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Rodríguez-Bayona B, Expósito Bey A, Balas A, González Escribano MF. Identification of the novel null allele HLA-DPB1*1449:01N by next-generation sequencing. HLA 2024; 103:e15449. [PMID: 38526319 DOI: 10.1111/tan.15449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
The novel HLA-DPB1*1449:01N allele differs from HLA-DPB1*16:01:01:01 by a nucleotide at codon 92 in exon 2.
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Affiliation(s)
- Beatriz Rodríguez-Bayona
- Servicio deInmunología, Instituto de Biomedicina deSevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad deSevilla, Sevilla, Spain
| | - Alba Expósito Bey
- Servicio deInmunología, Instituto de Biomedicina deSevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad deSevilla, Sevilla, Spain
| | - Antonio Balas
- Histocompatibilidad, Centro de Transfusión de la Comunidad de Madrid, Madrid, Spain
| | - María Francisca González Escribano
- Servicio deInmunología, Instituto de Biomedicina deSevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad deSevilla, Sevilla, Spain
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2
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Kar D, Manna D, Manjunath LE, Singh A, Som S, Vasu K, Eswarappa SM. Kinetics of Translating Ribosomes Determine the Efficiency of Programmed Stop Codon Readthrough. J Mol Biol 2023; 435:168274. [PMID: 37714299 DOI: 10.1016/j.jmb.2023.168274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 08/15/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
During translation, a stop codon on the mRNA signals the ribosomes to terminate the process. In certain mRNAs, the termination fails due to the recoding of the canonical stop codon, and ribosomes continue translation to generate C-terminally extended protein. This process, termed stop codon readthrough (SCR), regulates several cellular functions. SCR is driven by elements/factors that act immediately downstream of the stop codon. Here, we have analysed the process of SCR using a simple mathematical model to investigate how the kinetics of translating ribosomes influences the efficiency of SCR. Surprisingly, the analysis revealed that the rate of translation inversely regulates the efficiency of SCR. We tested this prediction experimentally in mammalian AGO1 and MTCH2 mRNAs. Reduction in translation either globally by harringtonine or locally by rare codons caused an increase in the efficiency of SCR. Thus, our study has revealed a hitherto unknown mode of regulation of SCR.
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Affiliation(s)
- Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/debaleenak8
| | - Debraj Manna
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/DebrajManna27
| | - Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/emlekha
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/Anumehasingh25
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India. https://twitter.com/SaubhikSom
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
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3
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Colson P, Delerce J, Fantini J, Pontarotti P, La Scola B, Raoult D. The return of the "Mistigri" (virus adaptative gain by gene loss) through the SARS-CoV-2 XBB.1.5 chimera that predominated in 2023. J Med Virol 2023; 95:e29146. [PMID: 37800455 DOI: 10.1002/jmv.29146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/03/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 XBB.1.5 is the first recombinant lineage to predominate at the country and global scales. Very interestingly, like the Marseille-4B subvariant (or B.1.160) and the pandemic variant B.1.1.7 (or Alpha) previously, it has its ORF8 gene inactivated by a stop codon. We aimed here to study the distribution of stop codons in ORF8 of XBB.1.5 and non-XBB.1.5 genomes. We identified that a stop codon was present at 89 (74%) ORF8 codons in ≥1 of 15 222 404 genomes available in GISAID. The mean proportion of genomes with a stop codon per codon was 0.11% (range, 0%-7.8%). In addition, a stop codon was detected at 15 (12%) codons in at least 1000 genomes. These 15 codons are notably located on seven stem-loop hairpin regions and in the signal peptide region for the case of the XBB.1.5 lineage (codon 8). Thus, it is very likely that stop codons in ORF8 gene contributed on at least three occasions and independently during the pandemic to the evolutionary success of a lineage that became transiently predominant. Such association of gene loss with evolutionary success, which suits the recently described Mistigri rule, is an important biological phenomenon very unknown in virology while largely described in cellular organisms.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | | | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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4
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Li R, Sun K, Tuplin A, Harris M. A structural and functional analysis of opal stop codon translational readthrough during Chikungunya virus replication. J Gen Virol 2023; 104:10.1099/jgv.0.001909. [PMID: 37862073 PMCID: PMC7615711 DOI: 10.1099/jgv.0.001909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Abstract
Chikungunya virus (CHIKV) is an alphavirus, transmitted by Aedes species mosquitoes. The CHIKV single-stranded positive-sense RNA genome contains two open reading frames, coding for the non-structural (nsP) and structural proteins of the virus. The non-structural polyprotein precursor is proteolytically cleaved to generate nsP1-4. Intriguingly, most isolates of CHIKV (and other alphaviruses) possess an opal stop codon close to the 3' end of the nsP3 coding sequence and translational readthrough is necessary to produce full-length nsP3 and the nsP4 RNA polymerase. Here we investigate the role of this stop codon by replacing the arginine codon with each of the three stop codons in the context of both a subgenomic replicon and infectious CHIKV. Both opal and amber stop codons were tolerated in mammalian cells, but the ochre was not. In mosquito cells all three stop codons were tolerated. Using SHAPE analysis we interrogated the structure of a putative stem loop 3' of the stop codon and used mutagenesis to probe the importance of a short base-paired region at the base of this structure. Our data reveal that this stem is not required for stop codon translational readthrough, and we conclude that other factors must facilitate this process to permit productive CHIKV replication.
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Affiliation(s)
- Raymond Li
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | | | - Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
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5
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Pandit M, Akhtar MN, Sundaram S, Sahoo S, Manjunath LE, Eswarappa SM. Termination codon readthrough of NNAT mRNA regulates calcium-mediated neuronal differentiation. J Biol Chem 2023; 299:105184. [PMID: 37611826 PMCID: PMC10506107 DOI: 10.1016/j.jbc.2023.105184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023] Open
Abstract
Termination codon readthrough (TCR) is a process in which ribosomes continue to translate an mRNA beyond a stop codon generating a C-terminally extended protein isoform. Here, we demonstrate TCR in mammalian NNAT mRNA, which encodes NNAT, a proteolipid important for neuronal differentiation. This is a programmed event driven by cis-acting RNA sequences present immediately upstream and downstream of the canonical stop codon and is negatively regulated by NONO, an RNA-binding protein known to promote neuronal differentiation. Unlike the canonical isoform NNAT, we determined that the TCR product (NNATx) does not show detectable interaction with the sarco/endoplasmic reticulum Ca2+-ATPase isoform 2 Ca2+ pump, cannot increase cytoplasmic Ca2+ levels, and therefore does not enhance neuronal differentiation in Neuro-2a cells. Additionally, an antisense oligonucleotide that targets a region downstream of the canonical stop codon reduced TCR of NNAT and enhanced the differentiation of Neuro-2a cells to cholinergic neurons. Furthermore, NNATx-deficient Neuro-2a cells, generated using CRISPR-Cas9, showed increased cytoplasmic Ca2+ levels and enhanced neuronal differentiation. Overall, these results demonstrate regulation of neuronal differentiation by TCR of NNAT. Importantly, this process can be modulated using a synthetic antisense oligonucleotide.
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Affiliation(s)
- Madhuparna Pandit
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Md Noor Akhtar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Susinder Sundaram
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bengaluru, India
| | - Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
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6
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Song Z, Zhang G, Huang S, Liu Y, Li G, Zhou X, Sun J, Gao P, Chen Y, Huang X, Liu J, Wang X. PE-STOP: A versatile tool for installing nonsense substitutions amenable for precise reversion. J Biol Chem 2023; 299:104942. [PMID: 37343700 PMCID: PMC10365944 DOI: 10.1016/j.jbc.2023.104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/23/2023] Open
Abstract
The rapid advances in genome editing technologies have revolutionized the study of gene functions in cell or animal models. The recent generation of double-stranded DNA cleavage-independent base editors has been suitably adapted for interrogation of protein-coding genes on the basis of introducing premature stop codons or disabling the start codons. However, such versions of stop/start codon-oriented genetic tools still present limitations on their versatility, base-level precision, and target specificity. Here, we exploit a newly developed prime editor (PE) that differs from base editors by its adoption of a reverse transcriptase activity, which enables incorporation of various types of precise edits templated by a specialized prime editing guide RNA. Based on such a versatile platform, we established a prime editing-empowered method (PE-STOP) for installation of nonsense substitutions, providing a complementary approach to the present gene-targeting tools. PE-STOP is bioinformatically predicted to feature substantially expanded coverage in the genome space. In practice, PE-STOP introduces stop codons with good efficiencies in human embryonic kidney 293T and N2a cells (with medians of 29% [ten sites] and 25% [four sites] editing efficiencies, respectively), while exhibiting minimal off-target effects and high on-target precision. Furthermore, given the fact that PE installs prime editing guide RNA-templated mutations, we introduce a unique strategy for precise genetic rescue of PE-STOP-dependent nonsense mutation via the same PE platform. Altogether, the present work demonstrates a versatile and specific tool for gene inactivation and for functional interrogation of nonsense mutations.
