1
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Tanjala AC, Jiang JX, Eckford PDW, Ramjeesingh M, Li C, Huan LJ, Langeveld G, Townsend C, Paone DV, Busch-Petersen J, Pekhletski R, Tang L, Raju V, Rowe SM, Bear CE. Comparison of a novel potentiator of CFTR channel activity to ivacaftor in ameliorating mucostasis caused by cigarette smoke in primary human bronchial airway epithelial cells. Respir Res 2024; 25:269. [PMID: 38982492 PMCID: PMC11234710 DOI: 10.1186/s12931-024-02889-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/19/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Cystic Fibrosis causing mutations in the gene CFTR, reduce the activity of the CFTR channel protein, and leads to mucus aggregation, airway obstruction and poor lung function. A role for CFTR in the pathogenesis of other muco-obstructive airway diseases such as Chronic Obstructive Pulmonary Disease (COPD) has been well established. The CFTR modulatory compound, Ivacaftor (VX-770), potentiates channel activity of CFTR and certain CF-causing mutations and has been shown to ameliorate mucus obstruction and improve lung function in people harbouring these CF-causing mutations. A pilot trial of Ivacaftor supported its potential efficacy for the treatment of mucus obstruction in COPD. These findings prompted the search for CFTR potentiators that are more effective in ameliorating cigarette-smoke (CS) induced mucostasis. METHODS Small molecule potentiators, previously identified in CFTR binding studies, were tested for activity in augmenting CFTR channel activity using patch clamp electrophysiology in HEK-293 cells, a fluorescence-based assay of membrane potential in Calu-3 cells and in Ussing chamber studies of primary bronchial epithelial cultures. Addition of cigarette smoke extract (CSE) to the solutions bathing the apical surface of Calu-3 cells and primary bronchial airway cultures was used to model COPD. Confocal studies of the velocity of fluorescent microsphere movement on the apical surface of CSE exposed airway epithelial cultures, were used to assess the effect of potentiators on CFTR-mediated mucociliary movement. RESULTS We showed that SK-POT1, like VX-770, was effective in augmenting the cyclic AMP-dependent channel activity of CFTR. SK-POT-1 enhanced CFTR channel activity in airway epithelial cells previously exposed to CSE and ameliorated mucostasis on the surface of primary airway cultures. CONCLUSION Together, this evidence supports the further development of SK-POT1 as an intervention in the treatment of COPD.
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Affiliation(s)
| | - Jia Xin Jiang
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Paul D W Eckford
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Mohabir Ramjeesingh
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Canhui Li
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Ling Jun Huan
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Gabrielle Langeveld
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | | | | | | | - Roman Pekhletski
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada
| | - LiPing Tang
- Department of Medicine, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vamsee Raju
- Department of Medicine, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven M Rowe
- Department of Medicine, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Christine E Bear
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Canada.
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2
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Tanjala AC, Jiang JX, Eckford PDW, Ramjeesingh M, Li C, Huan LJ, Langeveld G, Townsend C, Paone DV, Busch-Petersen J, Pekhletski R, Tang L, Raju V, Rowe SM, Bear CE. Comparison of a novel potentiator of CFTR channel activity to ivacaftor in ameliorating mucostasis caused by cigarette smoke in primary human bronchial airway epithelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582742. [PMID: 38496440 PMCID: PMC10942391 DOI: 10.1101/2024.03.01.582742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Cystic Fibrosis causing mutations in the gene CFTR , reduce the activity of the CFTR channel protein, and leads to mucus aggregation, airway obstruction and poor lung function. A role for CFTR in the pathogenesis of other muco-obstructive airway diseases such as Chronic Obstructive Pulmonary Disease (COPD) has been well established. The CFTR modulatory compound, Ivacaftor (VX-770), potentiates channel activity of CFTR and certain CF-causing mutations and has been shown to ameliorate mucus obstruction and improve lung function in people harbouring these CF-causing mutations. A pilot trial of Ivacaftor supported its potential efficacy for the treatment of mucus obstruction in COPD. These findings prompted the search for CFTR potentiators that are more effective in ameliorating cigarette-smoke (CS) induced mucostasis. Methods A novel small molecule potentiator (SK-POT1), previously identified in CFTR binding studies, was tested for its activity in augmenting CFTR channel activity using patch clamp electrophysiology in HEK-293 cells, a fluorescence-based assay of membrane potential in Calu-3 cells and in Ussing chamber studies of primary bronchial epithelial cultures. Addition of cigarette smoke extract (CSE) to the solutions bathing the apical surface of Calu-3 cells and primary bronchial airway cultures was used to model COPD. Confocal studies of the velocity of fluorescent microsphere movement on the apical surface of CSE exposed airway epithelial cultures, were used to assess the effect of potentiators on CFTR-mediated mucociliary movement. Results We showed that SK-POT1, like VX-770, was effective in augmenting the cyclic AMP-dependent channel activity of CFTR. SK-POT-1 enhanced CFTR channel activity in airway epithelial cells previously exposed to CSE and ameliorated mucostasis on the surface of primary airway cultures. Conclusion Together, this evidence supports the further development of SK-POT1 as an intervention in the treatment of COPD.
