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Mangkalaphiban K, Fu L, Du M, Thrasher K, Keeling KM, Bedwell DM, Jacobson A. Extended stop codon context predicts nonsense codon readthrough efficiency in human cells. Nat Commun 2024; 15:2486. [PMID: 38509072 PMCID: PMC10954755 DOI: 10.1038/s41467-024-46703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Protein synthesis terminates when a stop codon enters the ribosome's A-site. Although termination is efficient, stop codon readthrough can occur when a near-cognate tRNA outcompetes release factors during decoding. Seeking to understand readthrough regulation we used a machine learning approach to analyze readthrough efficiency data from published HEK293T ribosome profiling experiments and compared it to comparable yeast experiments. We obtained evidence for the conservation of identities of the stop codon, its context, and 3'-UTR length (when termination is compromised), but not the P-site codon, suggesting a P-site tRNA role in readthrough regulation. Models trained on data from cells treated with the readthrough-promoting drug, G418, accurately predicted readthrough of premature termination codons arising from CFTR nonsense alleles that cause cystic fibrosis. This predictive ability has the potential to aid development of nonsense suppression therapies by predicting a patient's likelihood of improvement in response to drugs given their nonsense mutation sequence context.
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Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
- Department of Genomics and Computational Biology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Ming Du
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kari Thrasher
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.
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2
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Li C, Liu Z, Anderson J, Liu Z, Tang L, Li Y, Peng N, Chen J, Liu X, Fu L, Townes TM, Rowe SM, Bedwell DM, Guimbellot J, Zhao R. Prime editing-mediated correction of the CFTR W1282X mutation in iPSCs and derived airway epithelial cells. PLoS One 2023; 18:e0295009. [PMID: 38019847 PMCID: PMC10686454 DOI: 10.1371/journal.pone.0295009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
A major unmet need in the cystic fibrosis (CF) therapeutic landscape is the lack of effective treatments for nonsense CFTR mutations, which affect approximately 10% of CF patients. Correction of nonsense CFTR mutations via genomic editing represents a promising therapeutic approach. In this study, we tested whether prime editing, a novel CRISPR-based genomic editing method, can be a potential therapeutic modality to correct nonsense CFTR mutations. We generated iPSCs from a CF patient homozygous for the CFTR W1282X mutation. We demonstrated that prime editing corrected one mutant allele in iPSCs, which effectively restored CFTR function in iPSC-derived airway epithelial cells and organoids. We further demonstrated that prime editing may directly repair mutations in iPSC-derived airway epithelial cells when the prime editing machinery is efficiently delivered by helper-dependent adenovirus (HDAd). Together, our data demonstrated that prime editing may potentially be applied to correct CFTR mutations such as W1282X.
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Affiliation(s)
- Chao Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zhong Liu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Justin Anderson
- Department of Pediatrics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zhongyu Liu
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Liping Tang
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yao Li
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ning Peng
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jianguo Chen
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Xueming Liu
- Key Laboratory of Imaging Processing and Intelligent Control, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tim M. Townes
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Steven M. Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David M. Bedwell
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jennifer Guimbellot
- Department of Pediatrics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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3
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Chen J, Thrasher K, Fu L, Wang W, Aghamohammadzadeh S, Wen H, Tang L, Keeling KM, Falk Libby E, Bedwell DM, Rowe SM. The synthetic aminoglycoside ELX-02 induces readthrough of G550X-CFTR producing super-functional protein that can be further enhanced by CFTR modulators. Am J Physiol Lung Cell Mol Physiol 2023; 324:L756-L770. [PMID: 37014818 DOI: 10.1152/ajplung.00038.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Ten percent of cystic fibrosis (CF) patients carry a Premature Termination Codon (PTC); no nutation-specific therapies exist for these individuals. ELX-02, a synthetic aminoglycoside, suppresses translation termination at PTCs (i.e., readthrough) by promoting the insertion of an amino acid at the PTC and restoring expression of full-length CFTR protein. The identity of amino acids inserted at PTCs affects the processing and function of the resulting full-length CFTR protein. We examined readthrough of the rare G550X-CFTR nonsense mutation due to its unique properties. We found that forskolin-induced swelling in G550X patient-derived intestinal organoids (PDOs) was significantly higher than in G542X PDOs (both UGA PTCs) with ELX-02 treatment, indicating greater CFTR function from the G550X allele. Using mass spectrometry, we identified tryptophan as the sole amino acid inserted in the G550X position during ELX-02 or G418 mediated readthrough, which differs from that three amino acids (cysteine, arginine, and tryptophan) inserted in the G542X position following treatment with G418. Compared to wildtype CFTR, FRT cells expressing the G550W-CFTR variant protein exhibited significantly increased forskolin-activated Cl- conductance, and G550W-CFTR channels showed increased PKA sensitivity and open probability. Following treatment with ELX-02 and CFTR correctors, CFTR function rescued from the G550X allele in FRTs reached 20%-40% of the wildtype level. These results suggest that readthrough of G550X produces greater CFTR function due to gain-of-function properties of the CFTR readthrough product that stems from its location in the signature LSGGQ motif found in ABC transporters. G550X may be a particularly sensitive target for translational readthrough therapy.
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Affiliation(s)
- Jianguo Chen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kari Thrasher
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Wei Wang
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | | | - Hui Wen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Liping Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Emily Falk Libby
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
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4
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Siddiqui A, Dundar H, Sharma J, Kaczmarczyk A, Echols J, Dai Y, Sun CR, Du M, Liu Z, Zhao R, Wood T, Sanders S, Rasmussen L, Bostwick JR, Augelli-Szafran C, Suto M, Rowe SM, Bedwell DM, Keeling KM. Triamterene Functions as an Effective Nonsense Suppression Agent for MPS I-H (Hurler Syndrome). Int J Mol Sci 2023; 24:4521. [PMID: 36901952 PMCID: PMC10003437 DOI: 10.3390/ijms24054521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Mucopolysaccharidosis I-Hurler (MPS I-H) is caused by the loss of α-L-iduronidase, a lysosomal enzyme that degrades glycosaminoglycans. Current therapies cannot treat many MPS I-H manifestations. In this study, triamterene, an FDA-approved, antihypertensive diuretic, was found to suppress translation termination at a nonsense mutation associated with MPS I-H. Triamterene rescued enough α-L-iduronidase function to normalize glycosaminoglycan storage in cell and animal models. This new function of triamterene operates through premature termination codon (PTC) dependent mechanisms that are unaffected by epithelial sodium channel activity, the target of triamterene's diuretic function. Triamterene represents a potential non-invasive treatment for MPS I-H patients carrying a PTC.
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Affiliation(s)
- Amna Siddiqui
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Halil Dundar
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Next Generation Sequencing Transplant Diagnostics, Thermo-Fisher Scientific, West Hills, CA 91304, USA
| | - Jyoti Sharma
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Division of Infectious Diseases, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aneta Kaczmarczyk
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- ARUP Laboratories, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Josh Echols
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yanying Dai
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chuanxi Richard Sun
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ming Du
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zhong Liu
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rui Zhao
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tim Wood
- Greenwood Genetic Center, Greenwood, SC 29646, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | | | | | | | - Mark Suto
- Southern Research, Birmingham, AL 35205, USA
| | - Steven M. Rowe
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David M. Bedwell
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim M. Keeling
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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5
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Long A, Liu H, Liu J, Daniel M, Bedwell DM, Korf B, Kesterson RA, Wallis D. Analysis of patient-specific NF1 variants leads to functional insights for Ras signaling that can impact personalized medicine. Hum Mutat 2021; 43:30-41. [PMID: 34694046 DOI: 10.1002/humu.24290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 01/04/2023]
Abstract
We have created a panel of 29 NF1 variant complementary DNAs (cDNAs) representing missense variants, many with clinically relevant phenotypes, in-frame deletions, splice variants, and nonsense variants. We have determined the functional consequences of the variants, assessing their ability to produce mature neurofibromin and restore Ras signaling activity in NF1 null (-/-) cells. cDNAs demonstrate variant-specific differences in neurofibromin protein levels, suggesting that some variants lead to neurofibromatosis type 1 (NF1) gene or protein instability or enhanced degradation. When expressed at high levels, some variant proteins are still able to repress Ras activity, indicating that the NF1 phenotype may be due to low protein abundance. In contrast, other variant proteins are incapable of repressing Ras activity, indicating that some do not functionally engage Ras and stimulate GTPase activity. We observed that effects on protein abundance and Ras activity can be mutually exclusive. These assays allow us to categorize variants by functional effects, may help to classify variants of unknown significance, and may have future implications for more directed therapeutics.
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Affiliation(s)
- Ashlee Long
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Hui Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jian Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael Daniel
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Bruce Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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6
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Sharma J, Du M, Wong E, Mutyam V, Li Y, Chen J, Wangen J, Thrasher K, Fu L, Peng N, Tang L, Liu K, Mathew B, Bostwick RJ, Augelli-Szafran CE, Bihler H, Liang F, Mahiou J, Saltz J, Rab A, Hong J, Sorscher EJ, Mendenhall EM, Coppola CJ, Keeling KM, Green R, Mense M, Suto MJ, Rowe SM, Bedwell DM. A small molecule that induces translational readthrough of CFTR nonsense mutations by eRF1 depletion. Nat Commun 2021; 12:4358. [PMID: 34272367 PMCID: PMC8285393 DOI: 10.1038/s41467-021-24575-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/22/2021] [Indexed: 11/09/2022] Open
Abstract
Premature termination codons (PTCs) prevent translation of a full-length protein and trigger nonsense-mediated mRNA decay (NMD). Nonsense suppression (also termed readthrough) therapy restores protein function by selectively suppressing translation termination at PTCs. Poor efficacy of current readthrough agents prompted us to search for better compounds. An NMD-sensitive NanoLuc readthrough reporter was used to screen 771,345 compounds. Among the 180 compounds identified with readthrough activity, SRI-37240 and its more potent derivative SRI-41315, induce a prolonged pause at stop codons and suppress PTCs associated with cystic fibrosis in immortalized and primary human bronchial epithelial cells, restoring CFTR expression and function. SRI-41315 suppresses PTCs by reducing the abundance of the termination factor eRF1. SRI-41315 also potentiates aminoglycoside-mediated readthrough, leading to synergistic increases in CFTR activity. Combining readthrough agents that target distinct components of the translation machinery is a promising treatment strategy for diseases caused by PTCs. Premature termination codons can cause early translation termination and lead to disease. Here the authors perform a screen to identify compounds with readthrough activity and show that these reduce eRF1 levels to suppress premature termination associated with cystic fibrosis.
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Affiliation(s)
- Jyoti Sharma
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Microbiology, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Ming Du
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Eric Wong
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Venkateshwar Mutyam
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Yao Li
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Jianguo Chen
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Jamie Wangen
- Department of Molecular Biology and Genetics and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kari Thrasher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Lianwu Fu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Ning Peng
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Liping Tang
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Kaimao Liu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | | | | | | | - Hermann Bihler
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Feng Liang
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Jerome Mahiou
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Josef Saltz
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Jeong Hong
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Eric J Sorscher
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Eric M Mendenhall
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Candice J Coppola
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Kim M Keeling
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin Mense
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | | | - Steven M Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Pediatrics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - David M Bedwell
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA. .,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.