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Affiliation(s)
- Ziguo Song
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guiquan Zhang
- Zhejiang Lab, Hangzhou, Zhejiang, China; State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center at Medical School of Nanjing University, Nanjing, China
| | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Liu
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xianhui Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayuan Sun
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Gao
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingxu Huang
- Zhejiang Lab, Hangzhou, Zhejiang, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jianghuai Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center at Medical School of Nanjing University, Nanjing, China.
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China.
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7
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Zhang HH, Xiang J, Yin BC, Ye BC. Overcoming Multidrug Resistance by Base-Editing-Induced Codon Mutation. ACS Pharmacol Transl Sci 2023; 6:812-819. [PMID: 37200813 PMCID: PMC10186359 DOI: 10.1021/acsptsci.3c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Indexed: 05/20/2023]
Abstract
Multidrug resistance (MDR) is the main obstacle in cancer chemotherapy. ATP binding cassette (ABC) transporters on the MDR cell membrane can transport a wide range of antitumor drugs out of cells, which is one of the main causes of MDR. Therefore, disturbing ABC transporters becomes the key to reversing MDR. In this study, we implement a cytosine base editor (CBE) system to knock out the gene encoding ABC transporters by base editing. When the CBE system works in MDR cells, the MDR cells are manipulated, and the genes encoding ABC transporters can be inactivated by precisely changing single in-frame nucleotides to induce stop (iSTOP) codons. In this way, the expression of ABC efflux transporters is reduced and intracellular drug retention is significantly increased in MDR cells. Ultimately, the drug shows considerable cytotoxicity to the MDR cancer cells. Moreover, the substantial downregulation of P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) implies the successful application of the CBE system in the knockout of different ABC efflux transporters. The recovery of chemosensitivity of MDR cancer cells to the chemotherapeutic drugs revealed that the system has a satisfactory universality and applicability. We believe that the CBE system will provide valuable clues for the use of CRISPR technology to defeat the MDR of cancer cells.
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Affiliation(s)
- He-Hua Zhang
- Lab
of Biosystem and Microanalysis, State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing
Technology, East China University of Science
and Technology, Shanghai 200237, China
| | - Jian Xiang
- Lab
of Biosystem and Microanalysis, State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing
Technology, East China University of Science
and Technology, Shanghai 200237, China
| | - Bin-Cheng Yin
- Lab
of Biosystem and Microanalysis, State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing
Technology, East China University of Science
and Technology, Shanghai 200237, China
- Institute
of Engineering Biology and Health, Collaborative Innovation Center
of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical
Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Bang-Ce Ye
- Lab
of Biosystem and Microanalysis, State Key Laboratory of Bioreactor
Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing
Technology, East China University of Science
and Technology, Shanghai 200237, China
- Institute
of Engineering Biology and Health, Collaborative Innovation Center
of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical
Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832000, Xinjiang, China
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8
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. Wiley Interdiscip Rev RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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9
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Marin Rubio LA, Ontañon J. HLA-DQA1*05:01:11, a novel HLA-DQA1 allele with an ochre stop codon. HLA 2022; 101:561-562. [PMID: 36533682 DOI: 10.1111/tan.14941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
The DQA1*05:01:11 allele shows the TAA (UAA) stop codon instead of the common DQA1 TGA (UGA) stop codon.
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Affiliation(s)
- Luis A Marin Rubio
- Immunology Unit, Clinical Analysis Department, Albacete University Hospital Complex, Albacete, Spain
| | - Jesús Ontañon
- Immunology Unit, Clinical Analysis Department, Albacete University Hospital Complex, Albacete, Spain
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10
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Abstract
Nonsense mutations are a type of mutations which results in a premature termination codon occurrence. In general, these mutations have been considered to be among the most harmful ones which lead to premature protein translation termination and result in shortened nonfunctional polypeptide. However, there is evidence that not all nonsense mutations are harmful as well as some molecular mechanisms exist which allow to avoid pathogenic effects of these mutations. This review addresses relevant information on nonsense mutations in eukaryotic genomes, characteristics of these mutations, and different molecular mechanisms preventing or mitigating harmful effects thereof.
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Affiliation(s)
- Nadezhda A Potapova
- Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Moscow, 127051, Russia.
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11
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Coste T, Hervé D, Neau JP, Jouvent E, Ba F, Bergametti F, Lamy M, Cogez J, Derache N, Schneckenburger R, Grelet M, Gollion C, Lanotte L, Lauer V, Layet V, Urbanczyk C, Didic M, Raynouard I, Delaval L, Dassa J, Florea A, Badiu C, Nguyen K, Tournier-Lasserve E. Heterozygous HTRA1 nonsense or frameshift mutations are pathogenic. Brain 2021; 144:2616-2624. [PMID: 34270682 DOI: 10.1093/brain/awab271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Heterozygous missense HTRA1 mutations have been associated with an autosomal dominant cerebral small vessel disease (CSVD) whereas the pathogenicity of heterozygous HTRA1 stop codon variants is unclear. We performed a targeted high throughput sequencing of all known CSVD genes, including HTRA1, in 3853 unrelated consecutive CSVD patients referred for molecular diagnosis. The frequency of heterozygous HTRA1 mutations leading to a premature stop codon in this patient cohort was compared with their frequency in large control databases. An analysis of HTRA1 mRNA was performed in several stop codon carrier patients. Clinical and neuroimaging features were characterized in all probands. Twenty unrelated patients carrying a heterozygous HTRA1 variant leading to a premature stop codon were identified. A highly significant difference was observed when comparing our patient cohort with control databases: gnomAD v3.1.1 [P = 3.12 × 10-17, odds ratio (OR) = 21.9], TOPMed freeze 5 (P = 7.6 × 10-18, OR = 27.1) and 1000 Genomes (P = 1.5 × 10-5). Messenger RNA analysis performed in eight patients showed a degradation of the mutated allele strongly suggesting a haploinsufficiency. Clinical and neuroimaging features are similar to those previously reported in heterozygous missense mutation carriers, except for penetrance, which seems lower. Altogether, our findings strongly suggest that heterozygous HTRA1 stop codons are pathogenic through a haploinsufficiency mechanism. Future work will help to estimate their penetrance, an important information for genetic counselling.
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Affiliation(s)
- Thibault Coste
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, France
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
| | - Dominique Hervé
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
- AP-HP, CERVCO, Service de Neurologie, Hôpital Lariboisière, France
| | - Jean Philippe Neau
- Centre Hospitalier Universitaire de Poitiers, Service de Neurologie, Poitiers, France
| | - Eric Jouvent
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
- AP-HP, CERVCO, Service de Neurologie, Hôpital Lariboisière, France
| | - Fatoumata Ba
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, France
| | | | - Matthias Lamy
- Centre Hospitalier Universitaire de Poitiers, Service de Neurologie, Poitiers, France
| | - Julien Cogez
- Centre Hospitalier Universitaire de Caen, Service de Neurologie, Caen, France
| | - Nathalie Derache
- Centre Hospitalier Universitaire de Caen, Service de Neurologie, Caen, France
| | | | - Maude Grelet
- Centre Hospitalier Intercommunal de Toulon- La Seyne sur mer, Service de Génétique Médicale, Toulon, France
| | - Cédric Gollion
- Centre Hospitalier Universitaire de Toulouse, Service de Neurologie, Toulouse, France
| | - Livia Lanotte
- Hôpital De Hautepierre, Service de Neurologie, Strasbourg, France
| | - Valérie Lauer
- Hôpital De Hautepierre, Unité Neuro-Vasculaire, Strasbourg, France
| | - Valérie Layet
- Groupe Hospitalier Du havre, Service de Génétique Médicale, Le Havre, France
| | - Cédric Urbanczyk
- Centre Hospitalier Départemental La Roche-Sur-Yon, Service de Neurologie, La Roche-Sur-Yon, France
| | - Mira Didic
- APHM, Hôpital Timone Adultes, Service de Neurologie et Neuropsychologie, Marseille, France
- Aix Marseille Université, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - Igor Raynouard
- Fondation Adolphe de Rothschild, Service de Neurologie, Paris, France
| | - Laure Delaval
- AP-HP, Hôpital Bichat, Service de Médecine Interne, France
| | - Jérémie Dassa
- Centre Hospitalier Emile Roux, Service de Neurologie, Le Puy-en-Velay, France
| | - Alexandru Florea
- Centre Hospitalier Marie Madeleine, Service de Neurologie, Forbach, France
| | - Carmen Badiu
- Centre Hospitalier Metz-Thionville, Service de Neurologie, Metz, France
| | - Karine Nguyen
- APHM, Hôpital Timone Adultes, Département de Génétique, Marseille, France
| | - Elisabeth Tournier-Lasserve
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, France
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
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12
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Feng WX, Zhuo XW, Liu ZM, Li JW, Zhang WH, Wu Y, Han TL, Fang F. Case Report: A Variant Non-ketotic Hyperglycinemia With GLRX5 Mutations: Manifestation of Deficiency of Activities of the Respiratory Chain Enzymes. Front Genet 2021; 12:605778. [PMID: 34054912 PMCID: PMC8155699 DOI: 10.3389/fgene.2021.605778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Variant non-ketotic hyperglycinaemia (NKH) is a rare disorder characterized by variable clinical, biochemical, and imaging features. The variant form of NKH is rare and characterized by variable clinical, biochemical and imaging features. Subjects: Herein, we report a girl with variant NKH with two mutations in glutaredoxin 5 (GLRX5), which has been described in only three patients. Results: The clinical and biochemical phenotypes of the patient are also described. She suffered from developmental regression associated with spasticity, developmental delay, anemia and optic atrophy. The mitochondrial leukoencephalopathy was used to designate these disorders. An increased T2 signal from the medulla oblongata to the C6 spinal region was also observed on spinal cord MRI. Tandem mass analysis of a dried blood sample revealed elevated levels of glycine. The patient has two compound heterozygous mutations (c.151_153 del AAG and c.196C>T) in the GLRX5 gene. The c.196C>T mutation led to a stop codon (p.Q66Ter). Activities of mitochondrial respiratory chain (MRC) complexes II+III in the patient's fibroblasts were abnormal. Conclusions: We present the case of a girl with variant NKH who manifested spasticity and bilateral cavitating leukoencephalopathy. The patient had a deficiency of a respiratory chain enzyme, and this is the first report. Genetic testing is important for physicians to evaluate suspected variant NKH patients and to provide proper genetic counseling.
