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Milicevic N, Jenner L, Myasnikov A, Yusupov M, Yusupova G. mRNA reading frame maintenance during eukaryotic ribosome translocation. Nature 2024; 625:393-400. [PMID: 38030725 DOI: 10.1038/s41586-023-06780-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
One of the most critical steps of protein synthesis is coupled translocation of messenger RNA (mRNA) and transfer RNAs (tRNAs) required to advance the mRNA reading frame by one codon. In eukaryotes, translocation is accelerated and its fidelity is maintained by elongation factor 2 (eEF2)1,2. At present, only a few snapshots of eukaryotic ribosome translocation have been reported3-5. Here we report ten high-resolution cryogenic-electron microscopy (cryo-EM) structures of the elongating eukaryotic ribosome bound to the full translocation module consisting of mRNA, peptidyl-tRNA and deacylated tRNA, seven of which also contained ribosome-bound, naturally modified eEF2. This study recapitulates mRNA-tRNA2-growing peptide module progression through the ribosome, from the earliest states of eEF2 translocase accommodation until the very late stages of the process, and shows an intricate network of interactions preventing the slippage of the translational reading frame. We demonstrate how the accuracy of eukaryotic translocation relies on eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs. Our findings shed light on the mechanism of translation arrest by the anti-fungal eEF2-binding inhibitor, sordarin. We also propose that the sterically constrained environment imposed by diphthamide, a conserved eukaryotic posttranslational modification in eEF2, not only stabilizes correct Watson-Crick codon-anticodon interactions but may also uncover erroneous peptidyl-tRNA, and therefore contribute to higher accuracy of protein synthesis in eukaryotes.
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Affiliation(s)
- Nemanja Milicevic
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France
| | - Lasse Jenner
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France
| | | | - Marat Yusupov
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France
| | - Gulnara Yusupova
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR7104, INSERM U1258, University of Strasbourg, Strasbourg, France.
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2
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Romano R, Ghahremani S, Zimmerman T, Legere N, Thakar K, Ladha FA, Pettinato AM, Hinson JT. Reading Frame Repair of TTN Truncation Variants Restores Titin Quantity and Functions. Circulation 2022; 145:194-205. [PMID: 34905694 PMCID: PMC8766920 DOI: 10.1161/circulationaha.120.049997] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/18/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Titin truncation variants (TTNtvs) are the most common inheritable risk factor for dilated cardiomyopathy (DCM), a disease with high morbidity and mortality. The pathogenicity of TTNtvs has been associated with structural localization as A-band variants overlapping myosin heavy chain-binding domains are more pathogenic than I-band variants by incompletely understood mechanisms. Demonstrating why A-band variants are highly pathogenic for DCM could reveal new insights into DCM pathogenesis, titin (TTN) functions, and therapeutic targets. METHODS We constructed human cardiomyocyte models harboring DCM-associated TTNtvs within A-band and I-band structural domains using induced pluripotent stem cell and CRISPR technologies. We characterized normal TTN isoforms and variant-specific truncation peptides by their expression levels and cardiomyocyte localization using TTN protein gel electrophoresis and immunofluorescence, respectively. Using CRISPR to ablate A-band variant-specific truncation peptides through introduction of a proximal I-band TTNtv, we studied genetic mechanisms in single cardiomyocyte and 3-dimensional, biomimetic cardiac microtissue functional assays. Last, we engineered a full-length TTN protein reporter assay and used next-generation sequencing assays to develop a CRISPR therapeutic for somatic cell genome editing TTNtvs. RESULTS An A-band TTNtv dose-dependently impaired cardiac microtissue twitch force, reduced full-length TTN levels, and produced abundant TTN truncation peptides. TTN truncation peptides integrated into nascent myofibril-like structures and impaired myofibrillogenesis. CRISPR ablation of TTN truncation peptides using a proximal I-band TTNtv partially restored cardiac microtissue twitch force deficits. Cardiomyocyte genome editing using SpCas9 and a TTNtv-specific guide RNA restored the TTN protein reading frame, which increased full-length TTN protein levels, reduced TTN truncation peptides, and increased sarcomere function in cardiac microtissue assays. CONCLUSIONS An A-band TTNtv diminished sarcomere function greater than an I-band TTNtv in proportion to estimated DCM pathogenicity. Although both TTNtvs resulted in full-length TTN haploinsufficiency, only the A-band TTNtv produced TTN truncation peptides that impaired myofibrillogenesis and sarcomere function. CRISPR-mediated reading frame repair of the A-band TTNtv restored functional deficits, and could be adapted as a one-and-done genome editing strategy to target ≈30% of DCM-associated TTNtvs.
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Affiliation(s)
- Robert Romano
- University of Connecticut Health Center, Farmington, CT 06030, USA
| | | | - Talia Zimmerman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Nicholas Legere
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ketan Thakar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Feria A. Ladha
- University of Connecticut Health Center, Farmington, CT 06030, USA
| | | | - J. Travis Hinson
- University of Connecticut Health Center, Farmington, CT 06030, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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Decrulle AL, Frénoy A, Meiller-Legrand TA, Bernheim A, Lotton C, Gutierrez A, Lindner AB. Engineering gene overlaps to sustain genetic constructs in vivo. PLoS Comput Biol 2021; 17:e1009475. [PMID: 34624014 PMCID: PMC8528312 DOI: 10.1371/journal.pcbi.1009475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 10/20/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Evolution is often an obstacle to the engineering of stable biological systems due to the selection of mutations inactivating costly gene circuits. Gene overlaps induce important constraints on sequences and their evolution. We show that these constraints can be harnessed to increase the stability of costly genes by purging loss-of-function mutations. We combine computational and synthetic biology approaches to rationally design an overlapping reading frame expressing an essential gene within an existing gene to protect. Our algorithm succeeded in creating overlapping reading frames in 80% of E. coli genes. Experimentally, scoring mutations in both genes of such overlapping construct, we found that a significant fraction of mutations impacting the gene to protect have a deleterious effect on the essential gene. Such an overlap thus protects a costly gene from removal by natural selection by associating the benefit of this removal with a larger or even lethal cost. In our synthetic constructs, the overlap converts many of the possible mutants into evolutionary dead-ends, reducing the evolutionary potential of the system and thus increasing its stability over time. Genomes are translated by triplets of nucleotides on two different strands, allowing for six different reading frames. This permits the existence of gene overlaps, often observed in microbial genomes, where two different proteins are encoded on the same piece of DNA, but in different reading frames. Gene overlaps are classically considered an obstacle for both evolution and genetic engineering, as mutations in overlapping regions likely have pleitrotropic effects on several genes. In 2013, we identified specific evolutionary scenarios where the decrease in evolutionary potential caused by gene overlaps could instead be advantageous and selected for. In this work, we demonstrate the use of gene overlaps in another context where reducing evolutionary potential can be useful: preventing evolution from inactivating synthetic circuits. We show that gene overlaps can be engineered to increase the evolutionary stability of genes that are costly to their hosts, by entangling these costly genes with essential genes.
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Affiliation(s)
| | - Antoine Frénoy
- Université de Paris, INSERM U1001, Paris, France
- Université Grenoble Alpes, CNRS UMR5525, Grenoble, France
- * E-mail: (AF); (ABL)
| | | | | | | | | | - Ariel B. Lindner
- Université de Paris, INSERM U1001, Paris, France
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
- * E-mail: (AF); (ABL)
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Gupta A, Alland D. Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis. Nat Commun 2021; 12:4702. [PMID: 34349104 PMCID: PMC8339072 DOI: 10.1038/s41467-021-25055-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis can adapt to changing environments by non-heritable mechanisms. Frame-shifting insertions and deletions (indels) may also participate in adaptation through gene disruption, which could be reversed by secondary introduction of a frame-restoring indel. We present ScarTrek, a program that scans genomic data for indels, including those that together disrupt and restore a gene's reading frame, producing "frame-shift scars" suggestive of reversible gene inactivation. We use ScarTrek to analyze 5977 clinical M. tuberculosis isolates. We show that indel frequency inversely correlates with genomic linguistic complexity and varies with gene-position and gene-essentiality. Using ScarTrek, we detect 74 unique frame-shift scars in 48 genes, with a 3.74% population-level incidence of unique scar events. We find multiple scars in the ESX-1 gene cluster. Six scars show evidence of convergent evolution while the rest shared a common ancestor. Our results suggest that sequential indels are a mechanism for reversible gene silencing and adaptation in M. tuberculosis.
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Affiliation(s)
- Aditi Gupta
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ, USA.
| | - David Alland
- Center for Emerging Pathogens, New Jersey Medical School, Rutgers University, Newark, NJ, USA.
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Abstract
Web services are used through all disciplines in life sciences and the online landscape is growing by hundreds of novel servers annually. However, availability varies, and maintenance practices are largely inconsistent. We screened the availability of 2396 web tools published during the past 10 years. All servers were accessed over 133 days and 318 668 index files were stored in a local database. The number of accessible tools almost linearly increases in time with highest availability for 2019 and 2020 (∼90%) and lowest for tools published in 2010 (∼50%). In a 133-day test frame, 31% of tools were always working, 48.4% occasionally and 20.6% never. Consecutive downtimes were typically below 5 days with a median of 1 day, and unevenly distributed over the weekdays. A rescue experiment on 47 tools that were published from 2019 onwards but never accessible showed that 51.1% of the tools could be restored in due time. We found a positive association between the number of citations and the probability of a web server being reachable. We then determined common challenges and formulated categorical recommendations for researchers planning to develop web-based resources. As implication of our study, we propose to develop a repository for automatic API testing and sustainability indexing.
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Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken 66123, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken 66123, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany
- Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken 66123, Germany
- Department of Neurology and Neurological Sciences, Stanford University, Palo Alto, CA 94305, USA
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Abstract
Identification of the full complement of genes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial step towards gaining a fuller understanding of its molecular biology. However, short and/or overlapping genes can be difficult to detect using conventional computational approaches, whereas high-throughput experimental approaches - such as ribosome profiling - cannot distinguish translation of functional peptides from regulatory translation or translational noise. By studying regions showing enhanced conservation at synonymous sites in alignments of SARS-CoV-2 and related viruses (subgenus Sarbecovirus) and correlating the results with the conserved presence of an open reading frame (ORF) and a plausible translation mechanism, a putative new gene - ORF3c - was identified. ORF3c overlaps ORF3a in an alternative reading frame. A recently published ribosome profiling study confirmed that ORF3c is indeed translated during infection. ORF3c is conserved across the subgenus Sarbecovirus, and encodes a 40-41 amino acid predicted transmembrane protein.