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3
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Reporting Two Novel Mutations in Two Iranian Families with Cystic Fibrosis, Molecular and Bioinformatic Analysis. IRANIAN BIOMEDICAL JOURNAL 2022; 26:398-405. [PMID: 35468710 PMCID: PMC9763878 DOI: 10.52547/ibj.3713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Cystic fibrosis (CF) is the most common heredity disease among the Caucasian population. More than 350 known pathogenic variations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene (NM_000492.4) cause CF. Herein, we report the outcome of our investigation in two unrelated Iranian families with CF patients. Methods We conducted phenotypic examination, segregation, linkage analysis, and CFTR gene sequencing to define causative mutations. Results We found two novel mutations in the present study. The first one was a deletion causing frameshift, c.299delT p.(Leu100Profs*7), and the second one was a missense mutation, c.1857G>T, at nucleotide binding domain 1 of the CFTR protein. Haplotype segregation data supported our new mutation findings. Conclusion Findings of this study expand the spectrum of CFTR pathogenic variations and can improve prenatal diagnosis and genetic counseling for CF.
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Phenotyping Rare CFTR Mutations Reveal Functional Expression Defects Restored by TRIKAFTA TM. J Pers Med 2021; 11:jpm11040301. [PMID: 33920764 PMCID: PMC8071105 DOI: 10.3390/jpm11040301] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/15/2022] Open
Abstract
The rare Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) mutations, c.1826A > G (H609R) and c.3067_3072delATAGTG (I1023_V1024del), are associated with severe lung disease. Despite the existence of four CFTR targeted therapies, none have been approved for individuals with these mutations because the associated molecular defects were not known. In this study we examined the consequences of these mutations on protein processing and channel function in HEK293 cells. We found that, similar to F508del, H609R and I1023_V1024del-CFTR exhibited reduced protein processing and altered channel function. Because the I1023_V1024del mutation can be linked with the mutation, I148T, we also examined the protein conferred by transfection of a plasmid bearing both mutations. Interestingly, together with I148T, there was no further reduction in channel function exhibited by I1023-V1024del. Both H609R and I1023_V1024del failed to exhibit significant correction of their functional expression with lumacaftor and ivacaftor. In contrast, the triple modulator combination found in TRIKAFTATM, i.e., tezacaftor, elexacaftor and ivacaftor rescued trafficking and function of both of these mutants. These in-vitro findings suggest that patients harbouring H609R or I1023_V1024del, alone or with I148T, may benefit clinically from treatment with TRIKAFTATM.
