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Kaur R, Maan S, Batra K, Singh N, Chahal N, Kumar A. Rapid detection of porcine sapelovirus by reverse transcription recombinase polymerase amplification assay. Mol Biol Rep 2024; 51:178. [PMID: 38252231 DOI: 10.1007/s11033-023-09123-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/06/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Porcine Sapelovirus (PSV) infection has been confirmed in pigs worldwide, mostly asymptomatic, but in some cases, it can lead to significant issues in the gastrointestinal, respiratory, neurological, or reproductive systems. PSV is considered an emerging pathogen of porcine species. Recombinase polymerase amplification (RPA) is a simple and fast isothermal technique that uses three enzymes for amplification without the use of any sophisticated equipment. METHODS AND RESULTS The reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed and optimized for field based detection of PSV. The assay was developed by targeting 5´UTR region of PSV genome and optimized for reaction time, temperature, primer and MgOAc concentration. The analytical sensitivity and specificity of assay was determined. The assay was evaluated on 85 porcine faecal samples collected from field. In addition to conventional format, this assay was also optimized for visual dye-based detection format and lateral flow strips based detection (in combination with probe). The developed assay works at constant temperature of 35 °C for 20 min with forward primer concentration 20pm, reverse primer concentration 10pm and MgOAc concentration of 14mM. This assay is highly sensitive and detects up to 28 copies of viral nucleic acid both in the conventional as well as in fluorescent dye based detection format. Using the newly developed assay 21 samples out of 85 samples were found positive, showing positivity rate of 24.7%. The positivity rate of RT-RPA assay corroborated with the gold standard RT-PCR test. CONCLUSIONS This study presented the development of an RT-RPA isothermal assay for rapid and accurate detection of PSV. The assay is highly sensitive, specific, works at a low and constant temperature, does not require any high-end instrument and can be a potential diagnostics tool for pen-side testing of PSV in the field conditions. The newly developed RT-RPA assay could successfully detect PSV circulating in swine population of Haryana, India. This is a first report of this kind from the region.
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Affiliation(s)
- Ramandeep Kaur
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Sushila Maan
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India.
| | - Kanisht Batra
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Neha Singh
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Niharika Chahal
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Aman Kumar
- Department of Animal Biotechnology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
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Mills MG, Bruce E, Huang ML, Crothers JW, Hyrien O, Oura CAL, Blake L, Brown Jordan A, Hester S, Wehmas L, Mari B, Barby P, Lacoux C, Fassy J, Vial P, Vial C, Martinez JRW, Oladipo OO, Inuwa B, Shittu I, Meseko CA, Chammas R, Santos CF, Dionísio TJ, Garbieri TF, Parisi VA, Mendes-Correa MC, de Paula AV, Romano CM, Góes LGB, Minoprio P, Campos AC, Cunha MP, Vilela APP, Nyirenda T, Mkakosya RS, Muula AS, Dumm RE, Harris RM, Mitchell CA, Pettit S, Botten J, Jerome KR. An international, interlaboratory ring trial confirms the feasibility of an extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples. PLoS One 2022; 17:e0261853. [PMID: 35025926 PMCID: PMC8758094 DOI: 10.1371/journal.pone.0261853] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time-reverse transcription polymerase chain reaction (RT-PCR) is a transparent and accessible qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic.
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Affiliation(s)
- Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Emily Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jessica W. Crothers
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher A. L. Oura
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Lemar Blake
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | | | - Susan Hester
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Leah Wehmas
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Bernard Mari
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pascal Barby
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Caroline Lacoux
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Julien Fassy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pablo Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Jose R. W. Martinez
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | | | - Bitrus Inuwa
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Ismaila Shittu
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Clement A. Meseko
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Roger Chammas
- Faculdade de Medicina da Universidade de São Paulo, Departamento de Radiologia e Oncologia, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de São Paulo, São Paulo, Brazil
| | - Carlos Ferreira Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thiago José Dionísio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thais Francini Garbieri
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Viviane Aparecida Parisi
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | | | - Anderson V. de Paula
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Camila M. Romano
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Luiz Gustavo Bentim Góes
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Paola Minoprio
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Angelica C. Campos
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Marielton P. Cunha
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula P. Vilela
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Tonney Nyirenda
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Adamson S. Muula
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Rebekah E. Dumm
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rebecca M. Harris
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Constance A. Mitchell
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Syril Pettit
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Jason Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Jin S, Lin Q, Luo Y, Zhu Z, Liu G, Li Y, Chen K, Qiu JL, Gao C. Genome-wide specificity of prime editors in plants. Nat Biotechnol 2021; 39:1292-1299. [PMID: 33859403 DOI: 10.1038/s41587-021-00891-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [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: 05/28/2020] [Accepted: 03/12/2021] [Indexed: 02/07/2023]
Abstract
Although prime editors (PEs) have the potential to facilitate precise genome editing in therapeutic, agricultural and research applications, their specificity has not been comprehensively evaluated. To provide a systematic assessment in plants, we first examined the mismatch tolerance of PEs in plant cells and found that the editing frequency was influenced by the number and location of mismatches in the primer binding site and spacer of the prime editing guide RNA (pegRNA). Assessing the activity of 12 pegRNAs at 179 predicted off-target sites, we detected only low frequencies of off-target edits (0.00~0.23%). Whole-genome sequencing of 29 PE-treated rice plants confirmed that PEs do not induce genome-wide pegRNA-independent off-target single-nucleotide variants or small insertions/deletions. We also show that ectopic expression of the Moloney murine leukemia virus reverse transcriptase as part of the PE does not change retrotransposon copy number or telomere structure or cause insertion of pegRNA or messenger RNA sequences into the genome.
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Affiliation(s)
- Shuai Jin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qiupeng Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zixu Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Guanwen Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yunjia Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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4
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Abstract
Reverse transcription quantitative PCR (RT-qPCR) has delivered significant insights in understanding the gene expression landscape. Thanks to its precision, sensitivity, flexibility, and cost effectiveness, RT-qPCR has also found utility in advanced single-cell analysis. Single-cell RT-qPCR now represents a well-established method, suitable for an efficient screening prior to single-cell RNA sequencing (scRNA-Seq) experiments, or, oppositely, for validation of hypotheses formulated from high-throughput approaches. Here, we aim to provide a comprehensive summary of the scRT-qPCR method by discussing the limitations of single-cell collection methods, describing the importance of reverse transcription, providing recommendations for the preamplification and primer design, and summarizing essential data processing steps. With the detailed protocol attached in the appendix, this tutorial provides a set of guidelines that allow any researcher to perform scRT-qPCR measurements of the highest standard.
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Affiliation(s)
- Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden
| | - Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology CAS, 252 50 Vestec, Czech Republic; (D.Z.); (M.K.)
- Correspondence:
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5
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Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Res 2021; 49:5925-5942. [PMID: 33978756 PMCID: PMC8191761 DOI: 10.1093/nar/gkab342] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/18/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.
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Affiliation(s)
- Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas Gremminger
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Cheng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Jun Li
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Liming Qiu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Juan Ji
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
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Taylor HE, Calantone N, Lichon D, Hudson H, Clerc I, Campbell EM, D'Aquila RT. mTOR Overcomes Multiple Metabolic Restrictions to Enable HIV-1 Reverse Transcription and Intracellular Transport. Cell Rep 2021; 31:107810. [PMID: 32579936 DOI: 10.1016/j.celrep.2020.107810] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 02/28/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
Cellular metabolism governs the susceptibility of CD4 T cells to HIV-1 infection. Multiple early post-fusion steps of HIV-1 replication are restricted in resting peripheral blood CD4 T cells; however, molecular mechanisms that underlie metabolic control of these steps remain undefined. Here, we show that mTOR activity following T cell stimulatory signals overcomes metabolic restrictions in these cells by enabling the expansion of dNTPs to fuel HIV-1 reverse transcription (RT), as well as increasing acetyl-CoA to stabilize microtubules that transport RT products. We find that catalytic mTOR inhibition diminishes the expansion of pools of both of these metabolites by limiting glucose and glutamine utilization in several pathways, thereby suppressing HIV-1 infection. We demonstrate how mTOR-coordinated biosyntheses enable the early steps of HIV-1 replication, add metabolic mechanisms by which mTOR inhibitors block HIV-1, and identify some metabolic modules downstream of mTOR as druggable targets for HIV-1 inhibition.
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Affiliation(s)
- Harry E Taylor
- Department of Microbiology and Immunology, State University of New York (SUNY) Upstate Medical University, Syracuse, NY 13210, USA.
| | - Nina Calantone
- Division of Infectious Diseases and HIV Translational Research Center, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Drew Lichon
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Hannah Hudson
- Division of Infectious Diseases and HIV Translational Research Center, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Isabelle Clerc
- Division of Infectious Diseases and HIV Translational Research Center, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Richard T D'Aquila
- Division of Infectious Diseases and HIV Translational Research Center, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Kishimoto N, Yamamoto K, Abe T, Yasuoka N, Takamune N, Misumi S. Glucose-dependent aerobic glycolysis contributes to recruiting viral components into HIV-1 particles to maintain infectivity. Biochem Biophys Res Commun 2021; 549:187-193. [PMID: 33676187 DOI: 10.1016/j.bbrc.2021.02.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 01/22/2021] [Accepted: 02/17/2021] [Indexed: 12/11/2022]
Abstract
The cellular environment affects optimal viral replication because viruses cannot replicate without their host cells. In particular, metabolic resources such as carbohydrates, lipids, and ATP are crucial for viral replication, which is sensitive to cellular metabolism. Intriguingly, recent studies have demonstrated that human immunodeficiency virus type 1 (HIV-1) infection induces a metabolic shift from oxidative phosphorylation to aerobic glycolysis in CD4+ T cells to produce the virus efficiently. However, the importance of aerobic glycolysis in maintaining the quality of viral components and viral infectivity has not yet been fully investigated. Here, we show that aerobic glycolysis is necessary not only to override the inhibitory effect of virion-incorporated glycolytic enzymes, but also to maintain the enzymatic activity of reverse transcriptase and the adequate packaging of envelope proteins into HIV-1 particles. To investigate the effect of metabolic remodeling on the phenotypic properties of HIV-1 produced by infected cells, we replaced glucose with galactose in the culture medium because the cells grown in galactose-containing medium are forced to carry out oxidative metabolism instead of aerobic glycolysis. We found that the packaging levels of glyceraldehyde 3-phosphate dehydrogenase, alpha-enolase and pyruvate kinase muscle type 2, which decrease HIV-1 infectivity by packaging into viral particles, are increased in progeny viruses produced by the cells grown in galactose-containing medium. Furthermore, we found that the entry and reverse transcription efficiency of the progeny viruses were reduced, which was caused by a decrease in the enzymatic activity of reverse transcriptase in the viral particles and a decrease in the packaging levels of envelope proteins and reverse transcriptase. These results indicate that the aerobic glycolysis environment in HIV-1-infected cells may contribute to the quality control of viruses.