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Affiliation(s)
- Andrew E. Firth
- Division of Virology, Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
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7
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Lyu P, Yoo KW, Yadav MK, Atala A, Aartsma-Rus A, van Putten M, Duan D, Lu B. Sensitive and reliable evaluation of single-cut sgRNAs to restore dystrophin by a GFP-reporter assay. PLoS One 2020; 15:e0239468. [PMID: 32970732 PMCID: PMC7514106 DOI: 10.1371/journal.pone.0239468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/08/2020] [Indexed: 12/31/2022] Open
Abstract
Most Duchenne muscular dystrophy (DMD) cases are caused by deletions or duplications of one or more exons that disrupt the reading frame of DMD mRNA. Restoring the reading frame allows the production of partially functional dystrophin proteins, and result in less severe symptoms. Antisense oligonucleotide mediated exon skipping has been approved for DMD, but this strategy needs repeated treatment. CRISPR/Cas9 can also restore dystrophin reading frame. Although recent in vivo studies showed the efficacy of the single-cut reframing/exon skipping strategy, methods to find the most efficient single-cut sgRNAs for a specific mutation are lacking. Here we show that the insertion/deletion (INDEL) generating efficiency and the INDEL profiles both contribute to the reading frame restoring efficiency of a single-cut sgRNA, thus assays only examining INDEL frequency are not able to find the best sgRNAs. We therefore developed a GFP-reporter assay to evaluate single-cut reframing efficiency, reporting the combined effects of both aspects. We show that the GFP-reporter assay can reliably predict the performance of sgRNAs in myoblasts. This GFP-reporter assay makes it possible to efficiently and reliably find the most efficient single-cut sgRNA for restoring dystrophin expression.
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Affiliation(s)
- Pin Lyu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Kyung Whan Yoo
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Manish Kumar Yadav
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | | | | | - Dongsheng Duan
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Baisong Lu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- * E-mail:
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8
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Gelsinger DR, Dallon E, Reddy R, Mohammad F, Buskirk A, DiRuggiero J. Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution. Nucleic Acids Res 2020; 48:5201-5216. [PMID: 32382758 PMCID: PMC7261190 DOI: 10.1093/nar/gkaa304] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/09/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
High-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint of H. volcanii to be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% of H. volcanii transcriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.
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Affiliation(s)
| | - Emma Dallon
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
| | - Rahul Reddy
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jocelyne DiRuggiero
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
- Department of Earth and Planetary Sciences, the Johns Hopkins University, Baltimore, MD, USA
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9
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Ren XD, Liu DY, Guo HQ, Wang L, Zhao N, Su N, Wei K, Ren S, Qu XM, Dai XT, Huang Q. Sensitive detection of low-abundance in-frame deletions in EGFR exon 19 using novel wild-type blockers in real-time PCR. Sci Rep 2019; 9:8276. [PMID: 31164704 PMCID: PMC6547704 DOI: 10.1038/s41598-019-44792-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/24/2019] [Indexed: 01/29/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) mutations are associated with response of tyrosine kinase inhibitors (TKIs) for patients with advanced non-small cell lung cancer (NSCLC). However, the existing methods for detection of samples having rare mutations(i.e. ~0.01%) have limits in terms of specificity, time consumption or cost. In the current study, novel wild-type blocking (WTB) oligonucleotides modified with phosphorothioate or inverted dT at the 5'-termini were designed to precisely detect 11 common deletion mutations in exon 19 of EGFR gene (E19del) using a WTB-PCR assay. And internal competitive leptin amplifications were further applied to enhance the specificity of the WTB-PCR system. Our results showed that WTB-PCR could completely block amplification of wild-type EGFR when 200 ng of DNA was used as template. Furthermore, the current WTB-PCR assay facilitated the detection of E19del mutations with a selectivity of 0.01% and sensitivity as low as a single copy. And, the results showed that the current WTB-PCR system exceeded detection limits afforded by the ARMS-PCR assay. In conclusion, the current WTB-PCR strategy represents a simple and cost-effective method to precisely detect various low-abundance deletion mutations.
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Affiliation(s)
- Xiao-Dong Ren
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Ding-Yuan Liu
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Hai-Qin Guo
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Liu Wang
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Na Zhao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Ning Su
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Kun Wei
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Sai Ren
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China
| | - Xue-Mei Qu
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China
| | - Xiao-Tian Dai
- Department of Pulmonology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China.
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, P.R. China.
- Department of Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, P.R. China.
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10
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Lim KRQ, Echigoya Y, Nagata T, Kuraoka M, Kobayashi M, Aoki Y, Partridge T, Maruyama R, Takeda S, Yokota T. Efficacy of Multi-exon Skipping Treatment in Duchenne Muscular Dystrophy Dog Model Neonates. Mol Ther 2018; 27:76-86. [PMID: 30448197 DOI: 10.1016/j.ymthe.2018.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/14/2018] [Accepted: 10/16/2018] [Indexed: 12/12/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by mutations in DMD, which codes for dystrophin. Because the progressive and irreversible degeneration of muscle occurs from childhood, earlier therapy is required to prevent dystrophic progression. Exon skipping by antisense oligonucleotides called phosphorodiamidate morpholino oligomers (PMOs), which restores the DMD reading frame and dystrophin expression, is a promising candidate for use in neonatal patients, yet the potential remains unclear. Here, we investigate the systemic efficacy and safety of early exon skipping in dystrophic dog neonates. Intravenous treatment of canine X-linked muscular dystrophy in Japan dogs with a 4-PMO cocktail resulted in ∼3%-27% in-frame exon 6-9 skipping and dystrophin restoration across skeletal muscles up to 14% of healthy levels. Histopathology was ameliorated with the reduction of fibrosis and/or necrosis area and centrally nucleated fibers, significantly in the diaphragm. Treatment induced cardiac multi-exon skipping, though dystrophin rescue was not detected. Functionally, treatment led to significant improvement in the standing test. Toxicity was not observed from blood tests. This is the first study to demonstrate successful multi-exon skipping treatment and significant functional improvement in dystrophic dogs. Early treatment was most beneficial for respiratory muscles, with implications for addressing pulmonary malfunction in patients.
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Affiliation(s)
- Kenji Rowel Q Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Yusuke Echigoya
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; Laboratory of Biomedical Science, Department of Veterinary Medicine, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Tetsuya Nagata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Mutsuki Kuraoka
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Masanori Kobayashi
- Department of Reproduction, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-0023, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Terence Partridge
- Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC 20010, USA; Department of Integrative Systems Biology, George Washington University School of Medicine, Washington, DC 20010, USA
| | - Rika Maruyama
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan.
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G2H7, Canada; Muscular Dystrophy Canada Research Chair, Edmonton, AB T6G2H7, Canada.
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11
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Strauss BE, Silva GRO, de Luna Vieira I, Cerqueira OLD, Del Valle PR, Medrano RFV, Mendonça SA. Perspectives for cancer immunotherapy mediated by p19Arf plus interferon-beta gene transfer. Clinics (Sao Paulo) 2018; 73:e479s. [PMID: 30208166 PMCID: PMC6113850 DOI: 10.6061/clinics/2018/e479s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/22/2018] [Indexed: 12/13/2022] Open
Abstract
While cancer immunotherapy has gained much deserved attention in recent years, many areas regarding the optimization of such modalities remain unexplored, including the development of novel approaches and the strategic combination of therapies that target multiple aspects of the cancer-immunity cycle. Our own work involves the use of gene transfer technology to promote cell death and immune stimulation. Such immunogenic cell death, mediated by the combined transfer of the alternate reading frame (p14ARF in humans and p19Arf in mice) and the interferon-β cDNA in our case, was shown to promote an antitumor immune response in mouse models of melanoma and lung carcinoma. With these encouraging results, we are now setting out on the road toward translational and preclinical development of our novel immunotherapeutic approach. Here, we outline the perspectives and challenges that we face, including the use of human tumor and immune cells to verify the response seen in mouse models and the incorporation of clinically relevant models, such as patient-derived xenografts and spontaneous tumors in animals. In addition, we seek to combine our immunotherapeutic approach with other treatments, such as chemotherapy or checkpoint blockade, with the goal of reducing dosage and increasing efficacy. The success of any translational research requires the cooperation of a multidisciplinary team of professionals involved in laboratory and clinical research, a relationship that is fostered at the Cancer Institute of Sao Paulo.
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Affiliation(s)
- Bryan E Strauss
- Laboratório de Vetores Virais, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail: /
| | - Gissele Rolemberg Oliveira Silva
- Laboratório de Vetores Virais, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Igor de Luna Vieira
- Laboratório de Vetores Virais, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Otto Luiz Dutra Cerqueira
- Laboratório de Vetores Virais, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Paulo Roberto Del Valle
- Laboratório de Vetores Virais, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Ruan Felipe Vieira Medrano
- Laboratório de Vetores Virais, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Samir Andrade Mendonça
- Laboratório de Vetores Virais, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
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12
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Abstract
The same nucleotide sequence can encode two protein products in different reading frames. Overlapping gene regions encode higher levels of intrinsic structural disorder (ISD) than nonoverlapping genes (39% vs. 25% in our viral dataset). This might be because of the intrinsic properties of the genetic code, because one member per pair was recently born de novo in a process that favors high ISD, or because high ISD relieves increased evolutionary constraint imposed by dual-coding. Here, we quantify the relative contributions of these three alternative hypotheses. We estimate that the recency of de novo gene birth explains [Formula: see text] or more of the elevation in ISD in overlapping regions of viral genes. While the two reading frames within a same-strand overlapping gene pair have markedly different ISD tendencies that must be controlled for, their effects cancel out to make no net contribution to ISD. The remaining elevation of ISD in the older members of overlapping gene pairs, presumed due to the need to alleviate evolutionary constraint, was already present prior to the origin of the overlap. Same-strand overlapping gene birth events can occur in two different frames, favoring high ISD either in the ancestral gene or in the novel gene; surprisingly, most de novo gene birth events contained completely within the body of an ancestral gene favor high ISD in the ancestral gene (23 phylogenetically independent events vs. 1). This can be explained by mutation bias favoring the frame with more start codons and fewer stop codons.
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Affiliation(s)
- Sara Willis
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
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13
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Wu G, Fan L, Edmonson MN, Shaw T, Boggs K, Easton J, Rusch MC, Webb TR, Zhang J, Potter PM. Inhibition of SF3B1 by molecules targeting the spliceosome results in massive aberrant exon skipping. RNA 2018; 24:1056-1066. [PMID: 29844105 PMCID: PMC6049506 DOI: 10.1261/rna.065383.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/14/2018] [Indexed: 05/22/2023]
Abstract
The recent identification of compounds that interact with the spliceosome (sudemycins, spliceostatin A, and meayamycin) indicates that these molecules modulate aberrant splicing via SF3B1 inhibition. Through whole transcriptome sequencing, we have demonstrated that treatment of Rh18 cells with sudemycin leads to exon skipping as the predominant aberrant splicing event. This was also observed following reanalysis of published RNA-seq data sets derived from HeLa cells after spliceostatin A exposure. These results are in contrast to previous reports that indicate that intron retention was the major consequence of SF3B1 inhibition. Analysis of the exon junctions up-regulated by these small molecules indicated that these sequences were absent in annotated human genes, suggesting that aberrant splicing events yielded novel RNA transcripts. Interestingly, the length of preferred downstream exons was significantly longer than the skipped exons, although there was no difference between the lengths of introns flanking skipped exons. The reading frame of the aberrantly skipped exons maintained a ratio of 2:1:1, close to that of the cassette exons (3:1:1) present in naturally occurring isoforms, suggesting negative selection by the nonsense-mediated decay (NMD) machinery for out-of-frame transcripts. Accordingly, genes involved in NMD and RNAs encoding proteins involved in the splicing process were enriched in both data sets. Our findings, therefore, further elucidate the mechanisms by which SF3B1 inhibition modulates pre-mRNA splicing.
