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Zhao M, Ma J, Zhang L, Qi H. Engineering strategies for enhanced heterologous protein production by Saccharomyces cerevisiae. Microb Cell Fact 2024; 23:32. [PMID: 38247006 PMCID: PMC10801990 DOI: 10.1186/s12934-024-02299-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Microbial proteins are promising substitutes for animal- and plant-based proteins. S. cerevisiae, a generally recognized as safe (GRAS) microorganism, has been frequently employed to generate heterologous proteins. However, constructing a universal yeast chassis for efficient protein production is still a challenge due to the varying properties of different proteins. With progress in synthetic biology, a multitude of molecular biology tools and metabolic engineering strategies have been employed to alleviate these issues. This review first analyses the advantages of protein production by S. cerevisiae. The most recent advances in improving heterologous protein yield are summarized and discussed in terms of protein hyperexpression systems, protein secretion engineering, glycosylation pathway engineering and systems metabolic engineering. Furthermore, the prospects for efficient and sustainable heterologous protein production by S. cerevisiae are also provided.
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Affiliation(s)
- Meirong Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Jianfan Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Lei Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China
| | - Haishan Qi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), Tianjin University, Tianjin, 300350, China.
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2
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Mention K, Cavusoglu-Doran K, Joynt AT, Santos L, Sanz D, Eastman AC, Merlo C, Langfelder-Schwind E, Scallan MF, Farinha CM, Cutting GR, Sharma N, Harrison PT. Use of adenine base editing and homology-independent targeted integration strategies to correct the cystic fibrosis causing variant, W1282X. Hum Mol Genet 2023; 32:3237-3248. [PMID: 37649273 PMCID: PMC10656707 DOI: 10.1093/hmg/ddad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/21/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023] Open
Abstract
Small molecule drugs known as modulators can treat ~90% of people with cystic fibrosis (CF), but do not work for premature termination codon variants such as W1282X (c.3846G>A). Here we evaluated two gene editing strategies, Adenine Base Editing (ABE) to correct W1282X, and Homology-Independent Targeted Integration (HITI) of a CFTR superexon comprising exons 23-27 (SE23-27) to enable expression of a CFTR mRNA without W1282X. In Flp-In-293 cells stably expressing a CFTR expression minigene bearing W1282X, ABE corrected 24% of W1282X alleles, rescued CFTR mRNA from nonsense mediated decay and restored protein expression. However, bystander editing at the adjacent adenine (c.3847A>G), caused an amino acid change (R1283G) that affects CFTR maturation and ablates ion channel activity. In primary human nasal epithelial cells homozygous for W1282X, ABE corrected 27% of alleles, but with a notably lower level of bystander editing, and CFTR channel function was restored to 16% of wild-type levels. Using the HITI approach, correct integration of a SE23-27 in intron 22 of the CFTR locus in 16HBEge W1282X cells was detected in 5.8% of alleles, resulting in 7.8% of CFTR transcripts containing the SE23-27 sequence. Analysis of a clonal line homozygous for the HITI-SE23-27 produced full-length mature protein and restored CFTR anion channel activity to 10% of wild-type levels, which could be increased three-fold upon treatment with the triple combination of CF modulators. Overall, these data demonstrate two different editing strategies can successfully correct W1282X, the second most common class I variant, with a concomitant restoration of CFTR function.