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Affiliation(s)
- Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Kengo Yamamoto
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Towa Abe
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Norito Yasuoka
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan
| | - Nobutoki Takamune
- Kumamoto Innovative Development Organization, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto, 862-0973, Japan.
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Jang WS, Lim DH, Yoon J, Kim A, Lim M, Nam J, Yanagihara R, Ryu SW, Jung BK, Ryoo NH, Lim CS. Development of a multiplex Loop-Mediated Isothermal Amplification (LAMP) assay for on-site diagnosis of SARS CoV-2. PLoS One 2021; 16:e0248042. [PMID: 33657176 PMCID: PMC7928493 DOI: 10.1371/journal.pone.0248042] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [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: 12/27/2020] [Accepted: 02/18/2021] [Indexed: 12/28/2022] Open
Abstract
A newly identified coronavirus, designated as severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), has spread rapidly from its epicenter in China to more than 150 countries across six continents. In this study, we have designed three reverse-transcription loop-mediated isothermal amplification (RT-LAMP) primer sets to detect the RNA-dependent RNA polymerase (RdRP), Envelope (E) and Nucleocapsid protein (N) genes of SARS CoV-2. For one tube reaction, the detection limits for five combination SARS CoV-2 LAMP primer sets (RdRP/E, RdRP/N, E/N, RdRP/E/N and RdRP/N/Internal control (actin beta)) were evaluated with a clinical nasopharyngeal swab sample. Among the five combination, the RdRP/E and RdRP/N/IC multiplex LAMP assays showed low detection limits. The sensitivity and specificity of the RT-LAMP assay were evaluated and compared to that of the widely used Allplex™ 2019-nCoV Assay (Seegene, Inc., Seoul, South Korea) and PowerChek™ 2019-nCoV Real-time PCR kit (Kogenebiotech, Seoul, South Korea) for 130 clinical samples from 91 SARS CoV-2 patients and 162 NP specimens from individuals with (72) and without (90) viral respiratory infections. The multiplex RdRP (FAM)/N (CY5)/IC (Hex) RT-LAMP assay showed comparable sensitivities (RdRP: 93.85%, N: 94.62% and RdRP/N: 96.92%) to that of the Allplex™ 2019-nCoV Assay (100%) and superior to those of PowerChek™ 2019-nCoV Real-time PCR kit (RdRP: 92.31%, E: 93.85% and RdRP/E: 95.38%).
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Affiliation(s)
- Woong Sik Jang
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Da Hye Lim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jung Yoon
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Ahran Kim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Minsup Lim
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Emergency Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Richard Yanagihara
- Pacific Center for Emerging Infectious Diseases Research, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Sook-Won Ryu
- Department of Laboratory Medicine, Kangwon National University, School of Medicine, Kangwondo, Republic of Korea
| | - Bo Kyeung Jung
- Department of Laboratory Medicine, Dankook University College of Medicine, Cheonan, Korea
| | - Nam-Hee Ryoo
- Department of Laboratory Medicine, Dongsan Medical Center, Keimyung University, Daegu, Korea
| | - Chae Seung Lim
- Departments of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
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9
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Abstract
BACKGROUND COVID-19 has spread rapidly around the world, affecting a large percentage of the population. When lifting certain mandatory measures for an economic restart, robust surveillance must be established and implemented, with nucleic acid detection for SARS-CoV-2 as an essential component. METHODS We tried to develop a one-tube detection platform based on RT-RPA (Reverse Transcription and Recombinase Polymerase Isothermal Amplification) and DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR) technology, termed OR-DETECTR, to detect SARS-CoV-2. We designed RT-RPA primers of the RdRp and N genes following the SARS-CoV-2 gene sequence. We optimized reaction components so that the detection process could be carried out in one tube. Specificity was demonstrated by detecting nucleic acid samples from pseudoviruses from seven human coronaviruses and Influenza A (H1N1). Clinical samples were used to validate the platform and all results were compared to rRT-PCR. RNA standards and pseudoviruses diluted by different gradients were used to demonstrate the detection limit. Additionally, we have developed a lateral flow assay based on OR-DETECTR for detecting COVID-19. RESULTS The OR-DETECTR detection process can be completed in one tube, which takes approximately 50 min. This method can specifically detect SARS-CoV-2 from seven human coronaviruses and Influenza A (H1N1), with a low detection limit of 2.5 copies/µl input (RNA standard) and 1 copy/µl input (pseudovirus). Results of six samples from SARS-CoV-2 patients, eight samples from patients with fever but no SARS-CoV-2 infection, and one mixed sample from 40 negative controls showed that OR-DETECTR is 100% consistent with rRT-PCR. The lateral flow assay based on OR-DETECTR can be used for the detection of COVID-19, and the detection limit is 2.5 copies/µl input. CONCLUSIONS The OR-DETECTR platform for the detection of COVID-19 is rapid, accurate, tube closed, easy-to-operate, and free of large instruments.
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Affiliation(s)
- Yangyang Sun
- Department of Urology, International Cancer Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518039, China
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518060, China
- The First Affiliated Hospital of Shantou University, Shantou, 515041, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Lei Yu
- Department of Urology, International Cancer Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518039, China
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518060, China
- The First Affiliated Hospital of Shantou University, Shantou, 515041, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Chengxi Liu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shanting Ye
- Department of Urology, International Cancer Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518039, China
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518060, China
- The First Affiliated Hospital of Shantou University, Shantou, 515041, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Wei Chen
- Department of Urology, International Cancer Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518039, China
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518060, China
- The First Affiliated Hospital of Shantou University, Shantou, 515041, China
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China
| | - Dechang Li
- Yuebei Second People's Hospital, Shaoguan, 512000, Guangdong, China.
| | - Weiren Huang
- Department of Urology, International Cancer Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen, 518039, China.
- International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518060, China.
- The First Affiliated Hospital of Shantou University, Shantou, 515041, China.
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China.
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10
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Lau YL, Ismail IB, Mustapa NIB, Lai MY, Tuan Soh TS, Haji Hassan A, Peariasamy KM, Lee YL, Abdul Kahar MKB, Chong J, Goh PP. Development of a reverse transcription recombinase polymerase amplification assay for rapid and direct visual detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). PLoS One 2021; 16:e0245164. [PMID: 33406112 PMCID: PMC7787525 DOI: 10.1371/journal.pone.0245164] [Citation(s) in RCA: 27] [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: 10/10/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
Rapid diagnosis is an important intervention in managing the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak. Real time reverse transcription polymerase chain reaction (RT-qPCR) remains the primary means for diagnosing the new virus strain but it is time consuming and costly. Recombinase polymerase amplification (RPA) is an isothermal amplification assay that does not require a PCR machine. It is an affordable, rapid, and simple assay. In this study, we developed and optimized a sensitive reverse transcription (RT)-RPA assay for the rapid detection of SARS-CoV-2 using SYBR Green I and/or lateral flow (LF) strip. The analytical sensitivity and specificity of the RT-RPA assay were tested by using 10-fold serial diluted synthetic RNA and genomic RNA of similar viruses, respectively. Clinical sensitivity and specificity of the RT-RPA assay were carried out using 78 positive and 35 negative nasopharyngeal samples. The detection limit of both RPA and RT-qPCR assays was 7.659 and 5 copies/μL RNA, respectively with no cross reactivity with other viruses. The clinical sensitivity and specificity of RT-RPA were 98% and 100%, respectively. Our study showed that RT-RPA represents a viable alternative to RT-qPCR for the detection of SARS-CoV-2, especially in areas with limited infrastructure.
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Affiliation(s)
- Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | | | - Yee Leng Lee
- Clinical Research Centre, Hospital Sungai Buloh, Selangor, Malaysia
| | | | - Jennifer Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Pik Pin Goh
- Institute for Clinical Research (ICR), National Institutes of Health (NIH), Ministry of Health Malaysia, Putrajaya, Malaysia
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11
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Rensen E, Mueller F, Scoca V, Parmar JJ, Souque P, Zimmer C, Di Nunzio F. Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages. EMBO J 2021; 40:e105247. [PMID: 33270250 PMCID: PMC7780146 DOI: 10.15252/embj.2020105247] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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: 04/09/2020] [Revised: 10/04/2020] [Accepted: 10/16/2020] [Indexed: 01/07/2023] Open
Abstract
In order to replicate, human immunodeficiency virus (HIV-1) reverse-transcribes its RNA genome into DNA, which subsequently integrates into host cell chromosomes. These two key events of the viral life cycle are commonly viewed as separate not only in time, but also in cellular space, since reverse transcription (RT) is thought to be completed in the cytoplasm before nuclear import and integration. However, the spatiotemporal organization of the early viral replication cycle in macrophages, the natural non-dividing target cells that constitute reservoirs of HIV-1 and an obstacle to curing AIDS, remains unclear. Here, we demonstrate that infected macrophages display large nuclear foci of viral DNA (vDNA) and viral RNA, in which multiple viral genomes cluster together. These clusters form in the absence of chromosomal integration, sequester the paraspeckle protein CPSF6, and localize to nuclear speckles. Surprisingly, these viral RNA clusters consist mostly of genomic, incoming RNA, both in cells where reverse transcription is pharmacologically suppressed and in untreated cells. We demonstrate that following temporary inhibition, reverse transcription can resume in the nucleus and lead to vDNA accumulation in these clusters. We further show that nuclear reverse transcription can result in transcription-competent viral DNA. These findings change our understanding of the early HIV-1 replication cycle and may have implications for addressing HIV-1 persistence.
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Affiliation(s)
- Elena Rensen
- Imaging and Modeling UnitInstitut PasteurUMR 3691 CNRSC3BI USR 3756 IP CNRSParisFrance
- Molecular Virology and VaccinologyInstitut PasteurParisFrance
| | - Florian Mueller
- Imaging and Modeling UnitInstitut PasteurUMR 3691 CNRSC3BI USR 3756 IP CNRSParisFrance
| | - Viviana Scoca
- Molecular Virology and VaccinologyInstitut PasteurParisFrance
| | - Jyotsana J Parmar
- Imaging and Modeling UnitInstitut PasteurUMR 3691 CNRSC3BI USR 3756 IP CNRSParisFrance
| | - Philippe Souque
- Molecular Virology and VaccinologyInstitut PasteurParisFrance
| | - Christophe Zimmer
- Imaging and Modeling UnitInstitut PasteurUMR 3691 CNRSC3BI USR 3756 IP CNRSParisFrance
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12
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Abstract
This chapter provides an overview on different methods for the characterization of RNAs in Trichoderma reesei. In the first section, protocols for the extraction of total RNA from fungal mycelia and the identification of 5' and 3' ends of certain RNAs of interest via rapid amplification of cDNA ends (RACE) are presented. In the next section, this knowledge on the transcriptional start and end points is used for in vitro synthesis and fluorescence labeling of the RNA of interest. The in vitro synthesized RNA can then be applied for in vitro analyses such as RNA electrophoretic mobility shift assays (RNA-EMSA) and RNA in vitro footprinting. RNA-EMSA is a method suitable for the identification and characterization of RNA-protein interactions or interactions of an RNA with other nucleic acids. RNA in vitro footprinting allows exact mapping of protein-binding sites on RNA molecules and also the determination of RNA secondary and tertiary structures at singe-nucleotide resolution. All protocols presented in this chapter are optimized for the analysis of noncoding RNAs (ncRNAs), especially long ncRNAs (lncRNAs) or other specific RNA species of more than 200 nt in length.
