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Hildebrandt ER, Sarkar A, Ravishankar R, Kim JH, Schmidt WK. Evaluating protein prenylation of human and viral CaaX sequences using a humanized yeast system. Dis Model Mech 2024; 17:dmm050516. [PMID: 38818856 PMCID: PMC11152559 DOI: 10.1242/dmm.050516] [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: 09/19/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Prenylated proteins are prevalent in eukaryotic biology (∼1-2% of proteins) and are associated with human disease, including cancer, premature aging and infections. Prenylated proteins with a C-terminal CaaX sequence are targeted by CaaX-type prenyltransferases and proteases. To aid investigations of these enzymes and their targets, we developed Saccharomyces cerevisiae strains that express these human enzymes instead of their yeast counterparts. These strains were developed in part to explore human prenyltransferase specificity because of findings that yeast FTase has expanded specificity for sequences deviating from the CaaX consensus (i.e. atypical sequence and length). The humanized yeast strains displayed robust prenyltransferase activity against CaaX sequences derived from human and pathogen proteins containing typical and atypical CaaX sequences. The system also recapitulated prenylation of heterologously expressed human proteins (i.e. HRas and DNAJA2). These results reveal that substrate specificity is conserved for yeast and human farnesyltransferases but is less conserved for type I geranylgeranyltransferases. These yeast systems can be easily adapted for investigating the prenylomes of other organisms and are valuable new tools for helping define the human prenylome, which includes physiologically important proteins for which the CaaX modification status is unknown.
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Affiliation(s)
- Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Rajani Ravishankar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - June H. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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2
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Yuan Y, Li P, Li J, Zhao Q, Chang Y, He X. Protein lipidation in health and disease: molecular basis, physiological function and pathological implication. Signal Transduct Target Ther 2024; 9:60. [PMID: 38485938 PMCID: PMC10940682 DOI: 10.1038/s41392-024-01759-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 03/18/2024] Open
Abstract
Posttranslational modifications increase the complexity and functional diversity of proteins in response to complex external stimuli and internal changes. Among these, protein lipidations which refer to lipid attachment to proteins are prominent, which primarily encompassing five types including S-palmitoylation, N-myristoylation, S-prenylation, glycosylphosphatidylinositol (GPI) anchor and cholesterylation. Lipid attachment to proteins plays an essential role in the regulation of protein trafficking, localisation, stability, conformation, interactions and signal transduction by enhancing hydrophobicity. Accumulating evidence from genetic, structural, and biomedical studies has consistently shown that protein lipidation is pivotal in the regulation of broad physiological functions and is inextricably linked to a variety of diseases. Decades of dedicated research have driven the development of a wide range of drugs targeting protein lipidation, and several agents have been developed and tested in preclinical and clinical studies, some of which, such as asciminib and lonafarnib are FDA-approved for therapeutic use, indicating that targeting protein lipidations represents a promising therapeutic strategy. Here, we comprehensively review the known regulatory enzymes and catalytic mechanisms of various protein lipidation types, outline the impact of protein lipidations on physiology and disease, and highlight potential therapeutic targets and clinical research progress, aiming to provide a comprehensive reference for future protein lipidation research.
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Affiliation(s)
- Yuan Yuan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyuan Li
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianghui Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
| | - Xingxing He
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China.
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3
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Sarkar A, Hildebrandt ER, Patel KV, Mai ET, Shah SS, Kim JH, Schmidt WK. Comprehensive analysis of CXXX sequence space reveals that S. cerevisiae GGTase-I mainly relies on a 2X substrate determinants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583369. [PMID: 38496651 PMCID: PMC10942308 DOI: 10.1101/2024.03.04.583369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Many proteins undergo a post-translational lipid attachment, which increases their hydrophobicity, thus strengthening their membrane association properties or aiding in protein interactions. Geranylgeranyltransferase-I (GGTase-I) is an enzyme involved in a three-step post-translational modification (PTM) pathway that attaches a 20-carbon lipid group called geranylgeranyl at the carboxy-terminal cysteine of proteins ending in a canonical CaaL motif (C - cysteine, a - aliphatic, L - often leucine, but can be phenylalanine, isoleucine, methionine, or valine). Genetic approaches involving two distinct reporters were employed in this study to assess S. cerevisiae GGTase-I specificity, for which limited data exists, towards all 8000 CXXX combinations. Orthogonal biochemical analyses and structure-based alignments were also performed to better understand the features required for optimal target interaction. These approaches indicate that yeast GGTase-I best modifies the Cxa[L/F/I/M/V] sequence that resembles but is not an exact match for the canonical CaaL motif. We also observed that minor modification of non-canonical sequences is possible. A consistent feature associated with well-modified sequences was the presence of a non-polar a2 residue and a hydrophobic terminal residue, which are features recognized by mammalian GGTase-I. These results thus support that mammalian and yeast GGTase-I exhibit considerable shared specificity.
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Affiliation(s)
- Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Khushi V. Patel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Emily T. Mai
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Sumil S. Shah
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - June H. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602
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Huang H, Wang S, Guan Y, Ren J, Liu X. Molecular basis and current insights of atypical Rho small GTPase in cancer. Mol Biol Rep 2024; 51:141. [PMID: 38236467 DOI: 10.1007/s11033-023-09140-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Atypical Rho GTPases are a subtype of the Rho GTPase family that are involved in diverse cellular processes. The typical Rho GTPases, led by RhoA, Rac1 and Cdc42, have been well studied, while relative studies on atypical Rho GTPases are relatively still limited and have great exploration potential. With the increase in studies, current evidence suggests that atypical Rho GTPases regulate multiple biological processes and play important roles in the occurrence and development of human cancers. Therefore, this review mainly discusses the molecular basis of atypical Rho GTPases and their roles in cancer. We summarize the sequence characteristics, subcellular localization and biological functions of each atypical Rho GTPase. Moreover, we review the recent advances and potential mechanisms of atypical Rho GTPases in the development of multiple cancers. A comprehensive understanding and extensive exploration of the biological functions of atypical Rho GTPases and their molecular mechanisms in tumors will provide important insights into the pathophysiology of tumors and the development of cancer therapeutic strategies.
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Affiliation(s)
- Hua Huang
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Sijia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Yifei Guan
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA (People's Liberation Army) General Hospital, Beijing, 100853, China.
| | - Xinhui Liu
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China.
- Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China.
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5
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Pham AC, Holstein SA, Borgstahl GE. Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy. Mol Cancer Ther 2024; 23:14-23. [PMID: 37756579 PMCID: PMC10762340 DOI: 10.1158/1535-7163.mct-23-0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Geranylgeranyl diphosphate synthase (GGDPS), the source of the isoprenoid donor in protein geranylgeranylation reactions, has become an attractive target for anticancer therapy due to the reliance of cancers on geranylgeranylated proteins. Current GGDPS inhibitor development focuses on optimizing the drug-target enzyme interactions of nitrogen-containing bisphosphonate-based drugs. To advance GGDPS inhibitor development, understanding the enzyme structure, active site, and ligand/product interactions is essential. Here we provide a comprehensive structure-focused review of GGDPS. We reviewed available yeast and human GGDPS structures and then used AlphaFold modeling to complete unsolved structural aspects of these models. We delineate the elements of higher-order structure formation, product-substrate binding, the electrostatic surface, and small-molecule inhibitor binding. With the rise of structure-based drug design, the information provided here will serve as a valuable tool for rationally optimizing inhibitor selectivity and effectiveness.
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Affiliation(s)
- Andrew C. Pham
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sarah A. Holstein
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Gloria E.O. Borgstahl
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska
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Deng DX, Li CY, Zheng ZY, Wen B, Liao LD, Zhang XJ, Li EM, Xu LY. Prenylated PALM2 Promotes the Migration of Esophageal Squamous Cell Carcinoma Cells Through Activating Ezrin. Mol Cell Proteomics 2023; 22:100593. [PMID: 37328063 PMCID: PMC10393820 DOI: 10.1016/j.mcpro.2023.100593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 05/28/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023] Open
Abstract
Proteins containing a CAAX motif at the C-terminus undergo prenylation for localization and activity and include a series of key regulatory proteins, such as RAS superfamily members, heterotrimeric G proteins, nuclear lamina protein, and several protein kinases and phosphatases. However, studies of prenylated proteins in esophageal cancer are limited. Here, through research on large-scale proteomic data of esophageal cancer in our laboratory, we found that paralemmin-2 (PALM2), a potential prenylated protein, was upregulated and associated with poor prognosis in patients. Low-throughput verification showed that the expression of PALM2 in esophageal cancer tissues was higher than that in their paired normal esophageal epithelial tissues, and it was generally expressed in the membrane and cytoplasm of esophageal cancer cells. PALM2 interacted with the two subunits of farnesyl transferase (FTase), FNTA and FNTB. Either the addition of an FTase inhibitor or mutation in the CAAX motif of PALM2 (PALM2C408S) impaired its membranous localization and reduced the membrane location of PALM2, indicating PALM2 was prenylated by FTase. Overexpression of PALM2 enhanced the migration of esophageal squamous cell carcinoma cells, whereas PALM2C408S lost this ability. Mechanistically, PALM2 interacted with the N-terminal FERM domain of ezrin of the ezrin/radixin/moesin (ERM) family. Mutagenesis indicated that lysine residues K253/K254/K262/K263 in ezrin's FERM domain and C408 in PALM2's CAAX motif were important for PALM2/ezrin interaction and ezrin activation. Knockout of ezrin prevented enhanced cancer cell migration by PALM2 overexpression. PALM2, depending on its prenylation, increased both ezrin membrane localization and phosphorylation of ezrin at Y146. In summary, prenylated PALM2 enhances the migration of cancer cells by activating ezrin.