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Affiliation(s)
- Karen Mention
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Kader Cavusoglu-Doran
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Anya T Joynt
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Lúcia Santos
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - David Sanz
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Alice C Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, 1800 Orleans St, Baltimore, MD 21287, United States
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Lenox Hill Hospital, 100 E. 77th Street, 4E, New York, NY 10075, United States
| | - Martina F Scallan
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Carlos M Farinha
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Patrick T Harrison
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
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3
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Woodall M, Tarran R, Lee R, Anfishi H, Prins S, Counsell J, Vergani P, Hart S, Baines D. Expression of gain-of-function CFTR in cystic fibrosis airway cells restores epithelial function better than wild-type or codon-optimized CFTR. Mol Ther Methods Clin Dev 2023; 30:593-605. [PMID: 37701179 PMCID: PMC10494266 DOI: 10.1016/j.omtm.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/10/2023] [Indexed: 09/14/2023]
Abstract
Class Ia/b cystic fibrosis transmembrane regulator (CFTR) variants cause severe lung disease in 10% of cystic fibrosis (CF) patients and are untreatable with small-molecule pharmaceuticals. Genetic replacement of CFTR offers a cure, but its effectiveness is limited in vivo. We hypothesized that enhancing protein levels (using codon optimization) and/or activity (using gain-of-function variants) of CFTR would more effectively restore function to CF bronchial epithelial cells. Three different variants of the CFTR protein were tested: codon optimized (high codon adaptation index [hCAI]), a gain-of-function (GOF) variant (K978C), and a combination of both (hˆK978C). In human embryonic kidney (HEK293T) cells, initial results showed that hCAI and hˆK978C produced greater than 10-fold more CFTR protein and displayed ∼4-fold greater activity than wild-type (WT) CFTR. However, functionality was profoundly different in CF bronchial epithelial cells. Here, K978C CFTR more potently restored essential epithelial functions (anion transport, airway surface liquid height, and pH) than WT CFTR. hCAI and hˆK978C CFTRs had limited impact because of mislocalization in the cell. These data provide a proof of principle showing that GOF variants may be more effective than codon-optimized forms of CFTR for CF gene therapy. Video abstract
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Affiliation(s)
- Maximillian Woodall
- Institute for Infection and Immunity, St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
| | - Robert Tarran
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Rhianna Lee
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Hafssa Anfishi
- Institute for Infection and Immunity, St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
| | - Stella Prins
- Neuroscience, Physiology, & Pharmacology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - John Counsell
- Genetics & Genomic Medicine Department, Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Paola Vergani
- Neuroscience, Physiology, & Pharmacology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Stephen Hart
- Genetics & Genomic Medicine Department, Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Deborah Baines
- Institute for Infection and Immunity, St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
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4
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Michaels WE, Pena-Rasgado C, Kotaria R, Bridges RJ, Hastings ML. Open reading frame correction using splice-switching antisense oligonucleotides for the treatment of cystic fibrosis. Proc Natl Acad Sci U S A 2022; 119:e2114886119. [PMID: 35017302 PMCID: PMC8784102 DOI: 10.1073/pnas.2114886119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
CFTR gene mutations that result in the introduction of premature termination codons (PTCs) are common in cystic fibrosis (CF). This mutation type causes a severe form of the disease, likely because of low CFTR messenger RNA (mRNA) expression as a result of nonsense-mediated mRNA decay, as well as the production of a nonfunctional, truncated CFTR protein. Current therapeutics for CF, which target residual protein function, are less effective in patients with these types of mutations due in part to low CFTR protein levels. Splice-switching antisense oligonucleotides (ASOs), designed to induce skipping of exons in order to restore the mRNA open reading frame, have shown therapeutic promise preclinically and clinically for a number of diseases. We hypothesized that ASO-mediated skipping of CFTR exon 23 would recover CFTR activity associated with terminating mutations in the exon, including CFTR p.W1282X, the fifth most common mutation in CF. Here, we show that CFTR lacking the amino acids encoding exon 23 is partially functional and responsive to corrector and modulator drugs currently in clinical use. ASO-induced exon 23 skipping rescued CFTR expression and chloride current in primary human bronchial epithelial cells isolated from a homozygote CFTR-W1282X patient. These results support the use of ASOs in treating CF patients with CFTR class I mutations in exon 23 that result in unstable CFTR mRNA and truncations of the CFTR protein.
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Affiliation(s)
- Wren E Michaels
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Science and Medicine, North Chicago, IL 60064
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Science and Medicine, North Chicago, IL 60064
| | - Cecilia Pena-Rasgado
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Science and Medicine, North Chicago, IL 60064
| | - Rusudan Kotaria
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Science and Medicine, North Chicago, IL 60064
| | - Robert J Bridges
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Science and Medicine, North Chicago, IL 60064;
| | - Michelle L Hastings
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Science and Medicine, North Chicago, IL 60064;
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5
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Gaither JBS, Lammi GE, Li JL, Gordon DM, Kuck HC, Kelly BJ, Fitch JR, White P. Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population. Gigascience 2021; 10:6211353. [PMID: 33822938 PMCID: PMC8023685 DOI: 10.1093/gigascience/giab023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/10/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
Background The role of synonymous single-nucleotide variants in human health and disease is poorly understood, yet evidence suggests that this class of “silent” genetic variation plays multiple regulatory roles in both transcription and translation. One mechanism by which synonymous codons direct and modulate the translational process is through alteration of the elaborate structure formed by single-stranded mRNA molecules. While tools to computationally predict the effect of non-synonymous variants on protein structure are plentiful, analogous tools to systematically assess how synonymous variants might disrupt mRNA structure are lacking. Results We developed novel software using a parallel processing framework for large-scale generation of secondary RNA structures and folding statistics for the transcriptome of any species. Focusing our analysis on the human transcriptome, we calculated 5 billion RNA-folding statistics for 469 million single-nucleotide variants in 45,800 transcripts. By considering the impact of all possible synonymous variants globally, we discover that synonymous variants predicted to disrupt mRNA structure have significantly lower rates of incidence in the human population. Conclusions These findings support the hypothesis that synonymous variants may play a role in genetic disorders due to their effects on mRNA structure. To evaluate the potential pathogenic impact of synonymous variants, we provide RNA stability, edge distance, and diversity metrics for every nucleotide in the human transcriptome and introduce a “Structural Predictivity Index” (SPI) to quantify structural constraint operating on any synonymous variant. Because no single RNA-folding metric can capture the diversity of mechanisms by which a variant could alter secondary mRNA structure, we generated a SUmmarized RNA Folding (SURF) metric to provide a single measurement to predict the impact of secondary structure altering variants in human genetic studies.
