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Carmody PJ, Roushar FJ, Tedman A, Wang W, Herwig M, Kim M, McDonald EF, Noguera K, Wong-Roushar J, Poirier JL, Zelt NB, Pockrass BT, McKee AG, Kuntz CP, Raju SV, Plate L, Penn WD, Schlebach JP. Ribosomal frameshifting selectively modulates the assembly, function, and pharmacological rescue of a misfolded CFTR variant. Proc Natl Acad Sci U S A 2024; 121:e2414768121. [PMID: 39388263 DOI: 10.1073/pnas.2414768121] [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: 08/01/2024] [Accepted: 08/19/2024] [Indexed: 10/12/2024] Open
Abstract
The cotranslational misfolding of the cystic fibrosis transmembrane conductance regulator chloride channel (CFTR) plays a central role in the molecular basis of CF. The misfolding of the most common CF variant (ΔF508) remodels both the translational regulation and quality control of CFTR. Nevertheless, it is unclear how the misassembly of the nascent polypeptide may directly influence the activity of the translation machinery. In this work, we identify a structural motif within the CFTR transcript that stimulates efficient -1 ribosomal frameshifting and triggers the premature termination of translation. Though this motif does not appear to impact the interactome of wild-type CFTR, silent mutations that disrupt this RNA structure alter the association of nascent ΔF508 CFTR with numerous translation and quality control proteins. Moreover, disrupting this RNA structure enhances the functional gating of the ΔF508 CFTR channel at the plasma membrane and its pharmacological rescue by the CFTR modulators contained in the CF drug Trikafta. The effects of the RNA structure on ΔF508 CFTR appear to be attenuated in the absence of the ER membrane protein complex, which was previously found to modulate ribosome collisions during "preemptive quality control" of a misfolded CFTR homolog. Together, our results reveal that ribosomal frameshifting selectively modulates the assembly, function, and pharmacological rescue of a misfolded CFTR variant. These findings suggest that interactions between the nascent chain, quality control machinery, and ribosome may dynamically modulate ribosomal frameshifting in order to tune the processivity of translation in response to cotranslational misfolding.
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Affiliation(s)
- Patrick J Carmody
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | - Francis J Roushar
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | - Austin Tedman
- The James Tarpo Junior and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Wei Wang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Madeline Herwig
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240
| | - Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37240
| | - Eli F McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240
| | - Karen Noguera
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | | | - Jon-Luc Poirier
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | - Nathan B Zelt
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | - Ben T Pockrass
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | - Andrew G McKee
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | - Charles P Kuntz
- The James Tarpo Junior and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - S Vamsee Raju
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37240
| | - Wesley D Penn
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN 47401
| | - Jonathan P Schlebach
- The James Tarpo Junior and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN 47907
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Carmody P, Roushar FJ, Tedman A, Wang W, Herwig M, Kim M, McDonald EF, Noguera K, Wong-Roushar J, Poirier JL, Zelt NB, Pockrass BT, McKee AG, Kuntz CP, Raju SV, Plate L, Penn WD, Schlebach JP. Ribosomal Frameshifting Selectively Modulates the Assembly, Function, and Pharmacological Rescue of a Misfolded CFTR Variant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.02.539166. [PMID: 39091758 PMCID: PMC11290997 DOI: 10.1101/2023.05.02.539166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The cotranslational misfolding of the cystic fibrosis transmembrane conductance regulator chloride channel (CFTR) plays a central role in the molecular basis of cystic fibrosis (CF). The misfolding of the most common CF variant (ΔF508) remodels both the translational regulation and quality control of CFTR. Nevertheless, it is unclear how the misassembly of the nascent polypeptide may directly influence the activity of the translation machinery. In this work, we identify a structural motif within the CFTR transcript that stimulates efficient -1 ribosomal frameshifting and triggers the premature termination of translation. Though this motif does not appear to impact the interactome of wild-type CFTR, silent mutations that disrupt this RNA structure alter the association of nascent ΔF508 CFTR with numerous translation and quality control proteins. Moreover, disrupting this RNA structure enhances the functional gating of the ΔF508 CFTR channel at the plasma membrane and its pharmacological rescue by the CFTR modulators contained in the CF drug Trikafta. The effects of the RNA structure on ΔF508 CFTR appear to be attenuated in the absence of the ER membrane protein complex (EMC), which was previously found to modulate ribosome collisions during "preemptive quality control" of a misfolded CFTR homolog. Together, our results reveal that ribosomal frameshifting selectively modulates the assembly, function, and pharmacological rescue of a misfolded CFTR variant. These findings suggest interactions between the nascent chain, quality control machinery, and ribosome may dynamically modulate ribosomal frameshifting in order to tune the processivity of translation in response to cotranslational misfolding.