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Affiliation(s)
- Wei-Xing Feng
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
| | - Xiu-Wei Zhuo
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
| | - Zhi-Mei Liu
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
| | - Jiu-Wei Li
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
| | - Wei-Hua Zhang
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yun Wu
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
| | - Tong-Li Han
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
| | - Fang Fang
- Neurology Department, National Center for Children's Health China, Beijing Children Hospital Affiliated to Capital Medical University, Beijing, China
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13
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Delbue S, D'Alessandro S, Signorini L, Dolci M, Pariani E, Bianchi M, Fattori S, Modenese A, Galli C, Eberini I, Ferrante P. Isolation of SARS-CoV-2 strains carrying a nucleotide mutation, leading to a stop codon in the ORF 6 protein. Emerg Microbes Infect 2021; 10:252-255. [PMID: 33525998 PMCID: PMC7894437 DOI: 10.1080/22221751.2021.1884003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was isolated from the oro/pharyngeal swabs of two Italian COVID-19 patients, physicians in a COVID-19 division hospital, with different courses of the disease. The complete genome sequences show that the two isolates belong to the B1.1 lineage, but contain a nucleotide mutation in the ORF6, leading to a stop codon and to the deletion of 6 amino acids in the C terminus. This deletion was unique, compared to the currently available sequences deposited in the GISAID and GenBank database. It did not affect the in vitro viral replication, neither the neutralizing activities of the patients' antibodies. Based on homology analysis with other Coronaviruses, the two isolated lacked the ORF6 aminoacidic portion responsible for the inhibition of the antiviral Interferon (IFN)-based host response. IFN seems to have a dual role of in SARS-CoV-2 infected patients: not only antiviral activity, but also a detrimental role in case of excessive production. A deletion in the SARS-CoV-2 ORF6 protein might have a specific, still unknown role in the viral pathogenesis.
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Affiliation(s)
- Serena Delbue
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Milano, Italy
| | - Sarah D'Alessandro
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Milano, Italy
| | - Lucia Signorini
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Milano, Italy
| | - Maria Dolci
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Milano, Italy
| | - Elena Pariani
- Department of Biomedical Science for Health, University of Milano, Milano, Italy
| | - Michele Bianchi
- Department of Cardiology, Istituto Clinico Città Studi, Milano, Italy
| | - Stefania Fattori
- Interdepartmental Center of Diabetic Foot, Istituto Clinico Città Studi, Milano, Italy
| | - Annalisa Modenese
- Laboratory of clinical analysis, Istituto Clinico Città Studi, Milano, Italy
| | - Cristina Galli
- Department of Biomedical Science for Health, University of Milano, Milano, Italy
| | - Ivano Eberini
- Department of Pharmacological and Biomolecular Sciences & DSRC, University of Milano, Milano, Italy
| | - Pasquale Ferrante
- Laboratory of Molecular Virology, Department of Biomedical, Surgical and Dental Sciences, University of Milano, Milano, Italy.,Health Direction, Istituto Clinico Città Studi, Milano, Italy
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14
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Sokolova EE, Vlasov PK, Egorova TV, Shuvalov AV, Alkalaeva EZ. [The Influence of A/G Composition of 3' Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes]. Mol Biol (Mosk) 2020; 54:837-848. [PMID: 33009793 DOI: 10.31857/s0026898420050080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/26/2020] [Indexed: 11/24/2022]
Abstract
Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don't explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA-for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency.
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Affiliation(s)
- E E Sokolova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - P K Vlasov
- Institute of Science and Technology, Klosterneuburg, 3400 Austria
| | - T V Egorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A V Shuvalov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E Z Alkalaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
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15
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Manjunath LE, Singh A, Sahoo S, Mishra A, Padmarajan J, Basavaraju CG, Eswarappa SM. Stop codon read-through of mammalian MTCH2 leading to an unstable isoform regulates mitochondrial membrane potential. J Biol Chem 2020; 295:17009-17026. [PMID: 33028634 PMCID: PMC7863902 DOI: 10.1074/jbc.ra120.014253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3' UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3' UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through-deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sarthak Sahoo
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Ashutosh Mishra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jinsha Padmarajan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
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16
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Roldan-Montes V, Cardoso DF, Hurtado-Lugo NA, do Nascimento AV, Santos DJDA, Scalez DCB, de Freitas AC, Herrera AC, Albuquerque LG, de Camargo GMF, Tonhati H. Polymorphisms in TLR4 Gene Associated With Somatic Cell Score in Water Buffaloes ( Bubalus bubalis). Front Vet Sci 2020; 7:568249. [PMID: 33251259 PMCID: PMC7676892 DOI: 10.3389/fvets.2020.568249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022] Open
Abstract
Considering the importance of the diseases affecting the productive performance of animals in the dairy industry worldwide, it is necessary to implement tools that help to control and limit the occurrence of such diseases. As the increased somatic cell counts (SCC) are a direct expression of the inflammatory process, they are candidates to become the usual parameter for assessing udder health regarding milk quality and for monitoring mastitis incidences. Toll-Like Receptors are membrane proteins that play a key role in immunity, recognizing pathogens and, subsequently, activating immune responses. The present study was conducted to identify single nucleotide polymorphisms in the TLR4 gene of buffaloes and to analyze its associations with somatic cell counts. DNA samples of 120 Murrah buffaloes were used. The whole coding region of the TLR4 gene was amplified by polymerase chain reaction reactions and sequenced for polymorphism scanning. A total of 13 polymorphisms were identified for the sequenced regions of the TLR4, most of which are in the coding region. The association with the somatic cell score was highly significant (p < 0.001) for all identified polymorphisms of TLR4 gene (g.54621T>A, g.54429G>T, g.54407T>A, g.46616C>A, g.46613T>G, g.46612A>G, g.46611C>A, g.46609T>G, g.46541C>G, g.46526C>A, g.46516T>C, g.46376C>T, g.46372T>C). Therefore, it is suggested that the markers of the TLR4 gene can be used as molecular markers for mastitis resistance in buffaloes, due to their association with somatic cell counts.
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Affiliation(s)
- Valentina Roldan-Montes
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Diercles Francisco Cardoso
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil.,Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | | | - André Vieira do Nascimento
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Daniel Jordan de Abreu Santos
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Daiane Cristina Becker Scalez
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil.,Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Ana Cláudia de Freitas
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Ana Cristina Herrera
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Lucia Galvão Albuquerque
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | | | - Humberto Tonhati
- Department of Animal Science, School of Agricultural and Veterinarian Science, São Paulo State University (UNESP), Jaboticabal, Brazil
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17
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Adachi H, Yu YT. Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context-independent. RNA 2020; 26:1247-1256. [PMID: 32434780 PMCID: PMC7430670 DOI: 10.1261/rna.076042.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/19/2020] [Indexed: 05/26/2023]
Abstract
We have previously shown that when the uridine of a stop codon (UAA, UAG, or UGA) is pseudouridylated, the ribosome reads through the modified stop codon. However, it is not clear as to whether or not the pseudouridine (Ψ)-mediated readthrough is dependent on the sequence context of mRNA. Here, we use several different approaches and the yeast system to address this question. We show that when a stop codon (premature termination codon, PTC) is introduced into the coding region of a reporter mRNA at several different positions (with different sequence contexts) and pseudouridylated, we detect similar levels of readthrough. Using mutational and selection/screen analyses, we also show that the upstream sequence (relative to PTC) as well as the nucleotides surrounding the PTC (upstream and downstream) play a minimal role (if at all) in Ψ-mediated ribosome readthrough. Interestingly, we detect no suppression of NMD (nonsense-mediated mRNA decay) by targeted PTC pseudouridylation in the yeast system. Our results indicate that Ψ-mediated nonsense suppression occurs at the translational level, and that the suppression is sequence context-independent, unlike some previously characterized rare stop codon readthrough events.