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Affiliation(s)
- Jeffrey B S Gaither
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - Grant E Lammi
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - James L Li
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - David M Gordon
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - Harkness C Kuck
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - Benjamin J Kelly
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - James R Fitch
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA
| | - Peter White
- Computational Genomics Group, The Institute for Genomic Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH 43215, USA.,Department of Pediatrics, College of Medicine, The Ohio State University, 370 W. 9th Avenue, Columbus, OH 43210, USA
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6
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Jakobson CM, Jarosz DF. What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? Annu Rev Genet 2020; 54:439-464. [PMID: 32897739 DOI: 10.1146/annurev-genet-021920-102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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7
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Chen Z, Zhao J, Qiao J, Li W, Li J, Xu R, Wang H, Liu Z, Xing B, Wendel JF, Grover CE. Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes. Mitochondrial DNA B Resour 2020; 5:2500-2506. [PMID: 33457843 PMCID: PMC7782173 DOI: 10.1080/23802359.2020.1780969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mitochondrial genomes favor codons that end in A or U, with a secondary preference for pyrimidine rich codons. These observations are similar to previous reports of codon usage in cotton nuclear genomes, possibly suggestive of a general bias spanning genomic compartment. Although evidence for codon usage bias is weak for most genes, we identified six genes (i.e. atp8, atp9, sdh3, sdh4, mttB and rpl2) with significant nonrandom codon usage. In general, we find multiple factors that influence cotton mitochondrial genome codon usage, which may include selection in a subset of genes.
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Affiliation(s)
- Zhiwen Chen
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Jianguo Zhao
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China.,College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Jun Qiao
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Weijia Li
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Jingwei Li
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Ran Xu
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Haiyan Wang
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Zehui Liu
- College of Chemistry and Environment Engineering, Shanxi Datong University, Datong, China
| | - Baoyan Xing
- Institute of Carbon Materials Science, Shanxi Datong University, Datong, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
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8
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Dershem R, Metpally RPR, Jeffreys K, Krishnamurthy S, Smelser DT, Hershfinkel M, Carey DJ, Robishaw JD, Breitwieser GE. Rare-variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations of orphan G protein-coupled receptors. J Biol Chem 2019; 294:18109-18121. [PMID: 31628190 DOI: 10.1074/jbc.ra119.009253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/08/2019] [Indexed: 02/02/2023] Open
Abstract
The pace of deorphanization of G protein-coupled receptors (GPCRs) has slowed, and new approaches are required. Small molecule targeting of orphan GPCRs can potentially be of clinical benefit even if the endogenous receptor ligand has not been identified. Many GPCRs lack common variants that lead to reproducible genome-wide disease associations, and rare-variant approaches have emerged as a viable alternative to identify disease associations for such genes. Therefore, our goal was to prioritize orphan GPCRs by determining their associations with human diseases in a large clinical population. We used sequence kernel association tests to assess the disease associations of 85 orphan or understudied GPCRs in an unselected cohort of 51,289 individuals. Using rare loss-of-function variants, missense variants predicted to be pathogenic or likely pathogenic, and a subset of rare synonymous variants that cause large changes in local codon bias as independent data sets, we found strong, phenome-wide disease associations shared by two or more variant categories for 39% of the GPCRs. To validate the bioinformatics and sequence kernel association test analyses, we functionally characterized rare missense and synonymous variants of GPR39, a family A GPCR, revealing altered expression or Zn2+-mediated signaling for members of both variant classes. These results support the utility of rare variant analyses for identifying disease associations for GPCRs that lack impactful common variants. We highlight the importance of rare synonymous variants in human physiology and argue for their routine inclusion in any comprehensive analysis of genomic variants as potential causes of disease.