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Haq IJ, Althaus M, Gardner AI, Yeoh HY, Joshi U, Saint-Criq V, Verdon B, Townshend J, O'Brien C, Ben-Hamida M, Thomas M, Bourke S, van der Sluijs P, Braakman I, Ward C, Gray MA, Brodlie M. Clinical and molecular characterization of the R751L-CFTR mutation. Am J Physiol Lung Cell Mol Physiol 2020; 320:L288-L300. [PMID: 33296276 PMCID: PMC8476205 DOI: 10.1152/ajplung.00137.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cystic fibrosis (CF) arises from mutations in the CF transmembrane conductance regulator (CFTR) gene, resulting in progressive and life-limiting respiratory disease. R751L is a rare CFTR mutation that is poorly characterized. Our aims were to describe the clinical and molecular phenotypes associated with R751L. Relevant clinical data were collected from three heterozygote individuals harboring R751L (2 patients with G551D/R751L and 1 with F508del/R751L). Assessment of R751L-CFTR function was made in primary human bronchial epithelial cultures (HBEs) and Xenopus oocytes. Molecular properties of R751L-CFTR were investigated in the presence of known CFTR modulators. Although sweat chloride was elevated in all three patients, the clinical phenotype associated with R751L was mild. Chloride secretion in F508del/R751L HBEs was reduced compared with non-CF HBEs and associated with a reduction in sodium absorption by the epithelial sodium channel (ENaC). However, R751L-CFTR function in Xenopus oocytes, together with folding and cell surface transport of R751L-CFTR, was not different from wild-type CFTR. Overall, R751L-CFTR was associated with reduced sodium chloride absorption but had functional properties similar to wild-type CFTR. This is the first report of R751L-CFTR that combines clinical phenotype with characterization of functional and biological properties of the mutant channel. Our work will build upon existing knowledge of mutations within this region of CFTR and, importantly, inform approaches for clinical management. Elevated sweat chloride and reduced chloride secretion in HBEs may be due to alternative non-CFTR factors, which require further investigation.
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Affiliation(s)
- Iram J Haq
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Mike Althaus
- Institute for Functional Gene Analytics, Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, Rheinbach, Germany
| | - Aaron Ions Gardner
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hui Ying Yeoh
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Urjita Joshi
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Vinciane Saint-Criq
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Bernard Verdon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jennifer Townshend
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Christopher O'Brien
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Mahfud Ben-Hamida
- Department of Paediatrics, West Cumberland Hospital, Whitehaven, United Kingdom
| | - Matthew Thomas
- Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Stephen Bourke
- Respiratory Medicine, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ineke Braakman
- Cellular Protein Chemistry, Science4Life, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Chris Ward
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael A Gray
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Malcolm Brodlie
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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6
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Brewington JJ, Backstrom J, Feldman A, Kramer EL, Moncivaiz JD, Ostmann AJ, Zhu X, Lu LJ, Clancy JP. Chronic β2AR stimulation limits CFTR activation in human airway epithelia. JCI Insight 2018; 3:93029. [PMID: 29467332 DOI: 10.1172/jci.insight.93029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 01/23/2018] [Indexed: 12/20/2022] Open
Abstract
Traditional pulmonary therapies for cystic fibrosis (CF) target the downstream effects of CF transmembrane conductance regulator (CFTR) dysfunction (the cause of CF). Use of one such therapy, β-adrenergic bronchodilators (such as albuterol), is nearly universal for airway clearance. Conversely, novel modulator therapies restore function to select mutant CFTR proteins, offering a disease-modifying treatment. Recent trials of modulators targeting F508del-CFTR, the most common CFTR mutation, suggest that chronic β-agonist use may undermine clinical modulator benefits. We therefore sought to understand the impact of chronic or excess β-agonist exposure on CFTR activation in human airway epithelium. The present studies demonstrate a greater than 60% reduction in both wild-type and modulator-corrected F508del-CFTR activation following chronic exposure to short- and long-acting β-agonists. This reduction was due to reduced cellular generation of cAMP downstream of the β-2 adrenergic receptor-G protein complex. Our results point towards a posttranscriptional reduction in adenylyl cyclase function as the mechanism of impaired CFTR activation produced by prolonged β-agonist exposure. β-Agonist-induced CFTR dysfunction was sufficient to abrogate VX809/VX770 modulation of F508del-CFTR in vitro. Understanding the clinical relevance of our observations is critical for CF patients using these drugs, and for investigators to inform future CFTR modulator drug trials.
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Affiliation(s)
| | | | - Amanda Feldman
- Division of Pulmonary Medicine, Department of Pediatrics, and
| | | | | | | | - Xiaoting Zhu
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - L Jason Lu
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - John P Clancy
- Division of Pulmonary Medicine, Department of Pediatrics, and
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7
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Zak SM, Clancy JP, Brewington JJ. CFTR functional assays in drug development. Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2017.1393413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sara M. Zak
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, USA
| | - John P. Clancy
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, USA
| | - John J. Brewington
- Department of Pediatrics, Division of Pulmonary Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, USA
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8
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Csizmok V, Follis AV, Kriwacki RW, Forman-Kay JD. Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling. Chem Rev 2016; 116:6424-62. [PMID: 26922996 DOI: 10.1021/acs.chemrev.5b00548] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins (IDPs) and regions (IDRs), which represent ∼30% of the proteome and enable unique regulatory mechanisms. In this review, we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of conformational ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as "ultrasensitivity" and "regulated folding and unfolding". We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information.
