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Mao XL, Eriani G, Zhou XL. ADATs: roles in tRNA editing and relevance to disease. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39034823 DOI: 10.3724/abbs.2024125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Transfer RNAs (tRNAs) play central roles in protein biosynthesis. Post-transcriptional RNA modifications affect tRNA function and stability. Among these modifications, RNA editing is a widespread RNA modification in three domains of life. Proteins of the adenosine deaminase acting on tRNA (ADAT) family were discovered more than 20 years ago. They catalyze the deamination of adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) during tRNA maturation. The most studied example is the TadA- or ADAT2/3-mediated A-to-I conversion of the tRNA wobble position in the anticodon of prokaryotic or eukaryotic tRNAs, respectively. This review provides detailed information on A-to-I and C-to-U editing of tRNAs in different domains of life, presents recent new findings on ADATs for DNA editing, and finally comments on the association of mutations in the ADAT3 gene with intellectual disability.
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Affiliation(s)
- Xue-Ling Mao
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Xiao-Long Zhou
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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Shen J, Xu X, Fan J, Chen H, Zhao Y, Huang W, Liu W, Zhang Z, Cui Q, Li Q, Niu Z, Jiang D, Cao G. APOBEC3-related mutations in the spike protein-encoding region facilitate SARS-CoV-2 evolution. Heliyon 2024; 10:e32139. [PMID: 38868014 PMCID: PMC11168432 DOI: 10.1016/j.heliyon.2024.e32139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
SARS-CoV-2 evolves gradually to cause COVID-19 epidemic. One of driving forces of SARS-CoV-2 evolution might be activation of apolipoprotein B mRNA editing catalytic subunit-like protein 3 (APOBEC3) by inflammatory factors. Here, we aimed to elucidate the effect of the APOBEC3-related viral mutations on the infectivity and immune evasion of SARS-CoV-2. The APOBEC3-related C > U mutations ranked as the second most common mutation types in the SARS-CoV-2 genome. mRNA expression of APOBEC3A (A3A), APOBEC3B (A3B), and APOBEC3G (A3G) in peripheral blood cells increased with disease severity. A3B, a critical member of the APOBEC3 family, was significantly upregulated in both severe and moderate COVID-19 patients and positively associated with neutrophil proportion and COVID-19 severity. We identified USP18 protein, a key molecule centralizing the protein-protein interaction network of key APOBEC3 proteins. Furthermore, mRNA expression of USP18 was significantly correlated to ACE2 and TMPRSS2 expression in the tissue of upper airways. Knockdown of USP18 mRNA significantly decreased A3B expression. Ectopic expression of A3B gene increased SARS-CoV-2 infectivity. C > U mutations at S371F, S373L, and S375F significantly conferred with the immune escape of SARS-CoV-2. Thus, APOBEC3, whose expression are upregulated by inflammatory factors, might promote SARS-CoV-2 evolution and spread via upregulating USP18 level and facilitating the immune escape. A3B and USP18 might be therapeutic targets for interfering with SARS-CoV-2 evolution.
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Affiliation(s)
- Jiaying Shen
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Xinxin Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Junyan Fan
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongsen Chen
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Weijin Huang
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Wenbin Liu
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Zihan Zhang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Qianqian Cui
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Qianqian Li
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), WHO Collaborating Center for Standardization and Evaluation of Biologicals, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, 102629 Beijing, China
| | - Zheyun Niu
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Dongming Jiang
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
| | - Guangwen Cao
- Tongji University School of Medicine, Tongji University, Shanghai 200120, China
- Key Laboratory of Biological Defense, Ministry of Education, China
- Shanghai Key Laboratory of Medical Bioprotection, China
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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Choi H, Hwang M, Cornelius L, Navarathna DH, Chatterjee P, Jinadatha C. Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak. Viruses 2024; 16:337. [PMID: 38543703 PMCID: PMC10974601 DOI: 10.3390/v16030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 05/23/2024] Open
Abstract
The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, we report the evolutionary trajectory of a unique Omicron lineage identified during an outbreak investigation that occurred in a residence unit in the healthcare system. The new lineage had four distinct non-synonymous and two distinct synonymous mutations apart from its parental lineage. Since this lineage of virus was exclusively found during the outbreak, we were able to track the detailed evolutionary history of the entire lineage along the transmission path. Furthermore, we estimated the evolutionary rate of the SARS-CoV-2 Omicron variant from the analysis of the evolution of the lineage. This new Omicron sub-lineage acquired 3 mutations in a 12-day period, and the evolutionary rate was estimated as 3.05 × 10-3 subs/site/year. This study provides more insight into an ever-evolving virus.