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7
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Leier A, Bedwell DM, Chen AT, Dickson G, Keeling KM, Kesterson RA, Korf BR, Marquez Lago TT, Müller UF, Popplewell L, Zhou J, Wallis D. Mutation-Directed Therapeutics for Neurofibromatosis Type I. Mol Ther Nucleic Acids 2020; 20:739-753. [PMID: 32408052 PMCID: PMC7225739 DOI: 10.1016/j.omtn.2020.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
Significant advances in biotechnology have led to the development of a number of different mutation-directed therapies. Some of these techniques have matured to a level that has allowed testing in clinical trials, but few have made it to approval by drug-regulatory bodies for the treatment of specific diseases. While there are still various hurdles to be overcome, recent success stories have proven the potential power of mutation-directed therapies and have fueled the hope of finding therapeutics for other genetic disorders. In this review, we summarize the state-of-the-art of various therapeutic approaches and assess their applicability to the genetic disorder neurofibromatosis type I (NF1). NF1 is caused by the loss of function of neurofibromin, a tumor suppressor and downregulator of the Ras signaling pathway. The condition is characterized by a variety of phenotypes and includes symptoms such as skin spots, nervous system tumors, skeletal dysplasia, and others. Hence, depending on the patient, therapeutics may need to target different tissues and cell types. While we also discuss the delivery of therapeutics, in particular via viral vectors and nanoparticles, our main focus is on therapeutic techniques that reconstitute functional neurofibromin, most notably cDNA replacement, CRISPR-based DNA repair, RNA repair, antisense oligonucleotide therapeutics including exon skipping, and nonsense suppression.
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Affiliation(s)
- Andre Leier
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ann T Chen
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - George Dickson
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Linda Popplewell
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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8
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Keeling KM, Bedwell DM. Finding sense in the context. eLife 2020; 9:55960. [PMID: 32202493 PMCID: PMC7089764 DOI: 10.7554/elife.55960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Ribosomal profiling has shed new light on how ribosomes can ignore stop codons in messenger RNA.
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Affiliation(s)
- Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, United States.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, United States
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, United States.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, United States
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9
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Xue X, Mutyam V, Thakerar A, Mobley J, Bridges RJ, Rowe SM, Keeling KM, Bedwell DM. Identification of the amino acids inserted during suppression of CFTR nonsense mutations and determination of their functional consequences. Hum Mol Genet 2017; 26:3116-3129. [PMID: 28575328 PMCID: PMC5886253 DOI: 10.1093/hmg/ddx196] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/14/2017] [Accepted: 05/17/2017] [Indexed: 11/13/2022] Open
Abstract
In-frame premature termination codons (PTCs) account for ∼11% of all disease-associated mutations. PTC suppression therapy utilizes small molecules that suppress translation termination at a PTC to restore synthesis of a full-length protein. PTC suppression is mediated by the base pairing of a near-cognate aminoacyl-tRNA with a PTC and subsequently, the amino acid becomes incorporated into the nascent polypeptide at the site of the PTC. However, little is known about the identity of the amino acid(s) inserted at a PTC during this process in mammalian cells, or how the surrounding sequence context influences amino acid incorporation. Here, we determined the amino acids inserted at the cystic fibrosis transmembrane conductance regulator (CFTR) W1282X PTC (a UGA codon) in the context of its three upstream and downstream CFTR codons during G418-mediated suppression. We found that leucine, cysteine and tryptophan are inserted during W1282X suppression. Interestingly, these amino acids (and their proportions) are significantly different from those recently identified following G418-mediated suppression of the CFTR G542X UGA mutation. These results demonstrate for the first time that local mRNA sequence context plays a key role in near-cognate aminoacyl-tRNA selection during PTC suppression. We also found that some variant CFTR proteins generated by PTC suppression exhibit reduced maturation and activity, indicating the complexity of nonsense suppression therapy. However, both a CFTR corrector and potentiator enhanced activity of protein variants generated by G418-mediated suppression. These results suggest that PTC suppression in combination with CFTR modulators may be beneficial for the treatment of CF patients with PTCs.
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Affiliation(s)
- Xiaojiao Xue
- Department of Biochemistry and Molecular Genetics
- Gregory Fleming James Cystic Fibrosis Research Center
| | - Venkateshwar Mutyam
- Gregory Fleming James Cystic Fibrosis Research Center
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amita Thakerar
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL 60064, USA
| | - James Mobley
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert J. Bridges
- Department of Physiology and Biophysics, Chicago Medical School, North Chicago, IL 60064, USA
| | - Steven M. Rowe
- Gregory Fleming James Cystic Fibrosis Research Center
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim M. Keeling
- Department of Biochemistry and Molecular Genetics
- Gregory Fleming James Cystic Fibrosis Research Center
| | - David M. Bedwell
- Department of Biochemistry and Molecular Genetics
- Gregory Fleming James Cystic Fibrosis Research Center
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10
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Mutyam V, Du M, Xue X, Keeling KM, White EL, Bostwick JR, Rasmussen L, Liu B, Mazur M, Hong JS, Falk Libby E, Liang F, Shang H, Mense M, Suto MJ, Bedwell DM, Rowe SM. Discovery of Clinically Approved Agents That Promote Suppression of Cystic Fibrosis Transmembrane Conductance Regulator Nonsense Mutations. Am J Respir Crit Care Med 2017; 194:1092-1103. [PMID: 27104944 DOI: 10.1164/rccm.201601-0154oc] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
RATIONALE Premature termination codons (PTCs) in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). Several agents are known to suppress PTCs but are poorly efficacious or toxic. OBJECTIVES To determine whether there are clinically available agents that elicit translational readthrough and improve CFTR function sufficient to confer therapeutic benefit to patients with CF with PTCs. METHODS Two independent screens, firefly luciferase and CFTR-mediated transepithelial chloride conductance assay, were performed on a library of 1,600 clinically approved compounds using fisher rat thyroid cells stably transfected with stop codons. Select agents were further evaluated using secondary screening assays including short circuit current analysis on primary cells from patients with CF. In addition, the effect of CFTR modulators (ivacaftor) was tested in combination with the most efficacious agents. MEASUREMENTS AND MAIN RESULTS From the primary screen, 48 agents were selected as potentially active. Following confirmatory tests in the transepithelial chloride conductance assay and prioritizing agents based on favorable pharmacologic properties, eight agents were advanced for secondary screening. Ivacaftor significantly increased short circuit current following forskolin stimulation in cells treated with pyranoradine tetraphosphate, potassium p-aminobenzoate, and escin as compared with vehicle control. Escin, an herbal agent, consistently induced readthrough activity as demonstrated by enhanced CFTR expression and function in vitro. CONCLUSIONS Clinically approved drugs identified as potential readthrough agents, in combination with ivacaftor, may induce nonsense suppression to restore therapeutic levels of CFTR function. One or more agents may be suitable to advance to human testing.
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Affiliation(s)
| | - Ming Du
- 2 Department of Microbiology
| | | | | | | | | | | | | | - Marina Mazur
- 4 Gregory Fleming James Cystic Fibrosis Research Center
| | - Jeong S Hong
- 4 Gregory Fleming James Cystic Fibrosis Research Center.,5 Department of Cell Developmental and Integrative Biology, and
| | | | - Feng Liang
- 6 Cystic Fibrosis Foundation Therapeutics, Boston, Massachusetts
| | - Haibo Shang
- 6 Cystic Fibrosis Foundation Therapeutics, Boston, Massachusetts
| | - Martin Mense
- 6 Cystic Fibrosis Foundation Therapeutics, Boston, Massachusetts
| | - Mark J Suto
- 3 Southern Research, Birmingham, Alabama; and
| | - David M Bedwell
- 2 Department of Microbiology.,4 Gregory Fleming James Cystic Fibrosis Research Center
| | - Steven M Rowe
- 1 Department of Medicine.,4 Gregory Fleming James Cystic Fibrosis Research Center.,5 Department of Cell Developmental and Integrative Biology, and.,7 Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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11
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Li K, Turner AN, Chen M, Brosius SN, Schoeb TR, Messiaen LM, Bedwell DM, Zinn KR, Anastasaki C, Gutmann DH, Korf BR, Kesterson RA. Mice with missense and nonsense NF1 mutations display divergent phenotypes compared with human neurofibromatosis type I. Dis Model Mech 2016; 9:759-67. [PMID: 27482814 PMCID: PMC4958313 DOI: 10.1242/dmm.025783] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/25/2016] [Indexed: 12/19/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a common genetic disorder characterized by the occurrence of nerve sheath tumors and considerable clinical heterogeneity. Some translational studies have been limited by the lack of animal models available for assessing patient-specific mutations. In order to test therapeutic approaches that might restore function to the mutated gene or gene product, we developed mice harboring NF1 patient-specific mutations including a nonsense mutation (c.2041C>T; p.Arg681*) and a missense mutation (c.2542G>C; p.Gly848Arg). The latter is associated with the development of multiple plexiform neurofibromas along spinal nerve roots. We demonstrate that the human nonsense NF1(Arg681*) and missense NF1(Gly848Arg) mutations have different effects on neurofibromin expression in the mouse and each recapitulates unique aspects of the NF1 phenotype, depending upon the genetic context when assessed in the homozygous state or when paired with a conditional knockout allele. Whereas the missense Nf1(Gly848Arg) mutation fails to produce an overt phenotype in the mouse, animals homozygous for the nonsense Nf1(Arg681*) mutation are not viable. Mice with one Nf1(Arg681*) allele in combination with a conditional floxed Nf1 allele and the DhhCre transgene (Nf1(4F/Arg681*); DhhCre) display disorganized nonmyelinating axons and neurofibromas along the spinal column, which leads to compression of the spinal cord and paralysis. This model will be valuable for preclinical testing of novel nonsense suppression therapies using drugs to target in-frame point mutations that create premature termination codons in individuals with NF1.
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Affiliation(s)
- Kairong Li
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ashley N Turner
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Min Chen
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephanie N Brosius
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA Medical Scientist Training Program, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Trenton R Schoeb
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ludwine M Messiaen
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kurt R Zinn
- Department of Radiology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Corina Anastasaki
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bruce R Korf
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert A Kesterson
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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12
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Kelly SP, Bedwell DM. Both the autophagy and proteasomal pathways facilitate the Ubp3p-dependent depletion of a subset of translation and RNA turnover factors during nitrogen starvation in Saccharomyces cerevisiae. RNA 2015; 21:898-910. [PMID: 25795416 PMCID: PMC4408797 DOI: 10.1261/rna.045211.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 01/05/2015] [Indexed: 05/20/2023]
Abstract
Protein turnover is an important regulatory mechanism that facilitates cellular adaptation to changing environmental conditions. Previous studies have shown that ribosome abundance is reduced during nitrogen starvation by a selective autophagy mechanism termed ribophagy, which is dependent upon the deubiquitinase Ubp3p. In this study, we asked whether the abundance of various translation and RNA turnover factors are reduced following the onset of nitrogen starvation in Saccharomyces cerevisiae. We found distinct differences in the abundance of the proteins tested following nitrogen starvation: (1) The level of some did not change; (2) others were reduced with kinetics similar to ribophagy, and (3) a few proteins were rapidly depleted. Furthermore, different pathways differentially degraded the various proteins upon nitrogen starvation. The translation factors eRF3 and eIF4GI, and the decapping enhancer Pat1p, required an intact autophagy pathway for their depletion. In contrast, the deadenylase subunit Pop2p and the decapping enzyme Dcp2p were rapidly depleted by a proteasome-dependent mechanism. The proteasome-dependent depletion of Dcp2p and Pop2p was also induced by rapamycin, suggesting that the TOR1 pathway influences this pathway. Like ribophagy, depletion of eIF4GI, eRF3, Dcp2p, and Pop2p was dependent upon Ubp3p to varying extents. Together, our results suggest that the autophagy and proteasomal pathways degrade distinct translation and RNA turnover factors in a Ubp3p-dependent manner during nitrogen starvation. While ribophagy is thought to mediate the reutilization of scarce resources during nutrient limitation, our results suggest that the selective degradation of specific proteins could also facilitate a broader reprogramming of the post-transcriptional control of gene expression.
