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Akaishi T. Recently Added Frameshift Mutation in Human Monkeypox Virus (hMPXV) OPG191 Gene. TOHOKU J EXP MED 2023; 261:103-107. [PMID: 37438121 DOI: 10.1620/tjem.2023.j057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Human monkeypox virus (hMPXV) has caused sporadic outbreaks intermittently across countries in recent years, with the largest outbreak in 2022. However, the underlying mechanisms remain unclear. This study searched for recently developed structural variants of the viral genome. A total of 22 hMPXV whole genome sequences were randomly selected from the National Center for Biotechnology Information GenBank sequence database for initial screening. As a result, a recent frameshift mutation based on a 2-base insertion in a coding region was identified at the 3' terminal of the OPG191 gene, which encodes MPXVgp168 (B7R) protein. With this insertion, the protein was prematurely truncated, and the last 11 amino acids were missing, with 3 alternative amino acids added. Among the hMPXV genome sequences registered in the GenBank database as of January 2023, 61 sequences lacked the 2-base insertion and 3,362 sequences were inserted. All 61 sequences without mutations were collected before 2020, whereas 3,358 (99.9%) of the 3,362 sequences with the insertion were collected during or after 2022. These findings imply that a 2-base insertion has recently emerged and has been fixed among the virus population that prevailed in 2022. In summary, a recently emerged frameshift mutation with a 2-base insertion was identified in hMPXV OPG191 gene. Although the structural and functional consequences of this mutation on virulence and infectivity are unknown, research on the possible associations between this mutation and recent hMPXV outbreaks is warranted.
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Affiliation(s)
- Tetsuya Akaishi
- Department of Education and Support for Regional Medicine, Tohoku University
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2
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Snobre J, Villellas MC, Coeck N, Mulders W, Tzfadia O, de Jong BC, Andries K, Rigouts L. Bedaquiline- and clofazimine- selected Mycobacterium tuberculosis mutants: further insights on resistance driven largely by Rv0678. Sci Rep 2023; 13:10444. [PMID: 37369740 DOI: 10.1038/s41598-023-36955-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Drug-resistant tuberculosis is a serious global health threat. Bedaquiline (BDQ) is a relatively new core drug, targeting the respiratory chain in Mycobacterium tuberculosis (Mtb). While mutations in the BDQ target gene, atpE, are rare in clinical isolates, mutations in the Rv0678 gene, a transcriptional repressor regulating the efflux pump MmpS5-MmpL5, are increasingly observed, and have been linked to worse treatment outcomes. Nevertheless, underlying mechanisms of (cross)-resistance remain incompletely resolved. Our study aims to distinguish resistance associated variants from other polymorphisms, by assessing the in vitro onset of mutations under drug pressure, combined with their impact on minimum inhibitory concentrations (MICs) and on protein stability. For this purpose, isolates were exposed in vitro to sub-lethal concentrations of BDQ or clofazimine (CFZ). Selected colonies had BDQ- and CFZ-MICs determined on 7H10 and 7H11 agar. Sanger sequencing and additional Deeplex Myc-TB and whole genome sequencing (WGS) for a subset of isolates were used to search for mutations in Rv0678, atpE and pepQ. In silico characterization of relevant mutations was performed using computational tools. We found that colonies that grew on BDQ medium had mutations in Rv0678, atpE or pepQ, while CFZ-exposed isolates presented mutations in Rv0678 and pepQ, but none in atpE. Twenty-eight Rv0678 mutations had previously been described among in vitro selected mutants or in patients' isolates, while 85 were new. Mutations were scattered across the Rv0678 gene without apparent hotspot. While most Rv0678 mutations led to an increased BDQ- and/or CFZ-MIC, only a part of them surpassed the critical concentration (69.1% for BDQ and 87.9% for CFZ). Among the mutations leading to elevated MICs for BDQ and CFZ, we report a synonymous Val1Val mutation in the Rv0678 start codon. Finally, in silico characterization of Rv0678 mutations suggests that especially the C46R mutant may render Rv0678 less stable.