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Affiliation(s)
- Petra Till
- Christian Doppler laboratory for optimized expression of carbohydrate-active enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
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13
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Wang H, Song P, Li X, Wang Y, Gui S, Liu Y, Lu F. Screening of the candidate inhibitory peptides of subtilisin by in vitro RNA display technique. Int J Biol Macromol 2020; 163:1162-1167. [PMID: 32673721 DOI: 10.1016/j.ijbiomac.2020.07.115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 11/19/2022]
Abstract
The application of inhibitors facilitates the stable preservation of enzyme in liquid detergent by mitigating the proteolytic activity of subtilisin. The conventionally used subtilisin inhibitors such as boric acid pose a threat to the environment and human health. Thus, the formulation of novel subtilisin inhibitors demands immediate attention. In the current study, we have screened the peptide inhibitors for subtilisin by employing the in vitro mRNA display technique. It is a sensitive screening technique with a high library capacity. The affinity screening was performed between the biotin-modified subtilisin immobilized on the streptavidin magnetic beads and the cDNA-mRNA-peptide fusion molecular library acquired from the in vitro translation and reverse transcription. The candidate peptides with high affinity were obtained after multiple rounds of screening. Furthermore, the inhibitory effect was evaluated, showing that some candidate peptides had inhibitory effects, but the isothermal titration calorimetry and time dependent experiments ultimately proved that these candidate peptides were not stable inhibitors. However, the in vitro mRNA display method explored in this study can be used as a preliminary screening method to provide candidate peptides for the screening of subtilisin inhibitors.
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Affiliation(s)
- Hongbin Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Ping Song
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xue Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yufa Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shuqi Gui
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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14
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Shen S, Xie Z, Cai D, Yu X, Zhang H, Kim ES, Zhou B, Hou J, Zhang X, Huang Q, Sun J, Guo H. Biogenesis and molecular characteristics of serum hepatitis B virus RNA. PLoS Pathog 2020; 16:e1008945. [PMID: 33079954 PMCID: PMC7575114 DOI: 10.1371/journal.ppat.1008945] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 06/10/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
HBV is an enveloped DNA virus that replicates its DNA genome via reverse transcription of a pregenomic (pg) RNA intermediate in hepatocytes. Interestingly, HBV RNA can be detected in virus-like particles in chronic hepatitis B (CHB) patient serum and has been utilized as a biomarker for intrahepatic cccDNA activity in treated patients. However, the biogenesis and molecular characteristics of serum HBV RNA remain to be fully defined. In this study, we found that the encapsidated serum HBV RNA predominately consists of pgRNA, which are detergent- and ribonuclease-resistant. Through blocking HBV DNA replication without affecting pgRNA encapsidation by using the priming-defective HBV mutant Y63D or 3TC treatment, we demonstrated that the cell culture supernatant contains a large amount of pgRNA-containing nonenveloped capsids and a minor population of pgRNA-containing virions. The formation of pgRNA-virion requires both capsid assembly and viral envelope proteins, which can be inhibited by capsid assembly modulators and an envelope-knockout mutant, respectively. Furthermore, the pgRNA-virion utilizes the multivesicular body pathway for egress, in a similar way as DNA-virion morphogenesis. Northern blotting, RT-PCR, and 3' RACE assays revealed that serum/supernatant HBV pgRNA are mainly spliced and devoid of the 3'-terminal sequences. Furthermore, pgRNA-virion collected from cells treated with a reversible HBV priming inhibitor L-FMAU was unable to establish infection in HepG2-NTCP cells. In summary, serum HBV RNA is secreted in noninfectious virion-like particle as spliced and poly(A)-free pgRNA. Our study will shed light on the molecular biology of serum HBV RNA in HBV life cycle, and aid the development of serum HBV RNA as a novel biomarker for CHB diagnosis and treatment prognosis.
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Affiliation(s)
- Sheng Shen
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Zhanglian Xie
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Dawei Cai
- Assembly Biosciences, Inc., South San Francisco, CA, United States of America
| | - Xiaoyang Yu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Hu Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Elena S. Kim
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Bin Zhou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Jinlin Hou
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoyong Zhang
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qi Huang
- Assembly Biosciences, Inc., South San Francisco, CA, United States of America
| | - Jian Sun
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
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15
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Wang C, Zhang K, Meng L, Zhang X, Song Y, Zhang Y, Gai Y, Zhang Y, Yu B, Wu J, Wang S, Yu X. The C-terminal domain of feline and bovine SAMHD1 proteins has a crucial role in lentiviral restriction. J Biol Chem 2020; 295:4252-4264. [PMID: 32075911 PMCID: PMC7105322 DOI: 10.1074/jbc.ra120.012767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/14/2020] [Indexed: 01/29/2023] Open
Abstract
SAM and HD domain-containing protein 1 (SAMHD1) is a host factor that restricts reverse transcription of lentiviruses such as HIV in myeloid cells and resting T cells through its dNTP triphosphohydrolase (dNTPase) activity. Lentiviruses counteract this restriction by expressing the accessory protein Vpx or Vpr, which targets SAMHD1 for proteasomal degradation. SAMHD1 is conserved among mammals, and the feline and bovine SAMHD1 proteins (fSAM and bSAM) restrict lentiviruses by reducing cellular dNTP concentrations. However, the functional regions of fSAM and bSAM that are required for their biological functions are not well-characterized. Here, to establish alternative models to investigate SAMHD1 in vivo, we studied the restriction profile of fSAM and bSAM against different primate lentiviruses. We found that both fSAM and bSAM strongly restrict primate lentiviruses and that Vpx induces the proteasomal degradation of both fSAM and bSAM. Further investigation identified one and five amino acid sites in the C-terminal domain (CTD) of fSAM and bSAM, respectively, that are required for Vpx-mediated degradation. We also found that the CTD of bSAM is directly involved in mediating bSAM's antiviral activity by regulating dNTPase activity, whereas the CTD of fSAM is not. Our results suggest that the CTDs of fSAM and bSAM have important roles in their antiviral functions. These findings advance our understanding of the mechanism of fSAM- and bSAM-mediated viral restriction and might inform strategies for improving HIV animal models.
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Affiliation(s)
- Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; The First Hospital and Institute of Immunology, Jilin University, Changchun 130012, China
| | - Kaikai Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xin Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yanan Song
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Ying Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yuepeng Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jiaxin Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
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16
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Zhang W, Eckwahl MJ, Zhou KI, Pan T. Sensitive and quantitative probing of pseudouridine modification in mRNA and long noncoding RNA. RNA 2019; 25:1218-1225. [PMID: 31227565 PMCID: PMC6800517 DOI: 10.1261/rna.072124.119] [Citation(s) in RCA: 30] [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] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/20/2019] [Indexed: 05/25/2023]
Abstract
Pseudouridine (Ψ) is the most abundant RNA modification in cellular RNA present in tRNA/rRNA/snRNA and also in mRNA and long noncoding RNA (lncRNA). Elucidation of Ψ function in mRNA/lncRNA requires mapping and quantitative assessment of its modification fraction at single-base resolution. The most widely used Ψ mapping method for mRNA/lncRNA relies on its reaction with N-Cyclohexyl-N'-(2-morpholinoethyl)carbodiimide (CMC), forming an adduct with the Ψ base in RNA that is detectable by reverse transcription (RT) stops. However, this method has not produced consistent Ψ maps in mRNAs; furthermore, available protocols do not lend confidence to the estimation of Ψ fraction at specific sites, which is a crucial parameter for investigating the biological relevance of mRNA modifications. Here we develop a quantitative RT-PCR based method that can detect and quantify the modification fraction of target Ψ sites in mRNA/lncRNA, termed CMC-RT and ligation assisted PCR analysis of Ψ modification (CLAP). The method still relies on RT stop at a CMC-Ψ site, but uses site-specific ligation and PCR to generate two distinct PCR products in the same sample, corresponding to the modified and unmodified site, that are visualized by gel electrophoresis. CLAP not only requires a small amount of cellular RNA to validate Ψ sites but also determines the Ψ fraction semiquantitatively at target sites in mRNA/lncRNA. We determined the Ψ status of four mRNA sites and one lncRNA site whose modification fractions range from 30% to 84% in three human cell lines. Our method enables precise mapping and assessment of Ψ modification levels in low abundance cellular RNAs.
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Affiliation(s)
- Wen Zhang
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
| | - Matthew J Eckwahl
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Katherine I Zhou
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
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17
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Conn V, Conn SJ. SplintQuant: a method for accurately quantifying circular RNA transcript abundance without reverse transcription bias. RNA 2019; 25:1202-1210. [PMID: 31151991 PMCID: PMC6800515 DOI: 10.1261/rna.070953.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 02/28/2019] [Accepted: 05/29/2019] [Indexed: 05/22/2023]
Abstract
Reverse transcription of RNA is fallible, introducing biases and confounding the quantification of transcript abundance. We demonstrate that circular RNAs (circRNAs) are more subjective to overestimation of transcript abundance than cognate linear RNAs due to their covalently closed, circular form, producing multiple concatameric products from a single priming of reverse transcriptase. We developed SplintQuant, where custom DNA oligonucleotides are ligated by PBCV-1 DNA ligase only when bound to their target RNA. These circRNA-specific DNA oligonucleotides are terminally tagged with universal primers, allowing SplintQuant to accurately quantify even lowly abundant circRNAs through highly specific quantitative PCR (qPCR) in the absence of reverse transcription. SplintQuant is sensitive, specific, highly reproducible, and applicable to the quantification of canonical and noncanonical RNA transcripts including alternative splice variants, gene fusions, and offers a gold-standard approach for accurately quantifying circRNAs.
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Affiliation(s)
- Vanessa Conn
- Flinders Centre for Innovation in Cancer, Flinders University, College of Medicine and Public Health, Bedford Park, South Australia 5042, Australia
- UniSA Cancer Research Institute, University of South Australia, School of Pharmacy and Medical Sciences, Adelaide, South Australia 5000, Australia
| | - Simon J Conn
- Flinders Centre for Innovation in Cancer, Flinders University, College of Medicine and Public Health, Bedford Park, South Australia 5042, Australia
- UniSA Cancer Research Institute, University of South Australia, School of Pharmacy and Medical Sciences, Adelaide, South Australia 5000, Australia
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18
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Kamitani M, Kashima M, Tezuka A, Nagano AJ. Lasy-Seq: a high-throughput library preparation method for RNA-Seq and its application in the analysis of plant responses to fluctuating temperatures. Sci Rep 2019; 9:7091. [PMID: 31068632 PMCID: PMC6506593 DOI: 10.1038/s41598-019-43600-0] [Citation(s) in RCA: 30] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/26/2019] [Indexed: 02/07/2023] Open
Abstract
RNA-Seq is a whole-transcriptome analysis method used to research biological mechanisms and functions but its use in large-scale experiments is limited by its high cost and labour requirements. In this study, we have established a high-throughput and cost-effective RNA-Seq library preparation method that does not require mRNA enrichment. The method adds unique index sequences to samples during reverse transcription (RT) that is conducted at a higher temperature (≥62 °C) to suppress RT of A-rich sequences in rRNA, and then pools all samples into a single tube. Both single-read and paired-end sequencing of libraries is enabled. We found that the pooled RT products contained large amounts of RNA, mainly rRNA, causing over-estimations of the quantity of DNA and unstable tagmentation results. Degradation of RNA before tagmentation was found to be necessary for the stable preparation of libraries. We named this protocol low-cost and easy RNA-Seq (Lasy-Seq) and used it to investigate temperature responses in Arabidopsis thaliana. We analysed how sub-ambient temperatures (10-30 °C) affected the plant transcriptomes using time-courses of RNA-Seq from plants grown in randomly fluctuating temperature conditions. Our results suggest that there are diverse mechanisms behind plant temperature responses at different time scales.