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Affiliation(s)
- Dan-Xia Deng
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Cheng-Yu Li
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, China; Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Cancer Research Cancer, Shantou University Medical College, Shantou, Guangdong, China
| | - Zhen-Yuan Zheng
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, China; Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Cancer Research Cancer, Shantou University Medical College, Shantou, Guangdong, China
| | - Bing Wen
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, China
| | - Lian-Di Liao
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiao-Jun Zhang
- Central Laboratory, Shantou University Medical College, Shantou, Guangdong, China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, Guangdong, China.
| | - Li-Yan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong, China; Guangdong Esophageal Cancer Research Institute, Shantou Sub-center, Cancer Research Cancer, Shantou University Medical College, Shantou, Guangdong, China.
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7
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Kim JH, Hildebrandt ER, Sarkar A, Yeung W, Waldon LRA, Kannan N, Schmidt WK. A comprehensive in vivo screen of yeast farnesyltransferase activity reveals broad reactivity across a majority of CXXX sequences. G3 (BETHESDA, MD.) 2023; 13:jkad094. [PMID: 37119806 PMCID: PMC10320760 DOI: 10.1093/g3journal/jkad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 05/01/2023]
Abstract
The current understanding of farnesyltransferase (FTase) specificity was pioneered through investigations of reporters like Ras and Ras-related proteins that possess a C-terminal CaaX motif that consists of 4 amino acid residues: cysteine-aliphatic1-aliphatic2-variable (X). These studies led to the finding that proteins with the CaaX motif are subject to a 3-step post-translational modification pathway involving farnesylation, proteolysis, and carboxylmethylation. Emerging evidence indicates, however, that FTase can farnesylate sequences outside the CaaX motif and that these sequences do not undergo the canonical 3-step pathway. In this work, we report a comprehensive evaluation of all possible CXXX sequences as FTase targets using the reporter Ydj1, an Hsp40 chaperone that only requires farnesylation for its activity. Our genetic and high-throughput sequencing approach reveals an unprecedented profile of sequences that yeast FTase can recognize in vivo, which effectively expands the potential target space of FTase within the yeast proteome. We also document that yeast FTase specificity is majorly influenced by restrictive amino acids at a2 and X positions as opposed to the resemblance of CaaX motif as previously regarded. This first complete evaluation of CXXX space expands the complexity of protein isoprenylation and marks a key step forward in understanding the potential scope of targets for this isoprenylation pathway.
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Affiliation(s)
- June H Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Emily R Hildebrandt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Anushka Sarkar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - La Ryel A Waldon
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Walter K Schmidt
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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8
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Jung D, Bachmann HS. Regulation of protein prenylation. Biomed Pharmacother 2023; 164:114915. [PMID: 37236024 DOI: 10.1016/j.biopha.2023.114915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Prenyltransferases (PTases) are known to play a role in embryonic development, normal tissue homeostasis and cancer by posttranslationally modifying proteins involved in these processes. They are being discussed as potential drug targets in an increasing number of diseases, ranging from Alzheimer's disease to malaria. Protein prenylation and the development of specific PTase inhibitors (PTIs) have been subject to intense research in recent decades. Recently, the FDA approved lonafarnib, a specific farnesyltransferase inhibitor that acts directly on protein prenylation; and bempedoic acid, an ATP citrate lyase inhibitor that might alter intracellular isoprenoid composition, the relative concentrations of which can exert a decisive influence on protein prenylation. Both drugs represent the first approved agent in their respective substance class. Furthermore, an overwhelming number of processes and proteins that regulate protein prenylation have been identified over the years, many of which have been proposed as molecular targets for pharmacotherapy in their own right. However, certain aspects of protein prenylation, such as the regulation of PTase gene expression or the modulation of PTase activity by phosphorylation, have attracted less attention, despite their reported influence on tumor cell proliferation. Here, we want to summarize the advances regarding our understanding of the regulation of protein prenylation and the potential implications for drug development. Additionally, we want to suggest new lines of investigation that encompass the search for regulatory elements for PTases, especially at the genetic and epigenetic levels.
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Affiliation(s)
- Dominik Jung
- Institute of Pharmacology and Toxicology, Center for Biomedical Education and Research (ZBAF), School of Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Hagen S Bachmann
- Institute of Pharmacology and Toxicology, Center for Biomedical Education and Research (ZBAF), School of Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany.
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García-España A, Philips MR. Origin and Evolution of RAS Membrane Targeting. Oncogene 2023; 42:1741-1750. [PMID: 37031342 PMCID: PMC10413328 DOI: 10.1038/s41388-023-02672-z] [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] [Received: 01/16/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 04/10/2023]
Abstract
KRAS, HRAS and NRAS proto-oncogenes belong to a family of 40 highly homologous genes, which in turn are a subset of a superfamily of >160 genes encoding small GTPases. RAS proteins consist of a globular G-domain (aa1-166) and a 22-23 aa unstructured hypervariable region (HVR) that mediates membrane targeting. The evolutionary origins of the RAS isoforms, their HVRs and alternative splicing of the KRAS locus has not been explored. We found that KRAS is basal to the RAS proto-oncogene family and its duplication generated HRAS in the common ancestor of vertebrates. In a second round of duplication HRAS generated NRAS and KRAS generated an additional RAS gene we have designated KRASBL, absent in mammals and birds. KRAS4A arose through a duplication and insertion of the 4th exon of NRAS into the 3rd intron of KRAS. We found evolutionary conservation of a short polybasic region (PBR1) in HRAS, NRAS and KRAS4A, a second polybasic region (PBR2) in KRAS4A, two neutralized basic residues (NB) and a serine in KRAS4B and KRASBL, and a modification of the CaaX motif in vertebrates with farnesyl rather than geranylgeranyl polyisoprene lipids, suggesting that a less hydrophobic membrane anchor is critical to RAS protein function. The persistence of four RAS isoforms through >400 million years of evolution argues strongly for differential function.
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Affiliation(s)
| | - Mark R Philips
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA.
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10
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Stick R, Peter A. CaaX-less lamins: Lophotrochozoa provide a glance at the playground of evolution. PROTOPLASMA 2023; 260:741-756. [PMID: 36102949 PMCID: PMC10125929 DOI: 10.1007/s00709-022-01809-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/01/2022] [Indexed: 05/05/2023]
Abstract
Nuclear lamins are the main components of the nuclear lamina in many eukaryotes. They are members of the intermediate filament (IF) protein family. Lamins differ from cytoplasmic IF proteins by the presence of a nuclear localisation sequence (NLS) and a C-terminal tetrapeptide, the CaaX motif. The CaaX motif is target of post-translational modifications including isoprenylation, proteolytic processing, and carboxyl-methylation. These modifications, in conjunction with the NLS, direct lamins to the inner nuclear membrane where they assemble into filaments. Lamins lacking a CaaX motif are unable to associate independently with nuclear membranes and remain in the nucleoplasm. So far, three species have been reported to exclusively express CaaX-less lamins. All three belong to the lophotrochozoan lineage. To find out whether they represent rare exceptions, we analysed lamins of representatives of 17 lophotrochozoan phyla. Here we report that all four clades of Rotifera as well as individual taxa of Mollusca and Annelida lack CaaX-lamins, but express lamins with alternative C-termini. Of note, the respective mollusc and annelid groups occupy very different phylogenetic ranks. Most of these alternative C-termini are rich in aromatic residues. A possible function of these residues in membrane association is discussed. Alternative splicing of terebellid lamin transcripts gives rise to two lamin variants, one with a CaaX motif and one with an alternative C-terminus. A similar situation is found in Arenicolidae, Opheliidae, Capitellidae, and Echiura. This points a way, how the switch from lamins carrying a CaaX motif to lamins with alternative C-termini may have occurred.
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Affiliation(s)
- Reimer Stick
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany.
| | - Annette Peter
- Department of Cell Biology, University of Bremen, P.O. Box 330440, 28334, Bremen, Germany
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Muehlebach ME, Holstein SA. Geranylgeranyl diphosphate synthase: Role in human health, disease and potential therapeutic target. Clin Transl Med 2023; 13:e1167. [PMID: 36650113 PMCID: PMC9845123 DOI: 10.1002/ctm2.1167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023] Open
Abstract
Geranylgeranyl diphosphate synthase (GGDPS), an enzyme in the isoprenoid biosynthesis pathway, is responsible for the production of geranylgeranyl pyrophosphate (GGPP). GGPP serves as a substrate for the post-translational modification (geranylgeranylation) of proteins, including those belonging to the Ras superfamily of small GTPases. These proteins play key roles in signalling pathways, cytoskeletal regulation and intracellular transport, and in the absence of the prenylation modification, cannot properly localise and function. Aberrant expression of GGDPS has been implicated in various human pathologies, including liver disease, type 2 diabetes, pulmonary disease and malignancy. Thus, this enzyme is of particular interest from a therapeutic perspective. Here, we review the physiological function of GGDPS as well as its role in pathophysiological processes. We discuss the current GGDPS inhibitors under development and the therapeutic implications of targeting this enzyme.