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Affiliation(s)
- J Snobre
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Internal Medicine Department, UZ Brussel, Brussels, Belgium
- Doctoral School of Life Sciences & Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - M C Villellas
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
| | - N Coeck
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - W Mulders
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - O Tzfadia
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - B C de Jong
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - K Andries
- Department of Infectious Diseases, Janssen Pharmaceutica, Beerse, Belgium
| | - L Rigouts
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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3
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Marchetti C, Ataseven B, Cassani C, Sassu CM, Congedo L, D'Indinosante M, Cappuccio S, Rhiem K, Hahnen E, Lucci Cordisco E, Arbustini E, Harter P, Minucci A, Scambia G, Fagotti A. Ovarian cancer onset across different BRCA mutation types: a view to a more tailored approach for BRCA mutated patients. Int J Gynecol Cancer 2023; 33:257-262. [PMID: 36581488 DOI: 10.1136/ijgc-2022-003893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE To evaluate the role of different specific types of germline breast cancer susceptibility BRCA mutations on the age of onset of high grade serous ovarian cancer. METHODS This was a multicenter, international, retrospective cohort of 474 patients diagnosed with recurrent or newly diagnosed high grade serous ovarian cancer, with known germline mutations in BRCA1/2 genes, treated between January 2011 and December 2020 in three academic centers in Europe. Patients were classified into four groups related to the type of BRCA1/2 genes mutation: frameshift, missense, nonsense, and splicing. Data from patients with splicing mutations were removed from the analysis because of the small numbers. The other three groups were compared. RESULTS Excluding the 29 patients with a splicing mutation, 474 patients were enrolled: 309 (65.2%) with frameshift mutations, 102 (21.5%) with nonsense mutations, and 63 (13.3%) with missense mutations. The BRCA1 gene was affected in 324 (68.4%) cases, while BRCA2 was involved in 150 (31.6%) women (p=0.06). We found a difference of more than 5 years in the age of onset of high grade serous ovarian cancer between BRCA1 and BRCA2 patients (mean 53.3 years vs 58.4 years; p=0.001), with a mean age of 55.1 years. Patients with nonsense germline mutations had the youngest age of onset, while women with frameshift mutations had the oldest age of onset of high grade serous ovarian cancer (mean 52.2 years vs mean 55.9 years), both in the BRCA1 and BRCA2 subgroups. There was no statistically significant difference in age of onset between early and advanced groups (mean 55.8 years vs 55.0 years; p=0.55). CONCLUSION Different types of germline BRCA mutations could determine different ages for onset of high grade serous ovarian cancer. If confirmed in larger series, this finding might have a clinical impact, potentially leading to a more tailored approach for risk reducing surgery for the prevention of high grade serous ovarian cancer.
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Affiliation(s)
- Claudia Marchetti
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Beyhan Ataseven
- Department of Gynecology and Gynecologic Oncology, Evangelische Kliniken Essen-Mitte, Evangelische Huyssens-Stiftung Essen-Huttrop, Essen, Germany
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Germany
| | - Chiara Cassani
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
- Unit of Obstetrics and Gynecology, IRCCS, Fondazione Policlinico San Matteo, Pavia, Italy
| | - Carolina Maria Sassu
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Luigi Congedo
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Marco D'Indinosante
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Serena Cappuccio
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Kerstin Rhiem
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Koln, Germany
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Koln, Germany
| | - Emanuela Lucci Cordisco
- UOC Genetica Medica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Medicina Genomica, Dipartimento Scienze della Vita e Sanità Pubblica, Universita Cattolica del Sacro Cuore, Roma, Italy
| | - Eloisa Arbustini
- Center for Inherited Cardiovascular Disease, IRCCS, Fondazione Policlinico San Matteo, Pavia, Italy
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Evangelische Kliniken Essen-Mitte, Evangelische Huyssens-Stiftung Essen-Huttrop, Essen, Germany
| | - Angelo Minucci
- Molecular and Genomic Diagnostics Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Giovanni Scambia
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Anna Fagotti
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italy
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Bogati B, Shore SFH, Nipper TD, Stoiculescu O, Fozo EM. Charged Amino Acids Contribute to ZorO Toxicity. Toxins (Basel) 2022; 15:32. [PMID: 36668852 PMCID: PMC9860968 DOI: 10.3390/toxins15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023] Open
Abstract
Chromosomally encoded toxin-antitoxin systems have been increasingly identified and characterized across bacterial species over the past two decades. Overproduction of the toxin gene results in cell growth stasis or death for the producing cell, but co-expression of its antitoxin can repress the toxic effects. For the subcategory of type I toxin-antitoxin systems, many of the described toxin genes encode a small, hydrophobic protein with several charged residues distributed across the sequence of the toxic protein. Though these charged residues are hypothesized to be critical for the toxic effects of the protein, they have not been studied broadly across different type I toxins. Herein, we mutated codons encoding charged residues in the type I toxin zorO, from the zor-orz toxin-antitoxin system, to determine their impacts on growth inhibition, membrane depolarization, ATP depletion, and the localization of this small protein. The non-toxic variants of ZorO accumulated both in the membrane and cytoplasm, indicating that membrane localization alone is not sufficient for its toxicity. While mutation of a charged residue could result in altered toxicity, this was dependent not only on the position of the amino acid within the protein but also on the residue to which it was converted, suggesting a complex role of charged residues in ZorO-mediated toxicity. A previous study indicated that additional copies of the zor-orz system improved growth in aminoglycosides: within, we note that this improved growth is independent of ZorO toxicity. By increasing the copy number of the zorO gene fused with a FLAG-tag, we were able to detect the protein expressed from its native promoter elements: an important step for future studies of toxin expression and function.