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Affiliation(s)
- Gang Wu
- Department of Computational Biology
| | - Liying Fan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
| | | | | | | | | | | | - Thomas R Webb
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
| | | | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA
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14
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Smaili W, Doubaj Y, Laarabi FZ, Lyahyai J, Kerbout M, Mikdame M, Sefiani A. CALR gene mutational profile in myeloproliferative neoplasms with non-mutated JAK2 in Moroccan patients: A case series and germline in-frame deletion. Curr Res Transl Med 2016; 65:15-19. [PMID: 28340692 DOI: 10.1016/j.retram.2016.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/05/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND The discovery of somatic mutations within the gene encoding calreticulin (CALR) in 2013 represented a major milestone in the molecular diagnosis of BCR-ABL negative myeloproliferative neoplasms (MPN). In fact, exome sequencing revealed that most patients with essential thrombocythemia (ET) or primary myelofibrosis (PMF) lacking JAK2 or MPL mutations, harbor somatic insertion and/or deletion in exon 9 of CALR gene. In this study, we identified the first CALR gene mutational landscape in Moroccan patients with MPN nonmutated for the JAK2 gene. METHODS We performed Sanger sequencing of exon 9 of CALR gene in blood samples obtained from 33 Moroccan patients with ET or PMF non-mutated for JAK2. RESULTS Of the 33 patients analyzed, we detected eight distinct variants in 15 patients (45.4%); six indel mutations, five with type 1 recurrent 52bp deletion, four with type 2 recurrent 5bp insertion and one in frame deletion which was found to be a germline variant suggesting a very rare condition in MPN. CONCLUSION This is the first cohort reported in CALR gene mutation analysis in Morocco. Our results were concordant with studies reported up to date and very encouraging in promoting the molecular diagnosis of myeloproliferative neoplasms in Moroccan patients. Moreover, the presence of a germline in frame deletion in a symptomatic patient should undermine the effectiveness of sizing assays without DNA sequencing in the diagnosis of CALR mutations.
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Affiliation(s)
- W Smaili
- Centre de génomique humaine, faculté de médecine et de pharmacie, université Mohamed V - Rabat, Rabat, Morocco; Département de génétique médicale, Institut national d'hygiène, 27, avenue Ibn Batouta, BP 769, 11400 Rabat, Morocco.
| | - Y Doubaj
- Centre de génomique humaine, faculté de médecine et de pharmacie, université Mohamed V - Rabat, Rabat, Morocco; Département de génétique médicale, Institut national d'hygiène, 27, avenue Ibn Batouta, BP 769, 11400 Rabat, Morocco
| | - F Z Laarabi
- Département de génétique médicale, Institut national d'hygiène, 27, avenue Ibn Batouta, BP 769, 11400 Rabat, Morocco
| | - J Lyahyai
- Centre de génomique humaine, faculté de médecine et de pharmacie, université Mohamed V - Rabat, Rabat, Morocco
| | - M Kerbout
- Service d'hématologie clinique, hôpital militaire d'instruction Mohammed V, université Mohamed V, Rabat, Morocco
| | - M Mikdame
- Service d'hématologie clinique, hôpital militaire d'instruction Mohammed V, université Mohamed V, Rabat, Morocco
| | - A Sefiani
- Centre de génomique humaine, faculté de médecine et de pharmacie, université Mohamed V - Rabat, Rabat, Morocco; Département de génétique médicale, Institut national d'hygiène, 27, avenue Ibn Batouta, BP 769, 11400 Rabat, Morocco
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15
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Fimmel E, Giannerini S, Gonzalez DL, Strüngmann L. Dinucleotide circular codes and bijective transformations. J Theor Biol 2015; 386:159-65. [PMID: 26423358 DOI: 10.1016/j.jtbi.2015.08.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 07/30/2015] [Accepted: 08/29/2015] [Indexed: 11/20/2022]
Abstract
The presence of circular codes in mRNA coding sequences is postulated to be involved in informational mechanisms aimed at detecting and maintaining the normal reading frame during protein synthesis. Most of the recent research is focused on trinucleotide circular codes. However, also dinucleotide circular codes are important since dinucleotides are ubiquitous in genomes and associated to important biological functions. In this work we adopt the group theoretic approach used for trinucleotide codes in Fimmel et al. (2015) to study dinucleotide circular codes and highlight their symmetry properties. Moreover, we characterize such codes in terms of n-circularity and provide a graph representation that allows to visualize them geometrically. The results establish a theoretical framework for the study of the biological implications of dinucleotide circular codes in genomic sequences.
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Affiliation(s)
- Elena Fimmel
- Institute for Mathematical Biology, Faculty of Computer Sciences, Mannheim University of Applied Sciences, 68163 Mannheim, Germany.
| | - Simone Giannerini
- Department of Statistical Sciences, University of Bologna, 40126, Bologna, Italy.
| | - Diego Luis Gonzalez
- CNR-IMM, Sezione di Bologna, Via Gobetti 101, I-40129, Bologna, Italia; Department of Statistical Sciences, University of Bologna, 40126, Bologna, Italy.
| | - Lutz Strüngmann
- Institute for Mathematical Biology, Faculty of Computer Sciences, Mannheim University of Applied Sciences, 68163 Mannheim, Germany.
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16
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Silva-Sanchez A, Liu CR, Vale AM, Khass M, Kapoor P, Elgavish A, Ivanov II, Ippolito GC, Schelonka RL, Schoeb TR, Burrows PD, Schroeder HW. Violation of an evolutionarily conserved immunoglobulin diversity gene sequence preference promotes production of dsDNA-specific IgG antibodies. PLoS One 2015; 10:e0118171. [PMID: 25706374 PMCID: PMC4338297 DOI: 10.1371/journal.pone.0118171] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/08/2015] [Indexed: 11/24/2022] Open
Abstract
Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3), which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (DH) gene segment sequence content by reading frame (RF) is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used DH RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1), which is rearranged by inversion. To determine the effect of altering this germline bias in DH gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type DH sequence did not. Thus, germline bias against the use of arginine enriched DH sequence helps to reduce the likelihood of producing self-reactive antibodies.
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Affiliation(s)
- Aaron Silva-Sanchez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Cun Ren Liu
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andre M. Vale
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Program in Immunobiology, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mohamed Khass
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Genetic Engineering Division, National Research Center of Egypt, Ad Doqi, Egypt
| | - Pratibha Kapoor
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ada Elgavish
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ivaylo I. Ivanov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Gregory C. Ippolito
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Robert L. Schelonka
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Trenton R. Schoeb
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter D. Burrows
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Harry W. Schroeder
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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17
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Wang QS, Jan E. Switch from cap- to factorless IRES-dependent 0 and +1 frame translation during cellular stress and dicistrovirus infection. PLoS One 2014; 9:e103601. [PMID: 25089704 PMCID: PMC4121135 DOI: 10.1371/journal.pone.0103601] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 07/03/2014] [Indexed: 11/18/2022] Open
Abstract
Internal ribosome entry sites (IRES) are utilized by a subset of cellular and viral mRNAs to initiate translation during cellular stress and virus infection when canonical cap-dependent translation is compromised. The intergenic region (IGR) IRES of the Dicistroviridae uses a streamlined mechanism in which it can directly recruit the ribosome in the absence of initiation factors and initiates translation using a non-AUG codon. A subset of IGR IRESs including that from the honey bee viruses can also direct translation of an overlapping +1 frame gene. In this study, we systematically examined cellular conditions that lead to IGR IRES-mediated 0 and +1 frame translation in Drosophila S2 cells. Towards this, a novel bicistronic reporter that exploits the 2A “stop-go” peptide was developed to allow the detection of IRES-mediated translation in vivo. Both 0 and +1 frame translation by the IGR IRES are stimulated under a number of cellular stresses and in S2 cells infected by cricket paralysis virus, demonstrating a switch from cap-dependent to IRES-dependent translation. The regulation of the IGR IRES mechanism ensures that both 0 frame viral structural proteins and +1 frame ORFx protein are optimally expressed during virus infection.
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Affiliation(s)
- Qing S. Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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18
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Abstract
Overall translational machinery in plastids is similar to that of E. coli. Initiation is the crucial step for translation and this step in plastids is somewhat different from that of E. coli. Unlike the Shine-Dalgarno sequence in E. coli, cis-elements for translation initiation are not well conserved in plastid mRNAs. Specific trans-acting factors are generally required for translation initiation and its regulation in plastids. During translation elongation, ribosomes pause sometimes on photosynthesis-related mRNAs due probably to proper insertion of nascent polypeptides into membrane complexes. Codon usage of plastid mRNAs is different from that of E. coli and mammalian cells. Plastid mRNAs do not have the so-called rare codons. Translation efficiencies of several synonymous codons are not always correlated with codon usage in plastid mRNAs.
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19
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Champiat S, Raposo RAS, Maness NJ, Lehman JL, Purtell SE, Hasenkrug AM, Miller JC, Dean H, Koff WC, Hong MA, Martin JN, Deeks SG, Spotts GE, Pilcher CD, Hecht FM, Kallas EG, Garrison KE, Nixon DF. Influence of HAART on alternative reading frame immune responses over the course of HIV-1 infection. PLoS One 2012; 7:e39311. [PMID: 22768072 PMCID: PMC3387156 DOI: 10.1371/journal.pone.0039311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 05/18/2012] [Indexed: 12/22/2022] Open
Abstract
Background Translational errors can result in bypassing of the main viral protein reading frames and the production of alternate reading frame (ARF) or cryptic peptides. Within HIV, there are many such ARFs in both sense and the antisense directions of transcription. These ARFs have the potential to generate immunogenic peptides called cryptic epitopes (CE). Both antiretroviral drug therapy and the immune system exert a mutational pressure on HIV-1. Immune pressure exerted by ARF CD8+ T cells on the virus has already been observed in vitro. HAART has also been described to select HIV-1 variants for drug escape mutations. Since the mutational pressure exerted on one location of the HIV-1 genome can potentially affect the 3 reading frames, we hypothesized that ARF responses would be affected by this drug pressure in vivo. Methodology/Principal findings In this study we identified new ARFs derived from sense and antisense transcription of HIV-1. Many of these ARFs are detectable in circulating viral proteins. They are predominantly found in the HIV-1 env nucleotide region. We measured T cell responses to 199 HIV-1 CE encoded within 13 sense and 34 antisense HIV-1 ARFs. We were able to observe that these ARF responses are more frequent and of greater magnitude in chronically infected individuals compared to acutely infected patients, and in patients on HAART, the breadth of ARF responses increased. Conclusions/Significance These results have implications for vaccine design and unveil the existence of potential new epitopes that could be included as vaccine targets.