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Affiliation(s)
- Molly E. Muehlebach
- Cancer Research Doctoral ProgramUniversity of Nebraska Medical CenterOmahaNebraskaUSA
| | - Sarah A. Holstein
- Department of Internal MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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12
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Ngo VA, Garcia AE. Millisecond molecular dynamics simulations of KRas-dimer formation and interfaces. Biophys J 2022; 121:3730-3744. [PMID: 35462078 PMCID: PMC9617078 DOI: 10.1016/j.bpj.2022.04.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 11/02/2022] Open
Abstract
Ras dimers have been proposed as building blocks for initiating the extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) cellular signaling pathway. To better examine the structure of possible dimer interfaces, the dynamics of Ras dimerization, and its potential signaling consequences, we performed molecular dynamics simulations totaling 1 ms of sampling, using an all-atom model of two full-length, farnesylated, guanosine triphosphate (GTP)-bound, wild-type KRas4b proteins diffusing on 29%POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine)-mixed POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membranes. Our simulations unveil an ensemble of thermodynamically weak KRas dimers spanning multiple conformations. The most stable conformations, having the largest interface areas, involve helix α2 and a hypervariable region (HVR). Among the dimer conformations, we found that the HVR of each KRas has frequent interactions with various parts of the dimer, thus potentially mediating the dimerization. Some dimer configurations have one KRas G-domain elevated above the lipid bilayer surface by residing on top of the other G-domain, thus likely contributing to the recruitment of cytosolic Raf kinases in the context of a stably formed multi-protein complex. We identified a variant of the α4-α5 KRas-dimer interface that is similar to the interfaces obtained with fluorescence resonance energy transfer (FRET) data of HRas on lipid bilayers. Interestingly, we found two arginine fingers, R68 and R149, that directly interact with the beta-phosphate of the GTP bound in KRas, in a manner similar to what is observed in a crystal structure of GAP-HRas complex, which can facilitate the GTP hydrolysis via the arginine finger of GTPase-activating protein (GAP).
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Affiliation(s)
- Van A Ngo
- Advanced Computing for Life Sciences and Engineering Group, Science Engagement Section, National Center for Computational Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee; Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Angel E Garcia
- Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory, Los Alamos, New Mexico.
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13
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Medical Advances in Hepatitis D Therapy: Molecular Targets. Int J Mol Sci 2022; 23:ijms231810817. [PMID: 36142728 PMCID: PMC9506394 DOI: 10.3390/ijms231810817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/25/2022] Open
Abstract
An approximate number of 250 million people worldwide are chronically infected with hepatitis B virus, making them susceptible to a coinfection with hepatitis D virus. The superinfection causes the most severe form of a viral hepatitis and thus drastically worsens the course of the disease. Until recently, the only available therapy consisted of interferon-α, only eligible for a minority of patients. In July 2020, the EMA granted Hepcludex conditional marketing authorization throughout the European Union. This first-in-class entry inhibitor offers the promise to prevent the spread in order to gain control and eventually participate in curing hepatitis B and D. Hepcludex is an example of how understanding the viral lifecycle can give rise to new therapy options. Sodium taurocholate co-transporting polypeptide, the virus receptor and the target of Hepcludex, and other targets of hepatitis D therapy currently researched are reviewed in this work. Farnesyltransferase inhibitors such as Lonafarnib, targeting another essential molecule in the HDV life cycle, represent a promising target for hepatitis D therapy. Farnesyltransferase attaches a farnesyl (isoprenyl) group to proteins carrying a C-terminal Ca1a2X (C: cysteine, a: aliphatic amino acid, X: C-terminal amino acid) motif like the large hepatitis D virus antigen. This modification enables the interaction of the HBV/HDV particle and the virus envelope proteins. Lonafarnib, which prevents this envelopment, has been tested in clinical trials. Targeting the lifecycle of the hepatitis B virus needs to be considered in hepatitis D therapy in order to cure a patient from both coexisting infections. Nucleic acid polymers target the hepatitis B lifecycle in a manner that is not yet understood. Understanding the possible targets of the hepatitis D virus therapy is inevitable for the improvement and development of a sufficient therapy that HDV patients are desperately in need of.
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14
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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: 0] [Impact Index Per Article: 0] [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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15
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Hossain MS, Zhang Z, Ashok S, Jenks AR, Lynch CJ, Hougland JL, Mozhdehi D. Temperature-Responsive Nano-Biomaterials from Genetically Encoded Farnesylated Disordered Proteins. ACS APPLIED BIO MATERIALS 2022; 5:1846-1856. [PMID: 35044146 PMCID: PMC9115796 DOI: 10.1021/acsabm.1c01162] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
Despite broad interest in understanding the biological implications of protein farnesylation in regulating different facets of cell biology, the use of this post-translational modification to develop protein-based materials and therapies remains underexplored. The progress has been slow due to the lack of accessible methodologies to generate farnesylated proteins with broad physicochemical diversities rapidly. This limitation, in turn, has hindered the empirical elucidation of farnesylated proteins' sequence-structure-function rules. To address this gap, we genetically engineered prokaryotes to develop operationally simple, high-yield biosynthetic routes to produce farnesylated proteins and revealed determinants of their emergent material properties (nano-aggregation and phase-behavior) using scattering, calorimetry, and microscopy. These outcomes foster the development of farnesylated proteins as recombinant therapeutics or biomaterials with molecularly programmable assembly.
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Affiliation(s)
- Md. Shahadat Hossain
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Zhe Zhang
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Sudhat Ashok
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Ashley R. Jenks
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Christopher J. Lynch
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - James L. Hougland
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
| | - Davoud Mozhdehi
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse: Institute for Material and Living Systems, Syracuse University, Syracuse, New York 13244, United States
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16
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Javaid S, Schaefer A, Goodwin CM, Nguyen VV, Massey FL, Pierobon M, Gambrell-Sanders D, Waters AM, Lambert KN, Diehl JN, Hobbs GA, Wood KC, Petricoin EF, Der CJ, Cox AD. Concurrent Inhibition of ERK and Farnesyltransferase Suppresses the Growth of HRAS Mutant Head and Neck Squamous Cell Carcinoma. Mol Cancer Ther 2022; 21:762-774. [PMID: 35247914 DOI: 10.1158/1535-7163.mct-21-0142] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/16/2021] [Accepted: 02/22/2022] [Indexed: 12/24/2022]
Abstract
Human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is a common cancer worldwide with an unmet need for more effective, less toxic treatments. Currently, both the disease and the treatment of HNSCC cause significant mortality and morbidity. Targeted therapies hold new promise for patients with HPV-negative status whose tumors harbor oncogenic HRAS mutations. Recent promising clinical results have renewed interest in the development of farnesyltransferase inhibitors (FTIs) as a therapeutic strategy for HRAS-mutant cancers. With the advent of clinical evaluation of the FTI tipifarnib for the treatment of HRAS-mutant HNSCC, we investigated the activity of tipifarnib and inhibitors of HRAS effector signaling in HRAS-mutant HNSCC cell lines. First, we validated that HRAS is a cancer driver in HRAS-mutant HNSCC lines. Second, we showed that treatment with the FTI tipifarnib largely phenocopied HRAS silencing, supporting HRAS as a key target of FTI antitumor activity. Third, we performed reverse-phase protein array analyses to profile FTI treatment-induced changes in global signaling, and conducted CRISPR/Cas9 genetic loss-of-function screens to identify previously unreported genes and pathways that modulate sensitivity to tipifarnib. Fourth, we determined that concurrent inhibition of HRAS effector signaling (ERK, PI3K, mTORC1) increased sensitivity to tipifarnib treatment, in part by overcoming tipifarnib-induced compensatory signaling. We also determined that ERK inhibition could block tipifarnib-induced epithelial-to-mesenchymal transition, providing a potential basis for the effectiveness of this combination. Our results support future investigations of these and other combination treatments for HRAS mutant HNSCC.
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Affiliation(s)
- Sehrish Javaid
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Antje Schaefer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Victoria V Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Frances L Massey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, Institute for Advanced Biomedical Research, George Mason University, Manassas, Virginia
| | | | - Andrew M Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kathryn N Lambert
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - J Nathaniel Diehl
- Curriculum in Genetics & Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - G Aaron Hobbs
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, Institute for Advanced Biomedical Research, George Mason University, Manassas, Virginia
| | - Channing J Der
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Adrienne D Cox
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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17
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Raisch T, Ciossani G, d’Amico E, Cmentowski V, Carmignani S, Maffini S, Merino F, Wohlgemuth S, Vetter IR, Raunser S, Musacchio A. Structure of the RZZ complex and molecular basis of Spindly‐driven corona assembly at human kinetochores. EMBO J 2022; 41:e110411. [PMID: 35373361 PMCID: PMC9058546 DOI: 10.15252/embj.2021110411] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022] Open
Abstract
In metazoans, a ≈1 megadalton (MDa) multiprotein complex comprising the dynein–dynactin adaptor Spindly and the ROD–Zwilch–ZW10 (RZZ) complex is the building block of a fibrous biopolymer, the kinetochore fibrous corona. The corona assembles on mitotic kinetochores to promote microtubule capture and spindle assembly checkpoint (SAC) signaling. We report here a high‐resolution cryo‐EM structure that captures the essential features of the RZZ complex, including a farnesyl‐binding site required for Spindly binding. Using a highly predictive in vitro assay, we demonstrate that the SAC kinase MPS1 is necessary and sufficient for corona assembly at supercritical concentrations of the RZZ–Spindly (RZZS) complex, and describe the molecular mechanism of phosphorylation‐dependent filament nucleation. We identify several structural requirements for RZZS polymerization in rings and sheets. Finally, we identify determinants of kinetochore localization and corona assembly of Spindly. Our results describe a framework for the long‐sought‐for molecular basis of corona assembly on metazoan kinetochores.