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Affiliation(s)
- Shane P Kelly
- Department of Cell, Developmental and Integrative Biology, Birmingham, Alabama 35294, USA
| | - David M Bedwell
- Department of Cell, Developmental and Integrative Biology, Birmingham, Alabama 35294, USA Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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13
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Xue X, Mutyam V, Tang L, Biswas S, Du M, Jackson LA, Dai Y, Belakhov V, Shalev M, Chen F, Schacht J, J Bridges R, Baasov T, Hong J, Bedwell DM, Rowe SM. Synthetic aminoglycosides efficiently suppress cystic fibrosis transmembrane conductance regulator nonsense mutations and are enhanced by ivacaftor. Am J Respir Cell Mol Biol 2014; 50:805-16. [PMID: 24251786 DOI: 10.1165/rcmb.2013-0282oc] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
New drugs are needed to enhance premature termination codon (PTC) suppression to treat the underlying cause of cystic fibrosis (CF) and other diseases caused by nonsense mutations. We tested new synthetic aminoglycoside derivatives expressly developed for PTC suppression in a series of complementary CF models. Using a dual-luciferase reporter system containing the four most prevalent CF transmembrane conductance regulator (CFTR) nonsense mutations (G542X, R553X, R1162X, and W1282X) within their local sequence contexts (the three codons on either side of the PTC), we found that NB124 promoted the most readthrough of G542X, R1162X, and W1282X PTCs. NB124 also restored full-length CFTR expression and chloride transport in Fischer rat thyroid cells stably transduced with a CFTR-G542XcDNA transgene, and was superior to gentamicin and other aminoglycosides tested. NB124 restored CFTR function to roughly 7% of wild-type activity in primary human bronchial epithelial (HBE) CF cells (G542X/delF508), a highly relevant preclinical model with endogenous CFTR expression. Efficacy was further enhanced by addition of the CFTR potentiator, ivacaftor (VX-770), to airway cells expressing CFTR PTCs. NB124 treatment rescued CFTR function in a CF mouse model expressing a human CFTR-G542X transgene; efficacy was superior to gentamicin and exhibited favorable pharmacokinetic properties, suggesting that in vitro results translated to clinical benefit in vivo. NB124 was also less cytotoxic than gentamicin in a tissue-based model for ototoxicity. These results provide evidence that NB124 and other synthetic aminoglycosides provide a 10-fold improvement in therapeutic index over gentamicin and other first-generation aminoglycosides, providing a promising treatment for a wide array of CFTR nonsense mutations.
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14
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Abstract
Nonsense suppression therapy encompasses approaches aimed at suppressing translation termination at in-frame premature termination codons (PTCs, also known as nonsense mutations) to restore deficient protein function. In this review, we examine the current status of PTC suppression as a therapy for genetic diseases caused by nonsense mutations. We discuss what is currently known about the mechanism of PTC suppression as well as therapeutic approaches under development to suppress PTCs. The approaches considered include readthrough drugs, suppressor tRNAs, PTC pseudouridylation, and inhibition of nonsense-mediated mRNA decay. We also discuss the barriers that currently limit the clinical application of nonsense suppression therapy and suggest how some of these difficulties may be overcome. Finally, we consider how PTC suppression may play a role in the clinical treatment of genetic diseases caused by nonsense mutations.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology and Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama 35294; , , ,
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15
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Tuggle KL, Birket SE, Cui X, Hong J, Warren J, Reid L, Chambers A, Ji D, Gamber K, Chu KK, Tearney G, Tang LP, Fortenberry JA, Du M, Cadillac JM, Bedwell DM, Rowe SM, Sorscher EJ, Fanucchi MV. Characterization of defects in ion transport and tissue development in cystic fibrosis transmembrane conductance regulator (CFTR)-knockout rats. PLoS One 2014; 9:e91253. [PMID: 24608905 PMCID: PMC3946746 DOI: 10.1371/journal.pone.0091253] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 02/10/2014] [Indexed: 11/28/2022] Open
Abstract
Animal models for cystic fibrosis (CF) have contributed significantly to our understanding of disease pathogenesis. Here we describe development and characterization of the first cystic fibrosis rat, in which the cystic fibrosis transmembrane conductance regulator gene (CFTR) was knocked out using a pair of zinc finger endonucleases (ZFN). The disrupted Cftr gene carries a 16 base pair deletion in exon 3, resulting in loss of CFTR protein expression. Breeding of heterozygous (CFTR+/−) rats resulted in Mendelian distribution of wild-type, heterozygous, and homozygous (CFTR−/−) pups. Nasal potential difference and transepithelial short circuit current measurements established a robust CF bioelectric phenotype, similar in many respects to that seen in CF patients. Young CFTR−/− rats exhibited histological abnormalities in the ileum and increased intracellular mucus in the proximal nasal septa. By six weeks of age, CFTR−/− males lacked the vas deferens bilaterally. Airway surface liquid and periciliary liquid depth were reduced, and submucosal gland size was abnormal in CFTR−/− animals. Use of ZFN based gene disruption successfully generated a CF animal model that recapitulates many aspects of human disease, and may be useful for modeling other CF genotypes, including CFTR processing defects, premature truncation alleles, and channel gating abnormalities.
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Affiliation(s)
- Katherine L. Tuggle
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Environmental Health Sciences, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Susan E. Birket
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Xiaoxia Cui
- SAGE Labs, Inc., St. Louis, Missouri, United States of America
| | - Jeong Hong
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joe Warren
- SAGE Labs, Inc., St. Louis, Missouri, United States of America
| | - Lara Reid
- SAGE Labs, Inc., St. Louis, Missouri, United States of America
| | - Andre Chambers
- SAGE Labs, Inc., St. Louis, Missouri, United States of America
| | - Diana Ji
- SAGE Labs, Inc., St. Louis, Missouri, United States of America
| | - Kevin Gamber
- SAGE Labs, Inc., St. Louis, Missouri, United States of America
| | - Kengyeh K. Chu
- Wellman Center for Photomedicine, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Guillermo Tearney
- Wellman Center for Photomedicine, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Li Ping Tang
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - James A. Fortenberry
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ming Du
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Animal Resources Program, Office of the Vice President for Research, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joan M. Cadillac
- Animal Resources Program, Office of the Vice President for Research, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David M. Bedwell
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Steven M. Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eric J. Sorscher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michelle V. Fanucchi
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Environmental Health Sciences, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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16
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Gunn G, Dai Y, Du M, Belakhov V, Kandasamy J, Schoeb TR, Baasov T, Bedwell DM, Keeling KM. Long-term nonsense suppression therapy moderates MPS I-H disease progression. Mol Genet Metab 2014; 111:374-381. [PMID: 24411223 PMCID: PMC3943726 DOI: 10.1016/j.ymgme.2013.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 01/16/2023]
Abstract
Nonsense suppression therapy is a therapeutic approach aimed at treating genetic diseases caused by in-frame premature termination codons (PTCs; also commonly known as nonsense mutations). This approach utilizes compounds that suppress translation termination at PTCs, which allows translation to continue and partial levels of deficient protein function to be restored. We hypothesize that suppression therapy can attenuate the lysosomal storage disease mucopolysaccharidosis type I-Hurler (MPS I-H), the severe form of α-L-iduronidase deficiency. α-L-iduronidase participates in glycosaminoglycan (GAG) catabolism and its insufficiency causes progressive GAG accumulation and onset of the MPS I-H phenotype, which consists of multiple somatic and neurological defects. 60-80% of MPS I-H patients carry a nonsense mutation in the IDUA gene. We previously showed that 2-week treatment with the designer aminoglycoside NB84 restored enough α-L-iduronidase function via PTC suppression to reduce tissue GAG accumulation in the Idua(tm1Kmke) MPS I-H mouse model, which carries a PTC homologous to the human IDUA-W402X nonsense mutation. Here we report that long-term NB84 administration maintains α-L-iduronidase activity and GAG reduction in Idua(tm1Kmke) mice throughout a 28-week treatment period. An examination of more complex MPS I-H phenotypes in Idua(tm1Kmke) mice following 28-week NB84 treatment revealed significant moderation of the disease in multiple tissues, including the brain, heart and bone, that are resistant to current MPS I-H therapies. This study represents the first demonstration that long-term nonsense suppression therapy can moderate progression of a genetic disease.
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Affiliation(s)
- Gwen Gunn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Yanying Dai
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Ming Du
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Valery Belakhov
- The Edith and Joseph Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Jeyakumar Kandasamy
- The Edith and Joseph Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel.
| | - Trenton R Schoeb
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Timor Baasov
- The Edith and Joseph Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel.
| | - David M Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Kim M Keeling
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA.
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17
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Zhang S, Ranganath NK, Skinner D, Bedwell DM, Buckley-Lanier JA, Sorscher EJ, Woodworth BA. Marked repression of CFTR mRNA in the transgenic Cftr(tm1kth) mouse model. J Cyst Fibros 2013; 13:351-2. [PMID: 24378376 DOI: 10.1016/j.jcf.2013.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/23/2013] [Accepted: 11/27/2013] [Indexed: 11/16/2022]
Affiliation(s)
- Shaoyan Zhang
- Department of Surgery, Division of Otolaryngology, University of Alabama at Birmingham, Birmingham, AL, United States; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Neel K Ranganath
- Department of Surgery, Division of Otolaryngology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Daniel Skinner
- Department of Surgery, Division of Otolaryngology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - David M Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jessica A Buckley-Lanier
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Eric J Sorscher
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Bradford A Woodworth
- Department of Surgery, Division of Otolaryngology, University of Alabama at Birmingham, Birmingham, AL, United States; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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18
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Aeffner F, Abdulrahman B, Hickman-Davis JM, Janssen PM, Amer A, Bedwell DM, Sorscher EJ, Davis IC. Heterozygosity for the F508del mutation in the cystic fibrosis transmembrane conductance regulator anion channel attenuates influenza severity. J Infect Dis 2013; 208:780-9. [PMID: 23749967 DOI: 10.1093/infdis/jit251] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Seasonal and pandemic influenza are significant public health concerns. Influenza stimulates respiratory epithelial Cl(-) secretion via the cystic fibrosis transmembrane conductance regulator (CFTR). The purpose of this study was to determine the contribution of this effect to influenza pathogenesis in mice with reduced CFTR activity. METHODS C57BL/6-congenic mice heterozygous for the F508del CFTR mutation (HET) and wild-type (WT) controls were infected intranasally with 10 000 focus-forming units of influenza A/WSN/33 (H1N1) per mouse. Body weight, arterial O2 saturation, and heart rate were monitored daily. Pulmonary edema and lung function parameters were derived from ratios of wet weight to dry weight and the forced-oscillation technique, respectively. Levels of cytokines and chemokines in bronchoalveolar lavage fluid were measured by enzyme-linked immunosorbent assay. RESULTS Relative to WT mice, influenza virus-infected HET mice showed significantly delayed mortality, which was accompanied by attenuated hypoxemia, cardiopulmonary dysfunction, and pulmonary edema. However, viral replication and weight loss did not differ. The protective HET phenotype was correlated with exaggerated alveolar macrophage and interleukin 6 responses to infection and was abrogated by alveolar macrophage depletion, using clodronate liposomes. CONCLUSIONS Reduced CFTR expression modulates the innate immune response to influenza and alters disease pathogenesis. CFTR-mediated Cl(-) secretion is therefore an important host determinant of disease, and CFTR inhibition may be of therapeutic benefit in influenza.