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Affiliation(s)
- Stephane Champiat
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Rui André Saraiva Raposo
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Nicholas J. Maness
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - John L. Lehman
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Biology, Saint Mary’s College of California, Moraga, California, United States of America
| | - Sean E. Purtell
- Department of Biology, Saint Mary’s College of California, Moraga, California, United States of America
| | - Aaron M. Hasenkrug
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jacob C. Miller
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Hansi Dean
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Wayne C. Koff
- International AIDS Vaccine Initiative, New York, New York, United States of America
| | - Marisa Ailin Hong
- Division of Clinical Immunology and Allergy, University of São Paulo, São Paulo, Brazil, and Institute Adolfo Lutz, São Paulo, Brazil
| | - Jeffrey N. Martin
- Epidemiology and Prevention Interventions Center, Division of Infectious Diseases, and The Positive Health Program, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Steven G. Deeks
- Positive Health Program, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Gerald E. Spotts
- Positive Health Program, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Christopher D. Pilcher
- Positive Health Program, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Fredrick M. Hecht
- Positive Health Program, Department of Medicine, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Esper G. Kallas
- University of São Paulo, São Paulo, Brazil, Division of Clinical Immunology and Allergy, University of São Paulo, São Paulo, Brazil
| | - Keith E. Garrison
- Department of Biology, Saint Mary’s College of California, Moraga, California, United States of America
| | - Douglas F. Nixon
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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20
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Korotkova MA, Kudryashov NA, Korotkov EV. An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity. Genomics Proteomics Bioinformatics 2012; 9:158-70. [PMID: 22196359 PMCID: PMC5054449 DOI: 10.1016/s1672-0229(11)60019-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/02/2011] [Indexed: 11/28/2022]
Abstract
The concept of the phase shift of triplet periodicity (TP) was used for searching potential DNA insertions in genes from 17 bacterial genomes. A mathematical algorithm for detection of these insertions has been developed. This approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large DNA fragments (>100 bases). New similarity measure between triplet matrixes was employed to improve the sensitivity for detecting the TP phase shift. Sequences of 17,220 bacterial genes with each consisting of more than 1,200 bases were analyzed, and the presence of a TP phase shift has been shown in ~16% of analysed genes (2,809 genes), which is about 4 times more than that detected in our previous work. We propose that shifts of the TP phase may indicate the shifts of reading frame in genes after insertions of the DNA fragments with lengths that are not multiples of three bases. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.
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Affiliation(s)
- Maria A. Korotkova
- National University of Nuclear Investigations (MIFI), Moscow 115409, Russia
| | | | - Eugene V. Korotkov
- National University of Nuclear Investigations (MIFI), Moscow 115409, Russia
- Centre of Bioengineering, Russian Academy of Sciences, Moscow 117312, Russia
- Corresponding author.
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21
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Mahowald GK, Mahowald MA, Moon C, Khor B, Sleckman BP. Out-of-frame T cell receptor beta transcripts are eliminated by multiple pathways in vivo. PLoS One 2011; 6:e21627. [PMID: 21765899 PMCID: PMC3135592 DOI: 10.1371/journal.pone.0021627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 06/03/2011] [Indexed: 11/21/2022] Open
Abstract
Non-productive antigen receptor genes with frame shifts generated during the assembly of these genes are found in many mature lymphocytes. Transcripts from these genes have premature termination codons (PTCs) and could encode truncated proteins if they are not either inactivated or destroyed by nonsense-mediated decay (NMD). In mammalian cells, NMD can be activated by pathways that rely on the presence of an intron downstream of the PTC; however, NMD can also be activated by pathways that do not rely on these downstream introns, and pathways independent of NMD can inactivate PTC-containing transcripts. Here, through the generation and analysis of mice with gene-targeted modifications of the endogenous T cell receptor beta (Tcrb) locus, we demonstrate that in T cells in vivo, optimal clearance of PTC-containing Tcrb transcripts depends on the presence of an intron downstream of the PTC.
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Affiliation(s)
- Grace K. Mahowald
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael A. Mahowald
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Clara Moon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bernard Khor
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Barry P. Sleckman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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22
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Ho JY, Lin TL, Li CY, Lee A, Cheng AN, Chen MC, Wu SH, Wang JT, Li TL, Tsai MD. Functions of some capsular polysaccharide biosynthetic genes in Klebsiella pneumoniae NTUH K-2044. PLoS One 2011; 6:e21664. [PMID: 21765903 PMCID: PMC3134468 DOI: 10.1371/journal.pone.0021664] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 06/05/2011] [Indexed: 11/24/2022] Open
Abstract
The growing number of Klebsiella pneumoniae infections, commonly acquired in hospitals, has drawn great concern. It has been shown that the K1 and K2 capsular serotypes are the most detrimental strains, particularly to those with diabetes. The K1 cps (capsular polysaccharide) locus in the NTUH-2044 strain of the pyogenic liver abscess (PLA) K. pneumoniae has been identified recently, but little is known about the functions of the genes therein. Here we report characterization of a group of cps genes and their roles in the pathogenesis of K1 K. pneumoniae. By sequential gene deletion, the cps gene cluster was first re-delimited between genes galF and ugd, which serve as up- and down-stream ends, respectively. Eight gene products were characterized in vitro and in vivo to be involved in the syntheses of UDP-glucose, UDP-glucuronic acid and GDP-fucose building units. Twelve genes were identified as virulence factors based on the observation that their deletion mutants became avirulent or lost K1 antigenicity. Furthermore, deletion of kp3706, kp3709 or kp3712 (ΔwcaI, ΔwcaG or Δatf, respectively), which are all involved in fucose biosynthesis, led to a broad range of transcriptional suppression for 52 upstream genes. The genes suppressed include those coding for unknown regulatory membrane proteins and six multidrug efflux system proteins, as well as proteins required for the K1 CPS biosynthesis. In support of the suppression of multidrug efflux genes, we showed that these three mutants became more sensitive to antibiotics. Taken together, the results suggest that kp3706, kp3709 or kp3712 genes are strongly related to the pathogenesis of K. pneumoniae K1.
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Affiliation(s)
- Jin-Yuan Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
| | - Tzu-Lung Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chun-Yen Li
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Arwen Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - An-Ning Cheng
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Bioinformatics and Structure Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Chuan Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- * E-mail: (JW); (TL); (MT)
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei, Taiwan
- * E-mail: (JW); (TL); (MT)
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Institute of Biochemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Science, National Taiwan University, Taipei, Taiwan
- * E-mail: (JW); (TL); (MT)
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23
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Matsuo M, Takeshima Y. [Mutation-specific treatments for Duchenne muscular dystrophy]. Brain Nerve 2009; 61:915-922. [PMID: 19697880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Duchenne muscular dystrophy (DMD) is the most common form of inherited muscle disease and is characterized by progressive muscle wasting ultimately resulting in death of the patients in their twenties. DMD is characterized by a deficiency of the muscle dystrophin as a result of mutations in the dystrophin gene. Currently, no effective treatment for DMD is available. Two promising treatments strategies have been proposed specifically for correcting the mutations in the dystrophin gene. Induction of exon skipping using antisense oligonucleotides is expected to correct the out-of-frame mutation into in-frame mutation of the translational reading frame of dystrophin mRNA. This strategy enables the production of truncated dystrophin production in DMD patients with out-of-frame exon-deletion mutations in the dystrophin gene. Our first treatment with antisense oligonucleotides against exon 19 was successful and resulted in the production of dystrophin in the skeletal muscle of a DMD patient with exon 20 deletion. It is anticipated that exon skipping will be applied extensively for the correction of deletion mutations. Induction of the read-through effect using gentamycin or PTC124 is expected to produce dystrophin in DMD patients with nonsense mutation. The treatment with PTC124 is currently under clinical trial. In this review, these treatments strategies have been summarized.
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Affiliation(s)
- Masafumi Matsuo
- Department of Pediatrics, Kobe Uni versity Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
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24
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Bouva MJ, Harteveld CL, Bakker-Verweij G, van Delft P, Giordano PC. Gγ −37 (A→T): A New Nondeletional Hereditary Persistence of Fetal Hemoglobin Determinant Associated with the Rare Codon 91 (+T) δ0-Thalassemia. Hemoglobin 2009; 30:371-7. [PMID: 16840228 DOI: 10.1080/03630260600755641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We recently described a rare frameshift mutation in the delta-globin gene in a Dutch patient, in association with a new mutation of the Ggamma-globin gene promoter [Ggamma -37 (A-->T)] with a moderately elevated Hb F level of 2.3%. The delta mutation at codon 91 (+T) has been described once before in our laboratory in 1989, in a complex Belgian family with Ggamma (Agammadeltabeta)0-thalassemia (thal) and moderately elevated Hb F levels, without the Ggamma (Agammadeltabeta)0-thal deletion in some individuals. Analysis of the patients from 1989 revealed the presence of the same Ggamma-globin gene mutation and moderately elevated Hb F in all patients, who were also carriers of the delta-globin gene frameshift. Further analysis demonstrated that the two mutations were in linkage with the same haplotype in both the Belgian family and the recently found patient, confirming the association of the elevated Hb F expression with the new Ggamma-globin gene mutation.
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Affiliation(s)
- Marelle J Bouva
- Department of Human and Clinical Genetics, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
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25
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Ahmed ZM, Masmoudi S, Kalay E, Belyantseva IA, Mosrati MA, Collin RWJ, Riazuddin S, Hmani-Aifa M, Venselaar H, Kawar MN, Abdelaziz T, van der Zwaag B, Khan SY, Ayadi L, Riazuddin SA, Morell RJ, Griffith AJ, Charfedine I, Çaylan R, Oostrik J, Karaguzel A, Ghorbel A, Riazuddin S, Friedman TB, Ayadi H, Kremer H. Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans. Nat Genet 2008; 40:1335-40. [PMID: 18953341 PMCID: PMC3404732 DOI: 10.1038/ng.245] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Accepted: 08/28/2008] [Indexed: 01/09/2023]
Abstract
Many proteins necessary for sound transduction have been identified through positional cloning of genes that cause deafness. We report here that mutations of LRTOMT are associated with profound nonsyndromic hearing loss at the DFNB63 locus on human chromosome 11q13.3-q13.4. LRTOMT has two alternative reading frames and encodes two different proteins, LRTOMT1 and LRTOMT2, detected by protein blot analyses. LRTOMT2 is a putative methyltransferase. During evolution, new transcripts can arise through partial or complete coalescence of genes. We provide evidence that in the primate lineage LRTOMT evolved from the fusion of two neighboring ancestral genes, which exist as separate genes (Lrrc51 and Tomt) in rodents.