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Affiliation(s)
- Mari Kamitani
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Shiga, Japan
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Makoto Kashima
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Shiga, Japan
| | - Ayumi Tezuka
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Shiga, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Shiga, Japan.
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19
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Abstract
Isolating a full-length clone of cDNA provides certainty that the entire protein-coding sequence of the mRNA has been identified and allows the 5' end of the mRNA to be precisely mapped onto the genomic DNA sequence. Unfortunately, partial clones that lack sequences corresponding to the 5' end of the target mRNA occur commonly in cDNA libraries. Rapid amplification of cDNA ends (RACE) provides a means to overcome this obstacle by amplifying the 5'-terminal sequences of cDNA. This technique differs from conventional polymerase chain reaction in that it only requires knowledge of a small region of sequence within either the target RNA or in a partial clone of cDNA. In the first step of 5'-RACE, extension of the primer by reverse transcriptase yields single-stranded cDNAs complementary to the 5' regions of the mRNA. In the second step, a homopolymeric tail or a primer-adaptor is added to the 3' ends of the cDNAs. This generates a primer-binding site upstream of the unknown 5'-sequence of the target mRNA. Finally, synthesis of the second cDNA strand and amplification of the resulting double-stranded cDNAs is performed using the gene-specific primer and the upstream primer. The double-stranded products of the final stage are purified and cloned into a vector for sequencing analysis and subsequent manipulation.
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20
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Abstract
cDNAs whose first-strand synthesis has been primed by oligo(dT) generally contain the 3' sequences of the RNA. However, cDNAs generated by internal gene-specific primers will usually lack one or both terminal regions of the parental mRNA. And alternate splicing or the presence of an internal A-rich tract can generate cDNA clones that lack 3' sequences. These sequences can be recovered using 3'-RACE (rapid amplification of cDNA ends), which can also be used to map the 3' termini of families of mRNAs with alternative polyadenylation sites. Briefly, a population of mRNAs is transcribed into cDNA using an adaptor-primer with a poly(T) at its 3' end and 30-40 nt containing the recognition sites for two or three restriction enzymes at its 5' end. Reverse transcription is usually followed by two successive rounds of polymerase chain reaction (PCR). The first is primed by a gene-specific sense oligonucleotide and the antisense (dT) adaptor-primer. The products of the first PCR can be used as templates for a second, nested PCR, which is primed by a gene-specific sense oligonucleotide internal to the first, and a second antisense oligonucleotide whose sequence is identical to the central region of the (dT) adaptor-primer. The products amplified in the second PCR are isolated, cleaved with a suitable restriction enzyme, cloned, and characterized.
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21
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Green MR, Sambrook J. Amplification of cDNA Generated by Reverse Transcription of mRNA: Two-Step Reverse Transcription-Polymerase Chain Reaction (RT-PCR). Cold Spring Harb Protoc 2019; 2019:2019/5/pdb.prot095190. [PMID: 31043555 DOI: 10.1101/pdb.prot095190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Reverse transcription-polymerase chain reaction (RT-PCR) is a powerful method to detect and synthesize cDNA copies of low-copy-number mRNAs. Two enzymes are used: reverse transcriptase to produce single-stranded cDNA copies, which are then used as templates in an amplification reaction catalyzed by a thermostable DNA polymerase. For this reason, the method is known as "two-step RT-PCR." This protocol describes the traditional method of RT-PCR in which the two synthetic reactions are performed separately and sequentially.
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22
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Wing PA, Davenne T, Wettengel J, Lai AG, Zhuang X, Chakraborty A, D'Arienzo V, Kramer C, Ko C, Harris JM, Schreiner S, Higgs M, Roessler S, Parish JL, Protzer U, Balfe P, Rehwinkel J, McKeating JA. A dual role for SAMHD1 in regulating HBV cccDNA and RT-dependent particle genesis. Life Sci Alliance 2019; 2:e201900355. [PMID: 30918010 PMCID: PMC6438393 DOI: 10.26508/lsa.201900355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 02/21/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B is one of the world's unconquered diseases with more than 240 million infected subjects at risk of developing liver disease and hepatocellular carcinoma. Hepatitis B virus reverse transcribes pre-genomic RNA to relaxed circular DNA (rcDNA) that comprises the infectious particle. To establish infection of a naïve target cell, the newly imported rcDNA is repaired by host enzymes to generate covalently closed circular DNA (cccDNA), which forms the transcriptional template for viral replication. SAMHD1 is a component of the innate immune system that regulates deoxyribonucleoside triphosphate levels required for host and viral DNA synthesis. Here, we show a positive role for SAMHD1 in regulating cccDNA formation, where KO of SAMHD1 significantly reduces cccDNA levels that was reversed by expressing wild-type but not a mutated SAMHD1 lacking the nuclear localization signal. The limited pool of cccDNA in infected Samhd1 KO cells is transcriptionally active, and we observed a 10-fold increase in newly synthesized rcDNA-containing particles, demonstrating a dual role for SAMHD1 to both facilitate cccDNA genesis and to restrict reverse transcriptase-dependent particle genesis.
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Affiliation(s)
- Peter Ac Wing
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tamara Davenne
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jochen Wettengel
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - Alvina G Lai
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anindita Chakraborty
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | | | - Catharina Kramer
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chunkyu Ko
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - James M Harris
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sabrina Schreiner
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Martin Higgs
- Institutes of Cancer and Genomic Sciences and Immunity and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Joanna L Parish
- Institutes of Cancer and Genomic Sciences and Immunity and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Peter Balfe
- Institutes of Cancer and Genomic Sciences and Immunity and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jane A McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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23
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Balasubramaniam M, Zhou J, Addai A, Martinez P, Pandhare J, Aiken C, Dash C. PF74 Inhibits HIV-1 Integration by Altering the Composition of the Preintegration Complex. J Virol 2019; 93:e01741-18. [PMID: 30567984 PMCID: PMC6401427 DOI: 10.1128/jvi.01741-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/06/2018] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 capsid protein (CA) facilitates reverse transcription and nuclear entry of the virus. However, CA's role in post-nuclear entry steps remains speculative. We describe a direct link between CA and integration by employing the capsid inhibitor PF74 as a probe coupled with the biochemical analysis of HIV-1 preintegration complexes (PICs) isolated from acutely infected cells. At a low micromolar concentration, PF74 potently inhibited HIV-1 infection without affecting reverse transcription. Surprisingly, PF74 markedly reduced proviral integration owing to inhibition of nuclear entry and/or integration. However, a 2-fold reduction in nuclear entry by PF74 did not quantitatively correlate with the level of antiviral activity. Titration of PF74 against the integrase inhibitor raltegravir showed an additive antiviral effect that is dependent on a block at the post-nuclear entry step. PF74's inhibitory effect was not due to the formation of defective viral DNA ends or a delay in integration, suggesting that the compound inhibits PIC-associated integration activity. Unexpectedly, PICs recovered from cells infected in the presence of PF74 exhibited elevated integration activity. PF74's effect on PIC activity is CA specific since the compound did not increase the integration activity of PICs of a PF74-resistant HIV-1 CA mutant. Sucrose gradient-based fractionation studies revealed that PICs assembled in the presence of PF74 contained lower levels of CA, suggesting a negative association between CA and PIC-associated integration activity. Finally, the addition of a CA-specific antibody or PF74 inhibited PIC-associated integration activity. Collectively, our results demonstrate that PF74's targeting of PIC-associated CA results in impaired HIV-1 integration.IMPORTANCE Antiretroviral therapy (ART) that uses various combinations of small molecule inhibitors has been highly effective in controlling HIV. However, the drugs used in the ART regimen are expensive, cause side effects, and face viral resistance. The HIV-1 CA plays critical roles in the virus life cycle and is an attractive therapeutic target. While currently there is no CA-based therapy, highly potent CA-specific inhibitors are being developed as a new class of antivirals. Efforts to develop a CA-targeted therapy can be aided through a clear understanding of the role of CA in HIV-1 infection. CA is well established to coordinate reverse transcription and nuclear entry of the virus. However, the role of CA in post-nuclear entry steps of HIV-1 infection is poorly understood. We show that a CA-specific drug PF74 inhibits HIV-1 integration revealing a novel role of this multifunctional viral protein in a post-nuclear entry step of HIV-1 infection.
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Affiliation(s)
- Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Jing Zhou
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amma Addai
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Phillip Martinez
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
| | - Christopher Aiken
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville, Tennessee, USA
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24
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Hagen B, Kraase M, Indikova I, Indik S. A high rate of polymerization during synthesis of mouse mammary tumor virus DNA alleviates hypermutation by APOBEC3 proteins. PLoS Pathog 2019; 15:e1007533. [PMID: 30768644 PMCID: PMC6395001 DOI: 10.1371/journal.ppat.1007533] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 08/30/2018] [Revised: 02/28/2019] [Accepted: 12/14/2018] [Indexed: 11/19/2022] Open
Abstract
Retroviruses have evolved multiple means to counteract host restriction factors such as single-stranded DNA-specific deoxycytidine deaminases (APOBEC3s, A3s). These include exclusion of A3s from virions by an A3-unreactive nucleocapsid or expression of an A3-neutralizing protein (Vif, Bet). However, a number of retroviruses package A3s and do not encode apparent vif- or bet-like genes, yet they replicate in the presence of A3s. The mode by which they overcome deleterious restriction remains largely unknown. Here we show that the prototypic betaretrovirus, mouse mammary tumor virus (MMTV), packages similar amounts of A3s as HIV-1ΔVif, yet its proviruses carry a significantly lower level of A3-mediated deamination events than the lentivirus. The G-to-A mutation rate increases when the kinetics of reverse transcription is reduced by introducing a mutation (F120L) to the DNA polymerase domain of the MMTV reverse transcriptase (RT). A similar A3-sensitizing effect was observed when the exposure time of single-stranded DNA intermediates to A3s during reverse transcription was lengthened by reducing the dNTP concentration or by adding suboptimal concentrations of an RT inhibitor to infected cells. Thus, the MMTV RT has evolved to impede access of A3s to transiently exposed minus DNA strands during reverse transcription, thereby alleviating inhibition by A3 family members. A similar mechanism may be used by other retroviruses and retrotransposons to reduce deleterious effects of A3 proteins.
