101
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Rajput B, Pruitt KD, Murphy TD. RefSeq curation and annotation of stop codon recoding in vertebrates. Nucleic Acids Res 2019; 47:594-606. [PMID: 30535227 PMCID: PMC6344875 DOI: 10.1093/nar/gky1234] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022] Open
Abstract
Recoding of stop codons as amino acid-specifying codons is a co-translational event that enables C-terminal extension of a protein. Synthesis of selenoproteins requires recoding of internal UGA stop codons to the 21st non-standard amino acid selenocysteine (Sec) and plays a vital role in human health and disease. Separately, canonical stop codons can be recoded to specify standard amino acids in a process known as stop codon readthrough (SCR), producing extended protein isoforms with potential novel functions. Conventional computational tools cannot distinguish between the dual functionality of stop codons as stop signals and sense codons, resulting in misannotation of selenoprotein gene products and failure to predict SCR. Manual curation is therefore required to correctly represent recoded gene products and their functions. Our goal was to provide accurately curated and annotated datasets of selenoprotein and SCR transcript and protein records to serve as annotation standards and to promote basic and biomedical research. Gene annotations were curated in nine vertebrate model organisms and integrated into NCBI's Reference Sequence (RefSeq) dataset, resulting in 247 selenoprotein genes encoding 322 selenoproteins, and 93 genes exhibiting SCR encoding 94 SCR isoforms.
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Affiliation(s)
- Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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102
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A common phytoene synthase mutation underlies white petal varieties of the California poppy. Sci Rep 2019; 9:11615. [PMID: 31406151 PMCID: PMC6690985 DOI: 10.1038/s41598-019-48122-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/30/2019] [Indexed: 11/29/2022] Open
Abstract
The California poppy (Eschscholzia californica) is renowned for its brilliant golden-orange flowers, though white petal variants have been described. By whole-transcriptome sequencing, we have discovered in multiple white petal varieties a single deletion leading to altered splicing and C-terminal truncation of phytoene synthase (PSY), a key enzyme in carotenoid biosynthesis. Our findings underscore the diverse roles of phytoene synthase in shaping horticultural traits, and resolve a longstanding mystery of the regaled golden poppy.
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103
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Lee J, Termglinchan V, Diecke S, Itzhaki I, Lam CK, Garg P, Lau E, Greenhaw M, Seeger T, Wu H, Zhang JZ, Chen X, Gil IP, Ameen M, Sallam K, Rhee JW, Churko JM, Chaudhary R, Chour T, Wang PJ, Snyder MP, Chang HY, Karakikes I, Wu JC. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy. Nature 2019; 572:335-340. [PMID: 31316208 PMCID: PMC6779479 DOI: 10.1038/s41586-019-1406-x] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 06/19/2019] [Indexed: 12/11/2022]
Abstract
Lamin A/C (LMNA) is one of the most frequently mutated genes associated with dilated cardiomyopathy (DCM). DCM related to mutations in LMNA is a common inherited cardiomyopathy that is associated with systolic dysfunction and cardiac arrhythmias. Here we modelled the LMNA-related DCM in vitro using patient-specific induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). Electrophysiological studies showed that the mutant iPSC-CMs displayed aberrant calcium homeostasis that led to arrhythmias at the single-cell level. Mechanistically, we show that the platelet-derived growth factor (PDGF) signalling pathway is activated in mutant iPSC-CMs compared to isogenic control iPSC-CMs. Conversely, pharmacological and molecular inhibition of the PDGF signalling pathway ameliorated the arrhythmic phenotypes of mutant iPSC-CMs in vitro. Taken together, our findings suggest that the activation of the PDGF pathway contributes to the pathogenesis of LMNA-related DCM and point to PDGF receptor-β (PDGFRB) as a potential therapeutic target.
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MESH Headings
- Arrhythmias, Cardiac/metabolism
- Arrhythmias, Cardiac/pathology
- Calcium/metabolism
- Cardiomyopathy, Dilated/genetics
- Cells, Cultured
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly/genetics
- Haploinsufficiency/genetics
- Homeostasis
- Humans
- In Vitro Techniques
- Induced Pluripotent Stem Cells/pathology
- Lamin Type A/genetics
- Models, Biological
- Mutation
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Nonsense Mediated mRNA Decay
- Platelet-Derived Growth Factor/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- Receptor, Platelet-Derived Growth Factor beta/metabolism
- Signal Transduction
- Single-Cell Analysis
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Affiliation(s)
- Jaecheol Lee
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea.
| | - Vittavat Termglinchan
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sebastian Diecke
- Berlin Institute of Health, Berlin, Germany
- Max Delbrueck Center, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Ilanit Itzhaki
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Chi Keung Lam
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Priyanka Garg
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Edward Lau
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Matthew Greenhaw
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Timon Seeger
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Haodi Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Joe Z Zhang
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Isaac Perea Gil
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohamed Ameen
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Karim Sallam
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - June-Wha Rhee
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Jared M Churko
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Rinkal Chaudhary
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Tony Chour
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Paul J Wang
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ioannis Karakikes
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA.
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
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104
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Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B. The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res 2019; 46:5822-5836. [PMID: 29596649 PMCID: PMC6009662 DOI: 10.1093/nar/gky225] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/16/2018] [Indexed: 12/16/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is important for RNA quality control and gene regulation in eukaryotes. NMD targets aberrant transcripts for decay and also directly influences the abundance of non-aberrant transcripts. In animals, the SMG1 kinase plays an essential role in NMD by phosphorylating the core NMD factor UPF1. Despite SMG1 being ubiquitous throughout the plant kingdom, little is known about its function, probably because SMG1 is atypically absent from the genome of the model plant, Arabidopsis thaliana. By combining our previously established SMG1 knockout in moss with transcriptome-wide analysis, we reveal the range of processes involving SMG1 in plants. Machine learning assisted analysis suggests that 32% of multi-isoform genes produce NMD-targeted transcripts and that splice junctions downstream of a stop codon act as the major determinant of NMD targeting. Furthermore, we suggest that SMG1 is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. Consistent with this, smg1 plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The potential involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants.
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Affiliation(s)
- James P B Lloyd
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Barry Causier
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Brendan Davies
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
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105
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Loss of function mutation of Eftud2, the gene responsible for mandibulofacial dysostosis with microcephaly (MFDM), leads to pre-implantation arrest in mouse. PLoS One 2019; 14:e0219280. [PMID: 31276534 PMCID: PMC6611600 DOI: 10.1371/journal.pone.0219280] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 05/23/2019] [Indexed: 11/19/2022] Open
Abstract
Mutations in EFTUD2 are responsible for the autosomal dominant syndrome named MFDM (mandibulofacial dysostosis with microcephaly). However, it is not clear how reduced levels of EFTUD2 cause abnormalities associated with this syndrome. To determine if the mouse can serve as a model for uncovering the etiology of abnormalities found in MFDM patients, we used in situ hybridization to characterize expression of Eftud2 during mouse development, and used CRISPR/Cas9 to generate a mutant mouse line with deletion of exon 2 of the mouse gene. We found that Eftud2 was expressed throughout embryonic development, though its expression was enriched in the developing head and craniofacial regions. Additionally, Eftud2 heterozygous mutant embryos had reduced EFTUD2 mRNA and protein levels. Moreover, Eftud2 heterozygous embryos were born at the expected Mendelian frequency, and were viable and fertile despite being developmentally delayed. In contrast, Eftud2 homozygous mutant embryos were not found post-implantation but were present at the expected Mendelian frequency at embryonic day (E) 3.5. Furthermore, only wild-type and heterozygous E3.5 embryos survived ex vivo culture. Our data indicate that Eftud2 expression is enriched in the precusor of structures affected in MFDM patients and show that heterozygous mice carrying deletion of exon 2 do not model MFDM. In addition, we uncovered a requirement for normal levels of Eftud2 for survival of pre-implantation zygotes.
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106
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Ling Z, Brockmöller T, Baldwin IT, Xu S. Evolution of Alternative Splicing in Eudicots. FRONTIERS IN PLANT SCIENCE 2019; 10:707. [PMID: 31244865 PMCID: PMC6581728 DOI: 10.3389/fpls.2019.00707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/13/2019] [Indexed: 05/30/2023]
Abstract
Alternative pre-mRNA splicing (AS) is prevalent in plants and is involved in many interactions between plants and environmental stresses. However, the patterns and underlying mechanisms of AS evolution in plants remain unclear. By analyzing the transcriptomes of four eudicot species, we revealed that the divergence of AS is largely due to the gains and losses of AS events among orthologous genes. Furthermore, based on a subset of AS, in which AS can be directly associated with specific transcripts, we found that AS that generates transcripts containing premature termination codons (PTC), are likely more conserved than those that generate non-PTC containing transcripts. This suggests that AS coupled with nonsense-mediated decay (NMD) might play an important role in affecting mRNA levels post-transcriptionally. To understand the mechanisms underlying the divergence of AS, we analyzed the key determinants of AS using a machine learning approach. We found that the presence/absence of alternative splice site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5' donor site and 3' acceptor site among the studied species, suggesting a relatively conserved AS mechanism. The comparative analysis further demonstrated that variations of the identified AS determinants significantly contributed to the AS divergence among closely related species in both Solanaceae and Brassicaceae taxa. Together, these results provide detailed insights into the evolution of AS in plants.
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Affiliation(s)
- Zhihao Ling
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Ian T. Baldwin
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Shuqing Xu
- Plant Adaptation-in-action Group, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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107
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Morton M, AlTamimi N, Butt H, Reddy ASN, Mahfouz M. Serine/Arginine-rich protein family of splicing regulators: New approaches to study splice isoform functions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:127-134. [PMID: 31128682 DOI: 10.1016/j.plantsci.2019.02.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 05/06/2023]
Abstract
Serine/arginine-rich (SR) proteins are conserved RNA-binding proteins that play major roles in RNA metabolism. They function as molecular adaptors, facilitate spliceosome assembly and modulate constitutive and alternative splicing of pre-mRNAs. Pre-mRNAs encoding SR proteins and many other proteins involved in stress responses are extensively alternatively spliced in response to diverse stresses. Hence, it is proposed that stress-induced changes in splice isoforms contribute to the adaptation of plants to stress responses. However, functions of most SR genes and their splice isoforms in stress responses are not known. Lack of easy and robust tools hindered the progress in this area. Emerging technologies such as CRISPR/Cas9 will facilitate studies of SR function by enabling the generation of single and multiple knock-out mutants of SR subfamily members. Moreover, CRISPR/Cas13 allows targeted manipulation of splice isoforms from SR and other genes in a constitutive or tissue-specific manner to evaluate functions of individual splice variants. Identification of the in vivo targets of SR proteins and their splice variants using the recently developed TRIBE (Targets of RNA-binding proteins Identified By Editing) and other methods will help unravel their mode of action and splicing regulatory elements under various conditions. These new approaches are expected to provide significant new insights into the roles of SRs and splice isoforms in plants adaptation to diverse stresses.