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Affiliation(s)
- Ridge Dershem
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Raghu P R Metpally
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Kirk Jeffreys
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Sarathbabu Krishnamurthy
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Diane T Smelser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Michal Hershfinkel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501 Israel
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- Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Janet D Robishaw
- Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Gerda E Breitwieser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822.
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9
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Guan DL, Qian ZQ, Ma LB, Bai Y, Xu SQ. Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates. Sci Rep 2019; 9:678. [PMID: 30679466 PMCID: PMC6345984 DOI: 10.1038/s41598-018-35760-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/09/2018] [Indexed: 01/08/2023] Open
Abstract
Damselflies and dragonflies, of the order Odonata, have distinct body plans and predatory abilities. Knowledge of their various evolutionary histories will allow for an understanding of the genetic and phenotypic evolution of insects. Mitogenomes are suitable materials to elucidate this, but the mitogenome of only a few odonates have been annotated. Herein, we report the complete mitogenome of nine odonates, including seven dragonflies and two damselflies, and a comprehensive analysis of the codon usage in 31 Odonata mitogenomes with the aim to estimate their evolutionary characteristics. Overall, a weak codon bias exists among odonate mitogenomes, although this favours AT-ending codons. Damselflies have a weaker codon usage bias than dragonflies, and 37 codons have significantly different usages. Both directional mutation and purifying selection shape damselfly and dragonfly mitogenomes. Although inevitable, directional mutation bias plays a minor role, whereas purifying selection pressure is the dominant evolutionary force. A higher selection pressure is observed in dragonflies than in damselflies, but it mainly acts on codon usage patterns rather than amino acid translation. Our findings suggest that dragonflies might have more efficient mitochondrial gene expression levels than damselflies, producing more proteins that support their locomotion and predatory abilities.
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Affiliation(s)
- De-Long Guan
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Zeng-Qiang Qian
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Li-Bin Ma
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Yi Bai
- School of Life Science, Taizhou University, Taizhou, 317000, P.R. China
| | - Sheng-Quan Xu
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China.
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10
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Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function. Biochem Soc Trans 2018; 46:937-944. [PMID: 30065107 DOI: 10.1042/bst20170422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/18/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022]
Abstract
Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a conserved feature of mRNA and have evolved to fine-tune protein folding, expression and function. Synonymous single-nucleotide polymorphisms (sSNPs) that alter programmed translational speed affect expression and function of the encoded protein. Synergistic advances in next-generation sequencing have led to the identification of sSNPs associated with disease penetrance. Here, we draw on studies with disease-related proteins to enhance our understanding of mechanistic contributions of sSNPs to functional alterations of the encoded protein. We emphasize the importance of identification of sSNPs along with disease-causing mutations to understand genotype-phenotype relationships.
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11
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Acosta-Sampson L, Döring K, Lin Y, Yu VY, Bukau B, Kramer G, Cate JHD. Role for ribosome-associated complex and stress-seventy subfamily B (RAC-Ssb) in integral membrane protein translation. J Biol Chem 2017; 292:19610-19627. [PMID: 28972146 DOI: 10.1074/jbc.m117.813857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 01/04/2023] Open
Abstract
Targeting of most integral membrane proteins to the endoplasmic reticulum is controlled by the signal recognition particle, which recognizes a hydrophobic signal sequence near the protein N terminus. Proper folding of these proteins is monitored by the unfolded protein response and involves protein degradation pathways to ensure quality control. Here, we identify a new pathway for quality control of major facilitator superfamily transporters that occurs before the first transmembrane helix, the signal sequence recognized by the signal recognition particle, is made by the ribosome. Increased rates of translation elongation of the N-terminal sequence of these integral membrane proteins can divert the nascent protein chains to the ribosome-associated complex and stress-seventy subfamily B chaperones. We also show that quality control of integral membrane proteins by ribosome-associated complex-stress-seventy subfamily B couples translation rate to the unfolded protein response, which has implications for understanding mechanisms underlying human disease and protein production in biotechnology.
