1
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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] [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: 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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2
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Kim HR, Byun DP, Thakur K, Ritchie J, Xie Y, Holewinski R, Suazo KF, Stevens M, Liechty H, Tagirasa R, Jing Y, Andresson T, Johnson SM, Yoo E. Discovery of a Tunable Heterocyclic Electrophile 4-Chloro-pyrazolopyridine That Defines a Unique Subset of Ligandable Cysteines. ACS Chem Biol 2024; 19:1082-1092. [PMID: 38629450 DOI: 10.1021/acschembio.4c00025] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Electrophilic small molecules with novel reactivity are powerful tools that enable activity-based protein profiling and covalent inhibitor discovery. Here, we report a reactive heterocyclic scaffold, 4-chloro-pyrazolopyridine (CPzP) for selective modification of proteins via a nucleophilic aromatic substitution (SNAr) mechanism. Chemoproteomic profiling reveals that CPzPs engage cysteines within functionally diverse protein sites including ribosomal protein S5 (RPS5), inosine monophosphate dehydrogenase 2 (IMPDH2), and heat shock protein 60 (HSP60). Through the optimization of appended recognition elements, we demonstrate the utility of CPzP for covalent inhibition of prolyl endopeptidase (PREP) by targeting a noncatalytic active-site cysteine. This study suggests that the proteome reactivity of CPzPs can be modulated by both electronic and steric features of the ring system, providing a new tunable electrophile for applications in chemoproteomics and covalent inhibitor design.
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Affiliation(s)
- Hong-Rae Kim
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - David P Byun
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Kalyani Thakur
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jennifer Ritchie
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yixin Xie
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ronald Holewinski
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21702, United States
| | - Kiall F Suazo
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21702, United States
| | - Mckayla Stevens
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Hope Liechty
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Ravichandra Tagirasa
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Yihang Jing
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, Maryland 21702, United States
| | - Steven M Johnson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Euna Yoo
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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Chen X, Crawford MC, Xiong Y, Shaik AB, Suazo KF, Penkalapati MS, Williams JH, Andressen T, Swenson RE, Meier JL. Paralogue-selective degradation of the lysine acetyltransferase EP300. bioRxiv 2024:2024.05.03.592353. [PMID: 38746397 PMCID: PMC11092752 DOI: 10.1101/2024.05.03.592353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The transcriptional coactivators EP300 and CREBBP are critical regulators of gene expression that share high sequence identity but exhibit non-redundant functions in basal and pathological contexts. Here, we report the development of a bifunctional small molecule, MC-1, capable of selectively degrading EP300 over CREBBP. Using a potent aminopyridine-based inhibitor of the EP300/CREBBP catalytic domain in combination with a VHL ligand, we demonstrate that MC-1 preferentially degrades EP300 in a proteasome-dependent manner. Mechanistic studies reveal that selective degradation cannot be predicted solely by target engagement or ternary complex formation, suggesting additional factors govern paralogue-specific degradation. MC-1 inhibits cell proliferation in a subset of cancer cell lines and provides a new tool to investigate the non-catalytic functions of EP300 and CREBBP. Our findings expand the repertoire of EP300/CREBBP-targeting chemical probes and offer insights into the determinants of selective degradation of highly homologous proteins.
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Davis GJ, Omole AO, Jung Y, Rut W, Holewinski R, Suazo KF, Kim HR, Yang M, Andresson T, Drag M, Yoo E. Chemical tools to define and manipulate interferon-inducible Ubl protease USP18. bioRxiv 2024:2024.04.08.588544. [PMID: 38645224 PMCID: PMC11030383 DOI: 10.1101/2024.04.08.588544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Ubiquitin-specific protease 18 (USP18) is a multifunctional cysteine protease primarily responsible for deconjugating interferon-inducible ubiquitin-like (Ubl) modifier ISG15 from protein substrates. Here, we report the design and synthesis of activity-based probes (ABPs) capable of selectively detecting USP18 activity over other ISG15 cross-reactive deubiquitinases (DUBs) by incorporating unnatural amino acids into the C-terminal tail of ISG15. Combining with a ubiquitin-based DUB ABP, the selective USP18 ABP is employed in a chemoproteomic screening platform to identify and assess inhibitors of DUBs including USP18. We further demonstrate that USP18 ABPs can be utilized to profile differential activities of USP18 in lung cancer cell lines, providing a strategy that will help define the activity-related landscape of USP18 in different disease states and unravel important (de)ISGylation-dependent biological processes.