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Affiliation(s)
- Famke Aeffner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
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19
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Keeling KM, Wang D, Dai Y, Murugesan S, Chenna B, Clark J, Belakhov V, Kandasamy J, Velu SE, Baasov T, Bedwell DM. Attenuation of nonsense-mediated mRNA decay enhances in vivo nonsense suppression. PLoS One 2013; 8:e60478. [PMID: 23593225 PMCID: PMC3622682 DOI: 10.1371/journal.pone.0060478] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/27/2013] [Indexed: 12/16/2022] Open
Abstract
Nonsense suppression therapy is an approach to treat genetic diseases caused by nonsense mutations. This therapeutic strategy pharmacologically suppresses translation termination at Premature Termination Codons (PTCs) in order to restore expression of functional protein. However, the process of Nonsense-Mediated mRNA Decay (NMD), which reduces the abundance of mRNAs containing PTCs, frequently limits this approach. Here, we used a mouse model of the lysosomal storage disease mucopolysaccharidosis I-Hurler (MPS I-H) that carries a PTC in the Idua locus to test whether NMD attenuation can enhance PTC suppression in vivo. Idua encodes alpha-L-iduronidase, an enzyme required for degradation of the glycosaminoglycans (GAGs) heparan sulfate and dermatan sulfate. We found that the NMD attenuator NMDI-1 increased the abundance of the PTC-containing Idua transcript. Furthermore, co-administration of NMDI-1 with the PTC suppression drug gentamicin enhanced alpha-L-iduronidase activity compared to gentamicin alone, leading to a greater reduction of GAG storage in mouse tissues, including the brain. These results demonstrate that NMD attenuation significantly enhances suppression therapy in vivo.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
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Abstract
In this review, we describe our current understanding of translation termination and pharmacological agents that influence the accuracy of this process. A number of drugs have been identified that induce suppression of translation termination at in-frame premature termination codons (PTCs; also known as nonsense mutations) in mammalian cells. We discuss efforts to utilize these drugs to suppress disease-causing PTCs that result in the loss of protein expression and function. In-frame PTCs represent a genotypic subset of mutations that make up ~11% of all known mutations that cause genetic diseases, and millions of patients have diseases attributable to PTCs. Current approaches aimed at reducing the efficiency of translation termination at PTCs (referred to as PTC suppression therapy) have the goal of alleviating the phenotypic consequences of a wide range of genetic diseases. Suppression therapy is currently in clinical trials for treatment of several genetic diseases caused by PTCs, and preliminary results suggest that some patients have shown clinical improvements. While current progress is promising, we discuss various approaches that may further enhance the efficiency of this novel therapeutic approach.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama, Birmingham, AL 35294-2170, USA
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21
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Conard SE, Buckley J, Dang M, Bedwell GJ, Carter RL, Khass M, Bedwell DM. Identification of eRF1 residues that play critical and complementary roles in stop codon recognition. RNA 2012; 18:1210-21. [PMID: 22543865 PMCID: PMC3358643 DOI: 10.1261/rna.031997.111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/15/2012] [Indexed: 05/31/2023]
Abstract
The initiation and elongation stages of translation are directed by codon-anticodon interactions. In contrast, a release factor protein mediates stop codon recognition prior to polypeptide chain release. Previous studies have identified specific regions of eukaryotic release factor one (eRF1) that are important for decoding each stop codon. The cavity model for eukaryotic stop codon recognition suggests that three binding pockets/cavities located on the surface of eRF1's domain one are key elements in stop codon recognition. Thus, the model predicts that amino acid changes in or near these cavities should influence termination in a stop codon-dependent manner. Previous studies have suggested that the TASNIKS and YCF motifs within eRF1 domain one play important roles in stop codon recognition. These motifs are highly conserved in standard code organisms that use UAA, UAG, and UGA as stop codons, but are more divergent in variant code organisms that have reassigned a subset of stop codons to sense codons. In the current study, we separately introduced TASNIKS and YCF motifs from six variant code organisms into eRF1 of Saccharomyces cerevisiae to determine their effect on stop codon recognition in vivo. We also examined the consequences of additional changes at residues located between the TASNIKS and YCF motifs. Overall, our results indicate that changes near cavities two and three frequently mediated significant effects on stop codon selectivity. In particular, changes in the YCF motif, rather than the TASNIKS motif, correlated most consistently with variant code stop codon selectivity.
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Affiliation(s)
- Sara E. Conard
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Jessica Buckley
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Mai Dang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Richard L. Carter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Mohamed Khass
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - David M. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Wang D, Belakhov V, Kandasamy J, Baasov T, Li SC, Li YT, Bedwell DM, Keeling KM. The designer aminoglycoside NB84 significantly reduces glycosaminoglycan accumulation associated with MPS I-H in the Idua-W392X mouse. Mol Genet Metab 2012; 105:116-25. [PMID: 22056610 PMCID: PMC3253910 DOI: 10.1016/j.ymgme.2011.10.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 12/20/2022]
Abstract
Suppression therapy utilizes compounds that suppress translation termination at in-frame premature termination codons (PTCs) to restore full-length, functional protein. This approach may provide a treatment for diseases caused by nonsense mutations such as mucopolysaccharidosis type I-Hurler (MPS I-H). MPS I-H is a lysosomal storage disease caused by severe α-L-iduronidase deficiency and subsequent lysosomal glycosaminoglycan (GAG) accumulation. MPS I-H represents a good target for suppression therapy because the majority of MPS I-H patients carry nonsense mutations, and restoration of even a small amount of functional α-L-iduronidase may attenuate the MPS I-H phenotype. In this study, we investigated the efficiency of suppression therapy agents to suppress the Idua-W392X nonsense mutation in an MPS I-H mouse model. The drugs tested included the conventional aminoglycosides gentamicin, G418, amikacin, and paromomycin. In addition, the designer aminoglycosides NB54 and NB84, two compounds previously designed to mediate efficient PTC suppression with reduced toxicity, were also examined. Overall, NB84 suppressed the Idua-W392X nonsense mutation much more efficiently than any of the other compounds tested. NB84 treatment restored enough functional α-L-iduronidase activity to partially reverse abnormal GAG accumulation and lysosomal abundance in mouse embryonic fibroblasts derived from the Idua-W392X mouse. Finally, in vivo administration of NB84 to Idua-W392X mice significantly reduced urine GAG excretion and tissue GAG storage. Together, these results suggest that NB84-mediated suppression therapy has the potential to attenuate the MPS I-H disease phenotype.
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Affiliation(s)
- Dan Wang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Valery Belakhov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Jeyakumar Kandasamy
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Timor Baasov
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Su-Chen Li
- Department of Biochemistry, Tulane University, New Orleans, LA 70112, USA
| | - Yu-Teh Li
- Department of Biochemistry, Tulane University, New Orleans, LA 70112, USA
| | - David M. Bedwell
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim M. Keeling
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Corresponding author: Kim M. Keeling, Address: Department of Microbiology, BBRB 456, 845 19 Street South, University of Alabama at Birmingham, Birmingham, AL 35294, USA. Telephone: 205-975-6585; Fax: 205-975-5482.
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Rowe SM, Sloane P, Tang LP, Backer K, Mazur M, Buckley-Lanier J, Nudelman I, Belakhov V, Bebok Z, Schwiebert E, Baasov T, Bedwell DM. Suppression of CFTR premature termination codons and rescue of CFTR protein and function by the synthetic aminoglycoside NB54. J Mol Med (Berl) 2011; 89:1149-61. [PMID: 21779978 DOI: 10.1007/s00109-011-0787-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/18/2011] [Accepted: 06/23/2011] [Indexed: 01/28/2023]
Abstract
Certain aminoglycosides are capable of inducing "translational readthrough" of premature termination codons (PTCs). However, toxicity and relative lack of efficacy deter treatment with clinically available aminoglycosides for genetic diseases caused by PTCs, including cystic fibrosis (CF). Using a structure-based approach, the novel aminoglycoside NB54 was developed that exhibits reduced toxicity and enhanced suppression of PTCs in cell-based reporter assays relative to gentamicin. We examined whether NB54 administration rescued CFTR protein and function in clinically relevant CF models. In a fluorescence-based halide efflux assay, NB54 partially restored halide efflux in a CF bronchial epithelial cell line (CFTR genotype W1282X/F508del), but not in a CF epithelial cell line lacking a PTC (F508del/F508del). In polarized airway epithelial cells expressing either a CFTR-W1282X or -G542X cDNA, treatment with NB54 increased stimulated short-circuit current (I (SC)) with greater efficiency than gentamicin. NB54 and gentamicin induced comparable increases in forskolin-stimulated I (SC) in primary airway epithelial cells derived from a G542X/F508del CF donor. Systemic administration of NB54 to Cftr-/- mice expressing a human CFTR-G542X transgene restored 15-17% of the average stimulated transepithelial chloride currents observed in wild-type (Cftr+/+) mice, comparable to gentamicin. NB54 exhibited reduced cellular toxicity in vitro and was tolerated at higher concentrations than gentamicin in vivo. These results provide evidence that synthetic aminoglycosides are capable of PTC suppression in relevant human CF cells and a CF animal model and support further development of these compounds as a treatment modality for genetic diseases caused by PTCs.
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Affiliation(s)
- Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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24
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Lazrak A, Jurkuvenaite A, Chen L, Keeling KM, Collawn JF, Bedwell DM, Matalon S. Enhancement of alveolar epithelial sodium channel activity with decreased cystic fibrosis transmembrane conductance regulator expression in mouse lung. Am J Physiol Lung Cell Mol Physiol 2011; 301:L557-67. [PMID: 21743028 DOI: 10.1152/ajplung.00094.2011] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We sought to establish whether the cystic fibrosis transmembrane conductance regulator (CFTR) regulates the activity of amiloride-sensitive sodium channels (ENaC) in alveolar epithelial cells of wild-type, heterozygous (Cftr(+/-)), knockout (Cftr(-/-)), and ΔF508-expressing mice in situ. RT-PCR studies confirmed the presence of CFTR message in freshly isolated alveolar type II (ATII) cells from wild-type mice. We patched alveolar type I (ATI) and ATII cells in freshly prepared lung slices from these mice and demonstrated the presence of 4-pS ENaC channels with the following basal open probabilities (P(o)): wild-type=0.21 ± 0.015: Cftr(+/-)=0.4 ± 0.03; ΔF508=0.55 ± 0.01; and Cftr(-/-)=and 0.81 ± 0.016 (means ± SE; n ≥ 9). Forskolin (5 μM) or trypsin (2 μM), applied in the pipette solution, increased the P(o) and number of channels in ATII cells of wild-type, Cftr(+/-), and ΔF508, but not in Cftr(-/-) mice, suggesting that the latter were maximally activated. Western blot analysis showed that lungs of all groups of mice had similar levels of α-ENaC; however, lungs of Cftr(+/-) and Cftr(-/-) mice had significantly higher levels of an α-ENaC proteolytic fragment (65 kDa) that is associated with active ENaC channels. Our results indicate that ENaC activity is inversely correlated to predicted CFTR levels and that CFTR heterozygous and homozygous mice have higher levels of proteolytically processed ENaC fragments in their lungs. This is the first demonstration of functional ENaC-CFTR interactions in alveolar epithelial cells in situ.