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Affiliation(s)
- Benedikt Hagen
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Martin Kraase
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ivana Indikova
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Stanislav Indik
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
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25
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Pollpeter D, Sobala A, Malim MH. Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells. J Vis Exp 2019:10.3791/58715. [PMID: 30774124 PMCID: PMC6682491 DOI: 10.3791/58715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Monitoring of nucleic acid intermediates during virus replication provides insights into the effects and mechanisms of action of antiviral compounds and host cell proteins on viral DNA synthesis. Here we address the lack of a cell-based, high-coverage, and high-resolution assay that is capable of defining retroviral reverse transcription intermediates within the physiological context of virus infection. The described method captures the 3'-termini of nascent complementary DNA (cDNA) molecules within HIV-1 infected cells at single nucleotide resolution. The protocol involves harvesting of whole cell DNA, targeted enrichment of viral DNA via hybrid capture, adaptor ligation, size fractionation by gel purification, PCR amplification, deep sequencing, and data analysis. A key step is the efficient and unbiased ligation of adaptor molecules to open 3'-DNA termini. Application of the described method determines the abundance of reverse transcripts of each particular length in a given sample. It also provides information about the (internal) sequence variation in reverse transcripts and thereby any potential mutations. In general, the assay is suitable for any questions relating to DNA 3'-extension, provided that the template sequence is known.
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Affiliation(s)
- Darja Pollpeter
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London;
| | - Andrew Sobala
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London
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26
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Green MR, Sambrook J. Quantification of RNA by Real-Time Reverse Transcription-Polymerase Chain Reaction (RT-PCR). Cold Spring Harb Protoc 2018; 2018:2018/10/pdb.prot095042. [PMID: 30275077 DOI: 10.1101/pdb.prot095042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This protocol describes a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay using a two-enzyme, two-tube approach, carried out using either SYBR Green I or TaqMan chemistries. The protocol uses a PCR volume of 20 µL (although most manufacturers recommend 50-µL reactions). However, if the PCR target is not very abundant (i.e., present at one to 10 copies per sample), a larger volume may yield better reproducibility between samples. Discussion on preparing high-quality RNA, choosing a priming method, selecting an enzyme, and selecting an endogenous reference gene is also included.
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27
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Benitez-Guijarro M, Lopez-Ruiz C, Tarnauskaitė Ž, Murina O, Mian Mohammad M, Williams TC, Fluteau A, Sanchez L, Vilar-Astasio R, Garcia-Canadas M, Cano D, Kempen MJH, Sanchez-Pozo A, Heras SR, Jackson AP, Reijns MA, Garcia-Perez JL. RNase H2, mutated in Aicardi-Goutières syndrome, promotes LINE-1 retrotransposition. EMBO J 2018; 37:e98506. [PMID: 29959219 PMCID: PMC6068448 DOI: 10.15252/embj.201798506] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [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: 10/26/2017] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 12/03/2022] Open
Abstract
Long INterspersed Element class 1 (LINE-1) elements are a type of abundant retrotransposons active in mammalian genomes. An average human genome contains ~100 retrotransposition-competent LINE-1s, whose activity is influenced by the combined action of cellular repressors and activators. TREX1, SAMHD1 and ADAR1 are known LINE-1 repressors and when mutated cause the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). Mutations in RNase H2 are the most common cause of AGS, and its activity was proposed to similarly control LINE-1 retrotransposition. It has therefore been suggested that increased LINE-1 activity may be the cause of aberrant innate immune activation in AGS Here, we establish that, contrary to expectations, RNase H2 is required for efficient LINE-1 retrotransposition. As RNase H1 overexpression partially rescues the defect in RNase H2 null cells, we propose a model in which RNase H2 degrades the LINE-1 RNA after reverse transcription, allowing retrotransposition to be completed. This also explains how LINE-1 elements can retrotranspose efficiently without their own RNase H activity. Our findings appear to be at odds with LINE-1-derived nucleic acids driving autoinflammation in AGS.
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Affiliation(s)
- Maria Benitez-Guijarro
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Cesar Lopez-Ruiz
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Olga Murina
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Mahwish Mian Mohammad
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Thomas C Williams
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Laura Sanchez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Raquel Vilar-Astasio
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marta Garcia-Canadas
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - David Cano
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marie-Jeanne Hc Kempen
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Antonio Sanchez-Pozo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Sara R Heras
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Martin Am Reijns
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Jose L Garcia-Perez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
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28
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Abstract
RNA has the intrinsic propensity to form base pairs, leading to complex intramolecular and intermolecular helices. Direct measurement of base pairing interactions in living cells is critical to solving transcriptome structure and interactions, and investigating their functions (Lu and Chang, Curr Opin Struct Biol 36:142-148, 2016). Toward this goal, we developed an experimental method, PARIS (Psoralen Analysis of RNA Interactions and Structures), to directly determine transcriptome-wide base pairing interactions (Lu et al., Cell 165(5):1267-1279, 2016). PARIS combines four critical steps, in vivo cross-linking, 2D gel purification, proximity ligation, and high-throughput sequencing to achieve high-throughput and near-base pair resolution determination of the RNA structurome and interactome in living cells. In this chapter, we aim to provide a comprehensive discussion on the principles behind the experimental and computational strategies, and a step-by-step description of the experiment and analysis.
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Affiliation(s)
- Zhipeng Lu
- Department of Dermatology, Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
| | - Jing Gong
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Haidian, Beijing, 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Haidian, Beijing, 100084, China.
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29
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Uchiyama H, Maehara S, Ohta H, Seki T, Tanaka Y. Elevenin regulates the body color through a G protein-coupled receptor NlA42 in the brown planthopper Nilaparvata lugens. Gen Comp Endocrinol 2018; 258:33-38. [PMID: 28743555 DOI: 10.1016/j.ygcen.2017.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/13/2017] [Accepted: 07/16/2017] [Indexed: 12/18/2022]
Abstract
The neuropeptide elevenin and similar neuropeptide precursors are common in some invertebrates but their physiological function in most species has not been explored. The brown planthopper, Nilaparvata lugens (Stål) has an elevenin-like peptide and a G protein-coupled receptor (GPCR) NlA42 that is homologous to the elevenin receptor of the annelid Platynereis dumerilii. RNA interference (RNAi)-mediated knockdown of either Nl-elevenin or the NlA42 gene resulted in cuticle melanization. Ion transport peptide (ITP) also induces melanization, but unlike ITP, knockdown of NlElevenin and NlA42 did not have any effect on wing expansion or activity after eclosion. In wild condition macropterous individuals show a darker body color when compared with brachypterous individuals, but RNAi experiments suggest that insulin-signaling and Nl-elevenin signaling regulate wing morph and body color independently. NlElevenin was predominantly expressed in the brain while NlA42 was highly expressed in the abdominal integument and brain. A signal Calcium assays using aequorin indicated that NlA42 heterologously expressed in HEK293 cells exhibited responses to synthetic Nl-elevenin peptide from concentrations as low as 10-9M. These results suggest that neuropeptide Nl-elevenin is involved in the regulation of melanization through its receptor NlA42. This is the first report of a physiological function for elevenin-like peptides in insects.
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Affiliation(s)
- Hironobu Uchiyama
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Shiori Maehara
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Hiroto Ohta
- Graduate School of Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Takehito Seki
- Department of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa 243-0034, Japan
| | - Yoshiaki Tanaka
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8634, Japan.
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30
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Geldreich A, Haas G, Kubina J, Bouton C, Tanguy M, Erhardt M, Keller M, Ryabova L, Dimitrova M. Formation of large viroplasms and virulence of Cauliflower mosaic virus in turnip plants depend on the N-terminal EKI sequence of viral protein TAV. PLoS One 2017; 12:e0189062. [PMID: 29253877 PMCID: PMC5734791 DOI: 10.1371/journal.pone.0189062] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/17/2017] [Indexed: 12/11/2022] Open
Abstract
Cauliflower mosaic virus (CaMV) TAV protein (TransActivator/Viroplasmin) plays a pivotal role during the infection cycle since it activates translation reinitiation of viral polycistronic RNAs and suppresses RNA silencing. It is also the major component of cytoplasmic electron-dense inclusion bodies (EDIBs) called viroplasms that are particularly evident in cells infected by the virulent CaMV Cabb B-JI isolate. These EDIBs are considered as virion factories, vehicles for CaMV intracellular movement and reservoirs for CaMV transmission by aphids. In this study, focused on different TAV mutants in vivo, we demonstrate that three physically separated domains collectively participate to the formation of large EDIBs: the N-terminal EKI motif, a sequence of the MAV domain involved in translation reinitiation and a C-terminal region encompassing the zinc finger. Surprisingly, EKI mutant TAVm3, corresponding to a substitution of the EKI motif at amino acids 11-13 by three alanines (AAA), which completely abolished the formation of large viroplasms, was not lethal for CaMV but highly reduced its virulence without affecting the rate of systemic infection. Expression of TAVm3 in a viral context led to formation of small irregularly shaped inclusion bodies, mild symptoms and low levels of viral DNA and particles accumulation, despite the production of significant amounts of mature capsid proteins. Unexpectedly, for CaMV-TAVm3 the formation of viral P2-containing electron-light inclusion body (ELIB), which is essential for CaMV aphid transmission, was also altered, thus suggesting an indirect role of the EKI tripeptide in CaMV plant-to-plant propagation. This important functional contribution of the EKI motif in CaMV biology can explain the strict conservation of this motif in the TAV sequences of all CaMV isolates.
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Affiliation(s)
- Angèle Geldreich
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Gabrielle Haas
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Julie Kubina
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Clément Bouton
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Mélanie Tanguy
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Mathieu Erhardt
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Mario Keller
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Lyubov Ryabova
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Maria Dimitrova
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
- * E-mail:
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Huo YY, Li GF, Qiu YH, Li WM, Zhang YJ. Rapid Detection of Prunus Necrotic Ringspot Virus by Reverse Transcription-cross-priming Amplification Coupled with Nucleic Acid Test Strip Cassette. Sci Rep 2017; 7:16175. [PMID: 29170535 PMCID: PMC5700948 DOI: 10.1038/s41598-017-16536-6] [Citation(s) in RCA: 8] [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: 08/31/2017] [Accepted: 11/13/2017] [Indexed: 11/09/2022] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) is one of the most devastating viruses to Prunus spp. In this study, we developed a diagnostic system RT-CPA-NATSC, wherein reverse transcription-cross-priming amplification (RT-CPA) is coupled with nucleic acid test strip cassette (NATSC), a vertical flow (VF) visualization, for PNRSV detection. The RT-CPA-NATSC assay targets the encoding gene of the PNRSV coat protein with a limit of detection of 72 copies per reaction and no cross-reaction with the known Prunus pathogenic viruses and viroids, demonstrating high sensitivity and specificity. The reaction is performed on 60 °C and can be completed less than 90 min with the prepared template RNA. Field sample test confirmed the reliability of RT-CPA-NATSC, indicating the potential application of this simple and rapid detection method in routine test of PNRSV.