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Affiliation(s)
- Mitchell Morton
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Nadia AlTamimi
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Anireddy S N Reddy
- Department of Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Magdy Mahfouz
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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108
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Morrow G, Dreumont N, Bourrelle-Langlois M, Roy V, Tanguay RM. Presence of three mutations in the fumarylacetoacetate hydrolase gene in a patient with atypical symptoms of hereditary tyrosinemia type I. Mol Genet Metab 2019; 127:58-63. [PMID: 30954369 DOI: 10.1016/j.ymgme.2019.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 11/16/2022]
Abstract
Hereditary tyrosinemia type 1 (HT1), the most severe disease of the tyrosine catabolic pathway, is caused by a deficiency of fumarylacetoacetate hydrolase (FAH). More than 90 disease-causing variants have been identified in the fah gene. We investigated the molecular defect in a patient who presented atypical symptoms for the disease. No immunoreactive FAH was found in the liver and RNA analysis by RT-PCR suggested the presence of splicing mutations. Indeed, the patient was revealed to be a compound heterozygote for IVS6-1 g- > t and two new variants, namely p.V259L and p.G398E. Using splicing minigene constructs transfected in HeLa cells, the c.775G > C variant (p.V259L) was shown to affect partially exon 9 splicing thereby allowing the production of some full-length double-mutant FAH transcripts. The p.G398E variant had a major impact on enzyme activity, which was worsened by the p.V259L variant. Surprisingly, the double mutant protein was expressed to similar level as the wild-type protein upon transfection in HeLa cells but was absent in the patient liver extract, suggesting a higher propensity to be degraded in the hepatocellular context.
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Affiliation(s)
- Geneviève Morrow
- Laboratoire de génétique cellulaire et développementale, IBIS and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, 1030 avenue de la Médecine, Université Laval, Québec G1V 0A6, Canada
| | - Natacha Dreumont
- Laboratoire de génétique cellulaire et développementale, IBIS and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, 1030 avenue de la Médecine, Université Laval, Québec G1V 0A6, Canada
| | - Maxime Bourrelle-Langlois
- Laboratoire de génétique cellulaire et développementale, IBIS and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, 1030 avenue de la Médecine, Université Laval, Québec G1V 0A6, Canada
| | - Vincent Roy
- Laboratoire de génétique cellulaire et développementale, IBIS and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, 1030 avenue de la Médecine, Université Laval, Québec G1V 0A6, Canada
| | - Robert M Tanguay
- Laboratoire de génétique cellulaire et développementale, IBIS and PROTEO, Département de biologie moléculaire, biochimie médicale et pathologie, Faculté de médecine, 1030 avenue de la Médecine, Université Laval, Québec G1V 0A6, Canada..
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109
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Xu W, Bao P, Jiang X, Wang H, Qin M, Wang R, Wang T, Yang Y, Lorenzini I, Liao L, Sattler R, Xu J. Reactivation of nonsense-mediated mRNA decay protects against C9orf72 dipeptide-repeat neurotoxicity. Brain 2019; 142:1349-1364. [PMID: 30938419 PMCID: PMC6487333 DOI: 10.1093/brain/awz070] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 01/04/2019] [Accepted: 01/27/2019] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis is a deleterious neurodegenerative disease without effective treatment options. Recent studies have indicated the involvement of the dysregulation of RNA metabolism in the pathogenesis of amyotrophic lateral sclerosis. Among the various RNA regulatory machineries, nonsense-mediated mRNA decay (NMD) is a stress responsive cellular surveillance system that degrades selected mRNA substrates to prevent the translation of defective or harmful proteins. Whether this pathway is affected in neurodegenerative diseases is unclear. Here we report the inhibition of NMD by arginine-rich dipeptide repeats derived from C9orf72 hexanucleotide repeat expansion, the most common cause of familial amyotrophic lateral sclerosis. Bioinformatic analysis of multiple transcriptome profiles revealed significant overlap of upregulated genes in NMD-defective cells with those in the brain tissues, micro-dissected motor neurons, or induced pluripotent stem cell-derived motor neurons specifically from amyotrophic lateral sclerosis patients carrying C9orf72 hexanucleotide repeat expansion, suggesting the suppression of NMD pathway in these patients. Using Drosophila as a model, we have validated that the C9orf72 hexanucleotide repeat expansion products could lead to the accumulation of the NMD substrates and identified arginine-rich dipeptide repeats, including poly glycine-arginine and poly proline-arginine, as the main culprits of NMD inhibition. Furthermore, in human SH-SY5Y neuroblastoma cells and in mouse brains, expression of glycine-arginine with 36 repeats (GR36) was sufficient to cause NMD inhibition. In cells expressing GR36, stress granule accumulation was accompanied by decreased processing body formation, which contributed to the inhibition of NMD. Remarkably, expression of UPF1, a core gene in the NMD pathway, efficiently blocked neurotoxicity caused by arginine-rich dipeptide repeats in both cellular and Drosophila models. Although not as effective as UPF1, expression of another NMD gene UPF2 also ameliorated the degenerative phenotypes in dipeptide repeat-expressing flies, indicating that genetically reactivating the NMD pathway could suppress dipeptide repeat toxicity. Finally, after validating tranilast as an NMD-activating drug, we demonstrated the therapeutic potential of this asthma drug in cellular and Drosophila models of C9orf72 dipeptide repeat neurotoxicity. Therefore, our study has revealed a cellular mechanism whereby arginine-rich C9orf72 dipeptide repeats could inhibit NMD activities by reducing the abundance of processing bodies. Furthermore, our results suggested that activation of the NMD pathway could be a potential therapeutic strategy for amyotrophic lateral sclerosis with defective RNA metabolism.
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Affiliation(s)
- Wangchao Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Puhua Bao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xin Jiang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meiling Qin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ruiqi Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tao Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Ileana Lorenzini
- Barrow Neurological Institute, Dignity Health, St. Joseph’s Hospital and Medical Center, Phoenix AZ, USA
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Rita Sattler
- Barrow Neurological Institute, Dignity Health, St. Joseph’s Hospital and Medical Center, Phoenix AZ, USA
| | - Jin Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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110
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Khan K, Zech M, Morgan AT, Amor DJ, Skorvanek M, Khan TN, Hildebrand MS, Jackson VE, Scerri TS, Coleman M, Rigbye KA, Scheffer IE, Bahlo M, Wagner M, Lam DD, Berutti R, Havránková P, Fečíková A, Strom TM, Han V, Dosekova P, Gdovinova Z, Laccone F, Jameel M, Mooney MR, Baig SM, Jech R, Davis EE, Katsanis N, Winkelmann J. Recessive variants in ZNF142 cause a complex neurodevelopmental disorder with intellectual disability, speech impairment, seizures, and dystonia. Genet Med 2019; 21:2532-2542. [PMID: 31036918 PMCID: PMC6821592 DOI: 10.1038/s41436-019-0523-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/15/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The purpose of this study was to expand the genetic architecture of neurodevelopmental disorders, and to characterize the clinical features of a novel cohort of affected individuals with variants in ZNF142, a C2H2 domain-containing transcription factor. METHODS Four independent research centers used exome sequencing to elucidate the genetic basis of neurodevelopmental phenotypes in four unrelated families. Following bioinformatic filtering, query of control data sets, and secondary variant confirmation, we aggregated findings using an online data sharing platform. We performed in-depth clinical phenotyping in all affected individuals. RESULTS We identified seven affected females in four pedigrees with likely pathogenic variants in ZNF142 that segregate with recessive disease. Affected cases in three families harbor either nonsense or frameshifting likely pathogenic variants predicted to undergo nonsense mediated decay. One additional trio bears ultrarare missense variants in conserved regions of ZNF142 that are predicted to be damaging to protein function. We performed clinical comparisons across our cohort and noted consistent presence of intellectual disability and speech impairment, with variable manifestation of seizures, tremor, and dystonia. CONCLUSION Our aggregate data support a role for ZNF142 in nervous system development and add to the emergent list of zinc finger proteins that contribute to neurocognitive disorders.
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Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA.,Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Angela T Morgan
- Murdoch Children's Research Institute and University of Melbourne Department of Paediatrics, Royal Children's Hospital, Parkville, Australia
| | - David J Amor
- Murdoch Children's Research Institute and University of Melbourne Department of Paediatrics, Royal Children's Hospital, Parkville, Australia
| | - Matej Skorvanek
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic.,Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Tahir N Khan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA.,Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Michael S Hildebrand
- Murdoch Children's Research Institute and University of Melbourne Department of Paediatrics, Royal Children's Hospital, Parkville, Australia.,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Victoria E Jackson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, and University of Melbourne Department of Medical Biology and School of Mathematics and Statistics, Parkville, VIC, Australia
| | - Thomas S Scerri
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, and University of Melbourne Department of Medical Biology and School of Mathematics and Statistics, Parkville, VIC, Australia
| | - Matthew Coleman
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Kristin A Rigbye
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, Australia.,University of Melbourne Department of Paediatrics, Royal Children's Hospital, and Florey and Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, and University of Melbourne Department of Medical Biology and School of Mathematics and Statistics, Parkville, VIC, Australia
| | - Matias Wagner
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Institut für Humangenetik, Technische Universität München, Munich, Germany
| | - Daniel D Lam
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Riccardo Berutti
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, Germany
| | - Petra Havránková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Anna Fečíková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Tim M Strom
- Institut für Humangenetik, Technische Universität München, Munich, Germany.,Institut für Humangenetik, Helmholtz Zentrum München, Munich, Germany
| | - Vladimir Han
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic.,Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Petra Dosekova
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic.,Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Zuzana Gdovinova
- Department of Neurology, P.J. Safarik University, Kosice, Slovak Republic.,Department of Neurology, University Hospital of L. Pasteur, Kosice, Slovak Republic
| | - Franco Laccone
- Institute of Medical Genetics, Medical School of Vienna, Vienna, Austria
| | - Muhammad Jameel
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Marie R Mooney
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Shahid M Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Robert Jech
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, Czech Republic
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA.
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany. .,Institut für Humangenetik, Technische Universität München, Munich, Germany. .,Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany. .,Munich Cluster for Systems Neurology, SyNergy, Munich, Germany.
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111
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Yusa A, Neriya Y, Hashimoto M, Yoshida T, Fujimoto Y, Hosoe N, Keima T, Tokumaru K, Maejima K, Netsu O, Yamaji Y, Namba S. Functional conservation of EXA1 among diverse plant species for the infection by a family of plant viruses. Sci Rep 2019; 9:5958. [PMID: 30976020 PMCID: PMC6459814 DOI: 10.1038/s41598-019-42400-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/20/2019] [Indexed: 12/20/2022] Open
Abstract
Since the propagation of plant viruses depends on various host susceptibility factors, deficiency in them can prevent viral infection in cultivated and model plants. Recently, we identified the susceptibility factor Essential for poteXvirus Accumulation 1 (EXA1) in Arabidopsis thaliana, and revealed that EXA1-mediated resistance was effective against three potexviruses. Although EXA1 homolog genes are found in tomato and rice, little is known about which viruses depend on EXA1 for their infection capability and whether the function of EXA1 homologs in viral infection is conserved across multiple plant species, including crops. To address these questions, we generated knockdown mutants using virus-induced gene silencing in two Solanaceae species, Nicotiana benthamiana and tomato. In N. benthamiana, silencing of an EXA1 homolog significantly compromised the accumulation of potexviruses and a lolavirus, a close relative of potexviruses, whereas transient expression of EXA1 homologs from tomato and rice complemented viral infection. EXA1 dependency for potexviral infection was also conserved in tomato. These results indicate that EXA1 is necessary for effective accumulation of potexviruses and a lolavirus, and that the function of EXA1 in viral infection is conserved among diverse plant species.