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Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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18
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Wang K, Romm EL, Kouznetsova VL, Tsigelny IF. Prediction of Premature Termination Codon Suppressing Compounds for Treatment of Duchenne Muscular Dystrophy Using Machine Learning. Molecules 2020; 25:molecules25173886. [PMID: 32858918 PMCID: PMC7503396 DOI: 10.3390/molecules25173886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/14/2020] [Accepted: 08/20/2020] [Indexed: 11/16/2022] Open
Abstract
A significant percentage of Duchenne muscular dystrophy (DMD) cases are caused by premature termination codon (PTC) mutations in the dystrophin gene, leading to the production of a truncated, non-functional dystrophin polypeptide. PTC-suppressing compounds (PTCSC) have been developed in order to restore protein translation by allowing the incorporation of an amino acid in place of a stop codon. However, limitations exist in terms of efficacy and toxicity. To identify new compounds that have PTC-suppressing ability, we selected and clustered existing PTCSC, allowing for the construction of a common pharmacophore model. Machine learning (ML) and deep learning (DL) models were developed for prediction of new PTCSC based on known compounds. We conducted a search of the NCI compounds database using the pharmacophore-based model and a search of the DrugBank database using pharmacophore-based, ML and DL models. Sixteen drug compounds were selected as a consensus of pharmacophore-based, ML, and DL searches. Our results suggest notable correspondence of the pharmacophore-based, ML, and DL models in prediction of new PTC-suppressing compounds.
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Affiliation(s)
- Kate Wang
- MAP program, University of California San Diego (UCSD), La Jolla, CA 92093, USA;
| | - Eden L. Romm
- Curematch Inc., 6440 Lusk Blvd, Suite D206, San Diego, CA 92121, USA;
| | - Valentina L. Kouznetsova
- San Diego Supercomputer Center, University of California San Diego (UCSD), La Jolla, CA 92093, USA;
| | - Igor F. Tsigelny
- Curematch Inc., 6440 Lusk Blvd, Suite D206, San Diego, CA 92121, USA;
- San Diego Supercomputer Center, University of California San Diego (UCSD), La Jolla, CA 92093, USA;
- Dept. of Neurosciences, University of California San Diego (UCSD), La Jolla, CA 92093, USA
- Correspondence:
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19
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Fisher C, Casey H, Kumer L, Tyler J, Shike H. A novel null allele, HLA-DPA1*01:35N in a European American Male from Pennsylvania, USA. HLA 2020; 96:378-379. [PMID: 32447839 DOI: 10.1111/tan.13944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 11/29/2022]
Abstract
A non-sense mutation in either DPA1*01:03:01:02 or DPA1*01:03:01:05/01:03:01:15 results in the novel allele, HLA-DPA1*01:35N.
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Affiliation(s)
- Carolyn Fisher
- Department of Pathology, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Heather Casey
- Department of Pathology, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Lorie Kumer
- Department of Pathology, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Jennifer Tyler
- Department of Pathology, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Hiroko Shike
- Department of Pathology, Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania, USA
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20
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Abstract
Although the constraints on a gene’s sequence are often assumed to reflect the functioning of that gene, here we propose transfer selection, a constraint operating on one class of genes transferred to another, mediated by shared binding factors. We show that such transfer can explain an otherwise paradoxical depletion of stop codons in long intergenic noncoding RNAs (lincRNAs). Serine/arginine-rich proteins direct the splicing machinery by binding exonic splice enhancers (ESEs) in immature mRNA. As coding exons cannot contain stop codons in one reading frame, stop codons should be rare within ESEs. We confirm that the stop codon density (SCD) in ESE motifs is low, even accounting for nucleotide biases. Given that serine/arginine-rich proteins binding ESEs also facilitate lincRNA splicing, a low SCD could transfer to lincRNAs. As predicted, multiexon lincRNA exons are depleted in stop codons, a result not explained by open reading frame (ORF) contamination. Consistent with transfer selection, stop codon depletion in lincRNAs is most acute in exonic regions with the highest ESE density, disappears when ESEs are masked, is consistent with stop codon usage skews in ESEs, and is diminished in both single-exon lincRNAs and introns. Owing to low SCD, the maximum lengths of pseudo-ORFs frequently exceed null expectations. This has implications for ORF annotation and the evolution of de novo protein-coding genes from lincRNAs. We conclude that not all constraints operating on genes need be explained by the functioning of the gene but may instead be transferred owing to shared binding factors.
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Affiliation(s)
- Liam Abrahams
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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21
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Montoyo-Rosario JG, Armenti ST, Zilberman Y, Nance J. The Role of pkc-3 and Genetic Suppressors in Caenorhabditis elegans Epithelial Cell Junction Formation. Genetics 2020; 214:941-59. [PMID: 32005655 DOI: 10.1534/genetics.120.303085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022] Open
Abstract
Epithelial cells form intercellular junctions to strengthen cell-cell adhesion and limit diffusion, allowing epithelia to function as dynamic tissues and barriers separating internal and external environments. Junctions form as epithelial cells differentiate; clusters of junction proteins first concentrate apically, then mature into continuous junctional belts that encircle and connect each cell. In mammals and Drosophila, atypical protein kinase C (aPKC) is required for junction maturation, although how it contributes to this process is poorly understood. A role for the Caenorhabditis elegans aPKC homolog PKC-3 in junction formation has not been described previously. Here, we show that PKC-3 is essential for junction maturation as epithelia first differentiate. Using a temperature-sensitive allele of pkc-3 that causes junction breaks in the spermatheca and leads to sterility, we identify intragenic and extragenic suppressors that render pkc-3 mutants fertile. Intragenic suppressors include an unanticipated stop-to-stop mutation in the pkc-3 gene, providing evidence for the importance of stop codon identity in gene activity. One extragenic pkc-3 suppressor is a loss-of-function allele of the lethal(2) giant larvae homolog lgl-1, which antagonizes aPKC within epithelia of Drosophila and mammals, but was not known previously to function in C. elegans epithelia. Finally, two extragenic suppressors are loss-of-function alleles of sups-1-a previously uncharacterized gene. We show that SUPS-1 is an apical extracellular matrix protein expressed in epidermal cells, suggesting that it nonautonomously regulates junction formation in the spermatheca. These findings establish a foundation for dissecting the role of PKC-3 and interacting genes in epithelial junction maturation.
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22
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Tate WP, Cridge AG, Brown CM. 'Stop' in protein synthesis is modulated with exquisite subtlety by an extended RNA translation signal. Biochem Soc Trans 2018; 46:1615-25. [PMID: 30420414 DOI: 10.1042/BST20180190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/30/2018] [Accepted: 10/04/2018] [Indexed: 02/08/2023]
Abstract
Translational stop codons, UAA, UAG, and UGA, form an integral part of the universal genetic code. They are of significant interest today for their underlying fundamental role in terminating protein synthesis, but also for their potential utilisation for programmed alternative translation events. In diverse organisms, UAA has wide usage, but it is puzzling that the high fidelity UAG is selected against and yet UGA, vulnerable to suppression, is widely used, particularly in those archaeal and bacterial genomes with a high GC content. In canonical protein synthesis, stop codons are interpreted by protein release factors that structurally and functionally mimic decoding tRNAs and occupy the decoding site on the ribosome. The release factors make close contact with the decoding complex through multiple interactions. Correct interactions cause conformational changes resulting in new and enhanced contacts with the ribosome, particularly between specific bases in the mRNA and rRNA. The base following the stop codon (fourth or +4 base) may strongly influence decoding efficiency, facilitating alternative non-canonical events like frameshifting or selenocysteine incorporation. The fourth base is drawn into the decoding site with a compacted stop codon in the eukaryotic termination complex. Surprisingly, mRNA sequences upstream and downstream of this core tetranucleotide signal have a significant influence on the strength of the signal. Since nine bases downstream of the stop codon are within the mRNA channel, their interactions with rRNA, and r-proteins may affect efficiency. With this understanding, it is now possible to design stop signals of desired strength for specific applied purposes.