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Affiliation(s)
- Zubair M Ahmed
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Rockville, MD, USA
| | - Saber Masmoudi
- Unité Cibles pour le Diagnostic et la Thérapie, Centre de Biotechnologie de Sfax, Tunisie
| | - Ersan Kalay
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Medical Biology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Rockville, MD, USA
| | - Mohamed Ali Mosrati
- Unité Cibles pour le Diagnostic et la Thérapie, Centre de Biotechnologie de Sfax, Tunisie
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Saima Riazuddin
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Rockville, MD, USA
| | - Mounira Hmani-Aifa
- Unité Cibles pour le Diagnostic et la Thérapie, Centre de Biotechnologie de Sfax, Tunisie
| | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Mayya N Kawar
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Rockville, MD, USA
| | - Tlili Abdelaziz
- Unité Cibles pour le Diagnostic et la Thérapie, Centre de Biotechnologie de Sfax, Tunisie
| | - Bert van der Zwaag
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Shahid Y Khan
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Leila Ayadi
- Unité Cibles pour le Diagnostic et la Thérapie, Centre de Biotechnologie de Sfax, Tunisie
| | - S Amer Riazuddin
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Robert J Morell
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Rockville, MD, USA
| | - Andrew J Griffith
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, Rockville, MD, USA
| | | | - Refik Çaylan
- Department of Otorhinolaryngology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ahmet Karaguzel
- Department of Medical Biology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | | | - Sheikh Riazuddin
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Rockville, MD, USA
| | - Hammadi Ayadi
- Unité Cibles pour le Diagnostic et la Thérapie, Centre de Biotechnologie de Sfax, Tunisie
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, the Netherlands
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26
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Lillo F, Krakauer DC. A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes. Biol Direct 2007; 2:22. [PMID: 17877818 PMCID: PMC2174442 DOI: 10.1186/1745-6150-2-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Accepted: 09/18/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among microbial genomes, genetic information is frequently compressed, exploiting redundancies in the genetic code in order to store information in overlapping genes. We investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution. RESULTS Using a variety of statistical null models we find patterns of compressive coding that can not be explained purely in terms of the selective processes favoring genome minimization or translational coupling. The distribution of overlap lengths follows a fat-tailed distribution, in which a significant proportion of overlaps are in excess of 100 base pairs in length. The phase of overlap--pairing of codon positions in complementary reading frames--is strongly predicted by the translation orientation of each gene. We find that as overlapping genes become longer, they have a tendency to alternate among alternative overlap phases. Some phases seem to reflect codon pairings reducing the probability of non-synonymous substitution. We analyze the lineage-dependent features of overlapping genes by tracing a number of different continuous characters through the prokaryotic phylogeny using squared-change parsimony and observe both clade-specific and species-specific patterns. CONCLUSION Overlapping reading frames preserve in their structure, features relating to mutational origination of new genes, but have undergone modification for both immediate benefits and for variational buffering and amplification. Genomes come under a variety of different mutational and selectional pressures, and the structure of redundancies in overlapping genes can be used to detect these pressures. No single mechanism is able to account for all the variability observed among the set of prokaryotic overlapping genes but a three-fold analysis of evolutionary events provides a more integrative framework.
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Affiliation(s)
- Fabrizio Lillo
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- Dipartimento di Fisicae Tecnologie Relative, Università di Palermo, Viale delle Scienze, I-90128 Palermo, Italy
| | - David C Krakauer
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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27
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Abstract
The roles of the ribosomal E site are not fully understood. Prior evidence suggests that deacyl-tRNA in the E site can prevent frameshifting. We hypothesized that if the E-site codon must dissociate from its tRNA to allow for frameshifting, then weak codon:anticodon duplexes should allow for greater frameshifting than stronger duplexes. Using the well-characterized Escherichia coli RF2 (prfB) programmed frameshift to study frameshifting, we mutagenized the E-site triplet to all Unn and Cnn codons. Those variants should represent a very wide range of duplex stability. Duplex stability was estimated using two different methods. Frameshifting is inversely correlated with stability, as estimated by either method. These findings indicate that pairing between the deacyl-tRNA and the E-site codon opposes frameshifting. We discuss the implications of these findings on frame maintenance and on the RF2 programmed frameshift mechanism.
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28
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Cock PJA, Whitworth DE. Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes. J Mol Evol 2007; 64:457-62. [PMID: 17479344 DOI: 10.1007/s00239-006-0180-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 01/22/2007] [Indexed: 10/23/2022]
Abstract
During a survey of two-component system genes, a list of neighboring histidine kinase and response regulator genes, encoded on the same strand, was compiled from over 200 fully sequenced bacteria. It was observed that many gene pairs overlapped, and although such overlaps can potentially occur in two phases (relative reading frames), one phase predominated for overlaps of seven or more nucleotides. Preference for a particular phase cannot be explained by arguments of sequence restraint (mutations in one gene differentially affect an overlapping gene, depending on phase). We have therefore investigated a potential explanation of the observed phase bias. For phase +1 gene overlaps, simulated point mutations in the overlapping region result in more severe changes to the downstream gene product than to the upstream gene product; vice versa in phase +2. Additionally, codon usage frequencies in nonoverlapping regions are more similar to those at the end of the upstream gene than the beginning of the downstream gene in overlaps. Taking both observations together, we propose that new gene overlaps generally arise by N-terminal extension of a downstream gene, creating a novel sequence at the start of the downstream gene. Sequence changes in this newly coding sequence will alter the sequences of both the new and the original coding sequence (the C-terminal region of the upstream gene). However, these changes will be less detrimental to the original coding sequence if the two genes overlap in phase +1, leading to selective retention during evolution of phase +1 overlaps relative to phase +2 overlaps.
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Affiliation(s)
- Peter J A Cock
- MOAC Doctoral Training Centre, University of Warwick, Coventry, UK
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29
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Kothe U, Rodnina MV. Codon reading by tRNAAla with modified uridine in the wobble position. Mol Cell 2007; 25:167-74. [PMID: 17218280 DOI: 10.1016/j.molcel.2006.11.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 11/02/2006] [Accepted: 11/14/2006] [Indexed: 10/23/2022]
Abstract
tRNAs reading four-codon families often have a modified uridine, cmo(5)U(34), at the wobble position of the anticodon. Here, we examine the effects on the decoding mechanism of a cmo(5)U modification in tRNA(1B)(Ala), anticodon C(36)G(35)cmo(5)U(34). tRNA(1B)(Ala) reads its cognate codons in a manner that is very similar to that of tRNA(Phe). As Ala codons are GC rich and Phe codons AU rich, this similarity suggests a uniform decoding mechanism that is independent of the GC content of the codon-anticodon duplex or the identity of the tRNA. The presence of cmo(5)U at the wobble position of tRNA(1B)(Ala) permits fairly efficient reading of non-Watson-Crick and nonwobble bases in the third codon position, e.g., the GCC codon. The ribosome accepts the C-cmo(5)U pair as an almost-correct base pair, unlike third-position mismatches, which lead to the incorporation of incorrect amino acids and are efficiently rejected.
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Affiliation(s)
- Ute Kothe
- Institute of Physical Biochemistry, University of Witten/Herdecke, 58448 Witten, Germany
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30
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Zhao X, McGirr KM, Buehring GC. Potential evolutionary influences on overlapping reading frames in the bovine leukemia virus pXBL region. Genomics 2007; 89:502-11. [PMID: 17239558 DOI: 10.1016/j.ygeno.2006.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 11/27/2006] [Accepted: 12/14/2006] [Indexed: 01/25/2023]
Abstract
Bovine leukemia virus contains a pXBL region encoding the 3' parts of four regulatory proteins (Tax, Rex, G4, R3) in overlapping reading frames. Here we report the pXBL polymorphisms of 30 isolates from four countries. Rates of overall and synonymous substitutions were consistently lower, and nucleotide/amino acid composition bias and codon bias higher, in more-overlapped than in less-overlapped regions. Ratios of nonsynonymous/synonymous substitutions were lowest in the tax gene and its subregions. The 5' parts of the four genes showed selection patterns corresponding to their genomic context outside of the pXBL region. Longer G4 variants due to a natural stop codon mutation had additional triple overlap with reduced sequence variability. These data support the concept that a higher level of overlapping in coding regions correlates with greater evolutionary constraint. Tax, the most conserved among the four regulatory proteins, showed purifying selection consistent with its importance in the viral life cycle.
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Affiliation(s)
- Xiangrong Zhao
- Graduate Program in Endocrinology, University of California at Berkeley, 3060 Valley Life Science Building, Berkeley, CA 94720-3140, USA.
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31
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Chappuis P, Callebert J, Quignon V, Woimant F, Laplanche JL. Late neurological presentations of Wilson disease patients in French population and identification of 8 novel mutations in the ATP7B gene. J Trace Elem Med Biol 2007; 21:37-42. [PMID: 17317524 DOI: 10.1016/j.jtemb.2006.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 11/12/2006] [Indexed: 01/28/2023]
Abstract
Wilson disease (WD) is an autosomal recessive disorder of copper biliary excretion caused by an impaired function of ATP7B, a metal-transporting P-type ATPase encoded by WD gene. It results in copper accumulation, mostly in liver and brain tissues. Mutation analysis was carried out on 11 WD French unrelated patients presenting a predominant neurological form of this illness. SSCP and dHPLC analysis followed by sequencing of the 21 exons and their flanking introns were performed. Thirteen different mutations in a total of 17, and, among them, 10 novel variants were evidenced. Two deletions (c.654_655delCC and c.1745_1746delTA), 4 missense mutations (p.F763Y, p.G843R, p.D918A and p.L979Q), 1 nonsense mutation (p.Q1200X), 1 splice site mutation (c.1947-1G>C) and 2 intronic silent substitutions (c.2448-25G>T and c.3412+13T>A) were detected. These data extend the mutational spectrum of the disease, already known to be a very heterogeneous genetic disorder. As compared to hepatic manifestations, the phenotypes associated to these mutations confirm that neurological presentations associated with other mutations than p.H1069Q are also often late in their onset. Most of these neurological forms probably correspond to an attenuated impairment of copper metabolism, as compared to hepatic forms of the disease, mostly diagnosed earlier.
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Affiliation(s)
- Philippe Chappuis
- Hôpital Lariboisière, Centre National Référence Bernard Pépin pour la Maladie de Wilson, Service de Biochimie et Biologie Moléculaire, 2, rue A. Paré, 75475 Paris Cedex 10, France.
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32
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Aartsma-Rus A, Van Deutekom JCT, Fokkema IF, Van Ommen GJB, Den Dunnen JT. Entries in the Leiden Duchenne muscular dystrophy mutation database: an overview of mutation types and paradoxical cases that confirm the reading-frame rule. Muscle Nerve 2006; 34:135-44. [PMID: 16770791 DOI: 10.1002/mus.20586] [Citation(s) in RCA: 460] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The severe Duchenne and milder Becker muscular dystrophy are both caused by mutations in the DMD gene. This gene codes for dystrophin, a protein important for maintaining the stability of muscle-fiber membranes. In 1988, Monaco and colleagues postulated an explanation for the phenotypic difference between Duchenne and Becker patients in the reading-frame rule: In Duchenne patients, mutations induce a shift in the reading frame leading to prematurely truncated, dysfunctional dystrophins. In Becker patients, in-frame mutations allow the synthesis of internally deleted, but largely functional dystrophins. Currently, over 4700 mutations have been reported in the Leiden DMD mutation database, of which 91% are in agreement with this rule. In this study we provide an update of the mutational variability in the DMD gene, particularly focusing on genotype-phenotype correlations and mutations that appear to be exceptions to the reading-frame rule.