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Affiliation(s)
- Ya-Yun Huo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Gui-Fen Li
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Yan-Hong Qiu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Wei-Min Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yong-Jiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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Naorem SS, Han J, Wang S, Lee WR, Heng X, Miller JF, Guo H. DGR mutagenic transposition occurs via hypermutagenic reverse transcription primed by nicked template RNA. Proc Natl Acad Sci U S A 2017; 114:E10187-E10195. [PMID: 29109248 PMCID: PMC5703328 DOI: 10.1073/pnas.1715952114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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] [Indexed: 11/18/2022] Open
Abstract
Diversity-generating retroelements (DGRs) are molecular evolution machines that facilitate microbial adaptation to environmental changes. Hypervariation occurs via a mutagenic retrotransposition process from a template repeat (TR) to a variable repeat (VR) that results in adenine-to-random nucleotide conversions. Here we show that reverse transcription of the Bordetella phage DGR is primed by an adenine residue in TR RNA and is dependent on the DGR-encoded reverse transcriptase (bRT) and accessory variability determinant (Avd ), but is VR-independent. We also find that the catalytic center of bRT plays an essential role in site-specific cleavage of TR RNA for cDNA priming. Adenine-specific mutagenesis occurs during reverse transcription and does not involve dUTP incorporation, indicating it results from bRT-catalyzed misincorporation of standard deoxyribonucleotides. In vivo assays show that this hybrid RNA-cDNA molecule is required for mutagenic transposition, revealing a unique mechanism of DNA hypervariation for microbial adaptation.
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Affiliation(s)
- Santa S Naorem
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Jin Han
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212
| | - Shufang Wang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212
| | - William R Lee
- Department of Biochemistry, University of Missouri, Columbia, MO 65212
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65212
| | - Jeff F Miller
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095;
- The California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - Huatao Guo
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212;
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Rehwinkel J, Maelfait J, Bridgeman A, Rigby R, Hayward B, Liberatore RA, Bieniasz PD, Towers GJ, Moita LF, Crow YJ, Bonthron DT, Reis e Sousa C. SAMHD1-dependent retroviral control and escape in mice. EMBO J 2013; 32:2454-62. [PMID: 23872947 PMCID: PMC3770946 DOI: 10.1038/emboj.2013.163] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/01/2013] [Indexed: 12/12/2022] Open
Abstract
SAMHD1 is a host restriction factor for human immunodeficiency virus 1 (HIV-1) in cultured human cells. SAMHD1 mutations cause autoimmune Aicardi-Goutières syndrome and are found in cancers including chronic lymphocytic leukaemia. SAMHD1 is a triphosphohydrolase that depletes the cellular pool of deoxynucleoside triphosphates, thereby preventing reverse transcription of retroviral genomes. However, in vivo evidence for SAMHD1's antiviral activity has been lacking. We generated Samhd1 null mice that do not develop autoimmune disease despite displaying a type I interferon signature in spleen, macrophages and fibroblasts. Samhd1(-/-) cells have elevated deoxynucleoside triphosphate (dNTP) levels but, surprisingly, SAMHD1 deficiency did not lead to increased infection with VSV-G-pseudotyped HIV-1 vectors. The lack of restriction is likely attributable to the fact that dNTP concentrations in SAMHD1-sufficient mouse cells are higher than the KM of HIV-1 reverse transcriptase (RT). Consistent with this notion, an HIV-1 vector mutant bearing an RT with lower affinity for dNTPs was sensitive to SAMHD1-dependent restriction in cultured cells and in mice. This shows that SAMHD1 can restrict lentiviruses in vivo and that nucleotide starvation is an evolutionarily conserved antiviral mechanism.
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Affiliation(s)
- Jan Rehwinkel
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, UK
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jonathan Maelfait
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rachel Rigby
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bruce Hayward
- Leeds Institute of Molecular Medicine, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Rachel A Liberatore
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - Luis F Moita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - David T Bonthron
- Leeds Institute of Molecular Medicine, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, UK
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Gao T, Tong Y, Cao M, Li X, Pang X. Evaluation of the inactivation of human Coxsackievirus by thermophilic and mesophilic anaerobic digestion using integrated cell culture and reverse transcription real-time quantitative PCR. Water Res 2013; 47:4259-4264. [PMID: 23764576 DOI: 10.1016/j.watres.2013.04.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/19/2013] [Accepted: 04/23/2013] [Indexed: 06/02/2023]
Abstract
The virucidal effects of anaerobic digestion were evaluated using human Coxsackievirus as a model for the Enterovirus family. Coxsackievirus was inactivated completely by thermophilic anaerobic digestion (TAD). By 4 h no living and infectious virus remained and no detectable viral RNA was present after 2 days in TAD (7.0 log reduction). Compared to TAD, 2.6 log reduction of viral RNA was achieved by 14 days in mesophilic anaerobic digestion (MAD) (p < 0.0001). Although cytopathogenic effect was not observed in the cultured cells, low levels of intracellular viral RNA were detected after one day of MAD treatment indicating that Coxsackievirus had infected the cells but could not replicate. The combination of thermal and biochemical effects in TAD plays a critical role for viral disinfection. The results of this study indicate that selection of the right configuration of anaerobic digestion for treatment of biowaste may reduce the risk of viral contamination to the environment and water source.
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Affiliation(s)
- Tiejun Gao
- Himark bioGas Inc., AFDP 6004-118 Street, Edmonton, Alberta, Canada.
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Feng H, Chen P, Zhao F, Nassal M, Hu K. Evidence for multiple distinct interactions between hepatitis B virus P protein and its cognate RNA encapsidation signal during initiation of reverse transcription. PLoS One 2013; 8:e72798. [PMID: 23977352 PMCID: PMC3748129 DOI: 10.1371/journal.pone.0072798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 06/04/2013] [Accepted: 07/11/2013] [Indexed: 12/27/2022] Open
Abstract
Replication of hepatitis B virus (HBV) via protein-primed reverse transcription is initiated by binding of the viral P protein to the conserved ε stem-loop on the pregenomic (pg) RNA. This triggers encapsidation of the complex and the ε-templated synthesis of a short P protein-linked DNA oligonucleotide (priming) for subsequent minus-strand DNA extension. ε consists of a lower and upper stem, a bulge containing the priming template, and an apical loop. The nonhelical subelements are considered important for DNA synthesis and pgRNA packaging whereas the role of the upper stem is not well characterized. Priming itself could until recently not be addressed because in vitro generated HBV P - ε complexes showed no activity. Focussing on the four A residues at the base and tip of the upper ε stem and the two U residues in the loop we first investigated the impact of 24 mutations on viral DNA accumulation in transfected cells. While surprisingly many mutations were tolerated, further analyzing the negatively acting mutations, including in a new cell-free priming system, revealed divergent position-related impacts on pgRNA packaging, priming activity and possibly initiation site selection. This genetic separability implies that the ε RNA undergoes multiple distinct interactions with P protein as pgRNA encapsidation and replication initiation progress, and that the strict conservation of ε in nature may reflect its optimal adaptation to comply with all of them. The data further define the most attractive mutants for future studies, including as decoys for interference with HBV replication.
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Affiliation(s)
- Hui Feng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ping Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Fei Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Michael Nassal
- University Hospital Freiburg, Department of Internal Medicine II/Molecular Biology, Freiburg, Germany
- * E-mail: (MN); (KH)
| | - Kanghong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Biomedical Center, Hubei University of Technology, Wuhan, China
- * E-mail: (MN); (KH)
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Monot C, Kuciak M, Viollet S, Mir AA, Gabus C, Darlix JL, Cristofari G. The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts. PLoS Genet 2013; 9:e1003499. [PMID: 23675310 PMCID: PMC3649969 DOI: 10.1371/journal.pgen.1003499] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [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: 10/25/2012] [Accepted: 03/22/2013] [Indexed: 01/18/2023] Open
Abstract
L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP) first uses its endonuclease (EN) to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A) tail, a process known as target-primed reverse transcription (TPRT). Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5′-TTTT/A-3′ sites) and frequently preceded by imperfect T-tracts. However, it is currently unclear whether—and to which degree—the liberated 3′-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A) tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3′ end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3′ overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3′ end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome. Jumping genes are DNA sequences present in the genome of most living organisms. They contribute to genome dynamics and occasionally result in hereditary genetic diseases or cancer. L1 elements are the only autonomously active jumping genes in the human genome. They replicate through an RNA–mediated copy-and-paste mechanism by cleaving the host genome and then using this new DNA end as a primer to reverse transcribe its own RNA, generating a new L1 DNA copy. The molecular determinants that influence L1 target site choice are not fully understood. Here we present a quantitative assay to measure the influence of DNA target site sequence and structure on the reverse transcription step. By testing more than 65 potential DNA primers, we observe that not all sites are equally extended by the L1 machinery, and we define the rules guiding this process. In particular, we highlight the importance of partial sequence complementarity between the target site and the L1 RNA extremity, but also the high level of flexibility of this process, since detrimental terminal mismatches can be compensated by an increasing number of interacting nucleotides. We propose that this mechanism contributes to the distribution of new L1 insertions within the human genome.
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Affiliation(s)
- Clément Monot
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Monika Kuciak
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Sébastien Viollet
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Ashfaq Ali Mir
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
| | - Caroline Gabus
- Ecole Normale Supérieure de Lyon, Human Virology Department, INSERM U758, Lyon, France
| | - Jean-Luc Darlix
- Ecole Normale Supérieure de Lyon, Human Virology Department, INSERM U758, Lyon, France
| | - Gaël Cristofari
- INSERM, U1081, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- CNRS, UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- University of Nice-Sophia-Antipolis, Faculty of Medicine, Nice, France
- * E-mail:
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Abstract
The fission yeast, Schizosaccharomyces pombe, is an important model species with a low intron density. Previous studies showed extensive intron losses during its evolution. To test the models of intron loss and gain in fission yeasts, we conducted a comparative genomic analysis in four Schizosaccharomyces species. Both intronization and de-intronization were observed, although both were at a low frequency. A de-intronization event was caused by a degenerative mutation in the branch site. Four cases of imprecise intron losses were identified, indicating that genomic deletion is not a negligible mechanism of intron loss. Most intron losses were precise deletions of introns, and were significantly biased to the 3′ sides of genes. Adjacent introns tended to be lost simultaneously. These observations indicated that the main force shaping the exon-intron structures of fission yeasts was precise intron losses mediated by reverse transcriptase. We found two cases of intron gains caused by tandem genomic duplication, but failed to identify the mechanisms for the majority of the intron gain events observed. In addition, we found that intron-lost and intron-gained genes had certain similar features, such as similar Gene Ontology categories and expression levels.