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Affiliation(s)
- Veronika Csizmok
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Ariele Viacava Follis
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center , Memphis, Tennessee 38163, United States
| | - Julie D Forman-Kay
- Molecular Structure & Function, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada.,Department of Biochemistry, University of Toronto , Toronto, ON M5S 1A8, Canada
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9
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Chuang CY, Chen LY, Fu RH, Chen SM, Ho MH, Huang JM, Hsu CC, Wang CC, Chen MS, Tsai RT. Involvement of the carboxyl-terminal region of the yeast peroxisomal half ABC transporter Pxa2p in its interaction with Pxa1p and in transporter function. PLoS One 2014; 9:e104892. [PMID: 25118695 PMCID: PMC4132065 DOI: 10.1371/journal.pone.0104892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 07/17/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The peroxisome is a single membrane-bound organelle in eukaryotic cells involved in lipid metabolism, including β-oxidation of fatty acids. The human genetic disorder X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ABCD1 gene (encoding ALDP, a peroxisomal half ATP-binding cassette [ABC] transporter). This disease is characterized by defective peroxisomal β-oxidation and a large accumulation of very long-chain fatty acids in brain white matter, adrenal cortex, and testis. ALDP forms a homodimer proposed to be the functional transporter, whereas the peroxisomal transporter in yeast is a heterodimer comprising two half ABC transporters, Pxa1p and Pxa2p, both orthologs of human ALDP. While the carboxyl-terminal domain of ALDP is engaged in dimerization, it remains unknown whether the same region is involved in the interaction between Pxa1p and Pxa2p. METHODS/PRINCIPAL FINDINGS Using a yeast two-hybrid assay, we found that the carboxyl-terminal region (CT) of Pxa2p, but not of Pxa1p, is required for their interaction. Further analysis indicated that the central part of the CT (designated CT2) of Pxa2p was indispensable for its interaction with the carboxyl terminally truncated Pxa1_NBD. An interaction between the CT of Pxa2p and Pxa1_NBD was not detected, but could be identified in the presence of Pxa2_NBD-CT1. A single mutation of two conserved residues (aligned with X-ALD-associated mutations at the same positions in ALDP) in the CT2 of the Pxa2_NBD-CT protein impaired its interaction with Pxa1_NBD or Pxa1_NBD-CT, resulting in a mutant protein that exhibited a proteinase K digestion profile different from that of the wild-type protein. Functional analysis of these mutant proteins on oleate plates indicated that they were defective in transporter function. CONCLUSIONS/SIGNIFICANCE The CT of Pxa2p is involved in its interaction with Pxa1p and in transporter function. This concept may be applied to human ALDP studies, helping to establish the pathological mechanism for CT-related X-ALD disease.
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Affiliation(s)
- Cheng-Yi Chuang
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ling-Yun Chen
- Department of Biochemistry, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ru-Huei Fu
- Graduate Institute of Immunology, China Medical University, Taichung, Taiwan
| | - Shih-Ming Chen
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ming-Hua Ho
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Jie-Mau Huang
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chia-Chi Hsu
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chien-Cheng Wang
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Meng-Shian Chen
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Rong-Tzong Tsai
- Institute of Biochemistry and Biotechnology, College of Medicine, Chung Shan Medical University, Taichung, Taiwan; Department of Biochemistry, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
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10
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Yuan J, Zhu Q, Liu B. Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes. PLoS One 2014; 9:e84330. [PMID: 24465405 PMCID: PMC3896360 DOI: 10.1371/journal.pone.0084330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/14/2013] [Indexed: 12/29/2022] Open
Abstract
The evolutionary history of living species is usually inferred through the phylogenetic analysis of molecular and morphological information using various mathematical models. New challenges in phylogenetic analysis are centered mostly on the search for accurate and efficient methods to handle the huge amounts of sequence data generated from newer genome sequencing. The next major challenge is the determination of relationships between the evolution of structural elements and their functional implementation, which is largely ignored in previous analyses. Here, we described the discovery of structural elements in metazoan mitochondrial genomes, termed key K-strings, that can serve as a basis for phylogenetic tree construction. Although comprising only a small fraction (0.73%) of all K-strings, these key K-strings are pivotal to the tree construction because they allow for a significant reduction in the computational time required to construct phylogenetic trees, and more importantly, they make significant improvement to the results of phylogenetic inference. The trees constructed from the key K-strings were consistent overall to our current view of metazoan phylogeny and exhibited a more rational topology than the trees constructed by using other conventional methods. Surprisingly, the key K-strings tended to accumulate in the conserved regions of the original sequences, which were most likely due to strong selection pressure. Furthermore, the special structural features of the key K-strings should have some potential applications in the study of the structures and functions relationship of proteins and in the determination of evolutionary trajectory of species. The novelty and potential importance of key K-strings lead us to believe that they are essential evolutionary elements. As such, they may play important roles in the process of species evolution and their physical existence. Further studies could lead to discoveries regarding the relationship between evolution and processes of speciation.