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Affiliation(s)
- Annemieke Aartsma-Rus
- Leiden University Medical Center, Department of Human Genetics, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
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33
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Abstract
Life depends on the faithful translation of the genetic information into proteins. Ribosomes have developed remarkable mechanisms to ensure the accurate synthesis of proteins. In the first part of this review various types of ribosomal errors and their importance for cell-life are surveyed, while in the second part two important aspects of the ribosomal E-site for the accuracy of translation are considered: (i) The fact that usually misincorporations are not harmful for the cell, since only one in about 400 misincorporations will affect the structure and/or function of a protein, is a function of the E-site. (ii) In contrast, an extremely harmful translational error is a loss of the reading frame, resulting in an immediate loss of the genetic information. Maintenance of the reading frame is one of the most remarkable achievements of the ribosome; only once in about 30,000 elongation cycles is the reading frame lost. A cognate tRNA at the E-site is an essential prerequisite for this high precision.
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Affiliation(s)
- Knud H Nierhaus
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, AG Ribosomen, D-14195 Berlin, Germany.
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34
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Phelps SS, Gaudin C, Yoshizawa S, Benitez C, Fourmy D, Joseph S. Translocation of a tRNA with an extended anticodon through the ribosome. J Mol Biol 2006; 360:610-22. [PMID: 16787653 DOI: 10.1016/j.jmb.2006.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/04/2006] [Accepted: 05/04/2006] [Indexed: 11/18/2022]
Abstract
Coordinated translocation of the tRNA-mRNA complex by the ribosome occurs in a precise, stepwise movement corresponding to a distance of three nucleotides along the mRNA. Frameshift suppressor tRNAs generally contain an extra nucleotide in the anticodon loop and they subvert the normal mechanisms used by the ribosome for frame maintenance. The mechanism by which suppressor tRNAs traverse the ribosome during translocation is poorly understood. Here, we demonstrate translocation of a tRNA by four nucleotides from the A site to the P site, and from the P site to the E site. We show that translocation of a punctuated mRNA is possible with an extra, unpaired nucleotide between codons. Interestingly, the NMR structure of the four nucleotide anticodon stem-loop reveals a conformation different from the canonical tRNA structure. Flexibility within the loop may allow conformational adjustment upon A site binding and for interacting with the four nucleotide codon in order to shift the mRNA reading frame.
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MESH Headings
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- Escherichia coli
- Hydrogen-Ion Concentration
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Nucleic Acid Conformation/drug effects
- Pliability/drug effects
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- Reading Frames/genetics
- Ribosomes/genetics
- Ribosomes/metabolism
- Salts/pharmacology
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Affiliation(s)
- Steven S Phelps
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0314, USA
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35
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Ho O, Green WR. Cytolytic CD8+T Cells Directed against a Cryptic Epitope Derived from a Retroviral Alternative Reading Frame Confer Disease Protection. J Immunol 2006; 176:2470-5. [PMID: 16456007 DOI: 10.4049/jimmunol.176.4.2470] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cytolytic CD8(+) T cells (CTL) are key to the immune response that controls virus infections and mediates disease protection. The ability of CTL to induce apoptosis of infected cells and/or limit viral replication is determined by recognition of processed viral peptide epitopes on the surface of the target cell. An understudied source of MHC class I-presented peptides is the aptly named "cryptic epitopes," defined by their nontraditional methods of generation, including derivation from alternative reading frames (ARFs). Although ARF-encoded epitopes have now been documented in a few systems, their potential functional relevance in vivo has been debated. In this study, we demonstrate the physiological significance of an ARF-derived CTL epitope in a retrovirus-induced disease model. We show that disease-susceptible CD8-deficient mice reconstituted with CTL specific for the retroviral ARF-derived SYNTGRFPPL epitope controlled an infection by the LP-BM5 retrovirus isolate, evidently at the level of viral clearance, resulting in protection of these mice from disease. These data indicate that ARF-derived epitopes are indeed relevant inducers of the immune system and demonstrate the importance of atypically generated peptides as functional Ag with a physiologic role in disease protection.
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Affiliation(s)
- On Ho
- Department of Microbiology and Immunology, Dartmouth Medical School, Lebanon, NH 03756, USA
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36
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Klase Z, Donio MJ, Blauvelt A, Marx PA, Jeang KT, Smith SM. A peptide-loaded dendritic cell based cytotoxic T-lymphocyte (CTL) vaccination strategy using peptides that span SIV Tat, Rev, and Env overlapping reading frames. Retrovirology 2006; 3:1. [PMID: 16398928 PMCID: PMC1360091 DOI: 10.1186/1742-4690-3-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2005] [Accepted: 01/06/2006] [Indexed: 11/17/2022] Open
Abstract
CTL based vaccine strategies in the macaque model of AIDS have shown promise in slowing the progression to disease. However, rapid CTL escape viruses can emerge rendering such vaccination useless. We hypothesized that such escape is made more difficult if the immunizing CTL epitope falls within a region of the virus that has a high density of overlapping reading frames which encode several viral proteins. To test this hypothesis, we immunized macaques using a peptide-loaded dendritic cell approach employing epitopes in the second coding exon of SIV Tat which spans reading frames for both Env and Rev. We report here that autologous dendritic cells, loaded with SIV peptides from Tat, Rev, and Env, induced a distinct cellular immune response measurable ex vivo. However, conclusive in vivo control of a challenge inoculation of SIVmac239 was not observed suggesting that CTL epitopes within densely overlapping reading frames are also subject to escape mutations.
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MESH Headings
- Animals
- CD4 Lymphocyte Count
- DNA Primers
- Dendritic Cells/immunology
- Enzyme-Linked Immunosorbent Assay
- Gene Products, env/chemistry
- Gene Products, env/genetics
- Gene Products, env/immunology
- Gene Products, rev/chemistry
- Gene Products, rev/genetics
- Gene Products, rev/immunology
- Gene Products, tat/chemistry
- Gene Products, tat/genetics
- Gene Products, tat/immunology
- Macaca mulatta
- Molecular Sequence Data
- Mutation
- Peptide Fragments/immunology
- Polymerase Chain Reaction
- Reading Frames/genetics
- Simian Immunodeficiency Virus/immunology
- T-Lymphocytes, Cytotoxic/immunology
- Vaccination
- Vaccines, Subunit
- Viral Load
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Affiliation(s)
- Zachary Klase
- Department of Infectious Diseases, Saint Michael's Medical Center, Newark, New Jersey, USA
| | - Michael J Donio
- Department of Infectious Diseases, Saint Michael's Medical Center, Newark, New Jersey, USA
| | - Andrew Blauvelt
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
- Dermatology Service, VA Medical Center, Portland, Oregon, USA
| | - Preston A Marx
- Tulane National Primate Research Center, Tulane University Health Sciences Center, Department of Tropical Medicine, Covington, Louisiana, USA
| | - Kuan-Teh Jeang
- Molecular Virology Section, Laboratory of Molecular Medicine, NIAID, NIH, Bethesda, Maryland, USA
| | - Stephen M Smith
- Department of Infectious Diseases, Saint Michael's Medical Center, Newark, New Jersey, USA
- Department of Preventive Medicine and Community Health, New Jersey Medical School, Newark, New Jersey, USA
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37
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Ivanov II, Schelonka RL, Zhuang Y, Gartland GL, Zemlin M, Schroeder HW. Development of the expressed Ig CDR-H3 repertoire is marked by focusing of constraints in length, amino acid use, and charge that are first established in early B cell progenitors. J Immunol 2005; 174:7773-80. [PMID: 15944280 DOI: 10.4049/jimmunol.174.12.7773] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To gain insight into the mechanisms that regulate the development of the H chain CDR3 (CDR-H3), we used the scheme of Hardy to sort mouse bone marrow B lineage cells into progenitor, immature, and mature B cell fractions, and then performed sequence analysis on V(H)7183-containing Cmu transcripts. The essential architecture of the CDR-H3 repertoire observed in the mature B cell fraction F was already established in the early pre-B cell fraction C. These architectural features include V(H) gene segment use preference, D(H) family usage, J(H) rank order, predicted structures of the CDR-H3 base and loop, and the amino acid composition and average hydrophobicity of the CDR-H3 loop. With development, the repertoire was focused by eliminating outliers to what appears to be a preferred repertoire in terms of length, amino acid composition, and average hydrophobicity. Unlike humans, the average length of CDR-H3 increased during development. The majority of this increase came from enhanced preservation of J(H) sequence. This was associated with an increase in the prevalence of tyrosine. With an accompanying increase in glycine, a shift in hydrophobicity was observed in the CDR-H3 loop from near neutral in fraction C (-0.08 +/- 0.03) to mild hydrophilic in fraction F (-0.17 +/- 0.02). Fundamental constraints on the sequence and structure of CDR-H3 are thus established before surface IgM expression.
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Affiliation(s)
- Ivaylo I Ivanov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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38
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Muralitharan S, Al Lamki Z, Dennison D, Christie BS, Wali YA, Zachariah M, Romana M, Bayoumi R, Krishnamoorthy R. An inframe perforin gene deletion in familial hemophagocytic lymphohistiocytosis is associated with perforin expression. Am J Hematol 2005; 78:59-63. [PMID: 15609274 DOI: 10.1002/ajh.20256] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Familial hemophagocytic lymphohistiocytosis is an autosomal recessive disease of early childhood manifested by hypercytokinemia and organ infiltration of macrophages and activated lymphocytes, and it is characterized by a fulminant clinical course. The molecular mechanism underlying this disease appears to be a deregulation of apoptosis of activated T cells and macrophages. Approximately 20-40% of patients with familial hemophagocytic lymphohistiocytosis reported worldwide had a perforin gene mutation. We report herein a novel perforin variant in the homozygous state in an Omani boy who was diagnosed 44 days after birth. Sequence analysis of the perforin gene coding region revealed a 12-base pair deletion (codon 284-287) resulting in the deletion of four amino acids in the membrane attack complex domain of the protein. This deletion maintains the reading frame of the perforin mRNA. Both parents were heterozygotes for this molecular defect. Flow-cytometric analysis revealed intracellular perforin expression at the lower end of the normal range in the cytotoxic T cells (CD3+/CD8+) and (CD3+/CD56+) and in around 50% of the natural killer cells (CD3-/CD56+). This is an additional example of a perforin variant which is associated with a significant level of cellular perforin expression and thus confirms that drastic reduction in its expression is not a constant feature in familial hemophagocytic lymphohistiocytosis type 2.
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Affiliation(s)
- Shanmugakonar Muralitharan
- Department of Child Health, Hematology, and Biochemistry, Sultan Qaboos University Hospital, Al-Khoud, Oman
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39
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Hasan MK, Yaguchi T, Minoda Y, Hirano T, Taira K, Wadhwa R, Kaul SC. Alternative reading frame protein (ARF)-independent function of CARF (collaborator of ARF) involves its interactions with p53: evidence for a novel p53-activation pathway and its negative feedback control. Biochem J 2004; 380:605-10. [PMID: 15109303 PMCID: PMC1224239 DOI: 10.1042/bj20040337] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Revised: 04/19/2004] [Accepted: 04/27/2004] [Indexed: 01/01/2023]
Abstract
CARF, a collaborator of ARF (alternative reading frame protein), was cloned as a novel ARF-binding protein from a yeast-interaction screen. It potentiated ARF-mediated p53 function, and also caused a moderate increase in p53 activity in the absence of ARF. We herein report the molecular mechanism of ARF-independent function of CARF. By employing a variety of approaches, including overexpression of CARF, its suppression by small interfering RNA and use of protease inhibitors, we demonstrate that: (i) CARF directly interacts with wild-type p53, causing its stabilization and functional activation; and (ii) CARF and p53 levels show an inverse relationship that is instigated by a negative-feedback control via a proteasome-mediated degradation pathway.