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Affiliation(s)
- Tobias Raisch
- Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Giuseppe Ciossani
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Ennio d’Amico
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Verena Cmentowski
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Sara Carmignani
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Felipe Merino
- Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Sabine Wohlgemuth
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Ingrid R Vetter
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Stefan Raunser
- Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Dortmund Germany
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology Max Planck Institute of Molecular Physiology Dortmund Germany
- Centre for Medical Biotechnology Faculty of Biology University Duisburg‐Essen Essen Germany
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18
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Safavi A, Ghodousi ES, Ghavamizadeh M, Sabaghan M, Azadbakht O, veisi A, Babaei H, Nazeri Z, Darabi MK, Zarezade V. Computational investigation of novel farnesyltransferase inhibitors using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking and molecular dynamics simulation studies: A new insight into cancer treatment. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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19
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Chamberlain SG, Gohlke A, Shafiq A, Squires IJ, Owen D, Mott HR. Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs. Proc Natl Acad Sci U S A 2021; 118:e2104219118. [PMID: 34480001 PMCID: PMC8433508 DOI: 10.1073/pnas.2104219118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022] Open
Abstract
RalA is a small GTPase and a member of the Ras family. This molecular switch is activated downstream of Ras and is widely implicated in tumor formation and growth. Previous work has shown that the ubiquitous Ca2+-sensor calmodulin (CaM) binds to small GTPases such as RalA and K-Ras4B, but a lack of structural information has obscured the functional consequences of these interactions. Here, we have investigated the binding of CaM to RalA and found that CaM interacts exclusively with the C terminus of RalA, which is lipidated with a prenyl group in vivo to aid membrane attachment. Biophysical and structural analyses show that the two RalA membrane-targeting motifs (the prenyl anchor and the polybasic motif) are engaged by distinct lobes of CaM and that CaM binding leads to removal of RalA from its membrane environment. The structure of this complex, along with a biophysical investigation into membrane removal, provides a framework with which to understand how CaM regulates the function of RalA and sheds light on the interaction of CaM with other small GTPases, including K-Ras4B.
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Affiliation(s)
- Samuel G Chamberlain
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Andrea Gohlke
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Arooj Shafiq
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Iolo J Squires
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
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20
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Yang W, Wang K, Wu H, Shao H, Chen H, Zhu J. Peptide scaffold‐derived peptidomimetic farnesyltransferase inhibitors. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wei Yang
- Department of Infectious Diseases, Taizhou Hospital Zhejiang University Taizhou China
| | - Kuifeng Wang
- Department of Infectious Diseases, Taizhou Hospital Zhejiang University Taizhou China
| | - Hongwei Wu
- Department of Infectious Diseases Affiliated Taizhou Hospital of Wenzhou Medical University Taizhou China
| | - Hui Shao
- Department of Infectious Diseases, Taizhou Hospital Zhejiang University Taizhou China
| | - Huazhong Chen
- Department of Infectious Diseases, Taizhou Hospital Zhejiang University Taizhou China
| | - Jiansheng Zhu
- Department of Infectious Diseases, Taizhou Hospital Zhejiang University Taizhou China
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21
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Campbell SL, Philips MR. Post-translational modification of RAS proteins. Curr Opin Struct Biol 2021; 71:180-192. [PMID: 34365229 DOI: 10.1016/j.sbi.2021.06.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022]
Abstract
Mutations of RAS genes drive cancer more frequently than any other oncogene. RAS proteins integrate signals from a wide array of receptors and initiate downstream signaling through pathways that control cellular growth. RAS proteins are fundamentally binary molecular switches in which the off/on state is determined by the binding of GDP or GTP, respectively. As such, the intrinsic and regulated nucleotide-binding and hydrolytic properties of the RAS GTPase were historically believed to account for the entirety of the regulation of RAS signaling. However, it is increasingly clear that RAS proteins are also regulated by a vast array of post-translational modifications (PTMs). The current challenge is to understand what are the functional consequences of these modifications and which are physiologically relevant. Because PTMs are catalyzed by enzymes that may offer targets for drug discovery, the study of RAS PTMs has been a high priority for RAS biologists.
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Affiliation(s)
| | - Mark R Philips
- Perlmutter Cancer Center, NYU Grossman School of Medicine, USA
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22
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Wang WH, Yuan T, Qian MJ, Yan FJ, Yang L, He QJ, Yang B, Lu JJ, Zhu H. Post-translational modification of KRAS: potential targets for cancer therapy. Acta Pharmacol Sin 2021; 42:1201-1211. [PMID: 33087838 PMCID: PMC8285426 DOI: 10.1038/s41401-020-00542-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/16/2020] [Indexed: 02/02/2023] Open
Abstract
Aberrant activation of the RAS superfamily is one of the critical factors in carcinogenesis. Among them, KRAS is the most frequently mutated one which has inspired extensive studies for developing approaches to intervention. Although the cognition toward KRAS remains far from complete, mounting evidence suggests that a variety of post-translational modifications regulate its activation and localization. In this review, we summarize the regulatory mode of post-translational modifications on KRAS including prenylation, post-prenylation, palmitoylation, ubiquitination, phosphorylation, SUMOylation, acetylation, nitrosylation, etc. We also highlight the recent studies targeting these modifications having exhibited potent anti-tumor activities.
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Affiliation(s)
- Wei-Hua Wang
- Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tao Yuan
- Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mei-Jia Qian
- Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Fang-Jie Yan
- Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Liu Yang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, China
| | - Qiao-Jun He
- Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jin-Jian Lu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
| | - Hong Zhu
- Zhejiang Province Key Laboratory of Anti-cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
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23
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Jo A, Lee Y, Kam TI, Kang SU, Neifert S, Karuppagounder SS, Khang R, Kang H, Park H, Chou SC, Oh S, Jiang H, Swing DA, Ham S, Pirooznia S, Umanah GKE, Mao X, Kumar M, Ko HS, Kang HC, Lee BD, Lee YI, Andrabi SA, Park CH, Lee JY, Kim H, Kim H, Kim H, Cho JW, Paek SH, Na CH, Tessarollo L, Dawson VL, Dawson TM, Shin JH. PARIS farnesylation prevents neurodegeneration in models of Parkinson's disease. Sci Transl Med 2021; 13:13/604/eaax8891. [PMID: 34321320 PMCID: PMC9990146 DOI: 10.1126/scitranslmed.aax8891] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/09/2020] [Accepted: 05/20/2021] [Indexed: 12/18/2022]
Abstract
Accumulation of the parkin-interacting substrate (PARIS; ZNF746), due to inactivation of parkin, contributes to Parkinson's disease (PD) through repression of peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α; PPARGC1A) activity. Here, we identify farnesol as an inhibitor of PARIS. Farnesol promoted the farnesylation of PARIS, preventing its repression of PGC-1α via decreasing PARIS occupancy on the PPARGC1A promoter. Farnesol prevented dopaminergic neuronal loss and behavioral deficits via farnesylation of PARIS in PARIS transgenic mice, ventral midbrain transduction of AAV-PARIS, adult conditional parkin KO mice, and the α-synuclein preformed fibril model of sporadic PD. PARIS farnesylation is decreased in the substantia nigra of patients with PD, suggesting that reduced farnesylation of PARIS may play a role in PD. Thus, farnesol may be beneficial in the treatment of PD by enhancing the farnesylation of PARIS and restoring PGC-1α activity.
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Affiliation(s)
- Areum Jo
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea.,Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yunjong Lee
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea.,Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Tae-In Kam
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Stewart Neifert
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Senthilkumar S Karuppagounder
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Rin Khang
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea
| | - Hojin Kang
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea.,Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyejin Park
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shih-Ching Chou
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sungtaek Oh
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Haisong Jiang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Deborah A Swing
- Neural Development Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21705, USA
| | - Sangwoo Ham
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea
| | - Sheila Pirooznia
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - George K E Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Xiaobo Mao
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Manoj Kumar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Han Seok Ko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA
| | - Ho Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, South Korea
| | - Byoung Dae Lee
- Neurodegeneration Control Research Center, Department of Neuroscience, Department of Physiology, Kyung Hee University School of Medicine, Seoul 02447, South Korea
| | - Yun-Il Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaida A Andrabi
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chi-Hu Park
- Research Core Facility, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea
| | - Ji-Yeong Lee
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea
| | - Hanna Kim
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea
| | - Hyein Kim
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea.,Research Core Facility, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea
| | - Hyojung Kim
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea
| | - Jin Whan Cho
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Chan Hyun Na
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lino Tessarollo
- Neural Development Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21705, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130-2685, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joo-Ho Shin
- Department of Pharmacology, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Suwon 16419, South Korea. .,Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Samsung Medical Center, Sungkyunkwan University School of Medicine, Samsung Biomedical Research Institute, Seoul 06351, South Korea
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24
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Veluthakal R, Thurmond DC. Emerging Roles of Small GTPases in Islet β-Cell Function. Cells 2021; 10:1503. [PMID: 34203728 PMCID: PMC8232272 DOI: 10.3390/cells10061503] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
Several small guanosine triphosphatases (GTPases) from the Ras protein superfamily regulate glucose-stimulated insulin secretion in the pancreatic islet β-cell. The Rho family GTPases Cdc42 and Rac1 are primarily involved in relaying key signals in several cellular functions, including vesicle trafficking, plasma membrane homeostasis, and cytoskeletal dynamics. They orchestrate specific changes at each spatiotemporal region within the β-cell by coordinating with signal transducers, guanine nucleotide exchange factors (GEFs), GTPase-activating factors (GAPs), and their effectors. The Arf family of small GTPases is involved in vesicular trafficking (exocytosis and endocytosis) and actin cytoskeletal dynamics. Rab-GTPases regulate pre-exocytotic and late endocytic membrane trafficking events in β-cells. Several additional functions for small GTPases include regulating transcription factor activity and mitochondrial dynamics. Importantly, defects in several of these GTPases have been found associated with type 2 diabetes (T2D) etiology. The purpose of this review is to systematically denote the identities and molecular mechanistic steps in the glucose-stimulated insulin secretion pathway that leads to the normal release of insulin. We will also note newly identified defects in these GTPases and their corresponding regulatory factors (e.g., GDP dissociation inhibitors (GDIs), GEFs, and GAPs) in the pancreatic β-cells, which contribute to the dysregulation of metabolism and the development of T2D.