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Affiliation(s)
- Jianbo Yuan
- Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | | | - Bin Liu
- Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang, China
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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11
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Phenotypic discordance in three siblings affected by atypical cystic fibrosis with the F508del/D614G genotype. J Cyst Fibros 2006; 5:193-5. [DOI: 10.1016/j.jcf.2005.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 11/30/2005] [Accepted: 12/01/2005] [Indexed: 11/20/2022]
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12
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Frelet A, Klein M. Insight in eukaryotic ABC transporter function by mutation analysis. FEBS Lett 2006; 580:1064-84. [PMID: 16442101 DOI: 10.1016/j.febslet.2006.01.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 11/21/2022]
Abstract
With regard to structure-function relations of ATP-binding cassette (ABC) transporters several intriguing questions are in the spotlight of active research: Why do functional ABC transporters possess two ATP binding and hydrolysis domains together with two ABC signatures and to what extent are the individual nucleotide-binding domains independent or interacting? Where is the substrate-binding site and how is ATP hydrolysis functionally coupled to the transport process itself? Although much progress has been made in the elucidation of the three-dimensional structures of ABC transporters in the last years by several crystallographic studies including novel models for the nucleotide hydrolysis and translocation catalysis, site-directed mutagenesis as well as the identification of natural mutations is still a major tool to evaluate effects of individual amino acids on the overall function of ABC transporters. Apart from alterations in characteristic sequence such as Walker A, Walker B and the ABC signature other parts of ABC proteins were subject to detailed mutagenesis studies including the substrate-binding site or the regulatory domain of CFTR. In this review, we will give a detailed overview of the mutation analysis reported for selected ABC transporters of the ABCB and ABCC subfamilies, namely HsCFTR/ABCC7, HsSUR/ABCC8,9, HsMRP1/ABCC1, HsMRP2/ABCC2, ScYCF1 and P-glycoprotein (Pgp)/MDR1/ABCB1 and their effects on the function of each protein.
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Affiliation(s)
- Annie Frelet
- Zurich Basel Plant Science Center, University of Zurich, Plant Biology, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
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13
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Chappe V, Hinkson DA, Howell LD, Evagelidis A, Liao J, Chang XB, Riordan JR, Hanrahan JW. Stimulatory and inhibitory protein kinase C consensus sequences regulate the cystic fibrosis transmembrane conductance regulator. Proc Natl Acad Sci U S A 2004; 101:390-5. [PMID: 14695900 PMCID: PMC314195 DOI: 10.1073/pnas.0303411101] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2003] [Accepted: 10/22/2003] [Indexed: 11/18/2022] Open
Abstract
Protein kinase C (PKC) phosphorylation stimulates the cystic fibrosis transmembrane conductance regulator (CFTR) channel and enhances its activation by protein kinase A (PKA) through mechanisms that remain poorly understood. We have examined the effects of mutating consensus sequences for PKC phosphorylation and report here evidence for both stimulatory and inhibitory sites. Sequences were mutated in subsets and the mutants characterized by patch clamping. Activation of a 4CA mutant (S707A/S790A/T791A/S809A) by PKA was similar to that of wild-type CFTR and was enhanced by PKC, whereas responses of 3CA (T582A/T604A/S641A) and 2CA (T682A/S686A) channels to PKA were both drastically reduced (>90%). When each mutation in the 3CA and 2CA constructs was studied individually in a wild-type background, T582, T604, and S686 were found to be essential for PKA activation. Responses were restored when these three residues were reintroduced simultaneously into a 9CA mutant lacking all nine PKC consensus sequences (R6CA revertant); however, PKC phosphorylation was not required for this rescue. Nevertheless, two of the sites (T604 and S686) were phosphorylated in vitro, and PKC alone partially activated wild-type CFTR, the 4CA mutant, and the point mutants T582A and T604A, but not S686A channels, indicating that PKC does act at S686. The region encompassing S641 and T682 is inhibitory, because S641A enhanced activation by PKA, and T682A channels had 4-fold larger responses to PKC compared to wild-type channels. These results identify functionally important PKC consensus sequences on CFTR and will facilitate studies of its convergent regulation by PKC and PKA.