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Affiliation(s)
- Md Kamrul Hasan
- Gene Function Research Center, National Institute of Advanced Industrial Science & Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
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40
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Pittis MG, Ricci V, Guerci VI, Marçais C, Ciana G, Dardis A, Gerin F, Stroppiano M, Vanier MT, Filocamo M, Bembi B. Acid sphingomyelinase: identification of nine novel mutations among Italian Niemann Pick type B patients and characterization of in vivo functional in-frame start codon. Hum Mutat 2004; 24:186-7. [PMID: 15241805 DOI: 10.1002/humu.9263] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Niemann Pick disease (NPD) is an autosomal recessive disorder due to the deficit of lysosomal acid sphingomyelinase, which results in intracellular accumulation of sphingomyelin. In the present work we studied 18 patients with NPD type B, including five individuals who presented an intermediate phenotype characterised by different levels of neurological involvement. We identified nine novel mutations in the SMPD1 gene including six single base changes c.2T>G, c.96G>A, c.308T>C, c.674T>C, c.732G>C, c.841G>A (p.M1_W32del, p.W32X, p.L103P, p.L225P, p.W244C, p.A281T) and three frameshift mutations c.100delC, c.565dupC, c.575dupC (p.G34fsX42, p.P189fsX1 and p.P192fsX14). The novel c.2T>G (p.M1_W32del) mutation inactivates the first in-frame translation start site of the SMPD1 gene and in the homozygous status causes NPD type B indicating that in'vivo translation of wild type SMPD1 initiates from the first in-frame ATG. Moreover, the new c.96G>A (p.W32X) introduces a premature stop codon before the second in-frame ATG. As a consequence of either c.2T>G (p.M1_W32del) or c.96G>A (p.W32X), impaired translation from the first in-frame ATG results in a mild NPD-B phenotype instead of the severe phenotype expected for a complete deficiency of the enzyme, suggesting that when the first ATG is not functional, the second initiation codon (ATG33) still produces a fairly functional sphingomyelinase. Analysis of the patients'clinical and molecular data demonstrated that all five patients with the intermediate phenotype carried at least one severe mutation. No association between the onset of pulmonary symptoms and genotype was observed. Finally, the presence of c.96G>A (p.W32X), the most frequent allele among Italian NPD type B population, and c.1799G>C (p.R600P) as compound heterozygotes in association with severe mutations suggested a beneficial effect for both mutations.
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Affiliation(s)
- M G Pittis
- Unità di Malattie Metaboliche, I.R.C.C.S. Burlo Garofolo, Trieste, Italy
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41
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Villesen P, Aagaard L, Wiuf C, Pedersen FS. Identification of endogenous retroviral reading frames in the human genome. Retrovirology 2004; 1:32. [PMID: 15476554 PMCID: PMC524368 DOI: 10.1186/1742-4690-1-32] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 10/11/2004] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs) comprise a large class of repetitive retroelements. Most HERVs are ancient and invaded our genome at least 25 million years ago, except for the evolutionary young HERV-K group. The far majority of the encoded genes are degenerate due to mutational decay and only a few non-HERV-K loci are known to retain intact reading frames. Additional intact HERV genes may exist, since retroviral reading frames have not been systematically annotated on a genome-wide scale. RESULTS By clustering of hits from multiple BLAST searches using known retroviral sequences we have mapped 1.1% of the human genome as retrovirus related. The coding potential of all identified HERV regions were analyzed by annotating viral open reading frames (vORFs) and we report 7836 loci as verified by protein homology criteria. Among 59 intact or almost-intact viral polyproteins scattered around the human genome we have found 29 envelope genes including two novel gammaretroviral types. One encodes a protein similar to a recently discovered zebrafish retrovirus (ZFERV) while another shows partial, C-terminal, homology to Syncytin (HERV-W/FRD). CONCLUSIONS This compilation of HERV sequences and their coding potential provide a useful tool for pursuing functional analysis such as RNA expression profiling and effects of viral proteins, which may, in turn, reveal a role for HERVs in human health and disease. All data are publicly available through a database at http://www.retrosearch.dk.
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Affiliation(s)
- Palle Villesen
- Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, Bldg. 090, DK-8000 Aarhus, Denmark
| | - Lars Aagaard
- Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, Bldg. 090, DK-8000 Aarhus, Denmark
| | - Carsten Wiuf
- Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, Bldg. 090, DK-8000 Aarhus, Denmark
| | - Finn Skou Pedersen
- Department of Molecular Biology, University of Aarhus, C. F. Møllers Allé, Bldg. 130, DK-8000 Aarhus, Denmark
- Department of Medical Microbiology and Immunology, University of Aarhus, DK-8000 Aarhus, Denmark
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42
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Zhang Y, Emmanuel N, Kamboj G, Chen J, Shurafa M, Van Dyke DL, Wiktor A, Rowley JD. PRDX4, a member of the peroxiredoxin family, is fused to AML1 (RUNX1) in an acute myeloid leukemia patient with a t(X;21)(p22;q22). Genes Chromosomes Cancer 2004; 40:365-70. [PMID: 15188461 DOI: 10.1002/gcc.20050] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The AML1 gene (also known as RUNX1) at 21q22 codes for core binding factor (CBF) alpha, which forms a heterodimer with CBF beta that acts as a transcriptional activating factor. CBF is a critical regulator in the generation and differentiation of definitive hematopoietic stem cells and is frequently disrupted in leukemia through chromosome translocations. We cloned a novel AML1 partner gene, PRDX4, in an X;21 translocation in a 74-year-old male patient diagnosed with acute myeloid leukemia-M2. Chromosome analysis detected a t(X;21)(p22;q22) as the sole abnormality in bone marrow samples. The involvement of AML1 was confirmed by fluorescence in situ hybridization studies. Using 3' RACE-PCR, we cloned a fusion between exon 5 of AML1 and exon 2 of PRDX4. RT-PCR confirmed the fusion and detected another fusion between exon 6 of AML1 and exon 2 of PRDX4, indicating alternative splicing of exon 6 of AML1 in the fusion transcripts. PRDX4 is one of six peroxiredoxin-family genes that are highly conserved in eukaryotes and prokaryotes and are ubiquitously expressed. Peroxiredoxin genes exhibit thioredoxin-dependent peroxidase activity and have been implicated in a number of other cellular functions such as cell proliferation and differentiation. PRDX4 plays a regulatory role in the activation of the transcription factor NF-kappaB and is significantly down-regulated in acute promyelocytic leukemia. This is the first example of antioxidant enzyme involvement in a chromosome translocation in leukemia.
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Affiliation(s)
- Yanming Zhang
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois 60637, USA
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43
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Boyer J, Badis G, Fairhead C, Talla E, Hantraye F, Fabre E, Fischer G, Hennequin C, Koszul R, Lafontaine I, Ozier-Kalogeropoulos O, Ricchetti M, Richard GF, Thierry A, Dujon B. Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae. Genome Biol 2004; 5:R72. [PMID: 15345056 PMCID: PMC522879 DOI: 10.1186/gb-2004-5-9-r72] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2004] [Revised: 07/13/2004] [Accepted: 07/26/2004] [Indexed: 03/24/2023] Open
Abstract
We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We selected 714 such fragments with a mean size of 700 base-pairs out of around 84,000 clones tested. These include 493 in-frame open reading frame fragments corresponding to 454 distinct genes (of which 91 are of unknown function), and 162 out-of-frame, antisense and intergenic genomic fragments, representing the largest collection of toxic inserts published so far in yeast.
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Affiliation(s)
- Jeanne Boyer
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Gwenaël Badis
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- Unité de Génétique des Interactions Macromoléculaires (URA2171 CNRS), Department of Structure and Dynamics of Genomes, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris-Cedex 15, France
| | - Cécile Fairhead
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Emmanuel Talla
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- CNRS-Laboratoire de Chimie Bactérienne, 31 Chemin Joseph Aiguier, 13402 Marseille-Cedex 20, France
| | - Florence Hantraye
- Unité de Génétique des Interactions Macromoléculaires (URA2171 CNRS), Department of Structure and Dynamics of Genomes, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris-Cedex 15, France
| | - Emmanuelle Fabre
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Gilles Fischer
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Christophe Hennequin
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- Laboratoire de Parasitologie, Faculté de Médecine St-Antoine, 27 rue de Chaligny, 75012 Paris, France
| | - Romain Koszul
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Ingrid Lafontaine
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | | | - Miria Ricchetti
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
- Unité de Génétique et Biochimie du Développement, Institut Pasteur, 25 rue du Dr Roux 75724 Paris-Cedex 15, France
| | - Guy-Franck Richard
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Agnès Thierry
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
| | - Bernard Dujon
- Unité de Génétique Moléculaire des Levures (URA2171 CNRS and UFR 927 Université Pierre et Marie Curie)
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44
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Couedel C, Lippert E, Bernardeau K, Bonneville M, Davodeau F. Allelic exclusion at the TCR delta locus and commitment to gamma delta lineage: different modalities apply to distinct human gamma delta subsets. J Immunol 2004; 172:5544-52. [PMID: 15100297 DOI: 10.4049/jimmunol.172.9.5544] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Expression of a beta-chain, as a pre-TCR, in T cell precursors prevents further rearrangements on the alternate beta allele through a strict allelic exclusion process and enables precursors to undergo differentiation. However, whether allelic exclusion applies to the TCR delta locus is unknown and the role of the gamma delta TCR in gamma delta lineage commitment is still unclear. Through the analysis of the rearrangement status of the TCR gamma, delta, and beta loci in human gamma delta T cell clones, expressing either the TCR V delta 1 or V delta 2 variable regions, we show that the rate of partial rearrangements at the delta locus is consistent with an allelic exclusion process. The overrepresentation of clones with two functional TCR gamma chains indicates that a gamma delta TCR selection process is required for the commitment of T cell precursors to the gamma delta lineage. Finally, while complete TCR beta rearrangements were observed in several V delta 2 T cell clones, these were seldom found in V delta 1 cells. This suggests a competitive alpha beta/gamma delta lineage commitment in the former subset and a precommitment to the gamma delta lineage in the latter. We propose that these distinct behaviors are related to the developmental stage at which rearrangements occur, as suggested by the patterns of accessibility to recombination sites that characterize the V delta 1 and V delta 2 subsets.