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Affiliation(s)
- Rajakrishnan Veluthakal
- Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope Beckman Research Institute, Duarte, CA 91010, USA
| | - Debbie C. Thurmond
- Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope Beckman Research Institute, Duarte, CA 91010, USA
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25
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Molecular and Pharmacological Characterization of the Interaction between Human Geranylgeranyltransferase Type I and Ras-Related Protein Rap1B. Int J Mol Sci 2021; 22:ijms22052501. [PMID: 33801503 PMCID: PMC7958859 DOI: 10.3390/ijms22052501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/20/2021] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
Geranylgeranyltransferase type-I (GGTase-I) represents an important drug target since it contributes to the function of many proteins that are involved in tumor development and metastasis. This led to the development of GGTase-I inhibitors as anti-cancer drugs blocking the protein function and membrane association of e.g., Rap subfamilies that are involved in cell differentiation and cell growth. In the present study, we developed a new NanoBiT assay to monitor the interaction of human GGTase-I and its substrate Rap1B. Different Rap1B prenylation-deficient mutants (C181G, C181S, and ΔCQLL) were designed and investigated for their interaction with GGTase-I. While the Rap1B mutants C181G and C181S still exhibited interaction with human GGTase-I, mutant ΔCQLL, lacking the entire CAAX motif (defined by a cysteine residue, two aliphatic residues, and the C-terminal residue), showed reduced interaction. Moreover, a specific, peptidomimetic and competitive CAAX inhibitor was able to block the interaction of Rap1B with GGTase-I. Furthermore, activation of both Gαs-coupled human adenosine receptors, A2A (A2AAR) and A2B (A2BAR), increased the interaction between GGTase-I and Rap1B, probably representing a way to modulate prenylation and function of Rap1B. Thus, A2AAR and A2BAR antagonists might be promising candidates for therapeutic intervention for different types of cancer that overexpress Rap1B. Finally, the NanoBiT assay provides a tool to investigate the pharmacology of GGTase-I inhibitors.
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26
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27
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Apken LH, Oeckinghaus A. The RAL signaling network: Cancer and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 361:21-105. [PMID: 34074494 DOI: 10.1016/bs.ircmb.2020.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The RAL proteins RALA and RALB belong to the superfamily of small RAS-like GTPases (guanosine triphosphatases). RAL GTPases function as molecular switches in cells by cycling through GDP- and GTP-bound states, a process which is regulated by several guanine exchange factors (GEFs) and two heterodimeric GTPase activating proteins (GAPs). Since their discovery in the 1980s, RALA and RALB have been established to exert isoform-specific functions in central cellular processes such as exocytosis, endocytosis, actin organization and gene expression. Consequently, it is not surprising that an increasing number of physiological functions are discovered to be controlled by RAL, including neuronal plasticity, immune response, and glucose and lipid homeostasis. The critical importance of RAL GTPases for oncogenic RAS-driven cellular transformation and tumorigenesis still attracts most research interest. Here, RAL proteins are key drivers of cell migration, metastasis, anchorage-independent proliferation, and survival. This chapter provides an overview of normal and pathological functions of RAL GTPases and summarizes the current knowledge on the involvement of RAL in human disease as well as current therapeutic targeting strategies. In particular, molecular mechanisms that specifically control RAL activity and RAL effector usage in different scenarios are outlined, putting a spotlight on the complexity of the RAL GTPase signaling network and the emerging theme of RAS-independent regulation and relevance of RAL.
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Affiliation(s)
- Lisa H Apken
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany
| | - Andrea Oeckinghaus
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Münster, Münster, Germany.
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28
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Wang Y, Kilic O, Csizmar CM, Ashok S, Hougland JL, Distefano MD, Wagner CR. Engineering reversible cell-cell interactions using enzymatically lipidated chemically self-assembled nanorings. Chem Sci 2020; 12:331-340. [PMID: 34168743 PMCID: PMC8179657 DOI: 10.1039/d0sc03194a] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/22/2020] [Indexed: 11/21/2022] Open
Abstract
Multicellular biology is dependent on the control of cell-cell interactions. These concepts have begun to be exploited for engineering of cell-based therapies. Herein, we detail the use of a multivalent lipidated scaffold for the rapid and reversible manipulation of cell-cell interactions. Chemically self-assembled nanorings (CSANs) are formed via the oligomerization of bivalent dihydrofolate reductase (DHFR2) fusion proteins using a chemical dimerizer, bis-methotrexate. With targeting proteins fused onto the DHFR2 monomers, the CSANs can target specific cellular antigens. Here, anti-EGFR or anti-EpCAM fibronectin-DHFR2 monomers incorporating a CAAX-box sequence were enzymatically prenylated, then assembled into the corresponding CSANs. Both farnesylated and geranylgeranylated CSANs efficiently modified the cell surface of lymphocytes and remained bound to the cell surface with a half-life of >3 days. Co-localization studies revealed a preference for the prenylated nanorings to associate with lipid rafts. The presence of antigen targeting elements in these bifunctional constructs enabled them to specifically interact with target cells while treatment with trimethoprim resulted in rapid CSAN disassembly and termination of the cell-cell interactions. Hence, we were able to determine that activated PBMCs modified with the prenylated CSANs caused irreversible selective cytotoxicity toward EGFR-expressing cells within 2 hours without direct engagement of CD3. The ability to disassemble these nanostructures in a temporally controlled manner provides a unique platform for studying cell-cell interactions and T cell-mediated cytotoxicity. Overall, antigen-targeted prenylated CSANs provide a general approach for the regulation of specific cell-cell interactions and will be valuable for a plethora of fundamental and therapeutic applications.
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Affiliation(s)
- Yiao Wang
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Ozgun Kilic
- Department of Medicinal Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Clifford M Csizmar
- Department of Medicinal Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Sudhat Ashok
- Department of Chemistry, Syracuse University Syracuse New York 13244 USA
| | - James L Hougland
- Department of Chemistry, Syracuse University Syracuse New York 13244 USA
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
- Department of Medicinal Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Carston R Wagner
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
- Department of Medicinal Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
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29
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Hodge RG, Schaefer A, Howard SV, Der CJ. RAS and RHO family GTPase mutations in cancer: twin sons of different mothers? Crit Rev Biochem Mol Biol 2020; 55:386-407. [PMID: 32838579 DOI: 10.1080/10409238.2020.1810622] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The RAS and RHO family comprise two major branches of the RAS superfamily of small GTPases. These proteins function as regulated molecular switches and control cytoplasmic signaling networks that regulate a diversity of cellular processes, including cell proliferation and cell migration. In the early 1980s, mutationally activated RAS genes encoding KRAS, HRAS and NRAS were discovered in human cancer and now comprise the most frequently mutated oncogene family in cancer. Only recently, exome sequencing studies identified cancer-associated alterations in two RHO family GTPases, RAC1 and RHOA. RAS and RHO proteins share significant identity in their amino acid sequences, protein structure and biochemistry. Cancer-associated RAS mutant proteins harbor missense mutations that are found primarily at one of three mutational hotspots (G12, G13 and Q61) and have been identified as gain-of-function oncogenic alterations. Although these residues are conserved in RHO family proteins, the gain-of-function mutations found in RAC1 are found primarily at a distinct hotspot. Unexpectedly, the cancer-associated mutations found with RHOA are located at different hotspots than those found with RAS. Furthermore, since the RHOA mutations suggested a loss-of-function phenotype, it has been unclear whether RHOA functions as an oncogene or tumor suppressor in cancer development. Finally, whereas RAS mutations are found in a broad spectrum of cancer types, RHOA and RAC1 mutations occur in a highly restricted range of cancer types. In this review, we focus on RHOA missense mutations found in cancer and their role in driving tumorigenesis, with comparisons to cancer-associated mutations in RAC1 and RAS GTPases.
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Affiliation(s)
- Richard G Hodge
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Antje Schaefer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah V Howard
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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30
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Chen M, Wan B, Zhu S, Zhang F, Jin J, Li X, Wang X, Lv Y, Chen C, Lv T, Song Y. Geranylgeranyl diphosphate synthase deficiency aggravates lung fibrosis in mice by modulating TGF-β1/BMP-4 signaling. Biol Chem 2020; 400:1617-1627. [PMID: 31120854 DOI: 10.1515/hsz-2019-0168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/12/2019] [Indexed: 02/06/2023]
Abstract
Geranylgeranyl diphosphate synthase (GGPPS) is an enzyme that catalyzes the synthesis of geranylgeranyl pyrophosphate (GGPP). GGPPS is implicated in many disorders, but its role in idiopathic pulmonary fibrosis (IPF) remains unclear. This study aimed to investigate the role of GGPPS in IPF. We established bleomycin-induced lung injury in a lung-specific GGPPS-deficient mouse (GGPPS-/-) and detected GGPPS expression in lung tissues by Western blot and immunohistochemistry analysis. We found that GGPPS expression increased during lung injury and fibrosis in mice induced by bleomycin, and GGPPS deficiency augmented lung fibrosis. GGPPS deficiency activated lung fibroblast by facilitating transforming growth factor β1 while antagonizing bone morphogenetic protein 4 signaling. Notably, the supplementation of exogenous GGPP mitigated lung fibrosis in GGPPS-/- mice induced by bleomycin. In conclusion, our findings suggest that GGPPS provides protection against pulmonary fibrosis and that the restoration of protein geranylgeranylation may benefit statin-induced lung injury.