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Affiliation(s)
- Akira Yusa
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
- Laboratory of Plant Pathology, School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi, 321-8505, Japan
| | - Masayoshi Hashimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tetsuya Yoshida
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuji Fujimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Naoi Hosoe
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takuya Keima
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kai Tokumaru
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kensaku Maejima
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Osamu Netsu
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
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112
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Elakhdar A, Ushijima T, Fukuda M, Yamashiro N, Kawagoe Y, Kumamaru T. Eukaryotic peptide chain release factor 1 participates in translation termination of specific cysteine-poor prolamines in rice endosperm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:223-231. [PMID: 30824055 DOI: 10.1016/j.plantsci.2018.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Prolamines are alcohol-soluble proteins classified as either cysteine-poor (CysP) or cysteine-rich (CysR) based on whether they can be alcohol-extracted without or with reducing agents, respectively. In rice esp1 mutants, various CysP prolamines exhibit both reduced and normal amounts of isoelectric focusing bands, indicating that the mutation affects only certain prolamine classes. To examine the genetic regulation of CysP prolamine synthesis and accumulation, we constructed a high-resolution genetic linkage map of ESP1. The ESP1 gene was mapped to within a 20 kb region on rice chromosome 7. Sequencing analysis of annotated genes in this region revealed a single-nucleotide polymorphism within eukaryotic peptide chain release factor (eRF1), which participates in stop-codon recognition and nascent-polypeptide release from ribosomes during translation. A subsequent complementation test revealed that ESP1 encodes eRF1. We also identified UAA as the stop codon of CysP prolamines with reduced concentration in esp1 mutants. Recognition assays and microarray analysis confirmed that ESP1/eRF1 recognizes UAA/UAG, but not UGA. Our results provide convincing evidence that ESP1/eRF1 participates in the translation termination of CysP prolamines during seed development.
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Affiliation(s)
- Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan; Field Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Tomokazu Ushijima
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Masako Fukuda
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Noriko Yamashiro
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - Yasushi Kawagoe
- Division of Plant Sciences, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Toshihiro Kumamaru
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan.
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Nakaminami K, Seki M. RNA Regulation in Plant Cold Stress Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1081:23-44. [PMID: 30288702 DOI: 10.1007/978-981-13-1244-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In addition to plants, all organisms react to environmental stimuli via the perception of signals and subsequently respond through alterations of gene expression. However, genes/mRNAs are usually not the functional unit themselves, and instead, resultant protein products with individual functions result in various acquired phenotypes. In order to fully characterize the adaptive responses of plants to environmental stimuli, it is essential to determine the level of proteins, in addition to the regulation of mRNA expression. This regulatory step, which is referred to as "mRNA posttranscriptional regulation," occurs subsequent to mRNA transcription and prior to translation. Although these RNA regulatory mechanisms have been well-studied in many organisms, including plants, it is not fully understood how plants respond to environmental stimuli, such as cold stress, via these RNA regulations.A recent study described several RNA regulatory factors in relation to environmental stress responses, including plant cold stress tolerance. In this chapter, the functions of RNA regulatory factors and comprehensive analyses related to the RNA regulations involved in cold stress response are summarized, such as mRNA maturation, including capping, splicing, polyadenylation of mRNA, and the quality control system of mRNA; mRNA degradation, including the decapping step; and mRNA stabilization. In addition, the putative roles of messenger ribonucleoprotein (mRNP) granules, such as processing bodies (PBs) and stress granules (SGs), which are cytoplasmic particles, are described in relation to RNA regulations under stress conditions. These RNA regulatory systems are important for adjusting or fine-tuning and determining the final levels of mRNAs and proteins in order to adapt or respond to environmental stresses. Collectively, these new areas of study revealed that plants possess precise novel regulatory mechanisms which specifically function in the response to cold stress.
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Affiliation(s)
- Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama, Japan
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Papageorgiou I, Loken MR, Brodersen LE, Gbadamosi M, Uy GL, Meshinchi S, Lamba JK. CCGG deletion (rs201074739) in CD33 results in premature termination codon and complete loss of CD33 expression: another key variant with potential impact on response to CD33-directed agents. Leuk Lymphoma 2019; 60:2287-2290. [PMID: 30721105 DOI: 10.1080/10428194.2019.1569232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Ioannis Papageorgiou
- Department of Pharmacotherapy and Translational Research, University of Florida , Gainesville , FL , USA.,Center for Pharmacogenetics, College of Pharmacy, University of Florida , Gainesville , FL , USA
| | | | | | - Mohammed Gbadamosi
- Department of Pharmacotherapy and Translational Research, University of Florida , Gainesville , FL , USA.,Center for Pharmacogenetics, College of Pharmacy, University of Florida , Gainesville , FL , USA
| | - Geoffrey L Uy
- Division of Oncology, Washington University , St Louis , MI , USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Center , Seattle , WA , USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy and Translational Research, University of Florida , Gainesville , FL , USA.,Center for Pharmacogenetics, College of Pharmacy, University of Florida , Gainesville , FL , USA
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115
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Karousis ED, Mühlemann O. Nonsense-Mediated mRNA Decay Begins Where Translation Ends. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032862. [PMID: 29891560 DOI: 10.1101/cshperspect.a032862] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is arguably the best-studied eukaryotic messenger RNA (mRNA) surveillance pathway, yet fundamental questions concerning the molecular mechanism of target RNA selection remain unsolved. Besides degrading defective mRNAs harboring premature termination codons (PTCs), NMD also targets many mRNAs encoding functional full-length proteins. Thus, NMD impacts on a cell's transcriptome and is implicated in a range of biological processes that affect a broad spectrum of cellular homeostasis. Here, we focus on the steps involved in the recognition of NMD targets and the activation of NMD. We summarize the accumulating evidence that tightly links NMD to translation termination and we further discuss the recruitment and activation of the mRNA degradation machinery and the regulation of this complex series of events. Finally, we review emerging ideas concerning the mechanistic details of NMD activation and the potential role of NMD as a general surveyor of translation efficacy.
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Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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Abstract
Melanocyte development is orchestrated by a complex interconnecting regulatory network of genes and synergistic interactions. Piebaldism and Waardenburg syndrome are neurocristopathies that arise from mutations in genes involved in this complex network. Our understanding of melanocyte development, Piebaldism, and Waardenburg syndrome has improved dramatically over the past decade. The diagnosis and classification of Waardenburg syndrome, first proposed in 1992 and based on phenotype, have expanded over the past three decades to include genotype. This review focuses on the current understanding of human melanocyte development and the evaluation and management of Piebaldism and Waardenburg syndrome. Management is often challenging and requires a multidisciplinary approach.
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117
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Ochkasova AS, Meschaninova MI, Venyaminova AG, Ivanov AV, Graifer DM, Karpova GG. The human ribosome can interact with the abasic site in mRNA via a specific peptide of the uS3 protein located near the mRNA entry channel. Biochimie 2018; 158:117-125. [PMID: 30594661 DOI: 10.1016/j.biochi.2018.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/25/2018] [Indexed: 12/12/2022]
Abstract
The small subunit ribosomal protein uS3 is a critically important player in the ribosome-mRNA interactions during translation and has numerous functions not directly related to protein synthesis in eukaryotes. A peculiar feature of the human uS3 protein is the ability of its fragment 55-64 exposed on the 40S subunit surface near the mRNA entry channel to form cross-links with 3'-terminal dialdehyde derivatives of various unstructured RNAs and with abasic sites in single-stranded DNAs. Here we showed that the ability of the above uS3 fragment to cross-link to abasic sites in DNAs is inherent only in mature cytoplasmic 40S subunits, but not nuclear pre-40S particles, which implies that it may be relevant to the ribosome-mRNA interplay. To clarify this issue, we investigated interactions of human ribosomes with synthetic mRNA analogues bearing an abasic site protected by a photocleavable group at the 3'-termini. We found that these mRNA analogues can form specific complexes with 80S ribosomes and 40S subunits, where the undamaged upstream part of the analogue is fixed in the mRNA binding channel by interaction with the P-site tRNA, and the downstream part located outside the ribosome is cross-linked to the uS3 fragment 55-64. The yield of cross-links of the mRNA analogues was rather high when their undamaged parts were bound to the mRNA channel prior to deprotection of the abasic site enabling its covalent attachment to the 40S subunit via the uS3 protein, but not vice versa. Based on our findings, one can assume that abasic sites, which can occur in mRNAs due to oxidative stress and ageing, are able to interact directly with the uS3 fragment exposed on the 40S subunit surface near the mRNA entry channel during translation. Consequently, the 40S subunit can be considered as a potential mRNA quality controller.
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Affiliation(s)
- Anastasia S Ochkasova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Aliya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Anton V Ivanov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
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118
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Fyfe JC, Hemker SL, Frampton A, Raj K, Nagy PL, Gibbon KJ, Giger U. Inherited selective cobalamin malabsorption in Komondor dogs associated with a CUBN splice site variant. BMC Vet Res 2018; 14:418. [PMID: 30591068 PMCID: PMC6309081 DOI: 10.1186/s12917-018-1752-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/19/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Three Komondor dogs in a small family and 3 sporadic cases exhibited a constellation of signs that included juvenile-onset of failure-to-thrive, inappetence, vomiting and/or diarrhea, and weakness. In each we documented dyshematopoiesis, increased anion gap, methylmalonic acidemia/-uria, and serum cobalamin deficiency. Urine protein electrophoresis demonstrated excretion of cubam ligands. All clinical signs and metabolic abnormalities, except proteinuria, were reversed by regular parenteral cobalamin administration. The pattern of occurrence and findings in the disorder suggested an autosomal recessive inheritance of cobalamin malabsorption with proteinuria, a condition in humans called Imerslund-Gräsbeck syndrome. The purpose of this study was to determine the molecular cause of this disorder in Komondors. RESULTS Whole genome sequencing of two affected Komondor dogs of unknown relatedness and one parent and a clinically-normal littermate of an affected dog revealed a pathogenic single-base change in the CUBN intron 55 splice donor consensus sequence (NM_001003148.1: c.8746 + 1G > A) that was homozygous in affected dogs and heterozygous in the unaffected parents. Alleles of the variant co-segregated with alleles of the disease locus in the entire family and all more distantly-related sporadic cases. A population study using a simple allele-specific DNA test indicated mutant allele frequencies of 8.3 and 4.5% among North American and Hungarian Komondors, respectively. CONCLUSIONS DNA testing can be used diagnostically in Komondors when clinical signs are suggestive of cobalamin deficiency or to inform Komondor breeders prospectively and prevent occurrence of future affected dogs. This represents the third cubilin variant causing inherited selective cobalamin malabsorption in a large animal ortholog of human Imerslund-Gräsbeck syndrome.