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Affiliation(s)
| | | | | | | | - Elizabeth M. Fozo
- Department of Microbiology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
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Wang X, Dong Q, Chen G, Zhang J, Liu Y, Cai Y. Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance. BMC Genomics 2022; 23:416. [PMID: 35655139 PMCID: PMC9164415 DOI: 10.1186/s12864-022-08435-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
Frameshift mutations have been considered of significant importance for the molecular evolution of proteins and their coding genes, while frameshift protein sequences encoded in the alternative reading frames of coding genes have been considered to be meaningless. However, functional frameshifts have been found widely existing. It was puzzling how a frameshift protein kept its structure and functionality while substantial changes occurred in its primary amino-acid sequence. This study shows that the similarities among frameshifts and wild types are higher than random similarities and are determined at different levels. Frameshift substitutions are more conservative than random substitutions in the standard genetic code (SGC). The frameshift substitutions score of SGC ranks in the top 2.0-3.5% of alternative genetic codes, showing that SGC is nearly optimal for frameshift tolerance. In many genes and certain genomes, frameshift-resistant codons and codon pairs appear more frequently than expected, suggesting that frameshift tolerance is achieved through not only the optimality of the genetic code but, more importantly, the further optimization of a specific gene or genome through the usages of codons/codon pairs, which sheds light on the role of frameshift mutations in molecular and genomic evolution.
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Crohn's-like Enteritis in X-Linked Agammaglobulinemia: A Case Series and Systematic Review. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 9:3466-3478. [PMID: 34029777 DOI: 10.1016/j.jaip.2021.04.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND X-linked agammaglobulinemia (XLA) is an inherited primary immunodeficiency that usually manifests clinically with recurrent sinopulmonary infections. Gastrointestinal manifestations are mostly driven by acute infections and disturbed mucosal immunity, but there is a notable prevalence of inflammatory bowel disease (IBD). Differentiating between XLA-associated enteritis, which can originate from recurrent infections, and IBD can be diagnostically and therapeutically challenging. OBJECTIVE This study presents a critical appraisal of the clinical, radiological, endoscopic, and histological features associated with XLA-associated Crohn disease (CD)-like enteritis. METHODS We report 3 cases and performed a systematic review of the literature describing the diagnoses and outcomes. RESULTS An XLA-related enteropathy presented in adolescence with an ileocolonic CD-like phenotype without perianal disease. Abdominal pain, noninfectious diarrhea, and weight loss were the most common symptoms. Imaging and endoscopic findings closely resemble CD. However, histologically, it presents without nodular lymphoid hyperplasia and only 2 studies reported the presence of granulomas. In addition, in XLA-associated enteritis, immunohistochemistry showed the absence or marked reduction in B cells and plasma cells. CONCLUSIONS An XLA-associated enteritis is a distinct pathological process that presents clinically in a manner similar to ileocolonic CD. It is important to evaluate for infectious diarrhea, which is common in XLA and can mimic IBD clinically. Complete multidisciplinary evaluation is, therefore, recommended for XLA patients with persistent gastrointestinal symptoms. Although more research is needed, therapeutic selection for XLA-associated enteritis is like that of IBD, and the possible risk of drug interactions and complications from increasing immunosuppression should be considered.