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Affiliation(s)
- Meizi Chen
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China.,Department of General Internal Medicine, The First People's Hospital of Chenzhou, Chenzhou 423000, Hunan, P.R. China
| | - Bing Wan
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Suhua Zhu
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Fang Zhang
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Jiajia Jin
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Xinying Li
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Xianghai Wang
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Yanling Lv
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Cen Chen
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Tangfeng Lv
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), Nanjing 210002, P.R. China
| | - Yong Song
- Department of Respiratory and Critical Medicine, Jinling Hospital, Nanjing Clinical School of Southern Medical University (Guangzhou), 305 Zhongshan Road, Nanjing 210002, P.R. China
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31
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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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32
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Souza ACO, Al Abdallah Q, DeJarnette K, Martin-Vicente A, Nywening AV, DeJarnette C, Sansevere EA, Ge W, Palmer GE, Fortwendel JR. Differential requirements of protein geranylgeranylation for the virulence of human pathogenic fungi. Virulence 2020; 10:511-526. [PMID: 31131706 PMCID: PMC6550545 DOI: 10.1080/21505594.2019.1620063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein prenylation is a crucial post-translational modification largely mediated by two heterodimeric enzyme complexes, farnesyltransferase and geranylgeranyltransferase type-I (GGTase-I), each composed of a shared α-subunit and a unique β-subunit. GGTase-I enzymes are validated drug targets that contribute to virulence in Cryptococcus neoformans and to the yeast-to-hyphal transition in Candida albicans. Therefore, we sought to investigate the importance of the α-subunit, RamB, and the β-subunit, Cdc43, of the A. fumigatus GGTase-I complex to hyphal growth and virulence. Deletion of cdc43 resulted in impaired hyphal morphogenesis and thermo-sensitivity, which was exacerbated during growth in rich media. The Δcdc43 mutant also displayed hypersensitivity to cell wall stress agents and to cell wall synthesis inhibitors, suggesting alterations of cell wall biosynthesis or stress signaling. In support of this, analyses of cell wall content revealed decreased amounts of β-glucan in the Δcdc43 strain. Despite strong in vitro phenotypes, the Δcdc43 mutant was fully virulent in two models of murine invasive aspergillosis, similar to the control strain. We further found that a strain expressing the α-subunit gene, ramB, from a tetracycline-inducible promoter was inviable under non-inducing in vitro growth conditions and was virtually avirulent in both mouse models. Lastly, virulence studies using C. albicans strains with tetracycline-repressible RAM2 or CDC43 expression revealed reduced pathogenicity associated with downregulation of either gene in a murine model of disseminated infection. Together, these findings indicate a differential requirement for protein geranylgeranylation for fungal virulence, and further inform the selection of specific prenyltransferases as promising antifungal drug targets for each pathogen.
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Affiliation(s)
- Ana Camila Oliveira Souza
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Qusai Al Abdallah
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Kaci DeJarnette
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Adela Martin-Vicente
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Ashley V Nywening
- b Department of Molecular Immunology and Biochemistry , College of Graduate Health Sciences, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Christian DeJarnette
- b Department of Molecular Immunology and Biochemistry , College of Graduate Health Sciences, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Emily A Sansevere
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Wenbo Ge
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Glen E Palmer
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
| | - Jarrod R Fortwendel
- a Department of Clinical Pharmacy and Translational Science , College of Pharmacy, University of Tennessee Health Science Center , Memphis , TN , USA
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33
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Rampogu S, Baek A, Son M, Park C, Yoon S, Parate S, Lee KW. Discovery of Lonafarnib-Like Compounds: Pharmacophore Modeling and Molecular Dynamics Studies. ACS OMEGA 2020; 5:1773-1781. [PMID: 32039312 PMCID: PMC7003205 DOI: 10.1021/acsomega.9b02263] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Progeria is a globally noticed rare genetic disorder manifested by premature aging with no effective treatment. Under these circumstances, farnesyltransferase inhibitors (FTIs) are marked as promising drug candidates. Correspondingly, a pharmacophore model was generated exploiting the features of lonafarnib. The selected pharmacophore model was allowed to screen the InterBioScreen natural compound database to retrieve the potential lead candidates. A series of filtering steps were applied to assess the drug-likeness of the compounds. The obtained compounds were advanced to molecular docking employing the CDOCKER module available with Discovery Studio (DS). Subsequently, three compounds (Hits) have displayed a higher dock score and demonstrated key residue interactions with stable molecular dynamics simulation results compared to the reference compound. Taken together, we therefore put forth three identified Hits as FTIs that may further serve as chemical spaces in designing new compounds.
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Affiliation(s)
- Shailima Rampogu
- Division of Life Science,
Division of Applied Life Science (BK21 Plus), Plant Molecular Biology
and Biotechnology Research Center (PMBBRC), Research Institute of
Natural Science (RINS), Gyeongsang National
University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Ayoung Baek
- Division of Life Science,
Division of Applied Life Science (BK21 Plus), Plant Molecular Biology
and Biotechnology Research Center (PMBBRC), Research Institute of
Natural Science (RINS), Gyeongsang National
University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Minky Son
- Division of Life Science,
Division of Applied Life Science (BK21 Plus), Plant Molecular Biology
and Biotechnology Research Center (PMBBRC), Research Institute of
Natural Science (RINS), Gyeongsang National
University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Chanin Park
- Division of Life Science,
Division of Applied Life Science (BK21 Plus), Plant Molecular Biology
and Biotechnology Research Center (PMBBRC), Research Institute of
Natural Science (RINS), Gyeongsang National
University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Sanghwa Yoon
- Division of Life Science,
Division of Applied Life Science (BK21 Plus), Plant Molecular Biology
and Biotechnology Research Center (PMBBRC), Research Institute of
Natural Science (RINS), Gyeongsang National
University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Shraddha Parate
- Division of Life Science,
Division of Applied Life Science (BK21 Plus), Plant Molecular Biology
and Biotechnology Research Center (PMBBRC), Research Institute of
Natural Science (RINS), Gyeongsang National
University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Life Science,
Division of Applied Life Science (BK21 Plus), Plant Molecular Biology
and Biotechnology Research Center (PMBBRC), Research Institute of
Natural Science (RINS), Gyeongsang National
University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
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34
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The Cellular Localization of the p42 and p46 Oligoadenylate Synthetase 1 Isoforms and Their Impact on Mitochondrial Respiration. Viruses 2019; 11:v11121122. [PMID: 31817188 PMCID: PMC6950736 DOI: 10.3390/v11121122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
The importance of the IFN-induced oligoadenylate synthetase (OAS) proteins and the OAS/RNase L pathway in the innate response against viral pathogens is well-established, however the observed differences in anti-viral activity between the human OAS1 p46 and p42 isoforms are not fully understood. The protein expression of these isoforms is determined by the SNP rs10774671, either being an A or a G allele resulting in expression of either the p42 or the p46 isoform. Using fluorescence microscopy and immunoblot analysis of fractionated cell samples, we show here that the CaaX motif is of key importance to the cellular localization. The OAS1 p42 isoform is mainly located in the cytosol, whereas the p46 isoform with a C-terminal CaaX motif is translocated to membranous organelles, like the mitochondria. We furthermore observed differences between p42 and p46 in their effect on mitochondrial physiology using high resolution respirometry and fluorometry. Overexpression of OAS1 p42 and IFN-β treatment of HeLa cells (AA genotype) resulted in significantly increased respiration, which was not seen with p46 overexpression. The difference in subcellular localization and mitochondrial effect of these two OAS1 isoforms might help to explain the anti-viral mechanisms that differentiate these proteins.
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35
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Messina S, De Simone G, Ascenzi P. Cysteine-based regulation of redox-sensitive Ras small GTPases. Redox Biol 2019; 26:101282. [PMID: 31386964 PMCID: PMC6695279 DOI: 10.1016/j.redox.2019.101282] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/21/2019] [Accepted: 07/24/2019] [Indexed: 12/22/2022] Open
Abstract
Reactive oxygen and nitrogen species (ROS and RNS, respectively) activate the redox-sensitive Ras small GTPases. The three canonical genes (HRAS, NRAS, and KRAS) are archetypes of the superfamily of small GTPases and are the most common oncogenes in human cancer. Oncogenic Ras is intimately linked to redox biology, mainly in the context of tumorigenesis. The Ras protein structure is highly conserved, especially in effector-binding regions. Ras small GTPases are redox-sensitive proteins thanks to the presence of the NKCD motif (Asn116-Lys 117-Cys118-Asp119). Notably, the ROS- and RNS-based oxidation of Cys118 affects protein stability, activity, and localization, and protein-protein interactions. Cys residues at positions 80, 181, 184, and 186 may also help modulate these actions. Moreover, oncogenic mutations of Gly12Cys and Gly13Cys may introduce additional oxidative centres and represent actionable drug targets. Here, the pathophysiological involvement of Cys-redox regulation of Ras proteins is reviewed in the context of cancer and heart and brain diseases.