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Affiliation(s)
- John C. Fyfe
- Laboratory of Comparative Medical Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI 48824 USA
- Department of Microbiology & Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI 48824 USA
| | - Shelby L. Hemker
- Laboratory of Comparative Medical Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI 48824 USA
- Present address: Department of Pediatrics, Division of Nephrology, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, 4401 Penn Ave, Pittsburgh, PA 15224 USA
| | - Alycia Frampton
- Section of Medical Genetics, University of Pennsylvania, 3900 Delancey Street, Philadelphia, PA 19104-6010 USA
| | - Karthik Raj
- Section of Medical Genetics, University of Pennsylvania, 3900 Delancey Street, Philadelphia, PA 19104-6010 USA
| | - Peter L. Nagy
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University - College of Physicians & Surgeons, 630 West 168th Street, New York, NY 10032 USA
- Present address: MNG Laboratories™, 5424 Glenridge Drive NE, Atlanta, GA 30342 USA
| | - Kristi J. Gibbon
- Oregon Veterinary Referral Associates, 444 B Street, Springfield, OR 97477 USA
- Cottonwood Heights, USA
| | - Urs Giger
- Section of Medical Genetics, University of Pennsylvania, 3900 Delancey Street, Philadelphia, PA 19104-6010 USA
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119
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Ganesan R, Leszyk J, Jacobson A. Selective profiling of ribosomes associated with yeast Upf proteins. Methods 2018; 155:58-67. [PMID: 30593864 DOI: 10.1016/j.ymeth.2018.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/11/2018] [Accepted: 12/21/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomes associated with nonsense-mediated decay factors Upf1, Upf2, or Upf3 were purified by immunoprecipitation, and enrichment and stoichiometry of Upf factors and ribosomal proteins were analyzed by western blot and mass spectrometry. Using a small RNA library preparation protocol that eliminates in-gel RNA and cDNA size selection and incorporates four random nucleotides on each side of the ribosome-protected RNA fragment allowed recovery, detection, and analysis of all size classes of protected fragments from a sample simultaneously.
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Affiliation(s)
- Robin Ganesan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655-0122, United States
| | - John Leszyk
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655-0122, United States
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01655-0122, United States.
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120
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Zech M, Lam DD, Weber S, Berutti R, Poláková K, Havránková P, Fečíková A, Strom TM, Růžička E, Jech R, Winkelmann J. A unique de novo gain-of-function variant in CAMK4 associated with intellectual disability and hyperkinetic movement disorder. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003293. [PMID: 30262571 PMCID: PMC6318768 DOI: 10.1101/mcs.a003293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/04/2018] [Indexed: 01/12/2023] Open
Abstract
Calcium/calmodulin-dependent protein kinases (CaMKs) are key mediators of calcium signaling and underpin neuronal health. Although widely studied, the contribution of CaMKs to Mendelian disease is rather enigmatic. Here, we describe an unusual neurodevelopmental phenotype, characterized by milestone delay, intellectual disability, autism, ataxia, and mixed hyperkinetic movement disorder including severe generalized dystonia, in a proband who remained etiologically undiagnosed despite exhaustive testing. We performed trio whole-exome sequencing to identify a de novo essential splice-site variant (c.981+1G>A) in CAMK4, encoding CaMKIV. Through in silico evaluation and cDNA analyses, we demonstrated that c.981+1G>A alters CAMK4 pre-mRNA processing and results in a stable mRNA transcript containing a 77-nt out-of-frame deletion and a premature termination codon within the last exon. The expected protein, p.Lys303Serfs*28, exhibits selective loss of the carboxy-terminal regulatory domain of CaMKIV and bears striking structural resemblance to previously reported synthetic mutants that confer constitutive CaMKIV activity. Biochemical studies in proband-derived cells confirmed an activating effect of c.981+1G>A and indicated that variant-induced excessive CaMKIV signaling is sensitive to pharmacological manipulation. Additionally, we found that variants predicted to cause selective depletion of CaMKIV's regulatory domain are unobserved in diverse catalogs of human variation, thus revealing that c.981+1G>A is a unique molecular event. We propose that our proband's phenotype is explainable by a dominant CAMK4 splice-disrupting mutation that acts through a gain-of-function mechanism. Our findings highlight the importance of CAMK4 in human neurodevelopment, provide a foundation for future clinical research of CAMK4, and suggest the CaMKIV signaling pathway as a potential drug target in neurological disease.
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Affiliation(s)
- Michael Zech
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany.,Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Daniel D Lam
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany
| | - Sandrina Weber
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany
| | - Riccardo Berutti
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, 85764, Germany
| | - Kamila Poláková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Petra Havránková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Anna Fečíková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Tim M Strom
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, 85764, Germany.,Institut für Humangenetik, Technische Universität München, Munich, 81675, Germany
| | - Evžen Růžička
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Robert Jech
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany.,Institut für Humangenetik, Technische Universität München, Munich, 81675, Germany.,Lehrstuhl für Neurogenetik, Technische Universität München, Munich, 80333, Germany.,Munich Cluster for Systems Neurology, SyNergy, Munich, 81377, Germany
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121
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High-Resolution Profiling of NMD Targets in Yeast. Methods Enzymol 2018. [PMID: 30502940 DOI: 10.1016/bs.mie.2018.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Contemporary high-throughput sequencing methods, notably RNA-Seq, permit the systematic identification and characterization of transcripts whose levels change significantly in response to altered biological states. We have described methods for the application of this methodology to a definition of the transcripts regulated by the NMD pathway in the yeast Saccharomyces cerevisiae. In short, we outline methods for growing cells of wild-type or NMD-deficient yeast, isolating RNA from the different strains, depleting rRNA from each sample, preparing and sequencing the respective RNA-Seq libraries, and employing multiple software packages to characterize the resulting sequence reads meaningfully. Our experimental approach has identified approximately 900 transcripts that are commonly upregulated when yeast NMD is inactivated (Celik, Baker, He, & Jacobson, 2017).
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122
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Zhou Y, Fujikura K, Mkrtchian S, Lauschke VM. Computational Methods for the Pharmacogenetic Interpretation of Next Generation Sequencing Data. Front Pharmacol 2018; 9:1437. [PMID: 30564131 PMCID: PMC6288784 DOI: 10.3389/fphar.2018.01437] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
Up to half of all patients do not respond to pharmacological treatment as intended. A substantial fraction of these inter-individual differences is due to heritable factors and a growing number of associations between genetic variations and drug response phenotypes have been identified. Importantly, the rapid progress in Next Generation Sequencing technologies in recent years unveiled the true complexity of the genetic landscape in pharmacogenes with tens of thousands of rare genetic variants. As each individual was found to harbor numerous such rare variants they are anticipated to be important contributors to the genetically encoded inter-individual variability in drug effects. The fundamental challenge however is their functional interpretation due to the sheer scale of the problem that renders systematic experimental characterization of these variants currently unfeasible. Here, we review concepts and important progress in the development of computational prediction methods that allow to evaluate the effect of amino acid sequence alterations in drug metabolizing enzymes and transporters. In addition, we discuss recent advances in the interpretation of functional effects of non-coding variants, such as variations in splice sites, regulatory regions and miRNA binding sites. We anticipate that these methodologies will provide a useful toolkit to facilitate the integration of the vast extent of rare genetic variability into drug response predictions in a precision medicine framework.
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Affiliation(s)
- Yitian Zhou
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Kohei Fujikura
- Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Souren Mkrtchian
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M. Lauschke
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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123
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Gong P, Li J, He C. Exon junction complex (EJC) core genes play multiple developmental roles in Physalis floridana. PLANT MOLECULAR BIOLOGY 2018; 98:545-563. [PMID: 30426309 PMCID: PMC6280879 DOI: 10.1007/s11103-018-0795-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Molecular and functional characterization of four gene families of the Physalis exon junction complex (EJC) core improved our understanding of the evolution and function of EJC core genes in plants. The exon junction complex (EJC) plays significant roles in posttranscriptional regulation of genes in eukaryotes. However, its developmental roles in plants are poorly known. We characterized four EJC core genes from Physalis floridana that were named PFMAGO, PFY14, PFeIF4AIII and PFBTZ. They shared a similar phylogenetic topology and were expressed in all examined organs. PFMAGO, PFY14 and PFeIF4AIII were localized in both the nucleus and cytoplasm while PFBTZ was mainly localized in the cytoplasm. No protein homodimerization was observed, but they could form heterodimers excluding the PFY14-PFBTZ heterodimerization. Virus-induced gene silencing (VIGS) of PFMAGO or PFY14 aborted pollen development and resulted in low plant survival due to a leaf-blight-like phenotype in the shoot apex. Carpel functionality was also impaired in the PFY14 knockdowns, whereas pollen maturation was uniquely affected in PFBTZ-VIGS plants. Once PFeIF4AIII was strongly downregulated, plant survival was reduced via a decomposing root collar after flowering and Chinese lantern morphology was distorted. The expression of Physalis orthologous genes in the DYT1-TDF1-AMS-bHLH91 regulatory cascade that is associated with pollen maturation was significantly downregulated in PFMAGO-, PFY14- and PFBTZ-VIGS flowers. Intron-retention in the transcripts of P. floridana dysfunctional tapetum1 (PFDYT1) occurred in these mutated flowers. Additionally, the expression level of WRKY genes in defense-related pathways in the shoot apex of PFMAGO- or PFY14-VIGS plants and in the root collar of PFeIF4AIII-VIGS plants was significantly downregulated. Taken together, the Physalis EJC core genes play multiple roles including a conserved role in male fertility and newly discovered roles in Chinese lantern development, carpel functionality and defense-related processes. These data increase our understanding of the evolution and functions of EJC core genes in plants.
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Affiliation(s)
- Pichang Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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124
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May JP, Yuan X, Sawicki E, Simon AE. RNA virus evasion of nonsense-mediated decay. PLoS Pathog 2018; 14:e1007459. [PMID: 30452463 PMCID: PMC6277124 DOI: 10.1371/journal.ppat.1007459] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/03/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022] Open
Abstract
Nonsense-mediated decay (NMD) is a host RNA control pathway that removes aberrant transcripts with long 3' untranslated regions (UTRs) due to premature termination codons (PTCs) that arise through mutation or defective splicing. To maximize coding potential, RNA viruses often contain internally located stop codons that should also be prime targets for NMD. Using an agroinfiltration-based NMD assay in Nicotiana benthamiana, we identified two segments conferring NMD-resistance in the carmovirus Turnip crinkle virus (TCV) genome. The ribosome readthrough structure just downstream of the TCV p28 termination codon stabilized an NMD-sensitive reporter as did a frameshifting element from umbravirus Pea enation mosaic virus. In addition, a 51-nt unstructured region (USR) at the beginning of the TCV 3' UTR increased NMD-resistance 3-fold when inserted into an unrelated NMD-sensitive 3' UTR. Several additional carmovirus 3' UTRs also conferred varying levels of NMD resistance depending on the construct despite no sequence similarity in the analogous region. Instead, these regions displayed a marked lack of RNA structure immediately following the NMD-targeted stop codon. NMD-resistance was only slightly reduced by conversion of 19 pyrimidines in the USR to purines, but resistance was abolished when a 2-nt mutation was introduced downstream of the USR that substantially increased the secondary structure in the USR through formation of a stable hairpin. The same 2-nt mutation also enhanced the NMD susceptibility of a subgenomic RNA expressed independently of the genomic RNA. The conserved lack of RNA structure among most carmoviruses at the 5' end of their 3' UTR could serve to enhance subgenomic RNA stability, which would increase expression of the encoded capsid protein that also functions as the RNA silencing suppressor. These results demonstrate that the TCV genome has features that are inherently NMD-resistant and these strategies could be widespread among RNA viruses and NMD-resistant host mRNAs with long 3' UTRs.