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MESH Headings
- Adult
- Alleles
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cell Line, Tumor
- Cell Lineage/genetics
- Cell Lineage/immunology
- Clone Cells
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Gene Rearrangement, delta-Chain T-Cell Antigen Receptor/genetics
- Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor/genetics
- Genetic Markers/immunology
- Humans
- Infant, Newborn
- Reading Frames/genetics
- Reading Frames/immunology
- Receptors, Antigen, T-Cell, gamma-delta/biosynthesis
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Recombination, Genetic/immunology
- Stem Cells/cytology
- Stem Cells/immunology
- Stem Cells/metabolism
- T-Lymphocyte Subsets/cytology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
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Affiliation(s)
- Chrystelle Couedel
- Institut National de la Santé et de la Recherche Médicale Unité 463, Institut de Biologie, Nantes, France
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45
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Márquez V, Wilson DN, Tate WP, Triana-Alonso F, Nierhaus KH. Maintaining the ribosomal reading frame: the influence of the E site during translational regulation of release factor 2. Cell 2004; 118:45-55. [PMID: 15242643 DOI: 10.1016/j.cell.2004.06.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 04/27/2004] [Accepted: 05/03/2004] [Indexed: 11/26/2022]
Abstract
Maintenance of the translation reading frame is one of the most remarkable achievements of the ribosome while decoding the information of an mRNA. Loss of the reading frame through spontaneous frameshifting occurs with a frequency of one in 30,000 amino acid incorporations. However, at many recoding sites, the mechanism that controls reading frame maintenance is switched off. One such example is the programmed +1 frameshift site of the prfB gene encoding the termination factor RF2, in which slippage into the forward frame by one nucleotide can attain an efficiency of approximately 100%, namely, four orders of magnitude higher than normally observed. Here, using the RF2 frameshift window, we demonstrate that premature release of the E site tRNA from the ribosome is coupled with high-level frameshifting. Consistently, in a minimal system, the presence of the E site tRNA prevents the +1 frameshift event, illustrating the importance of the E site for reading-frame maintenance.
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Affiliation(s)
- Viter Márquez
- Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestrasse 73, D-14195 Berlin, Germany
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46
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Abstract
Human intestinal lamina propria plasma cells are considered to be the progeny of chronically stimulated germinal centers located in organized gut-associated lymphoid tissues such as Peyer's patches and isolated lymphoid follicles. We have sampled human colonic lamina propria plasma cells and naive and memory B cell subsets from human Peyer's patches by microdissection of immunohistochemically stained tissue sections and used PCR methods and sequence analysis to compare IgVlambdaJlambda rearrangements in the plasma cell and B cell populations. Rearrangements that were either in-frame or out-of-frame between V and J were compared. Usage of IgVlambda families in the in-frame rearrangements from the plasma cells resembled that observed in the mantle cells, suggesting that antigenic selection for cellular specificity does not dramatically favor any particular Vlambda segment. However, in marked contrast, out-of-frame rearrangements involving Vlambda1 and Vlambda2 families are rarely observed in intestinal plasma cells, whereas rearrangements involving Vlambda5 are increased. This resulted in significantly biased ratios of in-frame:out-of-frame rearrangements in these Vlambda families. Out-of-frame rearrangements of IgVlambdaJlambda from plasma cells, including those involving the Vlambda5 family, have a significant tendency not to involve Jlambda1, consistent with the hypothesis that this population includes rearrangements generated by secondary recombination events. We propose that modification of out-of-frame rearrangements of IgVlambdaJlambda exists, probably a consequence of secondary rearrangements. This may be a mechanism to avoid translocations to susceptible out-of-frame IgVlambdaJlambda rearrangements during somatic hypermutation.
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Affiliation(s)
- Wen Su
- Department of Histopathology, GKT Medical School, St Thomas' Campus, London, United Kingdom
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47
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Safley AM, Sebastian S, Collins TS, Tirado CA, Stenzel TT, Gong JZ, Goodman BK. Molecular and cytogenetic characterization of a novel translocation t(4;22) involving the breakpoint cluster region and platelet-derived growth factor receptor-alpha genes in a patient with atypical chronic myeloid leukemia. Genes Chromosomes Cancer 2004; 40:44-50. [PMID: 15034867 DOI: 10.1002/gcc.20014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We report a case of BCR-ABL-negative atypical chronic myeloid leukemia (CML) with translocation t(4;22) (q12;q11.2) juxtaposing the breakpoint cluster region (BCR) and platelet-derived growth factor receptor-alpha (PDGFRA) genes. The patient was a 57-year-old man with a history of stage IV diffuse large B-cell lymphoma, status post-6 cycles of combination chemotherapy in 1999, who presented in August 2002 with enlarged lymph nodes, anemia, and marked leukocytosis (50 x 10(9) g/dL) consistent with a myeloproliferative disorder (MPD). A bone marrow biopsy showed granulocytic hyperplasia, neutrophilia, and mild eosinophilia. Initial cytogenetic evaluation by interphase FISH for BCR-ABL, to rule out a translocation 9;22, showed a variant signal pattern consistent with rearrangement of BCR at 22q11.2, but not ABL at 9q34. Analysis of the patient's cDNA by polymerase chain reaction (PCR) for BCR-ABL was negative. Cytogenetic analysis showed an abnormal karyotype with rearrangement of chromosomes 4 and 22. PCR amplification and subsequent sequence analysis demonstrated an in-frame 5'-BCR/3'-PDGFRA fusion in the patient's cDNA. PDGFRA encodes a receptor tyrosine kinase and shares structural and organizational homology with the KIT and CSf1R receptor genes. However, although the incidence of MPD involving translocations of PDGFRB has been well established, to our knowledge there are only two previous reports describing a BCR-PDGFRA fusion gene, in 3 patients diagnosed with atypical CML. Here, we report the molecular and cytogenetic characterization of a patient with BCR-PDGFRA-positive MPD who had a complete hematologic response after treatment with imatinib mesylate.
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MESH Headings
- Chromosome Breakage/genetics
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 4/genetics
- Cytogenetic Analysis/methods
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Male
- Middle Aged
- Myeloproliferative Disorders/genetics
- Oncogene Proteins, Fusion/genetics
- Protein-Tyrosine Kinases
- Proto-Oncogene Proteins/genetics
- Proto-Oncogene Proteins c-bcr
- Reading Frames/genetics
- Receptor, Platelet-Derived Growth Factor alpha/genetics
- Translocation, Genetic/genetics
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48
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Zeng X, Witchel SF, Dobrowolski SF, Moulder PV, Jarvik JW, Telmer CA. Detection and assignment of CYP21 mutations using peptide mass signature genotyping. Mol Genet Metab 2004; 82:38-47. [PMID: 15110320 DOI: 10.1016/j.ymgme.2004.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Revised: 02/11/2004] [Accepted: 02/11/2004] [Indexed: 11/16/2022]
Abstract
Congenital adrenal hyperplasia (CAH) is a common inborn error of steroidogenesis. The clinical spectrum of CAH ranges from the severe classical form, which can be fatal in the newborn, to simple virilizing forms or a milder non-classical form which is often not diagnosed until puberty. Recessive mutations in the autosomal gene encoding 21-hydroxylase (CYP21) are responsible for approximately 95% of CAH cases. Since CYP21 genotype is generally predictive of the presence and severity of the disorder, accurate CYP21 genotyping is of clear medical significance. Determining the CYP21 genotype of an individual, using standard methods, is difficult due to the presence of a nearly identical pseudogene (CYP21P) in close proximity to the functional gene. To address the need for a comprehensive test for mutations in the CYP21 gene, we developed a multiplexed peptide mass signature genotyping (PMSG) assay and applied the assay to 151 DNA samples. CAH patients had been previously characterized for the 10 most common mutations. The PMSG assay detected all common mutations; in addition it identified six known rare mutations and also discovered four new mutations (two frameshifts in the first half of the gene, P42fs and S171fs, and two point mutations, H365Y and R479L). This assay has the potential to provide high-throughput, cost-effective analysis of the CYP21 gene to detect known mutations and identify novel variants in samples obtained from patients with CAH, individuals suspected to have CAH, and heterozygous carriers.
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Affiliation(s)
- Xuemei Zeng
- SpectraGenetics LLC, 4415 Fifth Avenue, Suite 160, Pittsburgh, PA 15213, USA
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Abstract
The involvement of Shine-Dalgarno sequences in the translation of mRNA in halophilic archaea was investigated for two gvp genes involved in gas vesicle formation in Halobacterium salinarum PHH1. With the exception of gvpA and gvpO, all reading frames of the p-gvpDEFGHIJKLM and p-gvpACNO mRNAs contained upstream of the AUG start codon a putative Shine-Dalgarno (SD) sequence that is complementary to the 3'-end of the small ribosomal subunit RNA. The importance of the SD sequences of gvpG and gvpH was investigated in Haloferax volcanii transformants, and an alteration of the SD sequence resulted in a reduction of the amount of the GvpG or GvpH protein. For a more quantitative analysis the region upstream of gvpH was fused to the bgaH reading frame encoding an enzyme with beta-galactosidase activity as reporter. Scanning mutagenesis within the mRNA leader demonstrated that mutations adjacent to the putative SD sequence GGAGGUCA did not influence the efficiency of translation, whereas constructs harbouring an altered SD sequence yielded only 5-50% of the beta-galactosidase activities obtained with the wild-type SD element. A complete mutation of the SD sequence still yielded 20% of the wild-type activity. Alterations in the spacing of the SD sequence and the translation initiation codon of gvpH indicated that a distance of 4 or 10 nucleotides yielded a similar beta-galactosidase activity as found with the 7 nt spacing of the SD element in wild type, whereas a distance of 1 nt resulted in the loss of translation. A complete deletion of the 5'-UTR resulting in a leaderless mRNA yielded an enhanced beta-galactosidase activity in transformants implying that the initiation of translation involved a mechanism other than a specific mRNA-rRNA interaction.
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Affiliation(s)
- Simone Sartorius-Neef
- Institut für Mikrobiologie und Genetik, Technische Universität Darmstadt, Schnittspahnstr. 10, D-64287 Darmstadt, Germany
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Taylor MS, Ponting CP, Copley RR. Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res 2004; 14:555-66. [PMID: 15059996 PMCID: PMC383299 DOI: 10.1101/gr.1977804] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Accepted: 11/17/2003] [Indexed: 11/24/2022]
Abstract
Nucleotide insertion and deletion (indel) events, together with substitutions, represent the major mutational processes of gene evolution. Through the alignment of 8148 orthologous genes from human, mouse, and rat, we have identified 1743 indel events within rodent protein-coding sequences. Using human as an out-group, we reconstructed the mutational event underlying each of these indels. Overall, we found an excess of deletions over insertions, particularly for the rat lineage (70% excess). Sequence slippage accounts for at least 52% of insertions and 38% of deletions. We have also evaluated the selective tolerance of identifiable protein structures to indels. Transmembrane domains are the least, and low complexity regions, the most tolerant. Mapping of indels onto known protein structures demonstrated that structural cores are markedly less tolerant to indels than are loop regions. There is a specific enrichment of CpG dinucleotides in close proximity to insertion events, and both insertions and deletions are more common in higher G+C content sequences.
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Affiliation(s)
- Martin S Taylor
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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