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Affiliation(s)
| | - Kristina Döring
- the Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,the German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany, and
| | - Yuping Lin
- From the Departments of Molecular and Cell Biology and
| | - Vivian Y Yu
- From the Departments of Molecular and Cell Biology and
| | - Bernd Bukau
- the Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,the German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany, and
| | - Günter Kramer
- the Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,the German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg D-69120, Germany, and
| | - Jamie H D Cate
- From the Departments of Molecular and Cell Biology and .,Chemistry, University of California, Berkeley, California 94720.,the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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12
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Cripwell RA, Rose SH, van Zyl WH. Expression and comparison of codon optimised Aspergillus tubingensis amylase variants in Saccharomyces cerevisiae. FEMS Yeast Res 2017. [DOI: 10.1093/femsyr/fox040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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13
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Kirchner S, Cai Z, Rauscher R, Kastelic N, Anding M, Czech A, Kleizen B, Ostedgaard LS, Braakman I, Sheppard DN, Ignatova Z. Alteration of protein function by a silent polymorphism linked to tRNA abundance. PLoS Biol 2017; 15:e2000779. [PMID: 28510592 PMCID: PMC5433685 DOI: 10.1371/journal.pbio.2000779] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 04/13/2017] [Indexed: 01/22/2023] Open
Abstract
Synonymous single nucleotide polymorphisms (sSNPs) are considered neutral for protein function, as by definition they exchange only codons, not amino acids. We identified an sSNP that modifies the local translation speed of the cystic fibrosis transmembrane conductance regulator (CFTR), leading to detrimental changes to protein stability and function. This sSNP introduces a codon pairing to a low-abundance tRNA that is particularly rare in human bronchial epithelia, but not in other human tissues, suggesting tissue-specific effects of this sSNP. Up-regulation of the tRNA cognate to the mutated codon counteracts the effects of the sSNP and rescues protein conformation and function. Our results highlight the wide-ranging impact of sSNPs, which invert the programmed local speed of mRNA translation and provide direct evidence for the central role of cellular tRNA levels in mediating the actions of sSNPs in a tissue-specific manner. Synonymous single nucleotide polymorphisms (sSNPs) occur at high frequency in the human genome and are associated with ~50 diseases in humans; the responsible molecular mechanisms remain enigmatic. Here, we investigate the impact of the common sSNP, T2562G, on cystic fibrosis transmembrane conductance regulator (CFTR). Although this sSNP, by itself, does not cause cystic fibrosis (CF), it is prevalent in patients with CFTR-related disorders. T2562G sSNP modifies the local translation speed at the Thr854 codon, leading to changes in CFTR stability and channel function. This sSNP introduces a codon pairing to a low-abundance tRNA, which is particularly rare in human bronchial epithelia, but not in other human tissues, suggesting a tissue-specific effect of this sSNP. Enhancement of the cellular concentration of the tRNA cognate to the mutant ACG codon rescues the stability and conduction defects of T2562G-CFTR. These findings reveal an unanticipated mechanism—inverting the programmed local speed of mRNA translation in a tRNA-dependent manner—for sSNP-associated diseases.
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Affiliation(s)
- Sebastian Kirchner
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Zhiwei Cai
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Robert Rauscher
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Nicolai Kastelic
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Melanie Anding
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Andreas Czech
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Bertrand Kleizen
- Cellular Protein Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Lynda S. Ostedgaard
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ineke Braakman
- Cellular Protein Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - David N. Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
- * E-mail: (ZI); (DNS)
| | - Zoya Ignatova
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
- * E-mail: (ZI); (DNS)
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14
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Athanasiou D, Aguila M, Opefi CA, South K, Bellingham J, Bevilacqua D, Munro PM, Kanuga N, Mackenzie FE, Dubis AM, Georgiadis A, Graca AB, Pearson RA, Ali RR, Sakami S, Palczewski K, Sherman MY, Reeves PJ, Cheetham ME. Rescue of mutant rhodopsin traffic by metformin-induced AMPK activation accelerates photoreceptor degeneration. Hum Mol Genet 2017; 26:305-319. [PMID: 28065882 PMCID: PMC5351934 DOI: 10.1093/hmg/ddw387] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 01/29/2023] Open
Abstract
Protein misfolding caused by inherited mutations leads to loss of protein function and potentially toxic 'gain of function', such as the dominant P23H rhodopsin mutation that causes retinitis pigmentosa (RP). Here, we tested whether the AMPK activator metformin could affect the P23H rhodopsin synthesis and folding. In cell models, metformin treatment improved P23H rhodopsin folding and traffic. In animal models of P23H RP, metformin treatment successfully enhanced P23H traffic to the rod outer segment, but this led to reduced photoreceptor function and increased photoreceptor cell death. The metformin-rescued P23H rhodopsin was still intrinsically unstable and led to increased structural instability of the rod outer segments. These data suggest that improving the traffic of misfolding rhodopsin mutants is unlikely to be a practical therapy, because of their intrinsic instability and long half-life in the outer segment, but also highlights the potential of altering translation through AMPK to improve protein function in other protein misfolding diseases.