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5
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Puthenveetil R, Auger SA, Gómez-Navarro N, Rana MS, Das R, Healy LB, Suazo KF, Shi ZD, Swenson RE, Distefano MD, Banerjee A. Orthogonal Enzyme-Substrate Design Strategy for Discovery of Human Protein Palmitoyltransferase Substrates. J Am Chem Soc 2023; 145:22287-22292. [PMID: 37774000 PMCID: PMC10591334 DOI: 10.1021/jacs.3c04359] [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: 04/27/2023] [Indexed: 10/01/2023]
Abstract
Protein palmitoylation, with more than 5000 substrates, is the most prevalent form of protein lipidation. Palmitoylated proteins participate in almost all areas of cellular physiology and have been linked to several human diseases. Twenty-three zDHHC enzymes catalyze protein palmitoylation with extensive overlap among the substrates of each zDHHC member. Currently, there is no global strategy to delineate the physiological substrates of individual zDHHC enzymes without perturbing the natural cellular pool. Here, we outline a general approach to accomplish this on the basis of synthetic orthogonal substrates that are only compatible with engineered zDHHC enzymes. We demonstrate the utility of this strategy by validating known substrates and use it to identify novel substrates of two human zDHHC enzymes. Finally, we employ this method to discover and explore conserved palmitoylation in a family of host restriction factors against pathogenic viruses, including SARS-CoV-2.
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Affiliation(s)
- Robbins Puthenveetil
- Section
on Structural and Chemical Biology, Neurosciences and Cellular and
Structural Biology Division, Eunice Kennedy Shriver National Institute
of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20817, United States
| | - Shelby A. Auger
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Natalia Gómez-Navarro
- Section
on Structural and Chemical Biology, Neurosciences and Cellular and
Structural Biology Division, Eunice Kennedy Shriver National Institute
of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20817, United States
| | - Mitra Shumsher Rana
- Section
on Structural and Chemical Biology, Neurosciences and Cellular and
Structural Biology Division, Eunice Kennedy Shriver National Institute
of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20817, United States
| | - Riki Das
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Liam Brendan Healy
- Section
on Structural and Chemical Biology, Neurosciences and Cellular and
Structural Biology Division, Eunice Kennedy Shriver National Institute
of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20817, United States
| | - Kiall F. Suazo
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zhen-Dan Shi
- The
Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Rolf E. Swenson
- The
Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Mark D. Distefano
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anirban Banerjee
- Section
on Structural and Chemical Biology, Neurosciences and Cellular and
Structural Biology Division, Eunice Kennedy Shriver National Institute
of Child Health and Human Development, National
Institutes of Health, Bethesda, Maryland 20817, United States
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Koehn OJ, Lorimer E, Unger B, Harris R, Das AS, Suazo KF, Auger S, Distefano M, Prokop JW, Williams CL. GTPase splice variants RAC1 and RAC1B display isoform-specific differences in localization, prenylation, and interaction with the chaperone protein SmgGDS. J Biol Chem 2023; 299:104698. [PMID: 37059183 DOI: 10.1016/j.jbc.2023.104698] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023] Open
Abstract
Identifying events that regulate the prenylation and localization of small GTPases will help define new strategies for therapeutic targeting of these proteins in disorders such as cancer, cardiovascular disease, and neurological deficits. Splice variants of the chaperone protein SmgGDS (encoded by RAP1GDS1) are known to regulate prenylation and trafficking of small GTPases. The SmgGDS-607 splice variant regulates prenylation by binding pre-prenylated small GTPases, but the effects of SmgGDS binding to the small GTPase RAC1 versus the splice variant RAC1B are not well defined. Here we report unexpected differences in the prenylation and localization of RAC1 and RAC1B, and their binding to SmgGDS. Compared to RAC1, RAC1B more stably associates with SmgGDS-607, is less prenylated, and accumulates more in the nucleus. We show that the small GTPase DIRAS1 inhibits binding of RAC1 and RAC1B to SmgGDS and reduces their prenylation. These results suggest that prenylation of RAC1 and RAC1B is facilitated by binding to SmgGDS-607, but the greater retention of RAC1B by SmgGDS-607 slows RAC1B prenylation. We show that inhibiting RAC1 prenylation by mutating the CAAX motif promotes RAC1 nuclear accumulation, suggesting that differences in prenylation contribute to the different nuclear localization of RAC1 versus RAC1B. Finally, we demonstrate RAC1 and RAC1B that cannot be prenylated bind GTP in cells, indicating that prenylation is not a prerequisite for activation. We report differential expression of RAC1 and RAC1B transcripts in tissues, consistent with these two splice variants having unique functions that might arise in part from their differences in prenylation and localization.
