-metabolites for unbiased profiling of cellular protein acylation, and suggest new approaches for studying the signaling functions of SCFAs in differentiation and disease.
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Affiliation(s)
- Wilson R Sinclair
- Chemical Biology Laboratory , Center for Cancer Research , National Cancer Institute , National Institutes of Health , Frederick , MD 21702 , USA .
| | - Jonathan H Shrimp
- Chemical Biology Laboratory , Center for Cancer Research , National Cancer Institute , National Institutes of Health , Frederick , MD 21702 , USA .
| | - Thomas T Zengeya
- Chemical Biology Laboratory , Center for Cancer Research , National Cancer Institute , National Institutes of Health , Frederick , MD 21702 , USA .
| | - Rhushikesh A Kulkarni
- Chemical Biology Laboratory , Center for Cancer Research , National Cancer Institute , National Institutes of Health , Frederick , MD 21702 , USA .
| | - Julie M Garlick
- Chemical Biology Laboratory , Center for Cancer Research , National Cancer Institute , National Institutes of Health , Frederick , MD 21702 , USA .
| | - Hans Luecke
- National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , MD 20817 , USA
| | - Andrew J Worth
- Penn SRP Center , Center for Excellence in Environmental Toxicology , University of Pennsylvania , Philadelphia , PA 19104 , USA
| | - Ian A Blair
- Penn SRP Center , Center for Excellence in Environmental Toxicology , University of Pennsylvania , Philadelphia , PA 19104 , USA
| | - Nathaniel W Snyder
- Drexel University , A.J. Drexel Autism Institute , 3020 Market St , Philadelphia , PA 19104 , USA
| | - Jordan L Meier
- Chemical Biology Laboratory , Center for Cancer Research , National Cancer Institute , National Institutes of Health , Frederick , MD 21702 , USA .
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28
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Shala-Lawrence A, Blanden MJ, Krylova SM, Gangopadhyay SA, Beloborodov SS, Hougland JL, Krylov SN. Simultaneous Analysis of a Non-Lipidated Protein and Its Lipidated Counterpart: Enabling Quantitative Investigation of Protein Lipidation’s Impact on Cellular Regulation. Anal Chem 2017; 89:13502-13507. [DOI: 10.1021/acs.analchem.7b03846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Agnesa Shala-Lawrence
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Melanie J. Blanden
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Svetlana M. Krylova
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | | | - Stanislav S. Beloborodov
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Sergey N. Krylov
- Department
of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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29
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Witten AJ, Ejendal KFK, Gengelbach LM, Traore MA, Wang X, Umulis DM, Calve S, Kinzer-Ursem TL. Fluorescent imaging of protein myristoylation during cellular differentiation and development. J Lipid Res 2017; 58:2061-2070. [PMID: 28754825 PMCID: PMC5625117 DOI: 10.1194/jlr.d074070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/26/2017] [Indexed: 11/20/2022] Open
Abstract
Protein post-translational modifications (PTMs) serve to give proteins new cellular functions and can influence spatial distribution and enzymatic activity, greatly enriching the complexity of the proteome. Lipidation is a PTM that regulates protein stability, function, and subcellular localization. To complement advances in proteomic identification of lipidated proteins, we have developed a method to image the spatial distribution of proteins that have been co- and post-translationally modified via the addition of myristic acid (Myr) to the N terminus. In this work, we use a Myr analog, 12-azidododecanoic acid (12-ADA), to facilitate fluorescent detection of myristoylated proteins in vitro and in vivo. The azide moiety of 12-ADA does not react to natural biological chemistries, but is selectively reactive with alkyne functionalized fluorescent dyes. We find that the spatial distribution of myristoylated proteins varies dramatically between undifferentiated and differentiated muscle cells in vitro. Further, we demonstrate that our methodology can visualize the distribution of myristoylated proteins in zebrafish muscle in vivo. Selective protein labeling with noncanonical fatty acids, such as 12-ADA, can be used to determine the biological function of myristoylation and other lipid-based PTMs and can be extended to study deregulated protein lipidation in disease states.
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Affiliation(s)
- Andrew J Witten
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
| | - Karin F K Ejendal
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
| | | | - Meghan A Traore
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
| | - Xu Wang
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN
| | - David M Umulis
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
- Agricultural and Biological Engineering, Purdue University, West Lafayette, IN
| | - Sarah Calve
- Weldon School of Biomedical Engineering Purdue University, West Lafayette, IN
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30
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Marakasova ES, Eisenhaber B, Maurer-Stroh S, Eisenhaber F, Baranova A. Prenylation of viral proteins by enzymes of the host: Virus-driven rationale for therapy with statins and FT/GGT1 inhibitors. Bioessays 2017; 39. [DOI: 10.1002/bies.201700014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Birgit Eisenhaber
- Bioinformatics Institute; Agency for Science; Technology and Research Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute; Agency for Science; Technology and Research Singapore
- Department of Biological Sciences; National University Singapore; Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute; Agency for Science; Technology and Research Singapore
- Department of Biological Sciences; National University Singapore; Singapore
- School of Computer Engineering; Nanyang Technological University; Singapore
| | - Ancha Baranova
- School of Systems Biology; George Mason University; Fairfax VA USA
- Research Centre for Medical Genetics; Russian Academy of Medical Sciences; Moscow Russia
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31
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Brioschi M, Martinez Fernandez A, Banfi C. Exploring the biochemistry of the prenylome and its role in disease through proteomics: progress and potential. Expert Rev Proteomics 2017; 14:515-528. [PMID: 28521569 DOI: 10.1080/14789450.2017.1332998] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Protein prenylation is a ubiquitous covalent post-translational modification characterized by the addition of farnesyl or geranylgeranyl isoprenoid groups to a cysteine residue located near the carboxyl terminal of a protein. It is essential for the proper localization and cellular activity of numerous proteins, including Ras family GTPases and G-proteins. In addition to its roles in cellular physiology, the prenylation process has important implications in human diseases and in the recent years, it has become attractive target of inhibitors with therapeutic potential. Areas covered: This review attempts to summarize the basic aspects of prenylation integrating them with biological functions in diseases and giving an account of the current status of prenylation inhibitors as potential therapeutics. We also summarize the methodologies for the characterization of this modification. Expert commentary: The growing body of evidence suggesting an important role of prenylation in diseases and the subsequent development of inhibitors of the enzymes responsible for this modification lead to the urgent need to identify the full spectrum of prenylated proteins that are altered in the disease or affected by drugs. Proteomic tools to analyze prenylated proteins are recently emerging, thanks to the advancement in the field of mass spectrometry coupled to enrichment strategies.
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