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Affiliation(s)
- Valerie Chappe
- Department of Physiology, McGill University, Montréal, QC, Canada H3G 1Y6.
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Gentzsch M, Aleksandrov A, Aleksandrov L, Riordan JR. Functional analysis of the C-terminal boundary of the second nucleotide binding domain of the cystic fibrosis transmembrane conductance regulator and structural implications. Biochem J 2002; 366:541-8. [PMID: 12020354 PMCID: PMC1222794 DOI: 10.1042/bj20020511] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2002] [Revised: 05/16/2002] [Accepted: 05/20/2002] [Indexed: 12/22/2022]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) contains two nucleotide-binding domains (NBDs) or ATP-binding cassettes (ABCs) that characterize a large family of membrane transporters. Although the three-dimensional structures of these domains from several ABC proteins have been determined, this is not the case for CFTR, and hence the domains are defined simply on the basis of sequence alignment. The functional C-terminal boundary of NBD1 of CFTR was located by analysis of chloride channel function [Chan, Csanady, Seto-Young, Nairn and Gadsby (2000) J. Gen. Physiol. 116, 163-180]. However, the boundary between the C-terminal end of NBD2 and sequences further downstream in the whole protein, that are important for its cellular localization and endocytotic turnover, has not been defined. We have now done this by assaying the influence of progressive C-terminal truncations on photolabelling of NBD2 by 8-azido-ATP, which reflects hydrolysis, as well as binding, at that domain, and on NBD2-dependent channel gating itself. The boundary defined in this way is between residues 1420 and 1424, which corresponds to the final beta-strand in aligned NBDs whose structures have been determined. Utilization of this information should facilitate the generation of monodisperse NBD2 polypeptides for structural analysis, which until now has not been possible. The established boundary includes within NBD2 a hydrophobic patch of four residues (1413-1416) previously shown to be essential for CFTR maturation and stability [Gentzsch and Riordan (2001) J. Biol. Chem. 276, 1291-1298]. This hydrophobic cluster is conserved in most ABC proteins, and on alignment with ones of known structure constitutes the penultimate beta-strand of the domain which is likely to participate in essential structure-stabilizing beta-sheet formation.
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Affiliation(s)
- Martina Gentzsch
- Mayo Foundation and Mayo Clinic Scottsdale, S. C. Johnson Medical Research Center, 13400 E. Shea Blvd., Scottsdale, AZ 85259, USA
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Abstract
While originally characterized as a collection of related syndromes, cystic fibrosis (CF) is now recognized as a single disease whose diverse symptoms stem from the wide tissue distribution of the gene product that is defective in CF, the ion channel and regulator, cystic fibrosis transmembrane conductance regulator (CFTR). Defective CFTR protein impacts the function of the pancreas and alters the consistency of mucosal secretions. The latter of these effects probably plays an important role in the defective resistance of CF patients to many pathogens. As the modalities of CF research have changed over the decades from empirical histological studies to include biophysical measurements of CFTR function, the clinical management of this disease has similarly evolved to effectively address the ever-changing spectrum of CF-related infectious diseases. These factors have led to the successful management of many CF-related infections with the notable exception of chronic lung infection with the gram-negative bacterium Pseudomonas aeruginosa. The virulence of P. aeruginosa stems from multiple bacterial attributes, including antibiotic resistance, the ability to utilize quorum-sensing signals to form biofilms, the destructive potential of a multitude of its microbial toxins, and the ability to acquire a mucoid phenotype, which renders this microbe resistant to both the innate and acquired immunologic defenses of the host.