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Affiliation(s)
- Samantha Messina
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, I-00146, Roma, Italy.
| | - Giovanna De Simone
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, I-00146, Roma, Italy
| | - Paolo Ascenzi
- Department of Science, Roma Tre University, Viale Guglielmo Marconi 446, I-00146, Roma, Italy
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36
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García-Torres D, Fierke CA. The chaperone SmgGDS-607 has a dual role, both activating and inhibiting farnesylation of small GTPases. J Biol Chem 2019; 294:11793-11804. [PMID: 31197034 DOI: 10.1074/jbc.ra119.007438] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/12/2019] [Indexed: 11/06/2022] Open
Abstract
Ras family small GTPases undergo prenylation (such as farnesylation) for proper localization to the plasma membrane, where they can initiate oncogenic signaling pathways. Small GTP-binding protein GDP-dissociation stimulator (SmgGDS) proteins are chaperones that bind and traffic small GTPases, although their exact cellular function is unknown. Initially, SmgGDS proteins were classified as guanine nucleotide exchange factors, but recent findings suggest that SmgGDS proteins also regulate prenylation of small GTPases in vivo in a substrate-selective manner. SmgGDS-607 recognizes the polybasic region and the CAAX box of several small GTPases and inhibits prenylation by impeding their entry into the geranylgeranylation pathway. Here, using recombinant and purified enzymes for prenylation and protein-binding assays, we demonstrate that SmgGDS-607 differentially regulates farnesylation of several small GTPases. SmgGDS-607 inhibited farnesylation of some proteins, such as DiRas1, by sequestering the protein and limiting modification catalyzed by protein farnesyltransferase (FTase). We found that the competitive binding affinities of the small GTPase for SmgGDS-607 and FTase dictate the extent of this inhibition. Additionally, we discovered that SmgGDS-607 increases the rate of farnesylation of HRas by enhancing product release from FTase. Our work indicates that SmgGDS-607 binds to a broad range of small GTPases and does not require a PBR for recognition. Together, these results provide mechanistic insight into SmgGDS-607-mediated regulation of farnesylation of small GTPases and suggest that SmgGDS-607 has multiple modes of substrate recognition.
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Affiliation(s)
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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37
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Booth DS, Szmidt-Middleton H, King N. Transfection of choanoflagellates illuminates their cell biology and the ancestry of animal septins. Mol Biol Cell 2018; 29:3026-3038. [PMID: 30281390 PMCID: PMC6333174 DOI: 10.1091/mbc.e18-08-0514] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/17/2022] Open
Abstract
As the closest living relatives of animals, choanoflagellates offer unique insights into animal origins and core mechanisms underlying animal cell biology. However, unlike traditional model organisms, such as yeast, flies, and worms, choanoflagellates have been refractory to DNA delivery methods for expressing foreign genes. Here we report a robust method for expressing transgenes in the choanoflagellate Salpingoeca rosetta, overcoming barriers that have previously hampered DNA delivery and expression. To demonstrate how this method accelerates the study of S. rosetta cell biology, we engineered a panel of fluorescent protein markers that illuminate key features of choanoflagellate cells. We then investigated the localization of choanoflagellate septins, a family of GTP-binding cytoskeletal proteins that are hypothesized to regulate multicellular rosette development in S. rosetta. Fluorescently tagged septins localized to the basal poles of S. rosetta single cells and rosettes in a pattern resembling septin localization in animal epithelia. The establishment of transfection in S. rosetta and its application to the study of septins represent critical advances in the use of S. rosetta as an experimental model for investigating choanoflagellate cell biology, core mechanisms underlying animal cell biology, and the origin of animals.
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Affiliation(s)
- David S. Booth
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Heather Szmidt-Middleton
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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38
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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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39
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Goel P, Alam O, Naim MJ, Nawaz F, Iqbal M, Alam MI. Recent advancement of piperidine moiety in treatment of cancer- A review. Eur J Med Chem 2018; 157:480-502. [DOI: 10.1016/j.ejmech.2018.08.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 03/26/2018] [Accepted: 08/04/2018] [Indexed: 12/23/2022]
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40
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Liu BS, Dai XY, Xia HW, Xu HJ, Tang QL, Gong QY, Nie YZ, Bi F. Geranylgeranyl transferase 1 inhibitor GGTI‑298 enhances the anticancer effect of gefitinib. Mol Med Rep 2018; 18:4023-4029. [PMID: 30106149 DOI: 10.3892/mmr.2018.9371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/11/2018] [Indexed: 02/05/2023] Open
Abstract
Dysregulation of epidermal growth factor receptor (EGFR) signaling is responsible for the resistance to EGFR tyrosine kinase inhibitors (TKIs), such as gefitinib and erlotinib, and is thereby associated with the progression of tumors in non‑small cell lung cancers (NSCLCs). Immunoblotting results revealed that geranylgeranyl transferase 1 inhibitor (GGTI)‑298, a geranylgeranyl transferase 1 inhibitor with potential antitumor effects, effectively inhibited the phosphorylation of EGFR and its downstream target protein kinase B (AKT). A combination of gefitinib and GGTI‑298 amplified the inhibition of the EGFR‑AKT signaling pathway. In addition, GGTI‑298 treatment produced a synergistic effect on the inhibition of proliferation as indicated by the combination index values of <1 when combined with gefitinib in the NSCLC cell lines HCC827 and A549. These synergistic effects were also observed to induce apoptosis and migration inhibition. Further mechanistic studies demonstrated that GGTI‑298 inhibited the activity of Ras homolog family member A (RhoA), and downregulation of RhoA with small interfering RNA impaired the phosphorylation of EGFR, which suggested that EGFR inhibition by GGTI‑298 may be exerted mainly through RhoA mediation. These results presented a novel, promising therapeutic strategy involving a combination of two drugs for targeting EGFR signaling in lung cancer.
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Affiliation(s)
- Bi-Sheng Liu
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xin-Yu Dai
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hong-Wei Xia
- Laboratory of Molecular Targeted Therapy in Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Huan-Ji Xu
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qiu-Lin Tang
- Laboratory of Molecular Targeted Therapy in Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qi-Yong Gong
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yong-Zhan Nie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digest Diseases, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Feng Bi
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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41
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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: 83] [Impact Index Per Article: 13.8] [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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42
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Wang X, Xu W, Zhan P, Xu T, Jin J, Miu Y, Zhou Z, Zhu Q, Wan B, Xi G, Ye L, Liu Y, Gao J, Li H, Lv T, Song Y. Overexpression of geranylgeranyl diphosphate synthase contributes to tumour metastasis and correlates with poor prognosis of lung adenocarcinoma. J Cell Mol Med 2018; 22:2177-2189. [PMID: 29377583 PMCID: PMC5867137 DOI: 10.1111/jcmm.13493] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022] Open
Abstract
This study aimed to evaluate the biological role of geranylgeranyl diphosphate synthase (GGPPS) in the progression of lung adenocarcinoma. GGPPS expression was detected in lung adenocarcinoma tissues by qRT‐PCR, tissue microarray (TMA) and western blotting. The relationships between GGPPS expression and the clinicopathological characteristics and prognosis of lung adenocarcinoma patients were assessed. GGPPS was down‐regulated in SPCA‐1, PC9 and A549 cells using siRNA and up‐regulated in A549 cells using an adenoviral vector. The biological roles of GGPPS in cell proliferation, apoptosis, migration and invasion were determined by MTT and colony formation assays, flow cytometry, and transwell and wound‐healing assays, respectively. In addition, the regulatory roles of GGPPS on the expression of several epithelial‐mesenchymal transition (EMT) markers were determined. Furthermore, the Rac1/Cdc42 prenylation was detected after knockdown of GGPPS in SPCA‐1 and PC9 cells. GGPPS expression was significantly increased in lung adenocarcinoma tissues compared to that in adjacent normal tissues. Overexpression of GGPPS was correlated with large tumours, high TNM stage, lymph node metastasis and poor prognosis in patients. Knockdown of GGPPS inhibited the migration and invasion of lung adenocarcinoma cells, but did not affect cell proliferation and apoptosis. Meanwhile, GGPPS inhibition significantly increased the expression of E‐cadherin and reduced the expression of N‐cadherin and vimentin in lung adenocarcinoma cells. In addition, the Rac1/Cdc42 geranylgeranylation was reduced by GGPPS knockdown. Overexpression of GGPPS correlates with poor prognosis of lung adenocarcinoma and contributes to metastasis through regulating EMT.
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Affiliation(s)
- Xiaoxia Wang
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China.,Intensive Care Unit, Inner Mongolia People's Hospital, Hohhot, China
| | - Wujian Xu
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Ping Zhan
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Tianxiang Xu
- Center of Tumor, Inner Mongolia People's Hospital, Hohhot, China
| | - Jiajia Jin
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Yingying Miu
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Zejun Zhou
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Qingqing Zhu
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Bing Wan
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Guangmin Xi
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Liang Ye
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Yafang Liu
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Jianwei Gao
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Huijuan Li
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Tangfeng Lv
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
| | - Yong Song
- Department of Respiratory Medicine, Jinling Hospital, Southern Medical University, Nanjing, China
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43
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Tebar F, Enrich C, Rentero C, Grewal T. GTPases Rac1 and Ras Signaling from Endosomes. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2018; 57:65-105. [PMID: 30097772 DOI: 10.1007/978-3-319-96704-2_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The endocytic compartment is not only the functional continuity of the plasma membrane but consists of a diverse collection of intracellular heterogeneous complex structures that transport, amplify, sustain, and/or sort signaling molecules. Over the years, it has become evident that early, late, and recycling endosomes represent an interconnected vesicular-tubular network able to form signaling platforms that dynamically and efficiently translate extracellular signals into biological outcome. Cell activation, differentiation, migration, death, and survival are some of the endpoints of endosomal signaling. Hence, to understand the role of the endosomal system in signal transduction in space and time, it is therefore necessary to dissect and identify the plethora of decoders that are operational in the different steps along the endocytic pathway. In this chapter, we focus on the regulation of spatiotemporal signaling in cells, considering endosomes as central platforms, in which several small GTPases proteins of the Ras superfamily, in particular Ras and Rac1, actively participate to control cellular processes like proliferation and cell mobility.