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Affiliation(s)
| | - Monica Aguila
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, UK
| | - Chikwado A. Opefi
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex, UK
| | - Kieron South
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex, UK
| | | | | | - Peter M. Munro
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, UK
| | - Naheed Kanuga
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, UK
| | | | - Adam M. Dubis
- Moorfields Eye Hospital NHS Trust, 162 City Road, London, UK
| | | | - Anna B. Graca
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, UK
| | | | - Robin R. Ali
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, UK
| | - Sanae Sakami
- Department of Pharmacology, and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, USA
| | - Michael Y. Sherman
- Department of Biochemistry, Boston University Medical School, Boston, Massachusetts, MA, USA
| | - Philip J. Reeves
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex, UK
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15
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Webster GR, Teh AYH, Ma JKC. Synthetic gene design-The rationale for codon optimization and implications for molecular pharming in plants. Biotechnol Bioeng 2016; 114:492-502. [PMID: 27618314 DOI: 10.1002/bit.26183] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 08/10/2016] [Accepted: 09/05/2016] [Indexed: 12/14/2022]
Abstract
Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as "silent" as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised. Multiple inter-linked factors affecting protein expression need to be taken into consideration when optimizing a gene sequence. Over the years, various computer programmes have been developed to aid in the gene sequence optimization process. However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the "optimal" gene sequence. In this review, codon usage bias and factors affecting codon selection will be discussed and the evidence for codon optimization impact will be reviewed for recombinant protein expression using plants as a case study. These developments will be relevant to all recombinant expression systems; however, molecular pharming in plants is an area which has consistently encountered difficulties with low levels of recombinant protein expression, and should benefit from an evidence based rational approach to synthetic gene design. Biotechnol. Bioeng. 2017;114: 492-502. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Gina R Webster
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
| | - Audrey Y-H Teh
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
| | - Julian K-C Ma
- Molecular Immunology Unit, Institute for Infection and Immunity, St. George's University of London, SW17 0RE, London, UK
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16
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Bartoszewski R, Króliczewski J, Piotrowski A, Jasiecka AJ, Bartoszewska S, Vecchio-Pagan B, Fu L, Sobolewska A, Matalon S, Cutting GR, Rowe SM, Collawn JF. Codon bias and the folding dynamics of the cystic fibrosis transmembrane conductance regulator. Cell Mol Biol Lett 2016; 21:23. [PMID: 28536625 PMCID: PMC5415761 DOI: 10.1186/s11658-016-0025-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/13/2016] [Indexed: 12/20/2022] Open
Abstract
Synonymous or silent mutations are often overlooked in genetic analyses for disease-causing mutations unless they are directly associated with potential splicing defects. More recent studies, however, indicate that some synonymous single polynucleotide polymorphisms (sSNPs) are associated with changes in protein expression, and in some cases, protein folding and function. The impact of codon usage and mRNA structural changes on protein translation rates and how they can affect protein structure and function is just beginning to be appreciated. Examples are given here that demonstrate how synonymous mutations alter the translational kinetics and protein folding and/or function. The mechanism for how this occurs is based on a model in which codon usage modulates the translational rate by introducing pauses caused by nonoptimal or rare codons or by introducing changes in the mRNA structure, and this in turn influences co-translational folding. Two examples of this include the multidrug resistance protein (p-glycoprotein) and the cystic fibrosis transmembrane conductance regulator gene (CFTR). CFTR is also used here as a model to illustrate how synonymous mutations can be examined using in silico predictive methods to identify which sSNPs have the potential to change protein structure. The methodology described here can be used to help identify "non-silent" synonymous mutations in other genes.
