1
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Schey GL, Hildebrandt ER, Wang Y, Diwan S, Passetti HA, Potts GW, Sprague-Getsy AM, Leoni ER, Kuebler TS, Sham YY, Hougland JL, Beese LS, Schmidt WK, Distefano MD. Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase. Int J Mol Sci 2024; 25:5324. [PMID: 38791363 PMCID: PMC11121372 DOI: 10.3390/ijms25105324] [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: 02/03/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.
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Affiliation(s)
- Garrett L. Schey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (E.R.L.); (W.K.S.)
| | - You Wang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; (Y.W.); (L.S.B.)
| | - Safwan Diwan
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
| | - Holly A. Passetti
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
| | - Gavin W. Potts
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
| | - Andrea M. Sprague-Getsy
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (A.M.S.-G.); (J.L.H.)
| | - Ethan R. Leoni
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (E.R.L.); (W.K.S.)
| | - Taylor S. Kuebler
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA; (T.S.K.); (Y.Y.S.)
| | - Yuk Y. Sham
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA; (T.S.K.); (Y.Y.S.)
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - James L. Hougland
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA; (A.M.S.-G.); (J.L.H.)
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Syracuse, Syracuse University, Syracuse, NY 13244, USA
| | - Lorena S. Beese
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; (Y.W.); (L.S.B.)
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA; (E.R.H.); (E.R.L.); (W.K.S.)
| | - Mark D. Distefano
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; (S.D.); (H.A.P.); (G.W.P.)
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2
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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. [PMID: 38654427 DOI: 10.1021/acs.bioconjchem.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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3
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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 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [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, 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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4
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Ashok S, Hildebrandt ER, Ruiz CS, Hardgrove DS, Coreno DW, Schmidt WK, Hougland JL. Protein Farnesyltransferase Catalyzes Unanticipated Farnesylation and Geranylgeranylation of Shortened Target Sequences. Biochemistry 2020; 59:1149-1162. [PMID: 32125828 DOI: 10.1021/acs.biochem.0c00081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein prenylation is a posttranslational modification involving the attachment of a C15 or C20 isoprenoid group to a cysteine residue near the C-terminus of the target substrate by protein farnesyltransferase (FTase) or protein geranylgeranyltransferase type I (GGTase-I), respectively. Both of these protein prenyltransferases recognize a C-terminal "CaaX" sequence in their protein substrates, but recent studies in yeast- and mammalian-based systems have demonstrated FTase can also accept sequences that diverge in length from the canonical four-amino acid motif, such as the recently reported five-amino acid C(x)3X motif. In this work, we further expand the substrate scope of FTase by demonstrating sequence-dependent farnesylation of shorter three-amino acid "Cxx" C-terminal sequences using both genetic and biochemical assays. Strikingly, biochemical assays utilizing purified mammalian FTase and Cxx substrates reveal prenyl donor promiscuity leading to both farnesylation and geranylgeranylation of these sequences. These findings expand the substrate pool of sequences that can be potentially prenylated, further refine our understanding of substrate recognition by FTase and GGTase-I, and suggest the possibility of a new class of prenylated proteins within proteomes.
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Affiliation(s)
- Sudhat Ashok
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Emily R Hildebrandt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Colby S Ruiz
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Daniel S Hardgrove
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - David W Coreno
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Walter K Schmidt
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - James L Hougland
- Department of Chemistry, Syracuse University, Syracuse, New York 13244, United States.,Syracuse Biomaterials Institute, Syracuse University, Syracuse, New York 13244, United States
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5
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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: 53] [Impact Index Per Article: 10.6] [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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6
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Protein Isoprenylation in Yeast Targets COOH-Terminal Sequences Not Adhering to the CaaX Consensus. Genetics 2018; 210:1301-1316. [PMID: 30257935 PMCID: PMC6283164 DOI: 10.1534/genetics.118.301454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
Protein isoprenylation targets a subset of COOH-terminal Cxxx tetrapeptide sequences that has been operationally defined as a CaaX motif. The specificity of the farnesyl transferase toward each of the possible 8000 combinations of Cxxx sequences, however, remains largely unresolved. In part, it has been difficult to consolidate results stemming from in vitro and in silico approaches that yield a wider array of prenylatable sequences relative to those known in vivo We have investigated whether this disconnect results from the multistep complexity of post-translational modification that occurs in vivo to CaaX proteins. For example, the Ras GTPases undergo isoprenylation followed by additional proteolysis and carboxymethylation events at the COOH-terminus. By contrast, Saccharomyces cerevisiae Hsp40 Ydj1p is isoprenylated but not subject to additional modification. In fact, additional modifications are detrimental to Ydj1p activity in vivo We have taken advantage of the properties of Ydj1p and a Ydj1p-dependent growth assay to identify sequences that permit Ydj1p isoprenylation in vivo while simultaneously selecting against nonprenylatable and more extensively modified sequences. The recovered sequences are largely nonoverlapping with those previously identified using an in vivo Ras-based yeast reporter. Moreover, most of the sequences are not readily predicted as isoprenylation targets by existing prediction algorithms. Our results reveal that the yeast CaaX-type prenyltransferases can utilize a range of sequence combinations that extend beyond the traditional constraints for CaaX proteins, which implies that more proteins may be isoprenylated than previously considered.