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Affiliation(s)
- Ahmed Lazrak
- Department of Anesthesiology, School of Medicine, University of Alabama at Birmingham, 35205-3703, USA
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25
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Keeling KM, Bedwell DM. Suppression of nonsense mutations as a therapeutic approach to treat genetic diseases. Wiley Interdiscip Rev RNA 2011; 2:837-52. [PMID: 21976286 DOI: 10.1002/wrna.95] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Suppression therapy is a treatment strategy for genetic diseases caused by nonsense mutations. This therapeutic approach utilizes pharmacological agents that suppress translation termination at in-frame premature termination codons (PTCs) to restore translation of a full-length, functional polypeptide. The efficiency of various classes of compounds to suppress PTCs in mammalian cells is discussed along with the current limitations of this therapy. We also elaborate on approaches to improve the efficiency of suppression that include methods to enhance the effectiveness of current suppression drugs and the design or discovery of new, more effective suppression agents. Finally, we discuss the role of nonsense-mediated mRNA decay (NMD) in limiting the effectiveness of suppression therapy, and describe tactics that may allow the efficiency of NMD to be modulated in order to enhance suppression therapy.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
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26
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Wang D, Shukla C, Liu X, Schoeb TR, Clarke LA, Bedwell DM, Keeling KM. Characterization of an MPS I-H knock-in mouse that carries a nonsense mutation analogous to the human IDUA-W402X mutation. Mol Genet Metab 2010; 99:62-71. [PMID: 19751987 PMCID: PMC2795040 DOI: 10.1016/j.ymgme.2009.08.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 08/17/2009] [Accepted: 08/17/2009] [Indexed: 02/01/2023]
Abstract
Here we report the characterization of a knock-in mouse model for the autosomal recessive disorder mucopolysaccharidosis type I-Hurler (MPS I-H), also known as Hurler syndrome. MPS I-H is the most severe form of alpha-l-iduronidase deficiency. alpha-l-iduronidase (encoded by the IDUA gene) is a lysosomal enzyme that participates in the degradation of dermatan sulfate and heparan sulfate. Using gene replacement methodology, a nucleotide change was introduced into the mouse Idua locus that resulted in a nonsense mutation at codon W392. The Idua-W392X mutation is analogous to the human IDUA-W402X mutation commonly found in MPS I-H patients. We found that the phenotype in homozygous Idua-W392X mice closely correlated with the human MPS I-H disease. Homozygous W392X mice showed no detectable alpha-l-iduronidase activity. We observed a defect in GAG degradation as evidenced by an increase in sulfated GAGs excreted in the urine and stored in multiple tissues. Histology and electron microscopy also revealed evidence of GAG storage in all tissues examined. Additional assessment revealed bone abnormalities and altered metabolism within the Idua-W392X mouse. This new mouse will provide an important tool to investigate therapeutic approaches for MPS I-H that cannot be addressed using current MPS I-H animal models.
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Affiliation(s)
- Dan Wang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Charu Shukla
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xiaoli Liu
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Trenton R. Schoeb
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lorne A. Clarke
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, CA
| | - David M. Bedwell
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim M. Keeling
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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27
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Vallabhaneni H, Fan-Minogue H, Bedwell DM, Farabaugh PJ. Connection between stop codon reassignment and frequent use of shifty stop frameshifting. RNA 2009; 15:889-897. [PMID: 19329535 PMCID: PMC2673066 DOI: 10.1261/rna.1508109] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 02/05/2009] [Indexed: 05/27/2023]
Abstract
Ciliated protozoa of the genus Euplotes have undergone genetic code reassignment, redefining the termination codon UGA to encode cysteine. In addition, Euplotes spp. genes very frequently employ shifty stop frameshifting. Both of these phenomena involve noncanonical events at a termination codon, suggesting they might have a common cause. We recently demonstrated that Euplotes octocarinatus peptide release factor eRF1 ignores UGA termination codons while continuing to recognize UAA and UAG. Here we show that both the Tetrahymena thermophila and E. octocarinatus eRF1 factors allow efficient frameshifting at all three termination codons, suggesting that UGA redefinition also impaired UAA/UAG recognition. Mutations of the Euplotes factor restoring a phylogenetically conserved motif in eRF1 (TASNIKS) reduced programmed frameshifting at all three termination codons. Mutation of another conserved residue, Cys124, strongly reduces frameshifting at UGA while actually increasing frameshifting at UAA/UAG. We will discuss these results in light of recent biochemical characterization of these mutations.
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Affiliation(s)
- Haritha Vallabhaneni
- Program in Molecular and Cell Biology, Department of Biological Sciences, University of Maryland Baltimore County, Baltimore,Maryland 21250, USA
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28
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Du M, Keeling KM, Fan L, Liu X, Bedwell DM. Poly-L-aspartic acid enhances and prolongs gentamicin-mediated suppression of the CFTR-G542X mutation in a cystic fibrosis mouse model. J Biol Chem 2009; 284:6885-92. [PMID: 19136563 DOI: 10.1074/jbc.m806728200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Aminoglycosides such as gentamicin have the ability to suppress translation termination at premature stop mutations, leading to a partial restoration of protein expression and function. This observation led to studies showing that this approach may provide a viable treatment for patients with genetic diseases such as cystic fibrosis that are caused by premature stop mutations. Although aminoglycoside treatment is sometimes associated with harmful side effects, several studies have shown that the co-administration of polyanions such as poly-L-aspartic acid (PAA) can both reduce toxicity and increase the intracellular aminoglycoside concentration. In the current study we examined how the co-administration of gentamicin with PAA influenced the readthrough of premature stop codons in cultured cells and a cystic fibrosis mouse model. Using a dual luciferase readthrough reporter system in cultured cells, we found that the co-administration of gentamicin with PAA increased readthrough 20-40% relative to cells treated with the same concentration of gentamicin alone. Using a Cftr-/- hCFTR-G542X mouse model, we found that PAA also increased the in vivo nonsense suppression induced by gentamicin. Following the withdrawal of gentamicin, PAA significantly prolonged the time interval during which readthrough could be detected, as shown by short circuit current measurements and immunofluorescence. Because the use of gentamicin to suppress disease-causing nonsense mutations will require their long term administration, the ability of PAA to reduce toxicity and increase both the level and duration of readthrough has important implications for this promising therapeutic approach.
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Affiliation(s)
- Ming Du
- Department of Microbiology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama 35294-2170, USA
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29
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Fan-Minogue H, Du M, Pisarev AV, Kallmeyer AK, Salas-Marco J, Keeling KM, Thompson SR, Pestova TV, Bedwell DM. Distinct eRF3 requirements suggest alternate eRF1 conformations mediate peptide release during eukaryotic translation termination. Mol Cell 2008; 30:599-609. [PMID: 18538658 DOI: 10.1016/j.molcel.2008.03.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 02/25/2008] [Accepted: 03/28/2008] [Indexed: 10/22/2022]
Abstract
Organisms that use the standard genetic code recognize UAA, UAG, and UGA as stop codons, whereas variant code species frequently alter this pattern of stop codon recognition. We previously demonstrated that a hybrid eRF1 carrying the Euplotes octocarinatus domain 1 fused to Saccharomyces cerevisiae domains 2 and 3 (Eo/Sc eRF1) recognized UAA and UAG, but not UGA, as stop codons. In the current study, we identified mutations in Eo/Sc eRF1 that restore UGA recognition and define distinct roles for the TASNIKS and YxCxxxF motifs in eRF1 function. Mutations in or near the YxCxxxF motif support the cavity model for stop codon recognition by eRF1. Mutations in the TASNIKS motif eliminated the eRF3 requirement for peptide release at UAA and UAG codons, but not UGA codons. These results suggest that the TASNIKS motif and eRF3 function together to trigger eRF1 conformational changes that couple stop codon recognition and peptide release during eukaryotic translation termination.
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Affiliation(s)
- Hua Fan-Minogue
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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30
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Abstract
Recent studies of prokaryotic ribosomes have dramatically increased our knowledge of ribosomal RNA (rRNA) structure, functional centers, and their interactions with antibiotics. However, much less is known about how rRNA function differs between prokaryotic and eukaryotic ribosomes. The core decoding sites are identical in yeast and human 18S rRNAs, suggesting that insights obtained in studies with yeast rRNA mutants can provide information about ribosome function in both species. In this study, we examined the importance of key nucleotides of the 18S rRNA decoding site on ribosome function and aminoglycoside susceptibility in Saccharomyces cerevisiae cells expressing homogeneous populations of mutant ribosomes. We found that residues G577, A1755, and A1756 (corresponding to Escherichia coli residues G530, A1492, and A1493, respectively) are essential for cell viability. We also found that residue G1645 (A1408 in E. coli) and A1754 (G1491 in E. coli) both make significant and distinct contributions to aminoglycoside resistance. Furthermore, we found that mutations at these residues do not alter the basal level of translational accuracy, but influence both paromomycin-induced misreading of sense codons and readthrough of stop codons. This study represents the most comprehensive mutational analysis of the eukaryotic decoding site to date, and suggests that many fundamental features of decoding site function are conserved between prokaryotes and eukaryotes.
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Affiliation(s)
- Hua Fan-Minogue
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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31
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Keeling KM, Salas-Marco J, Osherovich LZ, Bedwell DM. Tpa1p is part of an mRNP complex that influences translation termination, mRNA deadenylation, and mRNA turnover in Saccharomyces cerevisiae. Mol Cell Biol 2006; 26:5237-48. [PMID: 16809762 PMCID: PMC1592710 DOI: 10.1128/mcb.02448-05] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this report, we show that the Saccharomyces cerevisiae protein Tpa1p (for termination and polyadenylation) influences translation termination efficiency, mRNA poly(A) tail length, and mRNA stability. Tpa1p is encoded by the previously uncharacterized open reading frame YER049W. Yeast strains carrying a deletion of the TPA1 gene (tpa1Delta) exhibited increased readthrough of stop codons, and coimmunoprecipitation assays revealed that Tpa1p interacts with the translation termination factors eRF1 and eRF3. In addition, the tpa1Delta mutation led to a 1.5- to 2-fold increase in the half-lives of mRNAs degraded by the general 5'-->3' pathway or the 3'-->5' nonstop decay pathway. In contrast, this mutation did not have any affect on the nonsense-mediated mRNA decay pathway. Examination of mRNA poly(A) tail length revealed that poly(A) tails are longer than normal in a tpa1Delta strain. Consistent with a potential role in regulating poly(A) tail length, Tpa1p was also found to coimmunoprecipitate with the yeast poly(A) binding protein Pab1p. These results suggest that Tpa1p is a component of a messenger ribonucleoprotein complex bound to the 3' untranslated region of mRNAs that affects translation termination, deadenylation, and mRNA decay.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology, BBRB 432/Box 8, 1530 3rd Avenue South, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA.