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Affiliation(s)
- Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Jaroslaw Króliczewski
- Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Anna Janaszak Jasiecka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Briana Vecchio-Pagan
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Lianwu Fu
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - Aleksandra Sobolewska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416 Gdansk, Poland
| | - Sadis Matalon
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, USA.,Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - Garry R Cutting
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Steven M Rowe
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Departments of Medicine and Pediatrics, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
| | - James F Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA.,Gregory Fleming James Cystic Fibrosis Center, University of Alabama at Birmingham, Birmingham, USA
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17
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Critical reflections on synthetic gene design for recombinant protein expression. Curr Opin Struct Biol 2016; 38:155-62. [DOI: 10.1016/j.sbi.2016.07.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 11/17/2022]
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18
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Bali V, Lazrak A, Guroji P, Matalon S, Bebok Z. Mechanistic Approaches to Improve Correction of the Most Common Disease-Causing Mutation in Cystic Fibrosis. PLoS One 2016; 11:e0155882. [PMID: 27214033 PMCID: PMC4877091 DOI: 10.1371/journal.pone.0155882] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/05/2016] [Indexed: 12/28/2022] Open
Abstract
The most common mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene leads to deletion of the phenylalanine at position 508 (ΔF508) in the CFTR protein and causes multiple folding and functional defects. Contrary to large-scale efforts by industry and academia, no significant therapeutic benefit has been achieved with a single “corrector”. Therefore, investigations concentrate on drug combinations. Orkambi (Vertex Pharmaceuticals), the first FDA-approved drug for treatment of cystic fibrosis (CF) caused by this mutation, is a combination of a corrector (VX-809) that facilitates ΔF508 CFTR biogenesis and a potentiator (VX-770), which improves its function. Yet, clinical trials utilizing this combination showed only modest therapeutic benefit. The low efficacy Orkambi has been attributed to VX-770-mediated destabilization of VX-809-rescued ΔF508 CFTR. Here we report that the negative effects of VX-770 can be reversed by increasing the half-life of the endoplasmic reticulum (ER) form (band B) of ΔF508 CFTR with another corrector (Corr-4a.) Although Corr-4a alone has only minimal effects on ΔF508 CFTR rescue, it increases the half-life of ΔF508 CFTR band B when it is present during half-life measurements. Our data shows that stabilization of band B ΔF508 CFTR with Corr-4a and simultaneous rescue with VX-809, leads to a >2-fold increase in cAMP-activated, CFTRinh-172-inhibited currents compared to VX-809 alone, or VX-809+VX-770. The negative effects of VX-770 and the Corr-4a protection are specific to the native I507-ATT ΔF508 CFTR without affecting the inherently more stable, synonymous variant I507-ATC ΔF508 CFTR. Our studies emphasize that stabilization of ΔF508 CFTR band B in the ER might improve its functional rescue by Orkambi.
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Affiliation(s)
- Vedrana Bali
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ahmed Lazrak
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- The Lung Injury and Repair Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Purushotham Guroji
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Sadis Matalon
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- The Lung Injury and Repair Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Zsuzsanna Bebok
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- The Lung Injury and Repair Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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19
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Shah K, Bradbury NA. Lemur Tyrosine Kinase 2, a novel target in prostate cancer therapy. Oncotarget 2016; 6:14233-46. [PMID: 26008968 PMCID: PMC4546463 DOI: 10.18632/oncotarget.3899] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 04/25/2015] [Indexed: 11/25/2022] Open
Abstract
Progression from early forms of prostate cancer to castration-resistant disease is associated with an increase in signal transduction activity. The majority of castration-resistance cancers persist in the expression of the androgen receptor (AR), as well as androgen-dependent genes. The AR is regulated not only by it associated steroid hormone, but also by manifold regulatory and signaling molecules, including several kinases. We undertook evaluation of the role of Lemur Tyrosine Kinase 2 (LMTK2) in modulating AR activity, as several Genome Wide Association Studies (GWAS) have shown a marked association of LMTK2 activity with the development of prostate cancer. We confirm that not only is LMTK2 mRNA reduced in prostate cancer tissue, but also LMTK2 protein levels are markedly diminished. Knockdown of LMTK2 protein in prostate cell lines greatly increased the transcription of androgen-responsive genes. In addition, LMTK2 knockdown led to an increase in prostate cancer stem cell populations in LNCaP cells, indicative of increased tumorogenicity. Using multiple approaches, we also demonstrate that LMTK2 interacts with the AR, thus putting LMTK2 as a component of a signaling complex modulating AR activity. Our finding that LMTK2 is a negative regulator of AR activity defines a novel cellular pathway for activation of AR-responsive genes in castrate resistant-prostate cancer. Moreover, pharmacologic manipulation of LMTK2 activity will provide a novel therapeutic target for more effective treatments for patients with castrate-resistant prostate cancer.