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Affiliation(s)
- Jeffrey B. Lyczak
- Channing Laboratory, Brigham and Women's Hospital,, Harvard Medical School,, Children's Hospital, Boston, MA 02115
| | - Carolyn L. Cannon
- Channing Laboratory, Brigham and Women's Hospital,, Harvard Medical School,, Children's Hospital, Boston, MA 02115
| | - Gerald B. Pier
- Channing Laboratory, Brigham and Women's Hospital,, Harvard Medical School,, Children's Hospital, Boston, MA 02115
- Corresponding author. Mailing address: Channing Laboratory, 181 Longwood Ave., Boston, MA 02115. Phone: (617) 525-2269. Fax: (617) 525-2510.
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Hämmerle MM, Aleksandrov AA, Riordan JR. Disease-associated mutations in the extracytoplasmic loops of cystic fibrosis transmembrane conductance regulator do not impede biosynthetic processing but impair chloride channel stability. J Biol Chem 2001; 276:14848-54. [PMID: 11278813 DOI: 10.1074/jbc.m011017200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Consistent with its function as a chloride channel regulated entirely from the cytoplasmic side of the plasma membrane, the cystic fibrosis transmembrane conductance regulator (CFTR) glycoprotein exposes little of its mass on the exterior surface of cells. The first and fourth extracytoplasmic loops (ELs) contain approximately 15 and 30 residues, respectively; the other four ELs are extremely short. To examine the influence of missense mutants in ELs detected in patients with cystic fibrosis, we have expressed them in mammalian (baby hamster kidney (BHK21)) cells and assessed their biosynthetic processing and chloride channel activity. In contrast to previous findings that 18 of 30 disease-associated missense mutations in cytoplasmic loops caused retention of the nascent polypeptides in the endoplasmic reticulum, all the EL mutants studied matured and were transported to the cell surface. This pronounced asymmetry is consistent with the notion that endoplasmic reticulum quality control of nascent CFTR is exerted primarily on the cytoplasmic side of the membrane. Although this set of EL mutations has little effect on CFTR maturation, most of them seriously compromise its chloride channel activity. Substitutions at six different positions in EL1 and single positions in EL2 and EL4 all destabilized the open state, some of them severely, indicating that the ELs contribute to the stability of the CFTR ion pore.
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Affiliation(s)
- M M Hämmerle
- S. C. Johnson Medical Research Center, Mayo Clinic Scottsdale, Scottsdale, Arizona 85259, USA
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Chen JM, Scotet V, Ferec C. Definition of a "functional R domain" of the cystic fibrosis transmembrane conductance regulator. Mol Genet Metab 2000; 71:245-9. [PMID: 11001817 DOI: 10.1006/mgme.2000.3041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The R domain of the cystic fibrosis transmembrane conductance regulator (CFTR) was originally defined as 241 amino acids, encoded by exon 13. Such exon/intron boundaries provide a convenient way to define the R domain, but do not necessarily reflect the corresponding functional domain within CFTR. A two-domain model was later proposed based on a comparison of the R-domain sequences from 10 species. While RD1, the N-terminal third of the R domain is highly conserved, RD2, the large central region of the R domain has less rigid structural requirements. Although this two-domain model was given strong support by recent functional analysis data, the simple observation that two of the four main phosphorylation sites are excluded from RD2 clearly indicates that RD2 still does not satisfy the requirements of a "functional R domain." Nevertheless, knowledge of the CFTR structure and function accumulated over the past decade and reevaluated in the context of a comprehensive sequence comparison of 15 CFTR homologues made it possible to define such a "functional R domain," i.e., amino acids C647 to D836. This definition is validated primarily because it contains all of the important potential consensus phosphorylation sequences. In addition, it includes the highly charged motif from E822 to D836. Finally, it includes all of the deletions/insertions in this region. This definition also aids in understanding the effects of missense mutations occurring within this domain.
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Affiliation(s)
- J M Chen
- Etablissement Français du Sang-Bretagne, Site de Brest, Brest, France
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