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23
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LeBlanc F, Leadbeater S, Laflamme M, Gagné N. In vivo virulence and genomic comparison of infectious Salmon Anaemia Virus isolates from Atlantic Canada. J Fish Dis 2018; 41:1373-1384. [PMID: 29938793 DOI: 10.1111/jfd.12832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
The infectious salmon anaemia virus (ISAV) is capable of causing a significant disease in Atlantic salmon, which has resulted in considerable financial losses for salmon farmers around the world. Since the first detection of ISAV in Canada in 1996, it has been a high priority for aquatic animal health management and surveillance programmes have led to the identification of many genetically distinct ISAV isolates of variable virulence. In this study, we evaluated the virulence of three ISAV isolates detected in Atlantic Canada in 2012 by doing in vivo-controlled disease challenges with two sources of Atlantic salmon. We measured viral loads in fish tissues during the course of infection. Sequences of the full viral RNA genomes of these three ISAV isolates were obtained and compared to a high-virulence and previously characterized isolate detected in the Bay of Fundy in 2004, as well as a newly identified ISAV NA-HPR0 isolate. All three ISAV isolates studied were shown to be of low to mid-virulence with fish from source A having a lower mortality rate than fish from source B. Viral load estimation using an RT-qPCR assay targeting viral segment 8 showed a high degree of similarity between tissues. Through genomic comparison, we identified various amino acid substitutions unique to some isolates, including a stop codon in the segment 8 ORF2 not previously reported in ISAV, present in the isolate with the lowest observed virulence.
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Affiliation(s)
- Francis LeBlanc
- Fisheries & Oceans Canada, Gulf Fisheries Center, Moncton, NB, Canada
| | - Steven Leadbeater
- Fisheries & Oceans Canada, St Andrews Biological Station, St Andrews, NB, Canada
| | - Mark Laflamme
- Fisheries & Oceans Canada, Gulf Fisheries Center, Moncton, NB, Canada
| | - Nellie Gagné
- Fisheries & Oceans Canada, Gulf Fisheries Center, Moncton, NB, Canada
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Prabhakar A, Capece MC, Petrov A, Choi J, Puglisi JD. Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling. Cell Rep 2017; 20:161-72. [PMID: 28683310 DOI: 10.1016/j.celrep.2017.06.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/06/2017] [Accepted: 06/09/2017] [Indexed: 01/24/2023] Open
Abstract
During termination of translation, the nascent peptide is first released from the ribosome, which must be subsequently disassembled into subunits in a process known as ribosome recycling. In bacteria, termination and recycling are mediated by the translation factors RF, RRF, EF-G, and IF3, but their precise roles have remained unclear. Here, we use single-molecule fluorescence to track the conformation and composition of the ribosome in real time during termination and recycling. Our results show that peptide release by RF induces a rotated ribosomal conformation. RRF binds to this rotated intermediate to form the substrate for EF-G that, in turn, catalyzes GTP-dependent subunit disassembly. After the 50S subunit departs, IF3 releases the deacylated tRNA from the 30S subunit, thus preventing reassembly of the 70S ribosome. Our findings reveal the post-termination rotated state as the crucial intermediate in the transition from termination to recycling.
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25
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Lingaas F, Guttersrud OA, Arnet E, Espenes A. Neuronal ceroid lipofuscinosis in Salukis is caused by a single base pair insertion in CLN8. Anim Genet 2018; 49:52-58. [PMID: 29446145 DOI: 10.1111/age.12629] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 01/09/2023]
Abstract
Neuronal ceroid lipofuscinoses (NCLs) are heterogenic inherited lysosomal storage diseases that have been described in a number of species including humans, sheep, cattle, cats and a number of different dog breeds, including Salukis. Here we present a novel genetic variant associated with the disease in this particular breed of dog. In a clinical case, a Saluki developed progressive neurological signs, including disorientation, anxiety, difficulties in eating, seizures and loss of vision, and for welfare reasons, was euthanized at 22 months of age. Microscopy showed aggregation of autofluorescent storage material in the neurons of several brain regions and also in the retina. The aggregates showed positive staining with Sudan black B and periodic acid Schiff, all features consistent with NCL. Whole genome sequencing of the case and both its parents, followed by variant calling in candidate genes, identified a new variant in the CLN8 gene: a single bp insertion (c.349dupT) in exon 2, introducing an immediate stop codon (p.Glu117*). The case was homozygous for the insertion, and both parents were heterozygous. A retrospective study of a Saluki from Australia diagnosed with NCL identified this case as being homozygous for the same mutation. This is the fourth variant identified in CLN8 that causes NCL in dogs.
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Affiliation(s)
- F Lingaas
- Section of Genetics, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. box 8146 Dep, 0033, Oslo, Norway
| | - O-A Guttersrud
- Section of Genetics, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. box 8146 Dep, 0033, Oslo, Norway
| | - E Arnet
- Section of Genetics, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. box 8146 Dep, 0033, Oslo, Norway
| | - A Espenes
- Section of Anatomy & Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. box 8146 Dep, 0033, Oslo, Norway
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Salmaninejad A, Valilou SF, Bayat H, Ebadi N, Daraei A, Yousefi M, Nesaei A, Mojarrad M. Duchenne muscular dystrophy: an updated review of common available therapies. Int J Neurosci 2018; 128:854-864. [PMID: 29351004 DOI: 10.1080/00207454.2018.1430694] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND AND PURPOSE Duchenne muscular dystrophy (DMD) is a lethal progressive pediatric muscle disorder and genetically inherited as an X-linked disease that caused by mutations in the dystrophin gene. DMD leads to progressive muscle weakness, degeneration, and wasting; finally, follows with the premature demise in affected individuals due to respiratory and/or cardiac failure typically by age of 30. For decades, scientists tried massively to find an effective therapy method, but there is no absolute cure currently for patients with DMD, nevertheless, recent advanced progressions on the treatment of DMD will be hopeful in the future. Several promising gene therapies are currently under investigation. These include gene replacement, exon skipping, suppression of stop codons. More recently, a promising gene editing tool referred to as CRISPR/Cas9 offers exciting perspectives for restoring dystrophin expression in patients with DMD. This review intents to briefly describe these methods and comment on their advances. Since DMD is a genetic disorder, it should be treated by replacing the deficient DMD copy with a functional one. However, there are different types of mutations in this gene, so such therapeutic approaches are highly mutation specific and thus are personalized. Therefore, DMD has arisen as a model of genetic disorder for understanding and overcoming of the challenges of developing personalized genetic medicines, consequently, the lessons learned from these approaches will be applicable to many other disorders. CONCLUSIONS This review provides an update on the recent gene therapies for DMD that aim to compensate for dystrophin deficiency and the related clinical trials.
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Affiliation(s)
- Arash Salmaninejad
- a Drug Applied Research Center , Tabriz University of Medical Sciences , Tabriz , Iran.,b Student Research Committee, Department of Medical Genetics, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,c Medical Genetics Research Center, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Saeed Farajzadeh Valilou
- d Medical Genetics Network (MeGeNe) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
| | - Hadi Bayat
- e Department of Tissue Engineering, School of Advanced Technologies in Medicine , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Nader Ebadi
- f Department of Medical Genetics, Faculty of Medicine , Tehran University of Medical Science , Tehran , Iran
| | - Abdolreza Daraei
- g Genetic Department, Faculty of Medicine , Babol University of Medical Sciences , Babol , Iran
| | - Meysam Yousefi
- b Student Research Committee, Department of Medical Genetics, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,c Medical Genetics Research Center, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
| | - Abolfazl Nesaei
- h Department of Basic Sciences, Faculty of Medicine , Gonabad University of Medical Sciences , Gonabad , Iran
| | - Majid Mojarrad
- b Student Research Committee, Department of Medical Genetics, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran.,c Medical Genetics Research Center, Faculty of Medicine , Mashhad University of Medical Sciences , Mashhad , Iran
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27
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Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF. Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response. J Biol Chem 2018; 293:4434-4444. [PMID: 29386352 PMCID: PMC5868278 DOI: 10.1074/jbc.m117.818526] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/30/2018] [Indexed: 12/25/2022] Open
Abstract
Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian readthrough have only recently been uncovered by systems biology and comparative genomics approaches. Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. Four mRNAs display highly efficient stop codon readthrough, and these mRNAs have a UGA stop codon immediately followed by CUAG (UGA_CUAG) that is conserved throughout vertebrates. Extending on the identification of this readthrough motif, we here investigated stop codon readthrough, using tissue culture reporter assays, for all previously untested human genes containing UGA_CUAG. The readthrough efficiency of the annotated stop codon for the sequence encoding vitamin D receptor (VDR) was 6.7%. It was the highest of those tested but all showed notable levels of readthrough. The VDR is a member of the nuclear receptor superfamily of ligand-inducible transcription factors, and it binds its major ligand, calcitriol, via its C-terminal ligand-binding domain. Readthrough of the annotated VDR mRNA results in a 67 amino acid-long C-terminal extension that generates a VDR proteoform named VDRx. VDRx may form homodimers and heterodimers with VDR but, compared with VDR, VDRx displayed a reduced transcriptional response to calcitriol even in the presence of its partner retinoid X receptor.