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Affiliation(s)
- Tao Zhu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Deng-Ke Niu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
- * E-mail:
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Battivelli E, Lecossier D, Clavel F, Hance AJ. Delaying reverse transcription does not increase sensitivity of HIV-1 to human TRIM5α. PLoS One 2013; 8:e52434. [PMID: 23320071 PMCID: PMC3540060 DOI: 10.1371/journal.pone.0052434] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/14/2012] [Indexed: 01/08/2023] Open
Abstract
Background Because uncoating of the capsid is linked to reverse transcription, modifications that delay this process lead to the persistence in the cytoplasm of capsids susceptible to recognition by the human restriction factor TRIM5α (hTRIM5α). It is unknown, however, if increasing the time available for capsid-hTRIM5α interactions would actually render viruses more sensitive to hTRIM5α. Results Viral sensitivity to hTRIM5α was evaluated by comparing their replication in human U373-X4 cells in which hTRIM5α activity had or had not been inhibited by overexpression of human TRIM5γ. No differences were observed comparing wild-type HIV-1 and variants carrying mutations in reverse transcriptase or the central polypurine tract that delayed the completion of reverse transcription. In addition, the effect of delaying the onset of reverse transcription for several hours by treating target cells with nevirapine was evaluated using viral isolates with different sensitivities to hTRIM5α. Delaying reverse transcription led to a time-dependent loss in viral infectivity that was increased by inhibiting capsid-cyclophilin A interactions, but did not result in increased viral sensitivity to hTRIM5α, regardless of their intrinsic sensitivity to this restriction factor. Conclusions Consistent with prior studies, the HIV-1 capsid can be targeted for destruction by hTRIM5α, but different strains display considerable variability in their sensitivity to this restriction factor. Capsids can also be lost more slowly through a TRIM5α-independent process that is accelerated when capsid-cyclophilin A interactions are inhibited, an effect that may reflect changes in the intrinsic stability of the capsid. Blocking the onset or delaying reverse transcription does not, however, increase viral sensitivity to hTRIM5α, indicating that the recognition of the capsids by hTRIM5α is completed rapidly following entry into the cytoplasm, as previously observed for the simian restriction factors TRIM-Cyp and rhesus TRIM5α.
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Affiliation(s)
- Emilie Battivelli
- Institut National de la Santé et de la Recherche Médicale (INSERM) U941, Paris, France
- Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint-Louis, Paris, France
| | - Denise Lecossier
- Institut National de la Santé et de la Recherche Médicale (INSERM) U941, Paris, France
- Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint-Louis, Paris, France
| | - François Clavel
- Institut National de la Santé et de la Recherche Médicale (INSERM) U941, Paris, France
- Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint-Louis, Paris, France
| | - Allan J. Hance
- Institut National de la Santé et de la Recherche Médicale (INSERM) U941, Paris, France
- Institut Universitaire d'Hématologie, Université Paris Diderot, Hôpital Saint-Louis, Paris, France
- Service des Maladies Infectieuses et Tropicales, Assistance Publique - Hôpitaux de Paris, Hôpital Bichat - Claude Bernard, Paris, France
- * E-mail:
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Chamontin C, Yu B, Racine PJ, Darlix JL, Mougel M. MoMuLV and HIV-1 nucleocapsid proteins have a common role in genomic RNA packaging but different in late reverse transcription. PLoS One 2012; 7:e51534. [PMID: 23236513 PMCID: PMC3517543 DOI: 10.1371/journal.pone.0051534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 09/19/2012] [Accepted: 11/05/2012] [Indexed: 11/25/2022] Open
Abstract
Retroviral nucleocapsid proteins harbor nucleic acid chaperoning activities that mostly rely on the N-terminal basic residues and the CCHC zinc finger motif. Such chaperoning is essential for virus replication, notably for genomic RNA selection and packaging in virions, and for reverse transcription of genomic RNA into DNA. Recent data revealed that HIV-1 nucleocapsid restricts reverse transcription during virus assembly--a process called late reverse transcription--suggesting a regulation between RNA packaging and late reverse transcription. Indeed, mutating the HIV-1 nucleocapsid basic residues or the two zinc fingers caused a reduction in RNA incorporated and an increase in newly made viral DNA in the mutant virions. MoMuLV nucleocapsid has an N-terminal basic region similar to HIV-1 nucleocapsid but a unique zinc finger. This prompted us to investigate whether the N-terminal basic residues and the zinc finger of MoMuLV and HIV-1 nucleocapsids play a similar role in genomic RNA packaging and late reverse transcription. To this end, we analyzed the genomic RNA and viral DNA contents of virions produced by cells transfected with MoMuLV molecular clones where the zinc finger was mutated or completely deleted or with a deletion of the N-terminal basic residues of nucleocapsid. All mutant virions showed a strong defect in genomic RNA content indicating that the basic residues and zinc finger are important for genomic RNA packaging. In contrast to HIV-1 nucleocapsid-mutants, the level of viral DNA in mutant MoMuLV virions was only slightly increased. These results confirm that the N-terminal basic residues and zinc finger of MoMuLV nucleocapsid are critical for genomic RNA packaging but, in contrast to HIV-1 nucleocapsid, they most probably do not play a role in the control of late reverse transcription. In addition, these results suggest that virus formation and late reverse transcription proceed according to distinct mechanisms for MuLV and HIV-1.
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Affiliation(s)
| | - Bing Yu
- UMR5236 CNRS, UM1,UM2, CPBS, Montpellier, France
| | | | - Jena-Luc Darlix
- UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, Illkirch, France
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Crouzier L, Dubois C, Edwards SL, Lauridsen LH, Wengel J, Veedu RN. Efficient reverse transcription using locked nucleic acid nucleotides towards the evolution of nuclease resistant RNA aptamers. PLoS One 2012; 7:e35990. [PMID: 22558297 PMCID: PMC3338489 DOI: 10.1371/journal.pone.0035990] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 03/26/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Modified nucleotides are increasingly being utilized in the de novo selection of aptamers for enhancing their drug-like character and abolishing the need for time consuming trial-and-error based post-selection modifications. Locked nucleic acid (LNA) is one of the most prominent and successful nucleic acid analogues because of its remarkable properties, and widely explored as building blocks in therapeutic oligonucleotides. Evolution of LNA-modified RNA aptamers requires an efficient reverse transcription method for PCR enrichment of the selected RNA aptamer candidates. Establishing this key step is a pre-requisite for performing LNA-modified RNA aptamer selection. METHODOLOGY In this study three different reverse transcriptases were investigated towards the enzymatic recognition of LNA nucleotides. Both incorporation as well as reading capabilities of the LNA nucleotides was investigated to fully understand the limitations of the enzymatic recognition. CONCLUSIONS We found that SuperScript® III Reverse Transcriptase is an efficient enzyme for the recognition of LNA nucleotides, making it a prime candidate to be used in de novo selection of LNA containing RNA aptamers.
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Affiliation(s)
- Lucile Crouzier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- Institute Polytechnique LaSalle Beauvais, Beauvais, France
| | - Camille Dubois
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- Institute Polytechnique LaSalle Beauvais, Beauvais, France
| | - Stacey L. Edwards
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
| | - Lasse H. Lauridsen
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- The Novo Nordisk Foundation Center for Biosustainability, Scion DTU, Hørsholm, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | - Rakesh N. Veedu
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Brisbane, Queensland, Australia
- * E-mail:
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Darmanin-Sheehan A, Finlay WJJ, Cunningham O, Fennell BJ. Molecular scanning: combining random mutagenesis, ribosome display, and bioinformatic analysis for protein engineering. Methods Mol Biol 2012; 907:487-503. [PMID: 22907370 DOI: 10.1007/978-1-61779-974-7_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/25/2023]
Abstract
Protein engineering techniques can facilitate the direct de-convolution of specific domains, regions, and particular amino acids that contribute to protein function. Many tools are available to aid this enterprise and herein we describe one such tool, a technique we term "Molecular Scanning" (MS). MS is analogous to previously described alanine scanning in that it samples potentially functional sequence space, but differs in that it uses Error-Prone polymerase chain reaction to randomly introduce all amino acids across the sequence space, as opposed to simply introducing alanine at each desired position. We commonly use MS in conjunction with ribosome-display, selecting for specific character traits (e.g., improved affinity) which allows us to sample functionally relevant diversity on a reasonably large scale. This approach is amenable to a variety of different mutational techniques and display technologies as dictated by user requirements or needs. In this chapter we present a general outline of the process as we have previously successfully applied it.
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Abstract
Most chloroplast genes in land plants are represented by multiple transcript isoforms that arise via differential splicing, endo- and exo-nucleolytic processing, and/or RNA editing. Exploration of the functional significance and mechanisms of these processing events is an active area of current research. This chapter focuses on methods that can be used to define the termini of chloroplast RNAs, quantify the relative levels of alternative processed RNA isoforms, and identify the binding sites of proteins that mediate chloroplast RNA processing. Various approaches for defining the sequence specificity of chloroplast RNA binding proteins are discussed, as are the parameters to consider in designing in vitro assays for RNA binding activities. A protocol is provided for a poisoned-primer extension assay for quantifying different splice isoforms.
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Affiliation(s)
- Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
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Yoder KE, Espeseth A, Wang XH, Fang Q, Russo MT, Lloyd RS, Hazuda D, Sobol RW, Fishel R. The base excision repair pathway is required for efficient lentivirus integration. PLoS One 2011; 6:e17862. [PMID: 21448280 PMCID: PMC3063173 DOI: 10.1371/journal.pone.0017862] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [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: 11/22/2010] [Accepted: 02/11/2011] [Indexed: 12/24/2022] Open
Abstract
An siRNA screen has identified several proteins throughout the base excision repair (BER) pathway of oxidative DNA damage as important for efficient HIV infection. The proteins identified included early repair factors such as the base damage recognition glycosylases OGG1 and MYH and the late repair factor POLß, implicating the entire BER pathway. Murine cells with deletions of the genes Ogg1, Myh, Neil1 and Polß recapitulate the defect of HIV infection in the absence of BER. Defective infection in the absence of BER proteins was also seen with the lentivirus FIV, but not the gammaretrovirus MMLV. BER proteins do not affect HIV infection through its accessory genes nor the central polypurine tract. HIV reverse transcription and nuclear entry appear unaffected by the absence of BER proteins. However, HIV integration to the host chromosome is reduced in the absence of BER proteins. Pre-integration complexes from BER deficient cell lines show reduced integration activity in vitro. Integration activity is restored by addition of recombinant BER protein POLß. Lentiviral infection and integration efficiency appears to depend on the presence of BER proteins.