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32
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Kallmeyer AK, Keeling KM, Bedwell DM. Eukaryotic release factor 1 phosphorylation by CK2 protein kinase is dynamic but has little effect on the efficiency of translation termination in Saccharomyces cerevisiae. Eukaryot Cell 2006; 5:1378-87. [PMID: 16896221 PMCID: PMC1539132 DOI: 10.1128/ec.00073-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Accepted: 06/05/2006] [Indexed: 11/20/2022]
Abstract
Protein synthesis requires a large commitment of cellular resources and is highly regulated. Previous studies have shown that a number of factors that mediate the initiation and elongation steps of translation are regulated by phosphorylation. In this report, we show that a factor involved in the termination step of protein synthesis is also subject to phosphorylation. Our results indicate that eukaryotic release factor 1 (eRF1) is phosphorylated in vivo at serine 421 and serine 432 by the CK2 protein kinase (previously casein kinase II) in the budding yeast Saccharomyces cerevisiae. Phosphorylation of eRF1 has little effect on the efficiency of stop codon recognition or nonsense-mediated mRNA decay. Also, phosphorylation is not required for eRF1 binding to the other translation termination factor, eRF3. In addition, we provide evidence that the putative phosphatase Sal6p does not dephosphorylate eRF1 and that the state of eRF1 phosphorylation does not influence the allosuppressor phenotype associated with a sal6Delta mutation. Finally, we show that phosphorylation of eRF1 is a dynamic process that is dependent upon carbon source availability. Since many other proteins involved in protein synthesis have a CK2 protein kinase motif near their extreme C termini, we propose that this represents a common regulatory mechanism that is shared by factors involved in all three stages of protein synthesis.
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Affiliation(s)
- Adam K Kallmeyer
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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Du M, Keeling KM, Fan L, Liu X, Kovaçs T, Sorscher E, Bedwell DM. Clinical doses of amikacin provide more effective suppression of the human CFTR-G542X stop mutation than gentamicin in a transgenic CF mouse model. J Mol Med (Berl) 2006; 84:573-82. [PMID: 16541275 DOI: 10.1007/s00109-006-0045-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Accepted: 01/09/2006] [Indexed: 10/24/2022]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause the disease cystic fibrosis. We previously reported that gentamicin administration suppressed a CFTR premature stop mutation in a Cftr-/- mouse model carrying a human CFTR-G542X (hCFTR-G542X) transgene, resulting in the appearance of hCFTR protein and function. However, the high doses used in that study resulted in peak serum levels well beyond the levels typically administered to humans. To address this problem, we identified doses of both gentamicin and amikacin that resulted in peak serum levels within their accepted clinical ranges. We then asked whether these doses could suppress the hCFTR-G542X mutation in the Cftr-/- hCFTR-G542X mouse model. Our results indicate that low doses of each compound restored some hCFTR protein expression and function, as shown by immunofluorescence and short-circuit current measurements. However, we found that amikacin suppressed the hCFTR-G542X premature stop mutation more effectively than gentamicin when administered at these clinically relevant doses. Because amikacin is also less toxic than gentamicin, it may represent a superior choice for suppression therapy in patients that carry a premature stop mutation in the CFTR gene.
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Affiliation(s)
- Ming Du
- Department of Microbiology, The University of Alabama at Birmingham, 35294-2170, USA
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Kellermayer R, Szigeti R, Keeling KM, Bedekovics T, Bedwell DM. Aminoglycosides as potential pharmacogenetic agents in the treatment of Hailey-Hailey disease. J Invest Dermatol 2006; 126:229-31. [PMID: 16417242 DOI: 10.1038/sj.jid.5700031] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Salas-Marco J, Fan-Minogue H, Kallmeyer AK, Klobutcher LA, Farabaugh PJ, Bedwell DM. Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes. Mol Cell Biol 2006; 26:438-47. [PMID: 16382136 PMCID: PMC1346903 DOI: 10.1128/mcb.26.2.438-447.2006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code.
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Affiliation(s)
- Joe Salas-Marco
- Department of Microbiology, BBRB 432/Box 8, 1530 Third Avenue South, The University of Alabama at Birmingham, Birmingham, Alabama 35294-2170, USA
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Salas-Marco J, Bedwell DM. Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. J Mol Biol 2005; 348:801-15. [PMID: 15843014 DOI: 10.1016/j.jmb.2005.03.025] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 02/18/2005] [Accepted: 03/01/2005] [Indexed: 11/30/2022]
Abstract
The suppression of stop codons (termed translational readthrough) can be caused by a decreased accuracy of translation elongation or a reduced efficiency of translation termination. In previous studies, the inability to determine the extent to which each of these distinct processes contributes to a readthrough phenotype has limited our ability to evaluate how defects in the translational machinery influence the overall termination process. Here, we describe the combined use of misincorporation and readthrough reporter systems to determine which of these mechanisms contributes to translational readthrough in Saccharomyces cerevisiae. The misincorporation reporter system was generated by introducing a series of near-cognate mutations into functionally important residues in the firefly luciferase gene. These constructs allowed us to monitor the incidence of elongation errors by monitoring the level of firefly luciferase activity from a mutant allele inactivated by a single missense mutation. In this system, an increase in luciferase activity should reflect an increased level of misincorporation of the wild-type amino acid that provides an estimate of the overall fidelity of translation elongation. Surprisingly, we found that growth in the presence of paromomycin stimulated luciferase activity for only a small subset of the mutant proteins examined. This suggests that the ability of this aminoglycoside to induce elongation errors is limited to a subset of near-cognate mismatches. We also found that a similar bias in near-cognate misreading could be induced by the expression of a mutant form of ribosomal protein (r-protein) S9B or by depletion of r-protein L12. We used this misincorporation reporter in conjunction with a readthrough reporter system to show that alterations at different regions of the ribosome influence elongation fidelity and termination efficiency to different extents.
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Affiliation(s)
- Joe Salas-Marco
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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Csutora P, Strassz A, Boldizsár F, Németh P, Sipos K, Aiello DP, Bedwell DM, Miseta A. Inhibition of phosphoglucomutase activity by lithium alters cellular calcium homeostasis and signaling in Saccharomyces cerevisiae. Am J Physiol Cell Physiol 2005; 289:C58-67. [PMID: 15703203 DOI: 10.1152/ajpcell.00464.2004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Phosphoglucomutase is a key enzyme of glucose metabolism that interconverts glucose-1-phosphate and glucose-6-phosphate. Loss of the major isoform of phosphoglucomutase in Saccharomyces cerevisiae results in a significant increase in the cellular glucose-1-phosphate-to-glucose-6-phosphate ratio when cells are grown in medium containing galactose as carbon source. This imbalance in glucose metabolites was recently shown to also cause a six- to ninefold increase in cellular Ca2+ accumulation. We found that Li+ inhibition of phosphoglucomutase causes a similar elevation of total cellular Ca2+ and an increase in 45Ca2+ uptake in a wild-type yeast strain grown in medium containing galactose, but not glucose, as sole carbon source. Li+ treatment also reduced the transient elevation of cytosolic Ca2+ response that is triggered by exposure to external CaCl2 or by the addition of galactose to yeast cells starved of a carbon source. Finally, we found that the Ca2+ over-accumulation induced by Li+ exposure was significantly reduced in a strain lacking the vacuolar Ca2+-ATPase Pmc1p. These observations suggest that Li+ inhibition of phosphoglucomutase results in an increased glucose-1-phosphate-to-glucose-6-phosphate ratio, which results in an accelerated rate of vacuolar Ca2+ uptake via the Ca2+-ATPase Pmc1p.
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Affiliation(s)
- Péter Csutora
- Department of Laboratory Medicine, Faculty of Medicine, Pécs University, Ifjúság u. 13, 7624 Pécs, Hungary
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Abstract
Translation termination in eukaryotes is mediated by two release factors, eRF1 and eRF3. eRF1 recognizes each of the three stop codons (UAG, UAA, and UGA) and facilitates release of the nascent polypeptide chain. eRF3 is a GTPase that stimulates the translation termination process by a poorly characterized mechanism. In this study, we examined the functional importance of GTP hydrolysis by eRF3 in Saccharomyces cerevisiae. We found that mutations that reduced the rate of GTP hydrolysis also reduced the efficiency of translation termination at some termination signals but not others. As much as a 17-fold decrease in the termination efficiency was observed at some tetranucleotide termination signals (characterized by the stop codon and the first following nucleotide), while no effect was observed at other termination signals. To determine whether this stop signal-dependent decrease in the efficiency of translation termination was due to a defect in either eRF1 or eRF3 recycling, we reduced the level of eRF1 or eRF3 in cells by expressing them individually from the CUP1 promoter. We found that the limitation of either factor resulted in a general decrease in the efficiency of translation termination rather than a decrease at a subset of termination signals as observed with the eRF3 GTPase mutants. We also found that overproduction of eRF1 was unable to increase the efficiency of translation termination at any termination signals. Together, these results suggest that the GTPase activity of eRF3 is required to couple the recognition of translation termination signals by eRF1 to efficient polypeptide chain release.
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Affiliation(s)
- Joe Salas-Marco
- Department of Microbiology, BBRB 432/Box 8, 1530 Third Ave. South, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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Aiello DP, Fu L, Miseta A, Sipos K, Bedwell DM. The Ca2+ Homeostasis Defects in a pgm2Δ Strain of Saccharomyces cerevisiae Are Caused by Excessive Vacuolar Ca2+ Uptake Mediated by the Ca2+-ATPase Pmc1p. J Biol Chem 2004; 279:38495-502. [PMID: 15252028 DOI: 10.1074/jbc.m400833200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Loss of the major isoform of phosphoglucomutase (PGM) causes an accumulation of glucose 1-phosphate when yeast cells are grown with galactose as the carbon and energy source. Remarkably, the pgm2Delta strain also exhibits a severe imbalance in intracellular Ca(2+) homeostasis when grown under these conditions. In the present study, we examined how the pgm2Delta mutation alters yeast Ca(2+) homeostasis in greater detail. We found that a shift from glucose to galactose as the carbon source resulted in a 2-fold increase in the rate of cellular Ca(2+) uptake in wild-type cells, whereas Ca(2+) uptake increased 8-fold in the pgm2Delta mutant. Disruption of the PMC1 gene, which encodes the vacuolar Ca(2+)-ATPase Pmc1p, suppressed the Ca(2+)-related phenotypes observed in the pgm2Delta strain. This suggests that excessive vacuolar Ca(2+) uptake is tightly coupled to these defects in Ca(2+) homeostasis. An in vitro assay designed to measure Ca(2+) sequestration into intracellular compartments confirmed that the pgm2Delta mutant contained a higher level of Pmc1p-dependent Ca(2+) transport activity than the wild-type strain. We found that this increased rate of vacuolar Ca(2+) uptake also coincided with a large induction of the unfolded protein response in the pgm2Delta mutant, suggesting that Ca(2+) uptake into the endoplasmic reticulum compartment was reduced. These results indicate that the excessive Ca(2+) uptake and accumulation previously shown to be associated with the pgm2Delta mutation are due to a severe imbalance in the distribution of cellular Ca(2+) into different intracellular compartments.