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Affiliation(s)
- Francesc Tebar
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain.
| | - Carlos Enrich
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain
| | - Carles Rentero
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Facultat de Medicina i Ciències de la Salut, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Casanova 143, 08036, Barcelona, Spain
| | - Thomas Grewal
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
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44
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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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Court H, Ahearn IM, Amoyel M, Bach EA, Philips MR. Regulation of NOTCH signaling by RAB7 and RAB8 requires carboxyl methylation by ICMT. J Cell Biol 2017; 216:4165-4182. [PMID: 29051265 PMCID: PMC5716267 DOI: 10.1083/jcb.201701053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 01/15/2023] Open
Abstract
Isoprenylcysteine carboxyl methyltransferase (ICMT) methylesterifies C-terminal prenylcysteine residues of CaaX proteins and some RAB GTPases. Deficiency of either ICMT or NOTCH1 accelerates pancreatic neoplasia in Pdx1-Cre;LSL-KrasG12D mice, suggesting that ICMT is required for NOTCH signaling. We used Drosophila melanogaster wing vein and scutellar bristle development to screen Rab proteins predicted to be substrates for ICMT (ste14 in flies). We identified Rab7 and Rab8 as ICMT substrates that when silenced phenocopy ste14 deficiency. ICMT, RAB7, and RAB8 were all required for efficient NOTCH1 signaling in mammalian cells. Overexpression of RAB8 rescued NOTCH activation after ICMT knockdown both in U2OS cells expressing NOTCH1 and in fly wing vein development. ICMT deficiency induced mislocalization of GFP-RAB7 and GFP-RAB8 from endomembrane to cytosol, enhanced binding to RABGDI, and decreased GTP loading of RAB7 and RAB8. Deficiency of ICMT, RAB7, or RAB8 led to mislocalization and diminished processing of NOTCH1-GFP. Thus, NOTCH signaling requires ICMT in part because it requires methylated RAB7 and RAB8.
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Affiliation(s)
- Helen Court
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| | - Ian M Ahearn
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| | - Marc Amoyel
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, England, UK
| | - Erika A Bach
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY
| | - Mark R Philips
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY
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Computational Exploration for Lead Compounds That Can Reverse the Nuclear Morphology in Progeria. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5270940. [PMID: 29226142 PMCID: PMC5684607 DOI: 10.1155/2017/5270940] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/24/2017] [Indexed: 01/01/2023]
Abstract
Progeria is a rare genetic disorder characterized by premature aging that eventually leads to death and is noticed globally. Despite alarming conditions, this disease lacks effective medications; however, the farnesyltransferase inhibitors (FTIs) are a hope in the dark. Therefore, the objective of the present article is to identify new compounds from the databases employing pharmacophore based virtual screening. Utilizing nine training set compounds along with lonafarnib, a common feature pharmacophore was constructed consisting of four features. The validated Hypo1 was subsequently allowed to screen Maybridge, Chembridge, and Asinex databases to retrieve the novel lead candidates, which were then subjected to Lipinski's rule of 5 and ADMET for drug-like assessment. The obtained 3,372 compounds were forwarded to docking simulations and were manually examined for the key interactions with the crucial residues. Two compounds that have demonstrated a higher dock score than the reference compounds and showed interactions with the crucial residues were subjected to MD simulations and binding free energy calculations to assess the stability of docked conformation and to investigate the binding interactions in detail. Furthermore, this study suggests that the Hits may be more effective against progeria and further the DFT studies were executed to understand their orbital energies.
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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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Norton TS, Al Abdallah Q, Hill AM, Lovingood RV, Fortwendel JR. The Aspergillus fumigatus farnesyltransferase β-subunit, RamA, mediates growth, virulence, and antifungal susceptibility. Virulence 2017; 8:1401-1416. [PMID: 28489963 PMCID: PMC5711395 DOI: 10.1080/21505594.2017.1328343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Post-translational prenylation mechanisms, including farnesylation and geranylgeranylation, mediate both subcellular localization and protein-protein interaction in eukaryotes. The prenyltransferase complex is an αβ heterodimer in which the essential α-subunit is common to both the farnesyltransferase and the geranylgeranyltransferase type-I enzymes. The β-subunit is unique to each enzyme. Farnesyltransferase activity is an important mediator of protein localization and subsequent signaling for multiple proteins, including Ras GTPases. Here, we examined the importance of protein farnesylation in the opportunistic fungal pathogen Aspergillus fumigatus through generation of a mutant lacking the farnesyltransferase β-subunit, ramA. Although farnesyltransferase activity was found to be non-essential in A. fumigatus, diminished hyphal outgrowth, delayed polarization kinetics, decreased conidial viability, and irregular distribution of nuclei during polarized growth were noted upon ramA deletion (ΔramA). Although predicted to be a target of the farnesyltransferase enzyme complex, we found that localization of the major A. fumigatus Ras GTPase protein, RasA, was only partially regulated by farnesyltransferase activity. Furthermore, the farnesyltransferase-deficient mutant exhibited attenuated virulence in a murine model of invasive aspergillosis, characterized by decreased tissue invasion and development of large, swollen hyphae in vivo. However, loss of ramA also led to a Cyp51A/B-independent increase in resistance to triazole antifungal drugs. Our findings indicate that protein farnesylation underpins multiple cellular processes in A. fumigatus, likely due to the large body of proteins affected by ramA deletion.
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Affiliation(s)
- Tiffany S Norton
- a Department of Microbiology and Immunology , University of South Alabama , Mobile , AL , USA
| | - Qusai Al Abdallah
- b Department of Clinical Pharmacy , University of Tennessee Health Science Center , Memphis , TN , USA
| | - Amy M Hill
- a Department of Microbiology and Immunology , University of South Alabama , Mobile , AL , USA
| | - Rachel V Lovingood
- a Department of Microbiology and Immunology , University of South Alabama , Mobile , AL , USA
| | - Jarrod R Fortwendel
- b Department of Clinical Pharmacy , University of Tennessee Health Science Center , Memphis , TN , USA
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Noguera-Salvà MA, Guardiola-Serrano F, Martin ML, Marcilla-Etxenike A, Bergo MO, Busquets X, Escribá PV. Role of the C-terminal basic amino acids and the lipid anchor of the Gγ 2 protein in membrane interactions and cell localization. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1536-1547. [PMID: 28235469 DOI: 10.1016/j.bbamem.2017.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/16/2017] [Accepted: 02/18/2017] [Indexed: 12/25/2022]
Abstract
Heterotrimeric G proteins are peripheral membrane proteins that frequently localize to the plasma membrane where their presence in molar excess over G protein coupled receptors permits signal amplification. Their distribution is regulated by protein-lipid interactions, which has a clear influence on their activity. Gβγ dimer drives the interaction between G protein heterotrimers with cell membranes. We focused our study on the role of the C-terminal region of the Gγ2 protein in G protein interactions with cell membranes. The Gγ2 subunit is modified at cysteine (Cys) 68 by the addition of an isoprenyl lipid, which is followed by the proteolytic removal of the last three residues that leaves an isoprenylated and carboxyl methylated Cys-68 as the terminal amino acid. The role of Cys isoprenylation of the CAAX box has been defined for other proteins, yet the importance of proteolysis and carboxyl methylation of isoprenylated proteins is less clear. Here, we showed that not only geranylgeranylation but also proteolysis and carboxyl methylation are essential for the correct localization of Gγ2 in the plasma membrane. Moreover, we showed the importance of electrostatic interactions between the inner leaflet of the plasma membrane and the positively charged C-terminal domain of the Gγ2 subunit (amino acids Arg-62, Lys-64 and Lys-65) as a second signal to reach the plasma membrane. Indeed, single or multiple point mutations at Gγ2 C-terminal amino acids have a significant effect on Gγ2 protein-plasma membrane interactions and its localization to charged Ld (liquid disordered) membrane microdomains. This article is part of a Special Issue entitled: Membrane Lipid Therapy: Drugs Targeting Biomembranes edited by Pablo V. Escribá.
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Affiliation(s)
- Maria A Noguera-Salvà
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, E-07122 Palma, Balearic Islands, Spain
| | - Francisca Guardiola-Serrano
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, E-07122 Palma, Balearic Islands, Spain
| | - M Laura Martin
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, E-07122 Palma, Balearic Islands, Spain
| | - Amaia Marcilla-Etxenike
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, E-07122 Palma, Balearic Islands, Spain
| | - Martin O Bergo
- Sahlgrenska Cancer Center, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Xavier Busquets
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, E-07122 Palma, Balearic Islands, Spain.
| | - Pablo V Escribá
- Laboratory of Molecular Cell Biomedicine, Department of Biology, University of the Balearic Islands, E-07122 Palma, Balearic Islands, Spain
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50
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Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind. Methods Mol Biol 2017; 1561:139-169. [PMID: 28236237 DOI: 10.1007/978-1-4939-6798-8_9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many signaling and regulatory processes involve peptide-mediated protein interactions, i.e., the binding of a short stretch in one protein to a domain in its partner. Computational tools that generate accurate models of peptide-receptor structures and binding improve characterization and manipulation of known interactions, help to discover yet unknown peptide-protein interactions and networks, and bring into reach the design of peptide-based drugs for targeting specific systems of medical interest.Here, we present a concise overview of the Rosetta FlexPepDock protocol and its derivatives that we have developed for the structure-based characterization of peptide-protein binding. Rosetta FlexPepDock was built to generate precise models of protein-peptide complex structures, by effectively addressing the challenge of the considerable conformational flexibility of the peptide. Rosetta FlexPepBind is an extension of this protocol that allows characterizing peptide-binding affinities and specificities of various biological systems, based on the structural models generated by Rosetta FlexPepDock. We provide detailed descriptions and guidelines for the usage of these protocols, and on a specific example, we highlight the variety of different challenges that can be met and the questions that can be answered with Rosetta FlexPepDock.
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