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Affiliation(s)
- Olivia J Koehn
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Ellen Lorimer
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Bethany Unger
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Ra'Mal Harris
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Akansha S Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA
| | - Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USAA
| | - Shelby Auger
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USAA
| | - Mark Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USAA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA; Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - Carol L Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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9
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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] [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.
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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, Minnesota 55455, United States
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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11
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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] [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.
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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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Qu W, Suazo KF, Liu W, Cheng S, Jeong A, Hottman D, Yuan LL, Distefano MD, Li L. Neuronal Protein Farnesylation Regulates Hippocampal Synaptic Plasticity and Cognitive Function. Mol Neurobiol 2020; 58:1128-1144. [PMID: 33098528 DOI: 10.1007/s12035-020-02169-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022]
Abstract
Protein prenylation is a post-translational lipid modification that governs a variety of important cellular signaling pathways, including those regulating synaptic functions and cognition in the nervous system. Two enzymes, farnesyltransferase (FT) and geranylgeranyltransferase type I (GGT), are essential for the prenylation process. Genetic reduction of FT or GGT ameliorates neuropathology but only FT haplodeficiency rescues cognitive function in transgenic mice of Alzheimer's disease. A follow-up study showed that systemic or forebrain neuron-specific deficiency of GGT leads to synaptic and cognitive deficits under physiological conditions. Whether FT plays different roles in shaping neuronal functions and cognition remains elusive. This study shows that in contrast to the detrimental effects of GGT reduction, systemic haplodeficiency of FT has little to no impact on hippocampal synaptic plasticity and cognition. However, forebrain neuron-specific FT deletion also leads to reduced synaptic plasticity, memory retention, and hippocampal dendritic spine density. Furthermore, a novel prenylomic analysis identifies distinct pools of prenylated proteins that are affected in the brain of forebrain neuron-specific FT and GGT knockout mice, respectively. Taken together, this study uncovers that physiological levels of FT and GGT in neurons are essential for normal synaptic/cognitive functions and that the prenylation status of specific signaling molecules regulates neuronal functions.
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Affiliation(s)
- Wenhui Qu
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wenfeng Liu
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - Shaowu Cheng
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - Angela Jeong
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - David Hottman
- Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA
| | - Li-Lian Yuan
- Department of Physiology and Pharmacology, Des Moines University, Des Moines, IA, 50312, USA
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ling Li
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, 55455, USA. .,Department of Experimental and Clinical Pharmacology, University of Minnesota, McGuire Translational Research Facility (MTRF) 4-208, 2001 6th Street SE, Minneapolis, MN, 55455, USA. .,Graduate Program in Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA.
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Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Suazo KF, Schaber C, Palsuledesai CC, Odom John AR, Distefano MD. Global proteomic analysis of prenylated proteins in Plasmodium falciparum using an alkyne-modified isoprenoid analogue. Sci Rep 2016; 6:38615. [PMID: 27924931 PMCID: PMC5141570 DOI: 10.1038/srep38615] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/09/2016] [Indexed: 01/28/2023] Open
Abstract
Severe malaria due to Plasmodium falciparum infection remains a serious threat to health worldwide and new therapeutic targets are highly desirable. Small molecule inhibitors of prenyl transferases, enzymes that catalyze the post-translational isoprenyl modifications of proteins, exhibit potent antimalarial activity. The antimalarial actions of prenyltransferase inhibitors indicate that protein prenylation is required for malaria parasite development. In this study, we used a chemical biology strategy to experimentally characterize the entire complement of prenylated proteins in the human malaria parasite. In contrast to the expansive mammalian and fungal prenylomes, we find that P. falciparum possesses a restricted set of prenylated proteins. The prenylome of P. falciparum is dominated by Rab GTPases, in addition to a small number of prenylated proteins that also appear to function primarily in membrane trafficking. Overall, we found robust experimental evidence for a total of only thirteen prenylated proteins in P. falciparum, with suggestive evidence for an additional two probable prenyltransferase substrates. Our work contributes to an increasingly complete picture of essential, post-translational hydrophobic modifications in blood-stage P. falciparum.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Chad Schaber
- Departments of Pediatrics and of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | | | - Audrey R Odom John
- Departments of Pediatrics and of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
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