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Affiliation(s)
- David P Aiello
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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40
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Keeling KM, Lanier J, Du M, Salas-Marco J, Gao L, Kaenjak-Angeletti A, Bedwell DM. Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae. RNA 2004; 10:691-703. [PMID: 15037778 PMCID: PMC1262634 DOI: 10.1261/rna.5147804] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The Nonsense-Mediated mRNA Decay (NMD) pathway mediates the rapid degradation of mRNAs that contain premature stop mutations in eukaryotic organisms. It was recently shown that mutations in three yeast genes that encode proteins involved in the NMD process, UPF1, UPF2, and UPF3, also reduce the efficiency of translation termination. In the current study, we compared the efficiency of translation termination in a upf1Delta strain and a [PSI(+)] strain using a collection of translation termination reporter constructs. The [PSI(+)] state is caused by a prion form of the polypeptide chain release factor eRF3 that limits its availability to participate in translation termination. In contrast, the mechanism by which Upf1p influences translation termination is poorly understood. The efficiency of translation termination is primarily determined by a tetranucleotide termination signal consisting of the stop codon and the first nucleotide immediately 3' of the stop codon. We found that the upf1Delta mutation, like the [PSI(+)] state, decreases the efficiency of translation termination over a broad range of tetranucleotide termination signals in a unique, context-dependent manner. These results suggest that Upf1p may associate with the termination complex prior to polypeptide chain release. We also found that the increase in readthrough observed in a [PSI(+)]/upf1Delta strain was larger than the readthrough observed in strains carrying either defect alone, indicating that the upf1Delta mutation and the [PSI(+)] state influence the termination process in distinct ways. Finally, our analysis revealed that the mRNA destabilization associated with NMD could be separated into two distinct forms that correlated with the extent the premature stop codon was suppressed. The minor component of NMD was a 25% decrease in mRNA levels observed when readthrough was >/=0.5%, while the major component was represented by a larger decrease in mRNA abundance that was observed only when readthrough was </=0.5%. This low threshold for the onset of the major component of NMD indicates that mRNA surveillance is an ongoing process that occurs throughout the lifetime of an mRNA.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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41
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Miseta A, Tökés-Füzesi M, Aiello DP, Bedwell DM. A Saccharomyces cerevisiae mutant unable to convert glucose to glucose-6-phosphate accumulates excessive glucose in the endoplasmic reticulum due to core oligosaccharide trimming. Eukaryot Cell 2003; 2:534-41. [PMID: 12796298 PMCID: PMC161446 DOI: 10.1128/ec.2.3.534-541.2003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
D-Glucose is the preferred carbon and energy source for most eukaryotic cells. Immediately following its uptake, glucose is rapidly phosphorylated to glucose-6-phosphate (Glc-6-P). The yeast Saccharomyces cerevisiae has three enzymes (Hxk1p, Hxk2p, and Glk1p) that convert glucose to Glc-6-P. In the present study, we found that yeast mutants lacking any two of these enzymes retain the ability to efficiently convert glucose to Glc-6-P and thus maintain a low level of cellular glucose. However, a mutant strain lacking all three glucose-phosphorylating enzymes contained up to 225-fold more intracellular glucose than normal. Drugs that inhibit the synthesis or the trimming of the lipid-linked core oligosaccharide Glu(3)Man(9)GlcNac(2) effectively reduced the accumulation of glucose. Similarly, mutations that block the addition of glucose residues to the core oligosaccharide moiety, such as alg5Delta or alg6Delta, also diminished glucose accumulation. These results indicate that the intracellular glucose accumulation observed in the glucose phosphorylation mutant results primarily from the trimming of glucose residues from core oligosaccharide chains within the endoplasmic reticulum (ER). Consistent with this conclusion, both [(14)C]glucose exchange and subcellular fractionation experiments indicate that much of the accumulated glucose is retained within an intracellular compartment, suggesting that the efficient transport of glucose from the ER to the cytosol in yeast may be coupled to its rephosphorylation to Glc-6-P. The high level of cellular glucose was associated with an increased level of protein glycation and the release of glucose into the culture medium via its transit through the secretory pathway. Finally, we also found that the accumulation of glucose may lead to a subtle alteration in ion homeostasis, particularly Ca(2+) uptake. This suggests that this mutant strain may serve as a useful model to study the consequences of excessive glucose accumulation and protein glycation.
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Affiliation(s)
- Attila Miseta
- Department of Clinical Chemistry, University Medical School, Peçs, Hungary
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42
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Kellermayer R, Aiello DP, Miseta A, Bedwell DM. Extracellular Ca(2+) sensing contributes to excess Ca(2+) accumulation and vacuolar fragmentation in a pmr1Delta mutant of S. cerevisiae. J Cell Sci 2003; 116:1637-46. [PMID: 12640047 DOI: 10.1242/jcs.00372] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have suggested that yeast strains lacking the Ca(2+)-ATPase Pmr1p are unable to maintain an adequate level of Ca(2+) within the Golgi apparatus. It is thought that this compartmental store depletion induces a signal that causes an increased rate of Ca(2+) uptake and accumulation in a manner similar to the capacitative Ca(2+) entry (CCE) response in non-excitable mammalian cells. To explore this model further, we examined cellular Ca(2+) uptake and accumulation in a pmr1Delta strain grown in the presence of a reduced level of divalent cations. We found that the level of Ca(2+) uptake and accumulation in a pmr1Delta strain increased as the concentration of divalent cations in the growth medium decreased. These results are inconsistent with a model in which cellular Ca(2+) uptake and accumulation are determined solely by the depletion of Ca(2+) in an intracellular compartment. Instead, our results suggest that a second regulatory mechanism couples cellular Ca(2+) uptake to the availability of Ca(2+) in the extracellular environment. Furthermore, we found that various conditions that increase the level of cytosolic Ca(2+) correlate with vacuolar fragmentation in wild-type (WT), pmr1Delta and pmr1Delta/pmc1Delta yeast strains. This suggests that vacuolar fragmentation might function as a normal physiological response to Ca(2+) stress that increases the vacuolar surface/volume ratio, thereby maximizing the sequestration of this important signaling molecule.
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Affiliation(s)
- Richard Kellermayer
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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43
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Aiello DP, Fu L, Miseta A, Bedwell DM. Intracellular glucose 1-phosphate and glucose 6-phosphate levels modulate Ca2+ homeostasis in Saccharomyces cerevisiae. J Biol Chem 2002; 277:45751-8. [PMID: 12351653 DOI: 10.1074/jbc.m208748200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme phosphoglucomutase plays a key role in cellular metabolism by virtue of its ability to interconvert Glc-1-P and Glc-6-P. It was recently shown that a yeast strain lacking the major isoform of phosphoglucomutase (pgm2Delta) accumulates a high level of Glc-1-P and exhibits several phenotypes related to altered Ca(2+) homeostasis when d-galactose is utilized as the carbon source (Fu, L., Miseta, A., Hunton, D., Marchase, R. B., and Bedwell, D. M. (2000) J. Biol. Chem. 275, 5431-5440). These phenotypes include increased Ca(2+) uptake and accumulation and sensitivity to high environmental Ca(2+) levels. In the present study, we overproduced the enzyme UDP-Glc pyrophosphorylase to test whether the overproduction of a downstream metabolite produced from Glc-1-P can also mediate changes in Ca(2+) homeostasis. We found that overproduction of UDP-Glc did not cause any alterations in Ca(2+) uptake or accumulation. We also examined whether Glc-6-P can influence cellular Ca(2+) homeostasis. A yeast strain lacking the beta-subunit of phosphofructokinase (pfk2Delta) accumulates a high level of Glc-6-P (Huang, D., Wilson, W. A., and Roach, P. J. (1997) J. Biol. Chem. 272, 22495-22501). We found that this increase in Glc-6-P led to a 1.5-2-fold increase in total cellular Ca(2+). We also found that the pgm2Delta/pfk2Delta strain, which accumulated high levels of both Glc-6-P and Glc-1-P, no longer exhibited the Ca(2+)-related phenotypes associated with high Glc-1-P levels in the pgm2Delta mutant. These results provide strong evidence that cellular Ca(2+) homeostasis is coupled to the relative levels of Glc-6-P and Glc-1-P in yeast.
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Affiliation(s)
- David P Aiello
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294-2170, USA
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44
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Du M, Jones JR, Lanier J, Keeling KM, Lindsey JR, Tousson A, Bebök Z, Whitsett JA, Dey CR, Colledge WH, Evans MJ, Sorscher EJ, Bedwell DM. Aminoglycoside suppression of a premature stop mutation in a Cftr-/- mouse carrying a human CFTR-G542X transgene. J Mol Med (Berl) 2002; 80:595-604. [PMID: 12226741 DOI: 10.1007/s00109-002-0363-1] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2002] [Accepted: 05/17/2002] [Indexed: 11/26/2022]
Abstract
Cystic fibrosis (CF) is caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein. Since approximately 5% of all mutant CF alleles are stop mutations, it can be calculated that approximately 10% of CF patients carry a premature stop mutation in at least one copy of the CFTR gene. Certain ethnic groups, such as the Ashkenazi Jewish population, carry a much higher percentage of CF stop mutations. Consequently, a therapeutic strategy aimed at suppressing this class of mutation would be highly desirable for the treatment of this common genetic disease. We have shown previously that aminoglycoside antibiotics can suppress premature stop mutations in the CFTR gene in a bronchial epithelial cell line [Nat Med (1997) 3:1280]. To address whether aminoglycosides can suppress a CFTR premature stop mutation in an animal model, we constructed a transgenic mouse with a null mutation in the endogenous CFTR locus (Cftr-/-) that also expressed a human CFTR-G542X cDNA under control of the intestinal fatty acid binding protein promoter. We then investigated whether the daily administration of the aminoglycoside antibiotics gentamicin or tobramycin could restore the expression of a detectable level of CFTR protein. Immunofluorescence staining of intestinal tissues from Cftr-/- hCFTR-G542X mice revealed that gentamicin treatment resulted in the appearance of hCFTR protein at the apical surface of the glands of treated mice. Weaker staining was also observed in the intestinal glands following tobramycin treatment. Short-circuit current measurements made on intestinal tissues from these mice demonstrated that a significant number of positive cAMP-stimulated transepithelial chloride current measurements could be observed following gentamicin treatment (P=0.008) and a near significant number following tobramycin treatment (P=0.052). When taken together, these results indicate that gentamicin, and to a lesser extent tobramycin, can restore the synthesis of functional hCFTR protein by suppressing the hCFTR-G542X premature stop mutation in vivo.