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Affiliation(s)
- Gary Loughran
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland,
| | - Irwin Jungreis
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, and
| | - Ioanna Tzani
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Michael Power
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ruslan I Dmitriev
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivaylo P Ivanov
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, and
| | - John F Atkins
- From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, .,Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330
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28
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Fan Y, Evans CR, Barber KW, Banerjee K, Weiss KJ, Margolin W, Igoshin OA, Rinehart J, Ling J. Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness. Mol Cell 2017; 67:826-836.e5. [PMID: 28781237 PMCID: PMC5591071 DOI: 10.1016/j.molcel.2017.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/22/2017] [Accepted: 07/07/2017] [Indexed: 12/30/2022]
Abstract
Gene expression noise (heterogeneity) leads to phenotypic diversity among isogenic individual cells. Our current understanding of gene expression noise is mostly limited to transcription, as separating translational noise from transcriptional noise has been challenging. It also remains unclear how translational heterogeneity originates. Using a transcription-normalized reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, and individual cells with higher UGA readthrough grow faster from stationary phase. Our work also revealed that individual cells with lower protein synthesis levels exhibited higher UGA readthrough, which was confirmed with ribosome-targeting antibiotics (e.g., chloramphenicol). Further experiments and mathematical modeling suggest that varied competition between ternary complexes and release factors perturbs the UGA readthrough level. Our results indicate that fluctuations in the concentrations of translational components lead to UGA readthrough heterogeneity among single cells, which enhances phenotypic diversity of the genetically identical population and facilitates its adaptation to changing environments.
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MESH Headings
- Bacterial Proteins/biosynthesis
- Bacterial Proteins/genetics
- Codon, Terminator
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/genetics
- Gene Expression Regulation, Bacterial
- Genes, Reporter
- Genetic Fitness
- Genotype
- Kinetics
- Luminescent Proteins/biosynthesis
- Luminescent Proteins/genetics
- Microscopy, Fluorescence
- Models, Genetic
- One-Carbon Group Transferases
- Phenotype
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Transcription, Genetic
- Red Fluorescent Protein
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Affiliation(s)
- Yongqiang Fan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Christopher R Evans
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Karl W Barber
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kinshuk Banerjee
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Kalyn J Weiss
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Oleg A Igoshin
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jiqiang Ling
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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29
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Korkmaz G, Sanyal S. R213I mutation in release factor 2 (RF2) is one step forward for engineering an omnipotent release factor in bacteria Escherichia coli. J Biol Chem 2017; 292:15134-15142. [PMID: 28743745 DOI: 10.1074/jbc.m117.785238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/23/2017] [Indexed: 11/06/2022] Open
Abstract
The current understanding of the specificity of the bacterial class I release factors (RFs) in decoding stop codons has evolved beyond a simple tripeptide anticodon model. A recent molecular dynamics study for deciphering the principles for specific stop codon recognition by RFs identified Arg-213 as a crucial residue on Escherichia coli RF2 for discriminating guanine in the third position (G3). Interestingly, Arg-213 is highly conserved in RF2 and substituted by Ile-196 in the corresponding position in RF1. Another similar pair is Leu-126 in RF1 and Asp-143 in RF2, which are also conserved within their respective groups. With the hypothesis that replacement of Arg-213 and Asp-143 with the corresponding RF1 residues will reduce G3 discrimination by RF2, we swapped these residues between E. coli RF1 and RF2 by site-directed mutagenesis and characterized their preference for different codons using a competitive peptide release assay. Among these, the R213I mutant of RF2 showed 5-fold improved reading of the RF1-specific UAG codon relative to UAA, the universal stop codon, compared with the wild type (WT). In-depth fast kinetic studies revealed that the gain in UAG reading by RF2 R213I is associated with a reduced efficiency of termination on the cognate UAA codon. Our work highlights the notion that stop codon recognition involves complex interactions with multiple residues beyond the PXT/SPF motifs. We propose that the R213I mutation in RF2 brings us one step forward toward engineering an omnipotent RF in bacteria, capable of reading all three stop codons.
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Affiliation(s)
- Gürkan Korkmaz
- From the Department of Cell and Molecular Biology, Uppsala University, Box-596, 75124 Uppsala, Sweden
| | - Suparna Sanyal
- From the Department of Cell and Molecular Biology, Uppsala University, Box-596, 75124 Uppsala, Sweden
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30
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Friesen WJ, Trotta CR, Tomizawa Y, Zhuo J, Johnson B, Sierra J, Roy B, Weetall M, Hedrick J, Sheedy J, Takasugi J, Moon YC, Babu S, Baiazitov R, Leszyk JD, Davis TW, Colacino JM, Peltz SW, Welch EM. The nucleoside analog clitocine is a potent and efficacious readthrough agent. RNA 2017; 23:567-577. [PMID: 28096517 PMCID: PMC5340919 DOI: 10.1261/rna.060236.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/05/2017] [Indexed: 06/01/2023]
Abstract
Nonsense mutations resulting in a premature stop codon in an open reading frame occur in critical tumor suppressor genes in a large number of the most common forms of cancers and are known to cause or contribute to the progression of disease. Low molecular weight compounds that induce readthrough of nonsense mutations offer a new means of treating patients with genetic disorders or cancers resulting from nonsense mutations. We have identified the nucleoside analog clitocine as a potent and efficacious suppressor of nonsense mutations. We determined that incorporation of clitocine into RNA during transcription is a prerequisite for its readthrough activity; the presence of clitocine in the third position of a premature stop codon directly induces readthrough. We demonstrate that clitocine can induce the production of p53 protein in cells harboring p53 nonsense-mutated alleles. In these cells, clitocine restored production of full-length and functional p53 as evidenced by induced transcriptional activation of downstream p53 target genes, progression of cells into apoptosis, and impeded growth of nonsense-containing human ovarian cancer tumors in xenograft tumor models. Thus, clitocine induces readthrough of nonsense mutations by a previously undescribed mechanism and represents a novel therapeutic modality to treat cancers and genetic diseases caused by nonsense mutations.
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Affiliation(s)
| | | | - Yuki Tomizawa
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Jin Zhuo
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Briana Johnson
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Jairo Sierra
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Bijoyita Roy
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Marla Weetall
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Jean Hedrick
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | | | - James Takasugi
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | | | - Suresh Babu
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Ramil Baiazitov
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - John D Leszyk
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655-0122, USA
| | - Thomas W Davis
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | | | - Stuart W Peltz
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
| | - Ellen M Welch
- PTC Therapeutics, Inc., South Plainfield, New Jersey 07080, USA
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Abstract
The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes. We consider the possible molecular mechanisms allowing the use of certain codons as sense and stop signals simultaneously. The results obtained by studying these amazing organisms represent a new and exciting insight into the mechanism of stop codon decoding in eukaryotes. Also see the video abstract here.
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Affiliation(s)
- Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Mikhailova
- Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Moscow, Russia
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32
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Abstract
Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3. This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range.
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Affiliation(s)
- Yulong Wei
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Juan Wang
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada Ottawa Institute of Systems Biology, Ottawa, ON, Canada
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33
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Colson P, Ravaux I, Tamalet C, Glazunova O, Baptiste E, Chabriere E, Wiedemann A, Lacabaratz C, Chefrour M, Picard C, Stein A, Levy Y, Raoult D. HIV infection en route to endogenization: two cases. Clin Microbiol Infect 2014; 20:1280-8. [PMID: 25366539 PMCID: PMC4360783 DOI: 10.1111/1469-0691.12807] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 10/28/2014] [Accepted: 10/28/2014] [Indexed: 12/30/2022]
Abstract
The long-term spontaneous evolution of humans and the human immunodeficiency virus (HIV) is not well characterized; many vertebrate species, including humans, exhibit remnants of other retroviruses in their genomes that question such possible endogenization of HIV. We investigated two HIV-infected patients with no HIV-related disease and no detection with routine tests of plasma HIV RNA or cell-associated HIV DNA. We used Sanger and deep sequencing to retrieve HIV DNA sequences integrated in the human genome and tested the host humoral and cellular immune responses. We noticed that viruses from both patients were inactivated by the high prevalence of the transformation of tryptophan codons into stop codons (25% overall (3-100% per gene) and 24% overall (0-50% per gene)). In contrast, the humoral and/or cellular responses were strong for one patient and moderate for the other, indicating that a productive infection occurred at one stage of the infection. We speculate that the stimulation of APOBEC, the enzyme group that exchanges G for A in viral nucleic acids and is usually inhibited by the HIV protein Vif, has been amplified and made effective from the initial stage of the infection. Furthermore, we propose that a cure for HIV may occur through HIV endogenization in humans, as observed for many other retroviruses in mammals, rather than clearance of all traces of HIV from human cells, which defines viral eradication.