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Affiliation(s)
- Jared P. May
- Department of Cell Biology and Molecular Genetics, University of Maryland–College Park, College Park, Maryland, United States of America
| | - Xuefeng Yuan
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong Province, P.R.China
| | - Erika Sawicki
- Department of Cell Biology and Molecular Genetics, University of Maryland–College Park, College Park, Maryland, United States of America
| | - Anne E. Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland–College Park, College Park, Maryland, United States of America
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125
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Brambilla M, Martani F, Bertacchi S, Vitangeli I, Branduardi P. The Saccharomyces cerevisiae
poly (A) binding protein (Pab1): Master regulator of mRNA metabolism and cell physiology. Yeast 2018; 36:23-34. [DOI: 10.1002/yea.3347] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Affiliation(s)
- Marco Brambilla
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Francesca Martani
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Stefano Bertacchi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Ilaria Vitangeli
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 20126 Milan Italy
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126
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Caciotti A, Tonin R, Mort M, Cooper DN, Gasperini S, Rigoldi M, Parini R, Deodato F, Taurisano R, Sibilio M, Parenti G, Guerrini R, Morrone A. Mis-splicing of the GALNS gene resulting from deep intronic mutations as a cause of Morquio a disease. BMC MEDICAL GENETICS 2018; 19:183. [PMID: 30305043 PMCID: PMC6180571 DOI: 10.1186/s12881-018-0694-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/24/2018] [Indexed: 11/30/2022]
Abstract
Background Mucopolysaccharidosis-IVA (Morquio A disease) is a lysosomal disorder in which the abnormal accumulation of keratan sulfate and chondroitin-6-sulfate is consequent to mutations in the galactosamine-6-sulfatase (GALNS) gene. Since standard DNA sequencing analysis fails to detect about 16% of GALNS mutant alleles, gross DNA rearrangement screening and uniparental disomy evaluation are required to complete the molecular diagnosis. Despite this, the second pathogenic GALNS allele generally remains unidentified in ~ 5% of Morquio-A disease patients. Methods In an attempt to bridge the residual gap between clinical and molecular diagnosis, we performed an mRNA-based evaluation of three Morquio-A disease patients in whom the second mutant GALNS allele had not been identified. We also performed sequence analysis of the entire GALNS gene in two patients. Results Different aberrant GALNS mRNA transcripts were characterized in each patient. Analysis of these transcripts then allowed the identification, in one patient, of a disease-causing deep intronic GALNS mutation. The aberrant mRNA products identified in the other two individuals resulted in partial exon loss. Despite sequencing the entire GALNS gene region in these patients, the identity of a single underlying pathological lesion could not be unequivocally determined. We postulate that a combination of multiple variants, acting in cis, may synergise in terms of their impact on the splicing machinery. Conclusions We have identified GALNS variants located within deep intronic regions that have the potential to impact splicing. These findings have prompted us to incorporate mRNA analysis into our diagnostic flow procedure for the molecular analysis of Morquio A disease. Electronic supplementary material The online version of this article (10.1186/s12881-018-0694-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Caciotti
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, Viale Pieraccini n. 24, 50139, Florence, Italy
| | - Rodolfo Tonin
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, Viale Pieraccini n. 24, 50139, Florence, Italy.,Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, University of Florence, Florence, Italy
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Miriam Rigoldi
- Metabolic Unit, San Gerardo Hospital, Monza, Milan, Italy
| | | | - Federica Deodato
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Roberta Taurisano
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michelina Sibilio
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University of Naples, Naples, Italy
| | - Giancarlo Parenti
- Department of Translational Medical Sciences, Section of Pediatrics, Federico II University of Naples, Naples, Italy
| | - Renzo Guerrini
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, Viale Pieraccini n. 24, 50139, Florence, Italy.,Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, University of Florence, Florence, Italy
| | - Amelia Morrone
- Molecular and Cell Biology Laboratory of Neurometabolic Diseases, Paediatric Neurology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, Viale Pieraccini n. 24, 50139, Florence, Italy. .,Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino, University of Florence, Florence, Italy.
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127
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Karamyshev AL, Karamysheva ZN. Lost in Translation: Ribosome-Associated mRNA and Protein Quality Controls. Front Genet 2018; 9:431. [PMID: 30337940 PMCID: PMC6180196 DOI: 10.3389/fgene.2018.00431] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 12/15/2022] Open
Abstract
Aberrant, misfolded, and mislocalized proteins are often toxic to cells and result in many human diseases. All proteins and their mRNA templates are subject to quality control. There are several distinct mechanisms that control the quality of mRNAs and proteins during translation at the ribosome. mRNA quality control systems, nonsense-mediated decay, non-stop decay, and no-go decay detect premature stop codons, the absence of a natural stop codon, and stalled ribosomes in translation, respectively, and degrade their mRNAs. Defective truncated polypeptide nascent chains generated from faulty mRNAs are degraded by ribosome-associated protein quality control pathways. Regulation of aberrant protein production, a novel pathway, senses aberrant proteins by monitoring the status of nascent chain interactions during translation and triggers degradation of their mRNA. Here, we review the current progress in understanding of the molecular mechanisms of mRNA and protein quality controls at the ribosome during translation.
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Affiliation(s)
- Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Zemfira N Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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128
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The genetic architecture of aniridia and Gillespie syndrome. Hum Genet 2018; 138:881-898. [PMID: 30242502 PMCID: PMC6710220 DOI: 10.1007/s00439-018-1934-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022]
Abstract
Absence of part or all of the iris, aniridia, is a feature of several genetically distinct conditions. This review focuses on iris development and then the clinical features and molecular genetics of these iris malformations. Classical aniridia, a panocular eye malformation including foveal hypoplasia, is the archetypal phenotype associated with heterozygous PAX6 loss-of-function mutations. Since this was identified in 1991, many genetic mechanisms of PAX6 inactivation have been elucidated, the commonest alleles being intragenic mutations causing premature stop codons, followed by those causing C-terminal extensions. Rarely, aniridia cases are associated with FOXC1, PITX2 and/or their regulatory regions. Aniridia can also occur as a component of many severe global eye malformations. Gillespie syndrome—a triad of partial aniridia, non-progressive cerebellar ataxia and intellectual disability—is phenotypically and genotypically distinct from classical aniridia. The causative gene has recently been identified as ITPR1. The same characteristic Gillespie syndrome-like iris, with aplasia of the pupillary sphincter and a scalloped margin, is seen in ACTA2-related multisystemic smooth muscle dysfunction syndrome. WAGR syndrome (Wilms tumour, aniridia, genitourinary anomalies and mental retardation/intellectual disability), is caused by contiguous deletion of PAX6 and WT1 on chromosome 11p. Deletions encompassing BDNF have been causally implicated in the obesity and intellectual disability associated with the condition. Lastly, we outline a genetic investigation strategy for aniridia in light of recent developments, suggesting an approach based principally on chromosomal array and gene panel testing. This strategy aims to test all known aniridia loci—including the rarer, life-limiting causes—whilst remaining simple and practical.
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129
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Selenium-Related Transcriptional Regulation of Gene Expression. Int J Mol Sci 2018; 19:ijms19092665. [PMID: 30205557 PMCID: PMC6163693 DOI: 10.3390/ijms19092665] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
The selenium content of the body is known to control the expression levels of numerous genes, both so-called selenoproteins and non-selenoproteins. Selenium is a trace element essential to human health, and its deficiency is related to, for instance, cardiovascular and myodegenerative diseases, infertility and osteochondropathy called Kashin–Beck disease. It is incorporated as selenocysteine to the selenoproteins, which protect against reactive oxygen and nitrogen species. They also participate in the activation of the thyroid hormone, and play a role in immune system functioning. The synthesis and incorporation of selenocysteine occurs via a special mechanism, which differs from the one used for standard amino acids. The codon for selenocysteine is a regular in-frame stop codon, which can be passed by a specific complex machinery participating in translation elongation and termination. This includes a presence of selenocysteine insertion sequence (SECIS) in the 3′-untranslated part of the selenoprotein mRNAs. Nonsense-mediated decay is involved in the regulation of the selenoprotein mRNA levels, but other mechanisms are also possible. Recent transcriptional analyses of messenger RNAs, microRNAs and long non-coding RNAs combined with proteomic data of samples from Keshan and Kashin–Beck disease patients have identified new possible cellular pathways related to transcriptional regulation by selenium.
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130
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Ricci F, Candelori A, Brandi A, Alimenti C, Luporini P, Vallesi A. The Sub-Chromosomic Macronuclear Pheromone Genes of the Ciliate Euplotes raikovi: Comparative Structural Analysis and Insights into the Mechanism of Expression. J Eukaryot Microbiol 2018; 66:376-384. [PMID: 30076754 DOI: 10.1111/jeu.12677] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/16/2018] [Accepted: 07/25/2018] [Indexed: 12/23/2022]
Abstract
In Euplotes raikovi, we have determined the full-length sequences of a family of macronuclear genes that are the transcriptionally active versions of codominant alleles inherited at the mating-type (mat) locus of the micronuclear genome, and encode cell type-distinctive signaling pheromones. These genes include a 225-231-bp coding region flanked by a conserved 544-bp 5'-leader region and a more variable 3'-trailer region. Two transcription initiation start sites and two polyadenylation sites associated with nonconventional signals cooperate with a splicing phenomenon of a 326-bp intron residing in the 5'-leader region in the generation of multiple transcripts from the same gene. In two of them, the synthesis of functional products depends on the reassignment to a sense codon, or readthrough of a strictly conserved leaky UAG stop codon. That this reassignment may take place is suggested by the position this codon occupies in the transcripts, close to the transcript extremity and far from the poly(A) tail. In such a case, one product is a 69-amino acid protein in search of function and the second product is a 126-amino acid protein that represents a membrane-bound pheromone isoform candidate to function as a cell type-specific binding site (receptor) of the soluble pheromones.