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7
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Salanga CM, Salanga MC. Genotype to Phenotype: CRISPR Gene Editing Reveals Genetic Compensation as a Mechanism for Phenotypic Disjunction of Morphants and Mutants. Int J Mol Sci 2021; 22:ijms22073472. [PMID: 33801686 PMCID: PMC8036752 DOI: 10.3390/ijms22073472] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
Forward genetic screens have shown the consequences of deleterious mutations; however, they are best suited for model organisms with fast reproductive rates and large broods. Furthermore, investigators must faithfully identify changes in phenotype, even if subtle, to realize the full benefit of the screen. Reverse genetic approaches also probe genotype to phenotype relationships, except that the genetic targets are predefined. Until recently, reverse genetic approaches relied on non-genomic gene silencing or the relatively inefficient, homology-dependent gene targeting for loss-of-function generation. Fortunately, the flexibility and simplicity of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system has revolutionized reverse genetics, allowing for the precise mutagenesis of virtually any gene in any organism at will. The successful integration of insertions/deletions (INDELs) and nonsense mutations that would, at face value, produce the expected loss-of-function phenotype, have been shown to have little to no effect, even if other methods of gene silencing demonstrate robust loss-of-function consequences. The disjunction between outcomes has raised important questions about our understanding of genotype to phenotype and highlights the capacity for compensation in the central dogma. This review describes recent studies in which genomic compensation appears to be at play, discusses the possible compensation mechanisms, and considers elements important for robust gene loss-of-function studies.
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Affiliation(s)
- Cristy M. Salanga
- Office of the Vice President for Research, Northern Arizona University, Flagstaff, AZ 86011, USA;
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Matthew C. Salanga
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
- Correspondence:
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Manger PR, Patzke N, Spocter MA, Bhagwandin A, Karlsson KÆ, Bertelsen MF, Alagaili AN, Bennett NC, Mohammed OB, Herculano-Houzel S, Hof PR, Fuxe K. Amplification of potential thermogenetic mechanisms in cetacean brains compared to artiodactyl brains. Sci Rep 2021; 11:5486. [PMID: 33750832 PMCID: PMC7970898 DOI: 10.1038/s41598-021-84762-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 01/25/2023] Open
Abstract
To elucidate factors underlying the evolution of large brains in cetaceans, we examined 16 brains from 14 cetartiodactyl species, with immunohistochemical techniques, for evidence of non-shivering thermogenesis. We show that, in comparison to the 11 artiodactyl brains studied (from 11 species), the 5 cetacean brains (from 3 species), exhibit an expanded expression of uncoupling protein 1 (UCP1, UCPs being mitochondrial inner membrane proteins that dissipate the proton gradient to generate heat) in cortical neurons, immunolocalization of UCP4 within a substantial proportion of glia throughout the brain, and an increased density of noradrenergic axonal boutons (noradrenaline functioning to control concentrations of and activate UCPs). Thus, cetacean brains studied possess multiple characteristics indicative of intensified thermogenetic functionality that can be related to their current and historical obligatory aquatic niche. These findings necessitate reassessment of our concepts regarding the reasons for large brain evolution and associated functional capacities in cetaceans.
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Affiliation(s)
- Paul R Manger
- School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Nina Patzke
- School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Japan
| | - Muhammad A Spocter
- School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Adhil Bhagwandin
- School of Anatomical Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Clinical Anatomy and Biological Anthropology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | - Karl Æ Karlsson
- Biomedical Engineering, Reykjavik University, Reykjavik, Iceland
| | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nigel C Bennett
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Osama B Mohammed
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Suzana Herculano-Houzel
- Department of Psychology, Department of Biological Sciences, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kjell Fuxe
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Mankin AS. Frame-shifted proteins of a given gene are unlikely to retain the same function. RNA (NEW YORK, N.Y.) 2020; 26:1301-1302. [PMID: 32503919 PMCID: PMC7491333 DOI: 10.1261/rna.076398.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/30/2020] [Indexed: 05/05/2023]
Abstract
In a recently published paper, Huang and coworkers claim that proteins translated in different reading frames from the same mRNA can have similar functions. This conclusion is possibly incorrect due to the possibility that the wild-type protein could still be expressed.
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Affiliation(s)
- Alexander S Mankin
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, Illinois 60607, USA
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