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Affiliation(s)
- P Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Université, Marseille, France; Fondation Institut Hospitalo-Universitaire (IHU) MéiterranéInfection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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34
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Hanke A, Hamann E, Sharma R, Geelhoed JS, Hargesheimer T, Kraft B, Meyer V, Lenk S, Osmers H, Wu R, Makinwa K, Hettich RL, Banfield JF, Tegetmeyer HE, Strous M. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Front Microbiol 2014; 5:231. [PMID: 24904545 PMCID: PMC4032931 DOI: 10.3389/fmicb.2014.00231] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 04/30/2014] [Indexed: 11/13/2022] Open
Abstract
Sandy coastal sediments are global hotspots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective porewater flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfur oxidizing Gammaproteobacteria and members of the enigmatic BD1-5/SN-2 candidate phylum were abundant in situ (>10% and ~2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sediment in a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacteria (at 24 ± 2% abundance) and a member of the BD1-5/SN-2 candidate phylum (at 7 ± 6% abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gammaproteobacterium grew partially autotrophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2 candidate phylum enabled, for the first time, direct microscopic observation by fluorescent in situ hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.
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Affiliation(s)
- Anna Hanke
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Emmo Hamann
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Ritin Sharma
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, TN, USA ; Chemical Science Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Jeanine S Geelhoed
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Theresa Hargesheimer
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Beate Kraft
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Volker Meyer
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Sabine Lenk
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Harald Osmers
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Rong Wu
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Delft, Netherlands
| | - Kofi Makinwa
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Delft, Netherlands
| | - Robert L Hettich
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, TN, USA ; Chemical Science Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, Department of Environmental Science, Policy, and Management, University of California Berkeley, CA, USA
| | - Halina E Tegetmeyer
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; Center for Biotechnology, University of Bielefeld Bielefeld, Germany
| | - Marc Strous
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Department of Geoscience, University of Calgary Calgary, AB, Canada
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Zhai Y, Li J, Zhu Y, Xia Y, Wang W, Yu Y, Yao K. A nonsense mutation of γD-crystallin associated with congenital nuclear and posterior polar cataract in a Chinese family. Int J Med Sci 2014; 11:158-63. [PMID: 24465161 PMCID: PMC3894400 DOI: 10.7150/ijms.7567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/17/2013] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE The goal of this study was to characterize the disease-causing mutations in a Chinese family with congenital nuclear and posterior polar cataracts. METHODS Clinical data of patients in the family were recorded using slit-lamp photography and high definition video. Genomic DNA samples were extracted from the peripheral blood of the pedigree members and 100 healthy controls. Mutation screening was performed in the candidate genes by bi-directional sequencing of the amplified products. RESULTS The congenital cataract phenotype of the pedigree was identified by slit-lamp examinations and observation during surgery as nuclear and posterior polar cataracts. Through the sequencing of the candidate genes, a heterozygous c. 418C>T change was detected in the coding region of the γD-crystallin gene (CRYGD). As a result of this change, a highly conserved arginine residue was replaced by a stop codon (p. R140X). This change was discovered among all of the affected individuals with cataracts, but not among the unaffected family members or the 100 ethnically matched controls. CONCLUSIONS This study identified a novel congenital nuclear and posterior polar cataract phenotype caused by the recurrent mutation p. R140X in CRYGD.
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Affiliation(s)
- Yi Zhai
- 1. Eye Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China ; 2. Key Laboratory of Ophthalmology of Zhejiang Province, China
| | - Jinyu Li
- 1. Eye Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China ; 2. Key Laboratory of Ophthalmology of Zhejiang Province, China
| | - Yanan Zhu
- 1. Eye Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China ; 2. Key Laboratory of Ophthalmology of Zhejiang Province, China
| | - Yan Xia
- 3. Center for Structural Biology and Department of Chemistry and the Institute for Chemical Biology, Vanderbilt University Medical Center, USA
| | - Wei Wang
- 1. Eye Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China ; 2. Key Laboratory of Ophthalmology of Zhejiang Province, China
| | - Yinhui Yu
- 1. Eye Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China ; 2. Key Laboratory of Ophthalmology of Zhejiang Province, China
| | - Ke Yao
- 1. Eye Center, Second Affiliated Hospital of Medical College, Zhejiang University, Hangzhou, Zhejiang, China ; 2. Key Laboratory of Ophthalmology of Zhejiang Province, China
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Dunn JG, Foo CK, Belletier NG, Gavis ER, Weissman JS. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2013; 2:e01179. [PMID: 24302569 PMCID: PMC3840789 DOI: 10.7554/elife.01179] [Citation(s) in RCA: 260] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution. DOI: http://dx.doi.org/10.7554/eLife.01179.001.
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Affiliation(s)
- Joshua G Dunn
- California Institute of Quantitative Biosciences, San Francisco, United States
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Abstract
The mitochondrial (mt) genome of the scallop Mimachlamys senatoria (17,383 bp), an economically and ecologically important bivalve, was newly sequenced and annotated. Comparative analyses between M. senatoria and its congeneric sister species M. nobilis revealed three new findings: (1) M. senatoria is more prone to use G-rich start/stop codon, and variation in start/stop codon usage is species-correlated rather than gene-correlated, and in some extent, bears useful phylogenetic information; (2) The A + T content is unexpectedly low (54.1%) in MNR and that is unexpectedly high (65.4%) in atp8 in both congeneric scallops, which may represent a novel evolutionary pattern of mt genomic nucleotide composition; and (3) The tRNA gene cluster "NGV" locating upstream of the nad1 in M. senatoria is replaced by "NTGV" in M. nobilis, and a parsimonious explanation for the existence of trnT in M. nobilis is that this gene was derived from a recently duplicated trnG gene via an alloacceptor tRNA gene recruitment process.
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Affiliation(s)
- Xiangyun Wu
- Key Laboratory of Marine Bio-resource Sustainable Utilization, Chinese Academy of Sciences, Guangdong Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences , Guangzhou , China
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Abstract
The complete mitochondrial genome of the black cutworm Agrotis ipsilon (Lepidoptera: Noctuidae) was determined (GenBank accession No. KF163965). The length of this mitochondrial genome is 15,377 bp with an A + T content of 82.5%. There are 37 typical animal mitochondrial genes, that is, 13 protein-coding, 2 rRNA and 22 tRNA gene and an A + T-rich region. The tRNA gene trnM was rearranged to the upstream of the trnI-trnQ-trnM cluster compared with the pupative ancestral arrangement of insects. All protein-coding genes start with ATN start codon except for the gene cox1, which uses CGA as in other lepidopteran species. Ten protein-coding genes stop with termination codon TAA, whereas three protein-coding gene use incomplete stop codon T. The A + T-region is located between rrnS and trnM with a length of 332 bp and A + T content of 94.88%.
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Affiliation(s)
- Qiu-Ling Wu
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing , China and
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Zhang T, Huang Y, Chamberlain S, Romeo T, Zhu-Shimoni J, Hewitt D, Zhu M, Katta V, Mauger B, Kao YH. Identification of a single base-pair mutation of TAA ( Stop codon) → GAA (Glu) that causes light chain extension in a CHO cell derived IgG1. MAbs 2012; 4:694-700. [PMID: 23018810 PMCID: PMC3502236 DOI: 10.4161/mabs.22232] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We describe here the identification of a stop codon TAA (Stop) → GAA (Glu) = Stop221E mutation on the light chain of a recombinant IgG1 antibody expressed in a Chinese hamster ovary (CHO) cell line. The extended light chain variants, which were caused by translation beyond the mutated stop codon to the next alternative in-frame stop codon, were observed by mass spectra analysis. The abnormal peptide peaks present in tryptic and chymotryptic LC–MS peptide mapping were confirmed by N-terminal sequencing as C-terminal light chain extension peptides. Furthermore, LC-MS/MS of Glu-C peptide mapping confirmed the stop221E mutation, which is consistent with a single base-pair mutation in TAA (stop codon) to GAA (Glu). The light chain variants were approximately 13.6% of wild type light chain as estimated by RP-HPLC analysis. DNA sequencing techniques determined a single base pair stop codon mutation, instead of a stop codon read-through, as the cause of this light chain extension. To our knowledge, the stop codon mutation has not been reported for IgGs expressed in CHO cells. These results demonstrate orthogonal techniques should be implemented to characterize recombinant proteins and select appropriate cell lines for production of therapeutic proteins because modifications could occur at unexpected locations.
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Affiliation(s)
- Taylor Zhang
- Protein Analytical Chemistry, Genentech, South San Francisco, CA, USA.