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Affiliation(s)
- Francesca Ricci
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Annalisa Candelori
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Anna Brandi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Claudio Alimenti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Pierangelo Luporini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
| | - Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), 62032, Italy
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131
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Collaboration of tRNA modifications and elongation factor eEF1A in decoding and nonsense suppression. Sci Rep 2018; 8:12749. [PMID: 30143741 PMCID: PMC6109124 DOI: 10.1038/s41598-018-31158-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/13/2018] [Indexed: 01/27/2023] Open
Abstract
Transfer RNA (tRNA) from all domains of life contains multiple modified nucleosides, the functions of which remain incompletely understood. Genetic interactions between tRNA modification genes in Saccharomyces cerevisiae suggest that different tRNA modifications collaborate to maintain translational efficiency. Here we characterize such collaborative functions in the ochre suppressor tRNA SUP4. We quantified ochre read-through efficiency in mutants lacking either of the 7 known modifications in the extended anticodon stem loop (G26-C48). Absence of U34, U35, A37, U47 and C48 modifications partially impaired SUP4 function. We systematically combined modification defects and scored additive or synergistic negative effects on SUP4 performance. Our data reveal different degrees of functional redundancy between specific modifications, the strongest of which was demonstrated for those occurring at positions U34 and A37. SUP4 activity in the absence of critical modifications, however, can be rescued in a gene dosage dependent fashion by TEF1 which encodes elongation factor eEF1A required for tRNA delivery to the ribosome. Strikingly, the rescue ability of higher-than-normal eEF1A levels extends to tRNA modification defects in natural non-suppressor tRNAs suggesting that elevated eEF1A abundance can partially compensate for functional defects induced by loss of tRNA modifications.
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132
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Imagawa E, Albuquerque EVA, Isidor B, Mitsuhashi S, Mizuguchi T, Miyatake S, Takata A, Miyake N, Boguszewski MCS, Boguszewski CL, Lerario AM, Funari MA, Jorge AAL, Matsumoto N. Novel SUZ12 mutations in Weaver-like syndrome. Clin Genet 2018; 94:461-466. [PMID: 30019515 DOI: 10.1111/cge.13415] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 01/12/2023]
Abstract
SUZ12 is a core component of polycomb repressive complex 2 (PRC2) along with EZH2 and EED. Recently, germline mutations in the SUZ12, EZH2 and EED genes have been reported in Weaver syndrome (WS) or Weaver-like syndrome, suggesting a functional link between PRC2 deficits and WS. However, only one case of a SUZ12 mutation presenting with Weaver-like syndrome has been reported. Here, we report a missense and a frameshift mutation in SUZ12 (c.1797A>C; p.Gln599His and c.844_845del; p.Ala282Glnfs*7), both of which are novel, in two individuals. Their clinical features included postnatal overgrowth, increased bifrontal diameter, large ears, round face, horizontal chin crease and skeletal anomalies, but did not fulfill the WS diagnostic criteria. These data provide strong evidence that SUZ12 mutations cause Weaver-like syndrome.
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Affiliation(s)
- Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Edoarda V A Albuquerque
- Unidade de Endocrinologia Genetica (LIM25), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Hôtel-Dieu, Nantes, France
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | - César L Boguszewski
- Department of Internal Medicine, Endocrine Division (SEMPR), Federal University of Paraná, Curitiba, Brazil
| | - Antonio M Lerario
- Unidade de Endocrinologia Genetica (LIM25), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil.,Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan
| | - Mariana A Funari
- Laboratorio de Hormonios e Genetica Molecular (LIM/42), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genetica (LIM25), Hospital das Clinicas da Faculdade de Medicina, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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133
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Coban-Akdemir Z, White JJ, Song X, Jhangiani SN, Fatih JM, Gambin T, Bayram Y, Chinn IK, Karaca E, Punetha J, Poli C, Boerwinkle E, Shaw CA, Orange JS, Gibbs RA, Lappalainen T, Lupski JR, Carvalho CM, Carvalho CMB. Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles. Am J Hum Genet 2018; 103:171-187. [PMID: 30032986 DOI: 10.1016/j.ajhg.2018.06.009] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/14/2018] [Indexed: 12/14/2022] Open
Abstract
Premature termination codon (PTC)-bearing transcripts are often degraded by nonsense-mediated decay (NMD) resulting in loss-of-function (LoF) alleles. However, not all PTCs result in LoF mutations, i.e., some such transcripts escape NMD and are translated to truncated peptide products that result in disease due to gain-of-function (GoF) effects. Since the location of the PTC is a major factor determining transcript fate, we hypothesized that depletion of protein-truncating variants (PTVs) within the gene region predicted to escape NMD in control databases could provide a rank for genic susceptibility for disease through GoF versus LoF. We developed an NMD escape intolerance score to rank genes based on the depletion of PTVs that would render them able to escape NMD using the Atherosclerosis Risk in Communities Study (ARIC) and the Exome Aggregation Consortium (ExAC) control databases, which was further used to screen the Baylor-Center for Mendelian Genomics disease database. This analysis revealed 1,996 genes significantly depleted for PTVs that are predicted to escape from NMD, i.e., PTVesc; further studies provided evidence that revealed a subset as candidate genes underlying Mendelian phenotypes. Importantly, these genes have characteristically low pLI scores, which can cause them to be overlooked as candidates for dominant diseases. Collectively, we demonstrate that this NMD escape intolerance score is an effective and efficient tool for gene discovery in Mendelian diseases due to production of truncated or altered proteins. More importantly, we provide a complementary analytical tool to aid identification of genes associated with dominant traits through a mechanism distinct from LoF.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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134
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Abstract
During protein synthesis, ribosomes encounter many roadblocks, the outcomes of which are largely determined by substrate availability, amino acid features and reaction kinetics. Prolonged ribosome stalling is likely to be resolved by ribosome rescue or quality control pathways, whereas shorter stalling is likely to be resolved by ongoing productive translation. How ribosome function is affected by such hindrances can therefore have a profound impact on the translational output (yield) of a particular mRNA. In this Review, we focus on these roadblocks and the resumption of normal translation elongation rather than on alternative fates wherein the stalled ribosome triggers degradation of the mRNA and the incomplete protein product. We discuss the fundamental stages of the translation process in eukaryotes, from elongation through ribosome recycling, with particular attention to recent discoveries of the complexity of the genetic code and regulatory elements that control gene expression, including ribosome stalling during elongation, the role of mRNA context in translation termination and mechanisms of ribosome rescue that resemble recycling.
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Affiliation(s)
- Anthony P Schuller
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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135
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Zhang XO, Fu Y, Mou H, Xue W, Weng Z. The temporal landscape of recursive splicing during Pol II transcription elongation in human cells. PLoS Genet 2018; 14:e1007579. [PMID: 30148885 PMCID: PMC6110456 DOI: 10.1371/journal.pgen.1007579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/20/2018] [Indexed: 01/28/2023] Open
Abstract
Recursive splicing (RS) is an evolutionarily conserved process of removing long introns via multiple steps of splicing. It was first discovered in Drosophila and recently proven to occur also in humans. The detailed mechanism of recursive splicing is not well understood, in particular, whether it is kinetically coupled with transcription. To investigate the dynamic process that underlies recursive splicing, we systematically characterized 342 RS sites in three human cell types using published time-series data that monitored synchronized Pol II elongation and nascent RNA production with 4-thiouridine labeling. We found that half of the RS events occurred post-transcriptionally with long delays. For at least 18-47% RS introns, we detected RS junction reads only after detecting canonical splicing junction reads, supporting the notion that these introns were removed by both recursive splicing and canonical splicing. Furthermore, the choice of which splicing mechanism was used showed cell type specificity. Our results suggest that recursive splicing supplements, rather than replaces, canonical splicing for removing long introns.
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Affiliation(s)
- Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Yu Fu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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136
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Jackson DP, Ting JH, Pozniak PD, Meurice C, Schleidt SS, Dao A, Lee AH, Klinman E, Jordan-Sciutto KL. Identification and characterization of two novel alternatively spliced E2F1 transcripts in the rat CNS. Mol Cell Neurosci 2018; 92:1-11. [PMID: 29936143 DOI: 10.1016/j.mcn.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 06/05/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022] Open
Abstract
E2F1 is a transcription factor classically known to regulate G0/G1 to S phase progression in the cell cycle. In addition, E2F1 also regulates a wide range of apoptotic genes and thus has been well studied in the context of neuronal death and neurodegenerative diseases. However, its function and regulation in the mature central nervous system are not well understood. Alternative splicing is a well-conserved post-transcriptional mechanism common in cells of the CNS and is necessary to generate diverse functional modifications to RNA or protein products from genes. Heretofore, physiologically significant alternatively spliced E2F1 transcripts have not been reported. In the present study, we report the identification of two novel alternatively spliced E2F1 transcripts: E2F1b, an E2F1 transcript retaining intron 5, and E2F1c, an E2F1 transcript excluding exon 6. These alternatively spliced transcripts are observed in the brain and neural cell types including neurons, astrocytes, and undifferentiated oligodendrocytes. The expression of these E2F1 transcripts is distinct during maturation of primary hippocampal neuroglial cells. Pharmacologically-induced global translation inhibition with cycloheximide, anisomycin or thapsigargin lead to significantly reduced expression of E2F1a, E2F1b and E2F1c. Conversely, increasing neuronal activity by elevating the concentration of potassium chloride selectively increased the expression of E2F1b. Furthermore, experiments expressing these variants in vitro show the transcripts can be translated to generate a protein product. Taken together, our data suggest that the alternatively spliced E2F1 transcript behave differently than the E2F1a transcript, and our results provide a foundation for future investigation of the function of E2F1 splice variants in the CNS.
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Affiliation(s)
- Dan P Jackson
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Jenhao H Ting
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Paul D Pozniak
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Claire Meurice
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie S Schleidt
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Anh Dao
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Amy H Lee
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA
| | - Eva Klinman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kelly L Jordan-Sciutto
- Department of Pathology, School of Dental Medicine, University of Pennsylvania, 240 S. 40th St, Philadelphia, PA 19104, USA.
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137
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Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:7831-7836. [PMID: 29915080 PMCID: PMC6064979 DOI: 10.1073/pnas.1804971115] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The upstream ORFs (uORFs) in the 5′UTRs of mRNA often function as repressors of main ORF translation or triggers of nonsense-mediated mRNA decay. In this study, we report on transcription start site (TSS) selection when etiolated Arabidopsis seedlings are exposed to blue light, and reveal that transcription from uORF-avoiding TSSs is induced throughout the genome. It is possible that transcripts arising from TSSs downstream of uORFs evade uORF-mediated inhibition of gene expression. Thus, uORF-avoiding transcription starts are an important mechanism of gene expression regulation during a plant’s response to environmental changes. Plants adapt to alterations in light conditions by controlling their gene expression profiles. Expression of light-inducible genes is transcriptionally induced by transcription factors such as HY5. However, few detailed analyses have been carried out on the control of transcription start sites (TSSs). Of the various wavelengths of light, it is blue light (BL) that regulates physiological responses such as hypocotyl elongation and flowering time. To understand how gene expression is controlled not only by transcript abundance but also by TSS selection, we examined genome-wide TSS profiles in Arabidopsis seedlings after exposure to BL irradiation following initial growth in the dark. Thousands of genes use multiple TSSs, and some transcripts have upstream ORFs (uORFs) that take precedence over the main ORF (mORF) encoding proteins. The uORFs often function as translation inhibitors of the mORF or as triggers of nonsense-mediated mRNA decay (NMD). Transcription from TSSs located downstream of the uORFs in 220 genes is enhanced by BL exposure. This type of regulation is found in HY5 and HYH, major regulators of light-dependent gene expression. Translation efficiencies of the genes showing enhanced usage of these TSSs increased upon BL exposure. We also show that transcripts from TSSs upstream of uORFs in 45 of the 220 genes, including HY5, accumulated in a mutant of NMD. These results suggest that BL controls gene expression not only by enhancing transcriptions but also by choosing the TSS, and transcripts from downstream TSSs evade uORF-mediated inhibition to ensure high expression of light-regulated genes.