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Affiliation(s)
- Kristine E. Yoder
- Molecular Virology, Immunology, and Medical Genetics, Human Cancer Genetics, The Ohio State University Medical Center and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (KEY); (RF)
| | - Amy Espeseth
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania, United States of America
| | - Xiao-hong Wang
- University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Qingming Fang
- University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Maria Teresa Russo
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Rome, Italy
| | - R. Stephen Lloyd
- Center for Research on Occupational and Environmental Toxicology, Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Daria Hazuda
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania, United States of America
| | - Robert W. Sobol
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Richard Fishel
- Molecular Virology, Immunology, and Medical Genetics, Human Cancer Genetics, The Ohio State University Medical Center and Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Physics Department, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (KEY); (RF)
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Espeseth AS, Fishel R, Hazuda D, Huang Q, Xu M, Yoder K, Zhou H. siRNA screening of a targeted library of DNA repair factors in HIV infection reveals a role for base excision repair in HIV integration. PLoS One 2011; 6:e17612. [PMID: 21448273 PMCID: PMC3063162 DOI: 10.1371/journal.pone.0017612] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [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: 12/17/2010] [Accepted: 01/31/2011] [Indexed: 12/19/2022] Open
Abstract
Host DNA repair enzymes have long been assumed to play a role in HIV replication,
and many different DNA repair factors have been associated with HIV. In order to
identify DNA repair pathways required for HIV infection, we conducted a targeted
siRNA screen using 232 siRNA pools for genes associated with DNA repair. Mapping
the genes targeted by effective siRNA pools to well-defined DNA repair pathways
revealed that many of the siRNAs targeting enzymes associated with the short
patch base excision repair (BER) pathway reduced HIV infection. For six siRNA
pools targeting BER enzymes, the negative effect of mRNA knockdown was rescued
by expression of the corresponding cDNA, validating the importance of the gene
in HIV replication. Additionally, mouse embryo fibroblasts (MEFs) lacking
expression of specific BER enzymes had decreased transduction by HIV-based
retroviral vectors. Examining the role BER enzymes play in HIV infection
suggests a role for the BER pathway in HIV integration.
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Affiliation(s)
- Amy S. Espeseth
- Department of Antiviral Research, Merck
Research Laboratories, West Point, Pennsylvania, United States of
America
- * E-mail: (ASE); (DH)
| | - Rick Fishel
- Department of Molecular Virology, Immunology,
and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio,
United States of America
| | - Daria Hazuda
- Department of Antiviral Research, Merck
Research Laboratories, West Point, Pennsylvania, United States of
America
- * E-mail: (ASE); (DH)
| | - Qian Huang
- Department of Antiviral Research, Merck
Research Laboratories, West Point, Pennsylvania, United States of
America
| | - Min Xu
- Department of Antiviral Research, Merck
Research Laboratories, West Point, Pennsylvania, United States of
America
| | - Kristine Yoder
- Department of Molecular Virology, Immunology,
and Medical Genetics, The Ohio State University Medical Center, Columbus, Ohio,
United States of America
| | - Honglin Zhou
- Department of Antiviral Research, Merck
Research Laboratories, West Point, Pennsylvania, United States of
America
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Maekawa C, Kitahara T, Kizawa K, Okazaki S, Kamakura T, Horii A, Imai T, Doi K, Inohara H, Kiyama H. Expression and translocation of aquaporin-2 in the endolymphatic sac in patients with Meniere's disease. J Neuroendocrinol 2010; 22:1157-64. [PMID: 20722976 DOI: 10.1111/j.1365-2826.2010.02060.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [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] [Indexed: 11/29/2022]
Abstract
Meniere's disease, characterised by episodic vertigo, fluctuating hearing loss and tinnitus, can occur under conditions of stress. Its pathology was first revealed to be inner ear hydrops through temporal bone studies in 1938. Although its pathogenesis has been proposed to be a disorder of water transport in the inner ear, subsequently, it remains unsolved, until now. A recent study revealed that both plasma stress hormone, vasopressin (pAVP) and its receptor, V2 (V2R) expression in the inner ear endolymphatic sac were significantly higher in Meniere's patients. In the present study, to link V2R-related molecules and inner ear hydrops, we examined V2R-linked water channel molecule, aquaporin-2 (AQP2) expression and translocation in human endolymphatic sac. AQP2 mRNA expression in the endolymphatic sac was significantly higher in Meniere's patients by using real-time polymerase chain reaction, as further confirmed by western blotting. AQP2-like immunoreactivity (-LIR) was translocated from luminal to basolateral side with endosomal trapping in the endolymphatic sac at the time of AVP exposure in human endolymphatic sac tissue culture. The similar AQP2-LIR translocation was also demonstrated by forskolin and blocked by vasopressin/V2R specific antagonist, OPC31260 and protein kinase A (PKA) specific antagonists, H-89 and KT-5720. We concluded that in the pathogenesis of inner ear hydrops resulting in Meniere's attacks, pAVP elevation as a result of stress and subsequent V2R-cAMP-PKA-AQP2 activation and endosomal trapping of AQP2 in the endolymphatic sac, might be important as a basis of this disease. Further experimental and clinical studies are needed to better clarify the neuroscientific relationship between stress and Meniere's disease.
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Affiliation(s)
- C Maekawa
- Department of Otolaryngology, Osaka University, School of Medicine, Suita-city, Osaka, Japan
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Yoon OK, Brem RB. Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA 2010; 16:1256-67. [PMID: 20421314 PMCID: PMC2874177 DOI: 10.1261/rna.2038810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Surveys of transcription in many organisms have observed widespread expression of RNAs with no known function, encoded within and between canonical coding genes. The search to distinguish functional RNAs from transcriptional noise represents one of the great challenges in genomic biology. Here we report a next-generation sequencing technique designed to facilitate the inference of function of uncharacterized transcript forms by improving their coverage in sequencing libraries, in parallel with the detection of canonical mRNAs. We piloted this protocol, which is based on the capture of 3' ends of polyadenylated RNAs, in budding yeast. Analysis of transcript ends in coding regions uncovered hundreds of alternative-length coding forms, which harbored a unique sequence motif and showed signatures of regulatory function in particular gene categories; independent single-gene measurements confirmed the differential regulation of short coding forms during heat shock. In addition, our 3'-end RNA-seq method applied to wild-type strains detected putative noncoding transcripts previously reported only in RNA surveillance mutants, and many such transcripts showed differential expression in yeast cultures grown under chemical stress. Our results underscore the power of the 3'-end protocol to improve detection of noncanonical transcript forms in a sequencing experiment of standard depth, and our findings strongly suggest that many unannotated, polyadenylated RNAs may have as yet uncharacterized regulatory functions.
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Affiliation(s)
- Oh Kyu Yoon
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
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47
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Haque R, Ali FG, Biscoglia R, Abey J, Weller J, Klein D, Iuvone PM. CLOCK and NPAS2 have overlapping roles in the circadian oscillation of arylalkylamine N-acetyltransferase mRNA in chicken cone photoreceptors. J Neurochem 2010; 113:1296-306. [PMID: 20345751 PMCID: PMC2950611 DOI: 10.1111/j.1471-4159.2010.06698.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Circadian clocks in vertebrates are thought to be composed of transcriptional-translational feedback loops involving a highly conversed set of 'clock genes' namely, period (Per1-3) and cryptochrome (Cry1-2), which encode negative transcriptional regulators; and Bmal1, Clock, and Npas2, which encode positive regulators. Aanat, which encodes arylalkylamine N-acetyltransferase (AANAT), the key regulatory enzyme that drives the circadian rhythm of melatonin synthesis, contains a circadian E-box element (CACGTG) in its proximal promoter that is potentially capable of binding CLOCK : BMAL1 and NPAS2 : BMAL1 heterodimers. The present study was conducted to investigate whether CLOCK and/or NPAS2 regulates Aanat expression in photoreceptor cells. Npas2 and Clock are both expressed in photoreceptor cells in vivo and in vitro. To assess the roles of CLOCK and NPAS2 in Aanat expression, gene-specific micro RNA vectors were used to knock down expression of these clock genes in photoreceptor-enriched cell cultures. The knockdown of CLOCK protein significantly reduced the circadian expression of Npas2, Per2, and Aanat transcripts but had no effect on the circadian rhythm of Bmal1 transcript level. The knockdown of NPAS2 significantly damped the circadian rhythm of Aanat mRNAs but had no effect on circadian expression of any of clock genes examined, except Npas2 itself. Chromatin immunoprecipitation studies indicated that both CLOCK and NPAS2 bound to the Aanat promoter in situ. Thus, CLOCK and NPAS2 have overlapping roles in the clock output pathway that regulates the rhythmic expression of Aanat in photoreceptors. However, CLOCK plays the predominant role in the chicken photoreceptor circadian clockwork mechanism, including the regulation of NPAS2 expression.
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Affiliation(s)
- Rashidul Haque
- Department of Ophthalmology & Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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48
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Abstract
Quantitative reverse transcriptase polymerase chain reaction enables the accurate quantification of gene expression in cultured cells or small tissue samples. In this chapter, we describe the use of Taqman((R)) technology to measure expression of matrix metalloproteinases and related genes.
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Abstract
Members of the chemokine (Chemotactic cytokines) superfamily and their receptors play a major role in trafficking of immune cells under homeostatic and inflammatory conditions. The chemokine receptor CXCR3 is expressed mainly on activated T lymphocytes and binds three pro-inflammatory, interferon-gamma-inducible chemokines: monokine induced by IFN-gamma (Mig/CXCL9), IFN-gamma-induced protein-10 (IP-10/CXCL10) and IFN-gamma-inducible T-cell alpha-chemoattractant (I-TAC/CXCL11). CXCR3 and its agonists are involved in a variety of inflammatory pathologies, making this receptor an attractive target for the design of new anti-inflammatory drugs. Interestingly, a growing body of evidence suggests the existence of at least two novel variants of CXCR3, namely CXCR3-B and CXCR3-alt, which present challenges in the design of new anti-inflammatory drugs targeting CXCR3. In this chapter, we describe the collection, isolation and activation of human peripheral blood-derived T lymphocytes and methods to examine the expression of CXCR3 and its atypical variants at both mRNA and protein levels, as well as protocols for exploring the biochemical and functional responses of T lymphocytes to all known CXCR3 agonists.
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Affiliation(s)
- Anna Korniejewska
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, Slough, UK
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Siquieroli ACS, Vieira CU, Carvalho-Zilse GA, Goulart LR, Kerr WE, Bonetti AM. Analysis of the intercaste transcriptional profile of Melipona scutellaris Latreille, 1811 (Hymenoptera, Apidae, Meliponini) by mRNA differential display. Biol Res 2009; 42:107-110. [PMID: 19621138] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023] Open
Abstract
In colonies of Melipona scutellaris Latreille, 1811 workers can be found with four ganglion nerve cells, a morphological characteristic of the queen. It is hypothesized that these workers, called intercastes, or phenocopies, are phenotypically-like workers, but genotypically identical to queens due to this specific trait. Workers with the same number of ganglion as queens seem to be intercastes between queens and workers. Our objective was to analyze the mRNA pro files of workers, queens, and intercastes of M. scutellaris through DDRT-PCR. Three hundred (300) pupae with white eyes were collected and externally identified according to the number of abdominal nerve ganglions: workers (5 ganglions), queens (4 ganglions) and intercastes (4 ganglions). The analysis identified differentially expressed transcripts that were present only in workers, but absent in intercastes and queens, confirming the hypothesis, by demonstrating the environmental effect on the queen genotype that generated phenotype-like workers.
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