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Conard SE, Buckley J, Dang M, Bedwell GJ, Carter RL, Khass M, Bedwell DM. Identification of eRF1 residues that play critical and complementary roles in stop codon recognition. RNA 2012; 18:1210-21. [PMID: 22543865 PMCID: PMC3358643 DOI: 10.1261/rna.031997.111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 03/15/2012] [Indexed: 05/31/2023]
Abstract
The initiation and elongation stages of translation are directed by codon-anticodon interactions. In contrast, a release factor protein mediates stop codon recognition prior to polypeptide chain release. Previous studies have identified specific regions of eukaryotic release factor one (eRF1) that are important for decoding each stop codon. The cavity model for eukaryotic stop codon recognition suggests that three binding pockets/cavities located on the surface of eRF1's domain one are key elements in stop codon recognition. Thus, the model predicts that amino acid changes in or near these cavities should influence termination in a stop codon-dependent manner. Previous studies have suggested that the TASNIKS and YCF motifs within eRF1 domain one play important roles in stop codon recognition. These motifs are highly conserved in standard code organisms that use UAA, UAG, and UGA as stop codons, but are more divergent in variant code organisms that have reassigned a subset of stop codons to sense codons. In the current study, we separately introduced TASNIKS and YCF motifs from six variant code organisms into eRF1 of Saccharomyces cerevisiae to determine their effect on stop codon recognition in vivo. We also examined the consequences of additional changes at residues located between the TASNIKS and YCF motifs. Overall, our results indicate that changes near cavities two and three frequently mediated significant effects on stop codon selectivity. In particular, changes in the YCF motif, rather than the TASNIKS motif, correlated most consistently with variant code stop codon selectivity.
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Affiliation(s)
- Sara E. Conard
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Jessica Buckley
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Mai Dang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Richard L. Carter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Mohamed Khass
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - David M. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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Napthine S, Yek C, Powell ML, Brown TDK, Brierley I. Characterization of the stop codon readthrough signal of Colorado tick fever virus segment 9 RNA. RNA 2012; 18:241-252. [PMID: 22190746 PMCID: PMC3264911 DOI: 10.1261/rna.030338.111] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/06/2011] [Indexed: 05/31/2023]
Abstract
Termination codon readthrough is utilized as a mechanism of expression of a growing number of viral and cellular proteins, but in many cases the mRNA signals that promote readthrough are poorly characterized. Here, we investigated the readthrough signal of Colorado tick fever virus (CTFV) segment 9 RNA (Seg-9). CTFV is the type-species of the genus Coltivirus within the family Reoviridae and is a tick-borne, double-stranded, segmented RNA virus. Seg-9 encodes a 36-kDa protein VP9, and by readthrough of a UGA stop codon, a 65-kDa product, VP9'. Using a reporter system, we defined the minimal sequence requirements for readthrough and confirmed activity in both mammalian and insect cell-free translation systems, and in transfected mammalian cells. Mutational analysis revealed that readthrough was UGA specific, and that the local sequence context around the UGA influenced readthrough efficiency. Readthrough was also dependent upon a stable RNA stem-loop structure beginning eight bases downstream from the UGA codon. Mutational analysis of this stem-loop revealed a requirement for the stem region but not for substructures identified within the loop. Unexpectedly, we were unable to detect a ribosomal pause during translation of the CTFV signal, suggesting that the mechanism of readthrough, at least at this site, is unlikely to be dependent upon RNA secondary-structure induced ribosomal pausing at the recoded stop codon.
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Affiliation(s)
- Sawsan Napthine
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Christina Yek
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Michael L. Powell
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - T. David K. Brown
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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Young DJ, Edgar CD, Poole ES, Tate WP. The codon specificity of eubacterial release factors is determined by the sequence and size of the recognition loop. RNA 2010; 16:1623-33. [PMID: 20584893 PMCID: PMC2905760 DOI: 10.1261/rna.2117010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The two codon-specific eubacterial release factors (RF1: UAA/UAG and RF2: UAA/UGA) have specific tripeptide motifs (PXT/SPF) within an exposed recognition loop shown in recent structures to interact with stop codons during protein synthesis termination. The motifs have been inferred to be critical for codon specificity, but this study shows that they are insufficient to determine specificity alone. Swapping the motifs or the entire loop between factors resulted in a loss of codon recognition rather than a switch of codon specificity. From a study of chimeric eubacterial RF1/RF2 recognition loops and an atypical shorter variant in Caenorhabditis elegans mitochondrial RF1 that lacks the classical tripeptide motif PXT, key determinants throughout the whole loop have been defined. It reveals that more than one configuration of the recognition loop based on specific sequence and size can achieve the same desired codon specificity. This study has provided unexpected insight into why a combination of the two factors is necessary in eubacteria to exclude recognition of UGG as stop.
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Affiliation(s)
- David J Young
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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43
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Abstract
The distribution of sequences which induce non-standard decoding, especially of shift-prone sequences, is very unusual. On one hand, since they can disrupt standard genetic readout, they are avoided within the coding regions of most genes. On the other hand, they play important regulatory roles for the expression of those genes where they do occur. As a result, they are preserved among homologs and exhibit deep phylogenetic conservation. The combination of these two constraints results in a characteristic distribution of recoding sequences across genomes: they are highly conserved at specific locations while they are very rare in other locations. We term such sequences singular genomic elements to signify their rare occurrence and biological importance.
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Affiliation(s)
- John F. Atkins
- Molecular Biology Program, University of Utah, N. 2030 E. 15, Salt Late City, 84112-5330 U.S.A
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44
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Sunohara T, Jojima K, Yamamoto Y, Inada T, Aiba H. Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA. RNA 2004; 10:378-86. [PMID: 14970383 PMCID: PMC1370933 DOI: 10.1261/rna.5169404] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Accepted: 11/06/2003] [Indexed: 05/21/2023]
Abstract
Recent studies have established that tmRNA-mediated protein tagging occurs at stop codons depending on the C-terminal amino acid sequence of the nascent polypeptide immediately adjacent to those codons. We investigate here how the trans-translation at a stop codon occurs by using model crp genes encoding variants of cAMP receptor protein (CRP). We demonstrate that a truncated crp mRNA is efficiently produced along with a normal transcript from the model gene where tmRNA-mediated protein tagging occurs. The truncated crp mRNA was not detected in the presence of tmRNA, indicating that its degradation was facilitated by tmRNA. The major 3'-ends of the truncated crp mRNA in cells unable to express tmRNA were mapped at and near the stop codon. When RNA derived from the model crp-crr fusion gene was analyzed, crr mRNA was detected as a downstream cleavage product along with the upstream crp mRNA. These results are compatible with the hypothesis that ribosome stalling caused by the tagging-provoking sequences leads to endonucleolytic cleavage of mRNA around the stop codon, resulting in nonstop mRNA. In addition, the data are consistent with the view that mRNA cleavage is the cause of trans-translation at stop codons. Neither the bacterial toxin RelE nor the known major endoribonucleases are required for this cleavage, indicating that either other endoribonuclease(s) or the ribosome itself would be responsible for the mRNA cleavage in response to ribosome stalling caused by the particular nascent peptides.
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Affiliation(s)
- Takafumi Sunohara
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
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Carnes J, Jacobson M, Leinwand L, Yarus M. Stop codon suppression via inhibition of eRF1 expression. RNA 2003; 9:648-653. [PMID: 12756323 PMCID: PMC1370432 DOI: 10.1261/rna.5280103] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2003] [Accepted: 03/17/2003] [Indexed: 05/24/2023]
Abstract
In humans, recognition of a stop codon by protein release factor eRF1 leads to release of the nascent peptide from the ribosome. Although efficient eRF1 activity is usually desirable, numerous pathologies result from eRF1 recognition of premature stop mutations in essential genes. In these cases, decreased eRF1 activity could increase readthrough of the premature stop codon, thereby making full-length protein. To broaden the means available to beneficially decrease eRF1 activity, we have targeted eRF1 mRNA using siRNAs and antisense oligonucleotides. We show that both eRF1-targeted siRNA and antisense oligonucleotides decrease eRF1 mRNA and eRF1 protein concentrations, and increase UAG readthrough in cultured human cells.
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Affiliation(s)
- Jason Carnes
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA
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Abstract
We have studied the molecular basis of factor I (fI) deficiency in two Brazilian sisters from a consanguineous family. By reverse transcription-polymerase chain reaction we observed that all fI cDNA amplified products from one sister had the same size as those of normal cDNA, however, they were significantly less intense. Sequencing analysis of subcloned cDNA revealed a dinucleotide insertion (AT) between positions 1204 and 1205 in the 11th exon that creates a stop codon 13 bp downstream of the insertion site. Genomic DNA sequencing and heteroduplex analysis confirmed that both probands are homozygous for this mutation, whereas their parents are heterozygous. The stop codon and the diminished amounts of fI cDNA could indicate increased fI mRNA instability, perhaps due to a mechanism of nonsense-mediated decay. This hypothesis is consistent with our observation that treatment with the translation inhibitor cycloheximide stabilized fI mRNA expression in proband's fibroblasts.
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Affiliation(s)
- G V Baracho
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de S. Paulo, Brazil
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