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Affiliation(s)
- Patrick Carmody
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Francis J. Roushar
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Austin Tedman
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907
| | - Wei Wang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Madeline Herwig
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
| | - Minsoo Kim
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, USA 37240
| | - Eli F. McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
| | - Karen Noguera
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | | | - Jon-Luc Poirier
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Nathan B. Zelt
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Ben T. Pockrass
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Andrew G. McKee
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Charles P. Kuntz
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907
| | - S. Vamsee Raju
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA 35233
| | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37240
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA 37240
| | - Wesley D. Penn
- Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA 47401
| | - Jonathan P. Schlebach
- The James Tarpo Jr. and Margaret Tarpo Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907
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Ferreira FC, Buarque CD, Lopes-Pacheco M. Organic Synthesis and Current Understanding of the Mechanisms of CFTR Modulator Drugs Ivacaftor, Tezacaftor, and Elexacaftor. Molecules 2024; 29:821. [PMID: 38398574 PMCID: PMC10891718 DOI: 10.3390/molecules29040821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The monogenic rare disease Cystic Fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance (CFTR) protein, an anion channel expressed at the apical plasma membrane of epithelial cells. The discovery and subsequent development of CFTR modulators-small molecules acting on the basic molecular defect in CF-have revolutionized the standard of care for people with CF (PwCF), thus drastically improving their clinical features, prognosis, and quality of life. Currently, four of these drugs are approved for clinical use: potentiator ivacaftor (VX-770) alone or in combination with correctors lumacaftor, (VX-809), tezacaftor (VX-661), and elexacaftor (VX-445). Noteworthily, the triple combinatorial therapy composed of ivacaftor, tezacaftor, and elexacaftor constitutes the most effective modulator therapy nowadays for the majority of PwCF. In this review, we exploit the organic synthesis of ivacaftor, tezacaftor, and elexacaftor by providing a retrosynthetic drug analysis for these CFTR modulators. Furthermore, we describe the current understanding of the mechanisms of action (MoA's) of these compounds by discussing several studies that report the key findings on the molecular mechanisms underlying their action on the CFTR protein.
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Affiliation(s)
- Filipa C. Ferreira
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Camilla D. Buarque
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro (PUC-Rio), Rio de Janeiro 22435-900, RJ, Brazil
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
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McDonald EF, Meiler J, Plate L. CFTR Folding: From Structure and Proteostasis to Cystic Fibrosis Personalized Medicine. ACS Chem Biol 2023; 18:2128-2143. [PMID: 37730207 PMCID: PMC10595991 DOI: 10.1021/acschembio.3c00310] [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: 05/25/2023] [Accepted: 08/02/2023] [Indexed: 09/22/2023]
Abstract
Cystic fibrosis (CF) is a lethal genetic disease caused by mutations in the chloride ion channel cystic fibrosis transmembrane conductance regulator (CFTR). Class-II mutants of CFTR lack intermolecular interactions important for CFTR structural stability and lead to misfolding. Misfolded CFTR is detected by a diverse suite of proteostasis factors that preferentially bind and route mutant CFTR toward premature degradation, resulting in reduced plasma membrane CFTR levels and impaired chloride ion conductance associated with CF. CF treatment has been vastly improved over the past decade by the availability of small molecules called correctors. Correctors directly bind CFTR, stabilize its structure by conferring thermodynamically favorable interactions that compensate for mutations, and thereby lead to downstream folding fidelity. However, each of over 100 Class-II CF causing mutations causes unique structural defects and shows a unique response to drug treatment, described as theratype. Understanding CFTR structural defects, the proteostasis factors evaluating those defects, and the stabilizing effects of CFTR correctors will illuminate a path toward personalized medicine for CF. Here, we review recent advances in our understanding of CFTR folding, focusing on structure, corrector binding sites, the mechanisms of proteostasis factors that evaluate CFTR, and the implications for CF personalized medicine.
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Affiliation(s)
- Eli Fritz McDonald
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jens Meiler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Institute
for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Lars Plate
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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Sivadas A, McDonald EF, Shuster SO, Davis CM, Plate L. Site-Specific Crosslinking Reveals Phosphofructokinase-L Inhibition Drives Self-Assembly and Attenuation of Protein Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558525. [PMID: 37781627 PMCID: PMC10541129 DOI: 10.1101/2023.09.19.558525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Phosphofructokinase is the central enzyme in glycolysis and constitutes a highly regulated step. The liver isoform (PFKL) compartmentalizes during activation and inhibition in vitro and in vivo respectively. Compartmentalized PFKL is hypothesized to modulate metabolic flux consistent with its central role as the rate limiting step in glycolysis. PFKL tetramers self-assemble at two interfaces in the monomer (interface 1 and 2), yet how these interfaces contribute to PFKL compartmentalization and drive protein interactions remains unclear. Here, we used site-specific incorporation of noncanonical photocrosslinking amino acids to identify PFKL interactors at interface 1, 2, and the active site. Tandem mass tag-based quantitative interactomics reveals interface 2 as a hotspot for PFKL interactions, particularly with cytoskeletal, glycolytic, and carbohydrate derivative metabolic proteins. Furthermore, PFKL compartmentalization into puncta was observed in human cells using citrate inhibition. Puncta formation attenuated crosslinked protein-protein interactions with the cytoskeleton at interface 2. This result suggests that PFKL compartmentalization sequesters interface 2, but not interface 1, and may modulate associated protein assemblies with the cytoskeleton.
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Affiliation(s)
- Athira Sivadas
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Eli Fritz McDonald
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | | | | | - Lars Plate
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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Nimer RM, Abdel Rahman AM. Recent advances in proteomic-based diagnostics of cystic fibrosis. Expert Rev Proteomics 2023; 20:151-169. [PMID: 37766616 DOI: 10.1080/14789450.2023.2258282] [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: 01/03/2023] [Accepted: 07/06/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF. AREAS COVERED We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers. EXPERT OPINION Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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