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138
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Herzel L, Straube K, Neugebauer KM. Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome Res 2018; 28:1008-1019. [PMID: 29903723 PMCID: PMC6028129 DOI: 10.1101/gr.232025.117] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/24/2018] [Indexed: 12/13/2022]
Abstract
Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe. Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2, the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3′ end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation.
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Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Korinna Straube
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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139
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Ricci Hagman J, Hult AK, Westman JS, Hosseini-Maaf B, Jongruamklang P, Saipin J, Bejrachandra S, Olsson ML. Multiple miscarriages in two sisters of Thai origin with the rare P k phenotype caused by a novel nonsense mutation at the B3GALNT1 locus. Transfus Med 2018; 29:202-208. [PMID: 29873420 DOI: 10.1111/tme.12544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/20/2018] [Accepted: 05/14/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVES To determine the genetic background underlying the Pk phenotype in two Thai sisters suffering from multiple spontaneous abortions. BACKGROUND The P antigen is carried by globoside, an abundant glycosphingolipid in the red blood cell (RBC) membrane. Inactivating mutations in the 3-β-N-acetylgalactosaminyltransferase gene (B3GALNT1) give rise to the rare Pk phenotype, which lack the P and PX2 antigens. Consequently, naturally occurring anti-P may cause recurrent miscarriages following the cytotoxic attack of the globoside-rich fetal portion of the placenta. METHODS/MATERIALS P/P1/PX2/Pk antigens on RBCs and their corresponding antibodies were detected by haemagglutination and flow cytometry. The B3GALNT1 coding region was sequenced, and an allele-specific polymerase chain reaction (PCR) was developed. RESULTS The two sisters had suffered 8 and 11 miscarriages, most of which occurred in the first trimester. Anti-P and anti-PX2 were identified in their plasmas, and the RBCs typed as P-PX2-Pk +, i.e. had the Pk phenotype. Sequencing revealed homozygosity for a nonsense mutation, c.420T>G, in B3GALNT1. This substitution introduces a premature stop codon, p.Tyr140Ter, which is predicted to abolish enzymatic activity. Screening of 384 Thai donors indicated an allele frequency of 0·13%. CONCLUSION We describe a novel nonsense mutation (c.420T>G) in B3GALNT1 (GLOB*01N·13), which was added to the 12 alleles already known in the GLOB system.
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Affiliation(s)
- J Ricci Hagman
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Division of Laboratory Medicine, Office of Medical Services, Region Skåne, Sweden
| | - A K Hult
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Division of Laboratory Medicine, Office of Medical Services, Region Skåne, Sweden
| | - J S Westman
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - B Hosseini-Maaf
- Clinical Immunology and Transfusion Medicine, Division of Laboratory Medicine, Office of Medical Services, Region Skåne, Sweden
| | - P Jongruamklang
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - J Saipin
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - S Bejrachandra
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - M L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Division of Laboratory Medicine, Office of Medical Services, Region Skåne, Sweden
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140
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Sun N, Nasello C, Deng L, Wang N, Zhang Y, Xu Z, Song Z, Kwan K, King RA, Pang ZP, Xing J, Heiman GA, Tischfield JA. The PNKD gene is associated with Tourette Disorder or Tic disorder in a multiplex family. Mol Psychiatry 2018; 23:1487-1495. [PMID: 28894297 PMCID: PMC5847395 DOI: 10.1038/mp.2017.179] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 05/24/2017] [Accepted: 06/07/2017] [Indexed: 01/29/2023]
Abstract
Tourette Disorder (TD) is a childhood-onset neuropsychiatric and neurodevelopmental disorder characterized by the presence of both motor and vocal tics. The genetic architecture of TD is believed to be complex and heterogeneous. Nevertheless, DNA sequence variants co-segregating with TD phenotypes within multiplex families have been identified. This report examines whole exomes of affected and unaffected individuals in a multiplex TD family to discover genes involved in the TD etiology. We performed whole exome sequencing on six out of nine members in a three-generation TD multiplex family. Putative deleterious sequence variants co-segregating with TD patients were identified by our in-house bioinformatics pipeline. Induced pluripotent stem cells (iPSCs) were generated from one unaffected and two TD affected individuals. Neurons were derived from the iPSCs and biochemical assays were conducted to evaluate possible molecular differences between affected and unaffected. A rare heterozygous nonsense mutation in PNKD was co-segregated with TD in this multiplex family. Transcript and protein levels of the PNKD long isoform were reduced in neurons derived from the individuals with TD due to the nonsense mutation, indicating nonsense-mediated mRNA decay. We demonstrated that the PNKD long isoform monomer oligomerizes with itself as well as interacts with the synaptic active zone protein RIMS1α. We concluded that reduced PNKD long isoform levels are detected in all affected individuals and we provide evidence for a mechanism whereby this might contribute to the TD phenotype.
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Affiliation(s)
- Nawei Sun
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Cara Nasello
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Li Deng
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Nan Wang
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Yeting Zhang
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Zihui Xu
- Child Health Institute of New Jersey, New Brunswick, NJ, USA
| | - Zhichao Song
- Department of Cell Biology and Neuroscience, Piscataway, NJ, USA
| | - Kelvin Kwan
- Department of Cell Biology and Neuroscience, Piscataway, NJ, USA
| | - Robert A. King
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
| | - Zhiping P. Pang
- Child Health Institute of New Jersey, New Brunswick, NJ, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Gary A. Heiman
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Jay A. Tischfield
- Department of Genetics, Rutgers University, Piscataway, NJ, USA,Human Genetics Institute of New Jersey, Piscataway, NJ, USA
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141
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Suzuki N, Mutai H, Miya F, Tsunoda T, Terashima H, Morimoto N, Matsunaga T. A case report of reversible generalized seizures in a patient with Waardenburg syndrome associated with a novel nonsense mutation in the penultimate exon of SOX10. BMC Pediatr 2018; 18:171. [PMID: 29792164 PMCID: PMC5966879 DOI: 10.1186/s12887-018-1139-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 05/02/2018] [Indexed: 11/15/2022] Open
Abstract
Background Waardenburg syndrome type 1 (WS1) can be distinguished from Waardenburg syndrome type 2 (WS2) by the presence of dystopia canthorum. About 96% of WS1 are due to PAX3 mutations, and SOX10 mutations have been reported in 15% of WS2. Case presentation This report describes a patient with WS1 who harbored a novel SOX10 nonsense mutation (c.652G > T, p.G218*) in exon 3 which is the penultimate exon. The patient had mild prodromal neurological symptoms that were followed by severe attacks of generalized seizures associated with delayed myelination of the brain. The immature myelination recovered later and the neurological symptoms could be improved. This is the first truncating mutation in exon 3 of SOX10 that is associated with neurological symptoms in Waardenburg syndrome. Previous studies reported that the neurological symptoms that associate with WS are congenital and irreversible. These findings suggest that the reversible neurological phenotype may be associated with the nonsense mutation in exon 3 of SOX10. Conclusions When patients of WS show mild prodromal neurological symptoms, the clinician should be aware of the possibility that severe attacks of generalized seizures may follow, which may be associated with the truncating mutation in exon 3 of SOX10. Electronic supplementary material The online version of this article (10.1186/s12887-018-1139-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Noriomi Suzuki
- Department of Otolaryngology, National Center for Child Health and Development, Tokyo, Japan
| | - Hideki Mutai
- Division of Hearing and Balance Research, National Institute of Sensory Organs/ Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Terashima
- Devision of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Noriko Morimoto
- Department of Otolaryngology, National Center for Child Health and Development, Tokyo, Japan
| | - Tatsuo Matsunaga
- Department of Otolaryngology, National Center for Child Health and Development, Tokyo, Japan. .,Division of Hearing and Balance Research, National Institute of Sensory Organs/ Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo, 152-8902, Japan.
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142
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Nicholson P, Gkratsou A, Josi C, Colombo M, Mühlemann O. Dissecting the functions of SMG5, SMG7, and PNRC2 in nonsense-mediated mRNA decay of human cells. RNA (NEW YORK, N.Y.) 2018; 24:557-573. [PMID: 29348139 PMCID: PMC5855955 DOI: 10.1261/rna.063719.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/08/2018] [Indexed: 05/04/2023]
Abstract
The term "nonsense-mediated mRNA decay" (NMD) originally described the degradation of mRNAs with premature translation-termination codons (PTCs), but its meaning has recently been extended to be a translation-dependent post-transcriptional regulator of gene expression affecting 3%-10% of all mRNAs. The degradation of NMD target mRNAs involves both exonucleolytic and endonucleolytic pathways in mammalian cells. While the latter is mediated by the endonuclease SMG6, the former pathway has been reported to require a complex of SMG5-SMG7 or SMG5-PNRC2 binding to UPF1. However, the existence, dominance, and mechanistic details of these exonucleolytic pathways are divisive. Therefore, we have investigated the possible exonucleolytic modes of mRNA decay in NMD by examining the roles of UPF1, SMG5, SMG7, and PNRC2 using a combination of functional assays and interaction mapping. Confirming previous work, we detected an interaction between SMG5 and SMG7 and also a functional need for this complex in NMD. In contrast, we found no evidence for the existence of a physical or functional interaction between SMG5 and PNRC2. Instead, we show that UPF1 interacts with PNRC2 and that it triggers 5'-3' exonucleolytic decay of reporter transcripts in tethering assays. PNRC2 interacts mainly with decapping factors and its knockdown does not affect the RNA levels of NMD reporters. We conclude that PNRC2 is probably an important mRNA decapping factor but that it does not appear to be required for NMD.
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Affiliation(s)
- Pamela Nicholson
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
| | - Asimina Gkratsou
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Christoph Josi
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern 3012, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, Bern 3012, Switzerland
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143
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Espinar L, Schikora Tamarit MÀ, Domingo J, Carey LB. Promoter architecture determines cotranslational regulation of mRNA. Genome Res 2018; 28:509-518. [PMID: 29567675 PMCID: PMC5880241 DOI: 10.1101/gr.230458.117] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 02/27/2018] [Indexed: 01/08/2023]
Abstract
Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of cotranslational regulation on mRNA levels is determined by promoter architecture. By using a novel computational genetic screen of 6402 RNA-seq experiments, we identify the RNA helicase Dbp2 as the mechanism by which cotranslational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus, the ORF sequence is a major regulator of gene expression, and a nonlinear interaction between promoters and ORFs determines mRNA levels.