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Affiliation(s)
- Hosoon Choi
- Department of Research, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (M.H.); (P.C.)
| | - Munok Hwang
- Department of Research, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (M.H.); (P.C.)
| | - Lisa Cornelius
- Department of Medicine, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (L.C.); (C.J.)
| | - Dhammika H. Navarathna
- Department of Pathology and Laboratory Medicine Services, Central Texas Veterans Health Care System, Temple, TX 76504, USA;
| | - Piyali Chatterjee
- Department of Research, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (M.H.); (P.C.)
| | - Chetan Jinadatha
- Department of Medicine, Central Texas Veterans Health Care System, Temple, TX 76504, USA; (L.C.); (C.J.)
- School of Medicine, Texas A&M University, Bryan, TX 77807, USA
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Zhang K, Chen F, Shen HY, Zhang PP, Gao H, Peng H, Luo YS, Cheng ZS. Regulatory variants of APOBEC3 genes potentially associate with COVID-19 severity in populations with African ancestry. Sci Rep 2023; 13:22435. [PMID: 38105291 PMCID: PMC10725877 DOI: 10.1038/s41598-023-49791-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
Since November 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused the worldwide pandemic of the coronavirus disease 2019 (COVID-19), the impact of which is huge to the lives of world populations. Many studies suggested that such situation will continue due to the endless mutations in SARS-CoV-2 genome that result in complexity of the efforts for the control of SARS-CoV-2, since the special enrichment of nucleotide substitution C>U in SARS-CoV-2 sequences were discovered mainly due to the editing by human host factors APOBEC3 genes. The observation of SARS-CoV-2 variants Beta (B.1.351) and Omicron (B.1.1.529) firstly spreading in South Africa promoted us to hypothesize that genetic variants of APOBEC3 special in African populations may be attributed to the higher mutation rate of SARS-CoV-2 variants in Africa. Current study was conducted to search for functional variants of APOBEC3 genes associate with COVID-19 hospitalization in African population. By integrating data from the 1000 Genomes Project, Genotype-Tissue Expression (GTEx), and Host Genetics Initiative (HGI) of COVID-19, we identified potential functional SNPs close to APOBEC3 genes that are associated with COVID-19 hospitalization in African but not with other populations. Our study provides new insights on the potential contribution of APOBEC3 genes on the evolution of SARS-CoV-2 mutations in African population, but further replication is needed to confirm our results.
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Affiliation(s)
- Ke Zhang
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Fang Chen
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Hu-Yan Shen
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Ping-Ping Zhang
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 561113, China
| | - Han Gao
- The Department of Emergency ICU, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Hong Peng
- The Department of Emergency ICU, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yu-Si Luo
- The Department of Emergency ICU, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
- The Department of Emergency, Liupanshui Hospital of The Affiliated Hospital of Guizhou Medical University, Liupanshui, 553000, China.
| | - Zhong-Shan Cheng
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, 262 Danny Thomas Hospital, MS1122, Memphis, TN, 38105, USA.
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Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24109072. [PMID: 37240420 DOI: 10.3390/ijms24109072] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.
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Affiliation(s)
- Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Garcia-Segura
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Nil Novau-Ferré
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | | | - Pere Puigbò
- Department of Biology, University of Turku, 20500 Turku, Finland
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, 43007 Tarragona, Spain
- Eurecat, Technology Centre of Catalonia, Unit of Nutrition and Health, 43204 Reus, Spain
| | - Adrià Cereto-Massagué
- EURECAT Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Santiago Garcia-Vallve
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
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