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Affiliation(s)
- Kalpit Shah
- Department of Physiology and Biophysics, Rosalind Franklin University of Medicine & Sciences, The Chicago Medical School, North Chicago, IL 60064, USA
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Rosalind Franklin University of Medicine & Sciences, The Chicago Medical School, North Chicago, IL 60064, USA
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20
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Bali V, Lazrak A, Guroji P, Fu L, Matalon S, Bebok Z. A synonymous codon change alters the drug sensitivity of ΔF508 cystic fibrosis transmembrane conductance regulator. FASEB J 2015; 30:201-13. [PMID: 26336913 DOI: 10.1096/fj.15-273714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/31/2015] [Indexed: 11/11/2022]
Abstract
Synonymous mutations, such as I507-ATC→ATT, in deletion of Phe508 in cystic fibrosis transmembrane conductance regulator (ΔF508 CFTR), the most frequent disease-associated mutant of CFTR, may affect protein biogenesis, structure, and function and contribute to an altered disease phenotype. Small-molecule drugs are being developed to correct ΔF508 CFTR. To understand correction mechanisms and the consequences of synonymous mutations, we analyzed the effect of mechanistically distinct correctors, corrector 4a (C4) and lumacaftor (VX-809), on I507-ATT and I507-ATC ΔF508 CFTR biogenesis and function. C4 stabilized I507-ATT ΔF508 CFTR band B, but without considerable biochemical and functional correction. VX-809 biochemically corrected ∼10% of both of the variants, leading to stable, forskolin+3-isobutyl-1-methylxanthine (IBMX)-activated whole-cell currents in the presence of the corrector. Omitting VX-809 during whole-cell recordings led to a spontaneous decline of the currents, suggesting posttranslational stabilization by VX-809. Treatment of cells with the C4+VX-809 combination resulted in enhanced rescue and 2-fold higher forskolin+IBMX-activated currents of both I507-ATT and I507-ATC ΔF508 CFTR, compared with VX-809 treatment alone. The lack of an effect of C4 on I507-ATC ΔF508 CFTR, but its additive effect in combination with VX-809, implies that C4 acted on VX-809-modified I507-ATC ΔF508 CFTR. Our results suggest that binding of C4 and VX-809 to ΔF508 CFTR is conformation specific and provide evidence that synonymous mutations can alter the drug sensitivity of proteins.
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Affiliation(s)
- Vedrana Bali
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ahmed Lazrak
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Purushotham Guroji
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lianwu Fu
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sadis Matalon
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zsuzsanna Bebok
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Jai Y, Shah K, Bridges RJ, Bradbury NA. Evidence against resveratrol as a viable therapy for the rescue of defective ΔF508 CFTR. Biochim Biophys Acta Gen Subj 2015; 1850:2377-84. [PMID: 26342647 DOI: 10.1016/j.bbagen.2015.08.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/10/2015] [Accepted: 08/31/2015] [Indexed: 01/23/2023]
Abstract
BACKGROUND Resveratrol, a natural phenolic compound, has been reported to rescue mutant ΔF508 CFTR in expression systems and primary epithelial cells. Although this implies a therapeutic benefit to patients with CF, investigations were performed using resveratrol concentrations greatly in excess of those achievable in plasma. We evaluated the efficacy of resveratrol as a CFTR corrector in relevant primary airway cells, using physiologically achievable resveratrol concentrations. METHODS Cells expressing wt or ΔF508 CFTR were exposed to chronic or acute resveratrol. CFTR mRNA and protein expression were monitored. The effects of resveratrol on primary ΔF508 human airway cells were evaluated by equivalent current analysis using modified Ussing chambers. RESULTS Consistent with previously published data in heterologous expression systems, high doses of resveratrol increased CFTR expression; however physiologically relevant concentrations were without effect. In contrast to heterologous expression systems, resveratrol was unable to increase mutant CFTR channel activity in primary airway cells. Elevated amiloride-sensitive currents, indicative of sodium transport and characteristically elevated in CF airway cells, were also unaffected by resveratrol. CONCLUSIONS High concentrations of resveratrol can increase CFTR mRNA and protein in some cell types. In addition, acute resveratrol exposure can stimulate CFTR mediated chloride secretion, probably by increasing cellular cAMP levels. Resveratrol at physiologically achievable levels yielded no benefit in primary ΔF508 airway cells, either in terms of amiloride-sensitive currents of CFTR currents. GENERAL SIGNIFICANCE Taken together, our results do not support the use of resveratrol supplements as a therapy for patients with cystic fibrosis. It is possible that further modifications of the resveratrol backbone would yield a more efficacious compound.
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Affiliation(s)
- Ying Jai
- Department of Physiology and Biophysics, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Kalpit Shah
- Department of Physiology and Biophysics, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Robert J Bridges
- Department of Physiology and Biophysics, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Neil A Bradbury
- Department of Physiology and Biophysics, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA.
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