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Affiliation(s)
- Lorena Espinar
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | | | - Júlia Domingo
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.,EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Lucas B Carey
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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144
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Mugridge JS, Tibble RW, Ziemniak M, Jemielity J, Gross JD. Structure of the activated Edc1-Dcp1-Dcp2-Edc3 mRNA decapping complex with substrate analog poised for catalysis. Nat Commun 2018; 9:1152. [PMID: 29559651 PMCID: PMC5861098 DOI: 10.1038/s41467-018-03536-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/22/2018] [Indexed: 11/17/2022] Open
Abstract
The conserved decapping enzyme Dcp2 recognizes and removes the 5′ eukaryotic cap from mRNA transcripts in a critical step of many cellular RNA decay pathways. Dcp2 is a dynamic enzyme that functions in concert with the essential activator Dcp1 and a diverse set of coactivators to selectively and efficiently decap target mRNAs in the cell. Here we present a 2.84 Å crystal structure of K. lactis Dcp1–Dcp2 in complex with coactivators Edc1 and Edc3, and with substrate analog bound to the Dcp2 active site. Our structure shows how Dcp2 recognizes cap substrate in the catalytically active conformation of the enzyme, and how coactivator Edc1 forms a three-way interface that bridges the domains of Dcp2 to consolidate the active conformation. Kinetic data reveal Dcp2 has selectivity for the first transcribed nucleotide during the catalytic step. The heterotetrameric Edc1–Dcp1–Dcp2–Edc3 structure shows how coactivators Edc1 and Edc3 can act simultaneously to activate decapping catalysis. The decapping enzyme Dcp2 removes the 5′ eukaryotic cap from mRNA transcripts and acts in concert with its essential activator Dcp1 and various coactivators. Here the authors present the structure of the fully-activated mRNA decapping complex, which reveals how Dcp2 recognizes the cap substrate and coactivators Edc1 and Edc3 activate catalysis.
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Affiliation(s)
- Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ryan W Tibble
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA.,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland.,Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, CA, 94158, USA.
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145
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Schuller AP, Zinshteyn B, Enam SU, Green R. Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk. Nucleic Acids Res 2018; 46:2060-2073. [PMID: 29253221 PMCID: PMC5829565 DOI: 10.1093/nar/gkx1263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 01/02/2023] Open
Abstract
Upf1 is an SF1-family RNA helicase that is essential for the nonsense-mediated decay (NMD) process in eukaryotes. While Upf1 has been shown to interact with 80S ribosomes, the molecular details of this interaction were unknown. Using purified recombinant proteins and high-throughput sequencing combined with Fe-BABE directed hydroxyl radical probing (HTS-BABE) we have characterized the interaction between Upf1 and the yeast 80S ribosome. We identify the 1C domain of Upf1, an alpha-helical insertion in the RecA helicase core, to be essential for ribosome binding, and determine that the L1 stalk of 25S rRNA is the binding site for Upf1 on the ribosome. Using the cleavage sites identified by hydroxyl radical probing and high-resolution structures of both yeast Upf1 and the human 80S ribosome, we provide a model of a Upf1:80S structure. Our model requires that the L1 stalk adopt an open configuration as adopted by an un-rotated, or classical-state, ribosome. Our results shed light on the interaction between Upf1 and the ribosome, and suggest that Upf1 may specifically engage a classical-state ribosome during translation.
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Affiliation(s)
- Anthony P Schuller
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Syed Usman Enam
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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146
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Davidsson J, Puschmann A, Tedgård U, Bryder D, Nilsson L, Cammenga J. SAMD9 and SAMD9L in inherited predisposition to ataxia, pancytopenia, and myeloid malignancies. Leukemia 2018. [PMID: 29535429 PMCID: PMC5940635 DOI: 10.1038/s41375-018-0074-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Germline mutations in the SAMD9 and SAMD9L genes, located in tandem on chromosome 7, are associated with a clinical spectrum of disorders including the MIRAGE syndrome, ataxia-pancytopenia syndrome and myelodysplasia and leukemia syndrome with monosomy 7 syndrome. Germline gain-of-function mutations increase SAMD9 or SAMD9L's normal antiproliferative effect. This causes pancytopenia and generally restricted growth and/or specific organ hypoplasia in non-hematopoietic tissues. In blood cells, additional somatic aberrations that reverse the germline mutation's effect, and give rise to the clonal expansion of cells with reduced or no antiproliferative effect of SAMD9 or SAMD9L include complete or partial chromosome 7 loss or loss-of-function mutations in SAMD9 or SAMD9L. Furthermore, the complete or partial loss of chromosome 7q may cause myelodysplastic syndrome in these patients. SAMD9 mutations appear to associate with a more severe disease phenotype, including intrauterine growth restriction, developmental delay and hypoplasia of adrenal glands, testes, ovaries or thymus, and most reported patients died in infancy or early childhood due to infections, anemia and/or hemorrhages. SAMD9L mutations have been reported in a few families with balance problems and nystagmus due to cerebellar atrophy, and may lead to similar hematological disease as seen in SAMD9 mutation carriers, from early childhood to adult years. We review the clinical features of these syndromes, discuss the underlying biology, and interpret the genetic findings in some of the affected family members. We provide expert-based recommendations regarding diagnosis, follow-up, and treatment of mutation carriers.
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Affiliation(s)
- Josef Davidsson
- Department of Pediatric Hematology and Oncology, Skåne University Hospital, Lund, Sweden. .,Department of Molecular Hematology, Lund University, Lund, Sweden.
| | - Andreas Puschmann
- Skåne University Hospital, Department of Clinical Sciences Lund, Neurology, Lund University, Lund, Sweden
| | - Ulf Tedgård
- Department of Pediatric Hematology and Oncology, Skåne University Hospital, Lund, Sweden
| | - David Bryder
- Department of Molecular Hematology, Lund University, Lund, Sweden
| | - Lars Nilsson
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Jörg Cammenga
- Department of Hematology, University Hospital Linköping, Linköping, Sweden. .,Institution for Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
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147
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Son M, Wickner RB. Nonsense-mediated mRNA decay factors cure most [PSI+] prion variants. Proc Natl Acad Sci U S A 2018; 115:E1184-E1193. [PMID: 29358398 PMCID: PMC5819436 DOI: 10.1073/pnas.1717495115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The yeast prion [PSI+] is a self-propagating amyloid of Sup35p with a folded in-register parallel β-sheet architecture. In a genetic screen for antiprion genes, using the yeast knockout collection, UPF1/NAM7 and UPF3, encoding nonsense-mediated mRNA decay (NMD) factors, were frequently detected. Almost all [PSI+] variants arising in the absence of Upf proteins were eliminated by restored normal levels of these proteins, and [PSI+] arises more frequently in upf mutants. Upf1p, complexed with Upf2p and Upf3p, is a multifunctional protein with helicase, ATP-binding, and RNA-binding activities promoting efficient translation termination and degradation of mRNAs with premature nonsense codons. We find that the curing ability of Upf proteins is uncorrelated with these previously reported functions but does depend on their interaction with Sup35p and formation of the Upf1p-Upf2p-Upf3p complex (i.e., the Upf complex). Indeed, Sup35p amyloid formation in vitro is inhibited by substoichiometric Upf1p. Inhibition of [PSI+] prion generation and propagation by Upf proteins may be due to the monomeric Upf proteins and the Upf complex competing with Sup35p amyloid fibers for available Sup35p monomers. Alternatively, the association of the Upf complex with amyloid filaments may block the addition of new monomers. Our results suggest that maintenance of normal protein-protein interactions prevents prion formation and can even reverse the process.
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Affiliation(s)
- Moonil Son
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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148
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C-terminal short arginine/serine repeat sequence-dependent regulation of Y14 (RBM8A) localization. Sci Rep 2018; 8:612. [PMID: 29330450 PMCID: PMC5766523 DOI: 10.1038/s41598-017-18765-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/15/2017] [Indexed: 01/01/2023] Open
Abstract
Y14 (RBM8A) is an RNA recognition motif-containing protein that forms heterodimers with MAGOH and serves as a core factor of the RNA surveillance machinery for the exon junction complex (EJC). The role of the Y14 C-terminal serine/arginine (RS) repeat-containing region, which has been reported to undergo modifications such as phosphorylation and methylation, has not been sufficiently investigated. Thus, we aimed to explore the functional significance of the Y14 C-terminal region. Deletion or dephosphorylation mimic mutants of the C-terminal region showed a shift in localization from the nucleoplasmic region; in addition, the C-terminal RS repeat-containing sequence itself exhibited the potential for nucleolar localization. Additionally, the regulation of Y14 localization by the C-terminal region was further found to be exquisitely controlled by MAGOH binding. Cumulatively, our findings, which demonstrated that Y14 localization is regulated not only by the previously reported N-terminal localization signal but also by the C-terminal RS repeat-containing region through phosphorylation and MAGOH binding to Y14, provide new insights for the mechanism of localization of short RS repeat-containing proteins.
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149
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Wu Q, Han Y, Tong Q. Current Genetic Techniques in Neural Circuit Control of Feeding and Energy Metabolism. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1090:211-233. [PMID: 30390293 DOI: 10.1007/978-981-13-1286-1_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The current epidemic of obesity and its associated metabolic syndromes imposes unprecedented challenges to our society. Despite intensive research focus on obesity pathogenesis, an effective therapeutic strategy to treat and cure obesity is still lacking. The obesity development is due to a disturbed homeostatic control of feeding and energy expenditure, both of which are controlled by an intricate neural network in the brain. Given the inherent complexity of brain networks in controlling feeding and energy expenditure, the understanding of brain-based pathophysiology for obesity development is limited. One key limiting factor in dissecting neural pathways for feeding and energy expenditure is unavailability of techniques that can be used to effectively reduce the complexity of the brain network to a tractable paradigm, based on which a strong hypothesis can be tested. Excitingly, emerging techniques have been involved to be able to link specific groups of neurons and neural pathways to behaviors (i.e., feeding and energy expenditure). In this chapter, novel techniques especially those based on animal models and viral vector approaches will be discussed. We hope that this chapter will provide readers with a basis that can help to understand the literatures using these techniques and with a guide to apply these exciting techniques to investigate brain mechanisms underlying feeding and energy expenditure.
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Affiliation(s)
- Qi Wu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA. .,Children's Nutrition Research Center, Research Service of Department of Agriculture of USA, Houston, TX, USA.
| | - Yong Han
- Department of Pediatrics, Baylor College of Medicine, USDA-ARS, Houston, TX, USA
| | - Qingchun Tong
- Center for Metabolic and Degenerative Diseases, Brown Foundation Institute of Molecular Medicine, University of Texas McGovern Medical School, Houston, TX, USA.
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150
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Abstract
Site-specific incorporation of unnatural amino acids (UAAs) has greatly expanded the toolkit available to study biological phenomena in single cells. However, to address questions involving complex cellular interactions such as development, ageing, and the functions of the nervous system it is often necessary to use multicellular model organisms. The nematode Caenorhabditis elegans was the first organism to have its genetic code expanded. Due to its small size, ease of cultivation, and excellent UAA incorporation efficiency, C. elegans makes an ideal model organism to apply UAAs as tools to investigate the functioning of multicellular systems.Here, we describe methods to generate transgenic C. elegans capable of UAA incorporation, as well as how to deliver unnatural amino acids and test incorporation. Furthermore, we describe methods to uncage photosensitive unnatural amino acid derivatives.
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Affiliation(s)
- Lloyd Davis
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK
| | - Sebastian Greiss
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK.
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