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Affiliation(s)
- Ming Du
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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45
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Tökés-Füzesi M, Bedwell DM, Repa I, Sipos K, Sümegi B, Rab A, Miseta A. Hexose phosphorylation and the putative calcium channel component Mid1p are required for the hexose-induced transient elevation of cytosolic calcium response in Saccharomyces cerevisiae. Mol Microbiol 2002; 44:1299-308. [PMID: 12028380 DOI: 10.1046/j.1365-2958.2002.02956.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Saccharomyces cerevisiae responds to environ-mental stimuli such as an exposure to pheromone or to hexoses after carbon source limitation with a transient elevation of cytosolic calcium (TECC) response. In this study, we examined whether hexose transport and phosphorylation are necessary for the TECC response. We found that a mutant strain lacking most of the known hexose transporters was unable to carry out the TECC response when exposed to glucose. A mutant strain that lacked the ability to phosphorylate glucose was unable to respond to glucose addition, but displayed a normal TECC response after the addition of galactose. These results indicate that hexose uptake and phosphorylation are required to trigger the hexose-induced TECC response. We also found that the TECC response was significantly smaller than normal when the level of environmental calcium was reduced, and was abolished in a mid1 mutant that lacked a subunit of the high-affinity calcium channel of the yeast plasma membrane. These results indicate that most or all of the TECC response is mediated by an influx of calcium from the extracellular space. Our results indicate that this transient increase in plasma membrane calcium permeability may be linked to the accumulation of Glc-1-P (or a related glucose metabolite) in yeast.
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Affiliation(s)
- Margit Tökés-Füzesi
- Department of Clinical Chemistry, Faculty of Medicine, Pécs University, 13 Ifjuság u., Pécs 7624, Hungary
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46
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Keeling KM, Bedwell DM. Clinically relevant aminoglycosides can suppress disease-associated premature stop mutations in the IDUA and P53 cDNAs in a mammalian translation system. J Mol Med (Berl) 2002; 80:367-76. [PMID: 12072912 DOI: 10.1007/s00109-001-0317-z] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2001] [Accepted: 11/28/2001] [Indexed: 10/27/2022]
Abstract
Recent studies have suggested that the use of aminoglycosides to suppress disease-causing nonsense mutations may be a promising new therapy for a large number of genetic diseases. However, gentamicin is currently the only clinically relevant aminoglycoside shown to suppress premature stop mutations in a mammalian system. We compared the ability of the clinically approved aminoglycosides gentamicin, tobramycin, and amikacin to suppress premature stop mutations. Using readthrough reporter constructs as well as mammalian cDNAs containing naturally occurring premature stop mutations, we found that each of these aminoglycosides can suppress many premature stop mutations in a context-dependent manner in a mammalian translation system. Our results indicate that the tetranucleotide termination signal (the stop codon and the nucleotide 3' of the stop codon) is the primary determinant for aminoglycoside-mediated suppression. The levels of termination suppression achieved by tobramycin were substantially lower than those observed with gentamicin. In contrast, amikacin stimulated suppression in a manner that was generally similar to gentamicin. Amikacin produced higher levels of readthrough than gentamicin at some contexts, demonstrating a unique pattern of context dependence. Experiments with mammalian cDNAs confirmed these results and demonstrated that these aminoglycosides can also suppress disease-associated premature stop mutations previously identified in the IDUA gene (responsible for the lysosomal storage disease mucopolysaccharidosis I) and the P53 gene (associated with many forms of cancer). Taken together, these results suggest that amikacin represents an alternative to gentamicin for suppression therapy in certain contexts, thus providing a means of optimizing the efficacy of aminoglycoside-mediated suppression of premature stop mutations.
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Affiliation(s)
- Kim M Keeling
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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47
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Koh JY, Hájek P, Bedwell DM. Overproduction of PDR3 suppresses mitochondrial import defects associated with a TOM70 null mutation by increasing the expression of TOM72 in Saccharomyces cerevisiae. Mol Cell Biol 2001; 21:7576-86. [PMID: 11604494 PMCID: PMC99929 DOI: 10.1128/mcb.21.22.7576-7586.2001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most mitochondrial proteins are synthesized with cleavable amino-terminal targeting signals that interact with the mitochondrial import machinery to facilitate their import from the cytosol. We previously reported that the presequence of the F(1)-ATPase beta subunit precursor (pre-F(1)beta) acts as an intramolecular chaperone that maintains the precursor in an import-competent conformation prior to import (P. Hajek, J. Y. Koh, L. Jones, and D. M. Bedwell, Mol. Cell. Biol. 17:7169-7177, 1997). We also found that a mutant form of pre-F(1)beta with a minimal targeting signal (Delta 1,2 pre-F(1)beta) is inefficiently imported into mitochondria because it rapidly folds into an import-incompetent conformation. We have now analyzed the consequences of reducing the pre-F(1)beta targeting signal to a minimal unit in more detail. We found that Delta 1,2 pre-F(1)beta is more dependent upon the Tom70p receptor for import than WT pre-F(1)beta is, resulting in a growth defect on a nonfermentable carbon source at 15 degrees C. Experiments using an in vitro mitochondrial protein import system suggest that Tom70p functions to maintain a precursor containing the Delta 1,2 pre-F(1)beta import signal in an import-competent conformation. We also identified PDR3, a transcriptional regulator of the pleiotropic drug resistance network, as a multicopy suppressor of the mitochondrial import defects associated with Delta 1,2 pre-F(1)beta in a tom70 Delta strain. The overproduction of PDR3 mediated this effect by increasing the import of Delta 1,2 pre-F(1)beta into mitochondria. This increased the mitochondrial ATP synthase activity to the extent that growth of the mutant strain was restored under the selective conditions. Analysis of the transcription patterns of components of the mitochondrial outer membrane import machinery demonstrated that PDR3 overproduction increased the expression of TOM72, a little studied TOM70 homologue. These results suggest that Tom72p possesses overlapping functions with Tom70p and that the pleiotropic drug resistance network plays a previously unappreciated role in mitochondrial biogenesis.
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Affiliation(s)
- J Y Koh
- Department of Microbiology, University of Alabama at Birmingham, 35294-2170, USA
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48
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Clancy JP, Bebök Z, Ruiz F, King C, Jones J, Walker L, Greer H, Hong J, Wing L, Macaluso M, Lyrene R, Sorscher EJ, Bedwell DM. Evidence that systemic gentamicin suppresses premature stop mutations in patients with cystic fibrosis. Am J Respir Crit Care Med 2001; 163:1683-92. [PMID: 11401894 DOI: 10.1164/ajrccm.163.7.2004001] [Citation(s) in RCA: 200] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Here we report the effects of gentamicin treatment on cystic fibrosis transmembrane regulator (CFTR) production and function in CF airway cells and patients with CF with premature stop mutations. Using immunocytochemical and functional [6-methoxy-N- (3-sulfopropyl) quinolinium (SPQ)-based] techniques, ex vivo exposure of airway cells from stop mutation CF patients led to the identification of surface-localized CFTR in a dose-dependent fashion. Next, five patients with CF with stop mutations and five CF control subjects were treated with parenteral gentamicin for 1 wk, and underwent repeated in vivo measures of CFTR function (nasal potential difference [PD] measurements and sweat chloride [Cl(-)] testing). During the treatment period, the number of nasal PD readings in the direction of Cl(-) secretion was increased approximately 3-fold in the stop mutation patient group compared with controls (p < 0.001), and four of five stop mutation patients with CF had at least one reading during gentamicin treatment with a Cl(-) secretory response of more than -5 mV (hyperpolarized). A response of this magnitude was not seen in any of the CF control subjects (p < 0.05). In an independent series of experiments designed to test the ability of repeat nasal PDs to detect wild-type CFTR function, evidence of Cl(-) secretion was seen in 88% of control (non-CF) nasal PDs, and 71% were more than -5 mV hyperpolarized. Together, these results suggest that gentamicin treatment can suppress premature stop mutations in airway cells from patients with CF, and produce small increases in CFTR Cl(-) conductance (as measured by the nasal PD) in vivo.
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Affiliation(s)
- J P Clancy
- Department of Pediatrics, University of Alabama at Birmingham, USA.
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Keeling KM, Brooks DA, Hopwood JJ, Li P, Thompson JN, Bedwell DM. Gentamicin-mediated suppression of Hurler syndrome stop mutations restores a low level of alpha-L-iduronidase activity and reduces lysosomal glycosaminoglycan accumulation. Hum Mol Genet 2001; 10:291-9. [PMID: 11159948 DOI: 10.1093/hmg/10.3.291] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hurler syndrome is the most severe form of a lysosomal storage disease caused by loss of the enzyme alpha-L-iduronidase (encoded by the IDUA gene), which participates in the degradation of glycosaminoglycans (GAGs) within the lysosome. In some populations, premature stop mutations represent roughly two-thirds of the mutations that cause Hurler syndrome. In this study we investigated whether the aminoglycoside gentamicin can suppress stop mutations within the IDUA gene. We found that a Hurler syndrome fibroblast cell line heterozygous for the IDUA stop mutations Q70X and W402X showed a significant increase in alpha-L-iduronidase activity when cultured in the presence of gentamicin, resulting in the restoration of 2.8% of normal alpha-L-iduronidase activity. Determination of alpha-L-iduronidase protein levels by an immunoquantification assay indicated that gentamicin treatment produced a similar increase in alpha-L-iduronidase protein in Hurler cells. Both the alpha-L-iduronidase activity and protein level resulting from this treatment have previously been correlated with mild Hurler phenotypes. Although Hurler fibroblasts contain a much higher level of GAGs than normal, we found that gentamicin treatment reduced GAG accumulation in Hurler cells to a normal level. We also found that a reduced GAG level could be sustained for at least 2 days after gentamicin treatment was discontinued. The reduction in the GAG level was also reflected in a marked reduction in lysosomal vacuolation. Taken together, these results suggest that the suppression of premature stop mutations may provide an effective treatment for Hurler syndrome patients with premature stop mutations in the IDUA gene.
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Affiliation(s)
- K M Keeling
- Department of Human Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA
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Manuvakhova M, Keeling K, Bedwell DM. Aminoglycoside antibiotics mediate context-dependent suppression of termination codons in a mammalian translation system. RNA 2000; 6:1044-1055. [PMID: 10917599 PMCID: PMC1369979 DOI: 10.1017/s1355838200000716] [Citation(s) in RCA: 280] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The translation machinery recognizes codons that enter the ribosomal A site with remarkable accuracy to ensure that polypeptide synthesis proceeds with a minimum of errors. When a termination codon enters the A site of a eukaryotic ribosome, it is recognized by the release factor eRF1. It has been suggested that the recognition of translation termination signals in these organisms is not limited to a simple trinucleotide codon, but is instead recognized by an extended tetranucleotide termination signal comprised of the stop codon and the first nucleotide that follows. Interestingly, pharmacological agents such as aminoglycoside antibiotics can reduce the efficiency of translation termination by a mechanism that alters this ribosomal proofreading process. This leads to the misincorporation of an amino acid through the pairing of a near-cognate aminoacyl tRNA with the stop codon. To determine whether the sequence context surrounding a stop codon can influence aminoglycoside-mediated suppression of translation termination signals, we developed a series of readthrough constructs that contained different tetranucleotide termination signals, as well as differences in the three bases upstream and downstream of the stop codon. Our results demonstrate that the sequences surrounding a stop codon can play an important role in determining its susceptibility to suppression by aminoglycosides. Furthermore, these distal sequences were found to influence the level of suppression in remarkably distinct ways. These results suggest that the mRNA context influences the suppression of stop codons in response to subtle differences in the conformation of the ribosomal decoding site that result from aminoglycoside binding.
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Affiliation(s)
- M Manuvakhova
- Department of Microbiology, The University of Alabama at Birmingham, 35294-2170, USA
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