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7
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Jennings BC, Lawton AJ, Rizk Z, Fierke CA. SmgGDS-607 Regulation of RhoA GTPase Prenylation Is Nucleotide-Dependent. Biochemistry 2018; 57:4289-4298. [PMID: 29940100 DOI: 10.1021/acs.biochem.8b00567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Protein prenylation involves the attachment of a hydrophobic isoprenoid moiety to the C-terminus of proteins. Several small GTPases, including members of the Ras and Rho subfamilies, require prenylation for their normal and pathological functions. Recent work has suggested that SmgGDS proteins regulate the prenylation of small GTPases in vivo. Using RhoA as a representative small GTPase, we directly test this hypothesis using biochemical assays and present a mechanism describing the mode of prenylation regulation. SmgGDS-607 completely inhibits RhoA prenylation catalyzed by protein geranylgeranyltransferase I (GGTase-I) in an in vitro radiolabel incorporation assay. SmgGDS-607 inhibits prenylation by binding to and blocking access to the C-terminal tail of the small GTPase (substrate sequestration mechanism) rather than via inhibition of the prenyltransferase activity. The reactivity of GGTase-I with RhoA is unaffected by addition of nucleotides. In contrast, the affinity of SmgGDS-607 for RhoA varies with the nucleotide bound to RhoA; SmgGDS-607 has a higher affinity for RhoA-GDP compared to RhoA-GTP. Consequently, the prenylation blocking function of SmgGDS-607 is regulated by the bound nucleotide. This work provides mechanistic insight into a novel pathway for the regulation of small GTPase protein prenylation by SmgGDS-607 and demonstrates that peptides are a good mimic for full-length proteins when measuring GGTase-I activity.
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Affiliation(s)
- Benjamin C Jennings
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Alexis J Lawton
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Zeinab Rizk
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Carol A Fierke
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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8
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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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9
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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: 274] [Impact Index Per Article: 45.7] [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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10
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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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11
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Novotny CJ, Hamilton GL, McCormick F, Shokat KM. Farnesyltransferase-Mediated Delivery of a Covalent Inhibitor Overcomes Alternative Prenylation to Mislocalize K-Ras. ACS Chem Biol 2017; 12:1956-1962. [PMID: 28530791 DOI: 10.1021/acschembio.7b00374] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mutationally activated Ras is one of the most common oncogenic drivers found across all malignancies, and its selective inhibition has long been a goal in both pharma and academia. One of the oldest and most validated methods to inhibit overactive Ras signaling is by interfering with its post-translational processing and subsequent cellular localization. Previous attempts to target Ras processing led to the development of farnesyltransferase inhibitors, which can inhibit H-Ras localization but not K-Ras due to its ability to bypass farnesyltransterase inhibition through alternative prenylation by geranylgeranyltransferase. Here, we present the creation of a neo-substrate for farnesyltransferase that prevents the alternative prenlation by geranylgeranyltransferase and mislocalizes oncogenic K-Ras in cells.
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Affiliation(s)
- Chris J. Novotny
- Howard
Hughes Medical Institute and Department of Cellular and Molecular
Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Gregory L. Hamilton
- Howard
Hughes Medical Institute and Department of Cellular and Molecular
Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Frank McCormick
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National
Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland 21701, United States
- Diller Family Comprehensive
Cancer Center, University of California, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Howard
Hughes Medical Institute and Department of Cellular and Molecular
Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
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12
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Palsuledesai CC, Ochocki JD, Kuhns MM, Wang YC, Warmka JK, Chernick DS, Wattenberg EV, Li L, Arriaga EA, Distefano MD. Metabolic Labeling with an Alkyne-modified Isoprenoid Analog Facilitates Imaging and Quantification of the Prenylome in Cells. ACS Chem Biol 2016; 11:2820-2828. [PMID: 27525511 PMCID: PMC5074897 DOI: 10.1021/acschembio.6b00421] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein prenylation is a post-translational modification that is responsible for membrane association and protein-protein interactions. The oncogenic protein Ras, which is prenylated, has been the subject of intense study in the past 20 years as a therapeutic target. Several studies have shown a correlation between neurodegenerative diseases including Alzheimer's disease and Parkinson's disease and protein prenylation. Here, a method for imaging and quantification of the prenylome using microscopy and flow cytometry is described. We show that metabolically incorporating an alkyne isoprenoid into mammalian cells, followed by a Cu(I)-catalyzed alkyne azide cycloaddition reaction to a fluorophore, allows for detection of prenylated proteins in several cell lines and that different cell types vary significantly in their levels of prenylated proteins. The addition of a prenyltransferase inhibitor or the precursors to the native isoprenoid substrates lowers the levels of labeled prenylated proteins. Finally, we demonstrate that there is a significantly higher (22%) level of prenylated proteins in a cellular model of compromised autophagy as compared to normal cells, supporting the hypothesis of a potential involvement of protein prenylation in abrogated autophagy. These results highlight the utility of total prenylome labeling for studies on the role of protein prenylation in various diseases including aging-related disorders.
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Affiliation(s)
- Charuta C. Palsuledesai
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Joshua D. Ochocki
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michelle M. Kuhns
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yen-Chih Wang
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Janel K. Warmka
- Division
of Environmental Health Sciences, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Dustin S. Chernick
- Department
of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Elizabeth V. Wattenberg
- Division
of Environmental Health Sciences, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ling Li
- Department
of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Edgar A. Arriaga
- 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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