1
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Lelyveld VS, O'Flaherty DK, Zhou L, Izgu EC, Szostak JW. DNA polymerase activity on synthetic N3'→P5' phosphoramidate DNA templates. Nucleic Acids Res 2019; 47:8941-8949. [PMID: 31428779 PMCID: PMC6755091 DOI: 10.1093/nar/gkz707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/29/2019] [Accepted: 08/01/2019] [Indexed: 11/12/2022] Open
Abstract
Genetic polymers that could plausibly govern life in the universe might inhabit a broad swath of chemical space. A subset of these genetic systems can exchange information with RNA and DNA and could therefore form the basis for model protocells in the laboratory. N3'→P5' phosphoramidate (NP) DNA is defined by a conservative linkage substitution and has shown promise as a protocellular genetic material, but much remains unknown about its functionality and fidelity due to limited enzymatic tools. Conveniently, we find widespread NP-DNA-dependent DNA polymerase activity among reverse transcriptases, an observation consistent with structural studies of the RNA-like conformation of NP-DNA duplexes. Here, we analyze the consequences of this unnatural template linkage on the kinetics and fidelity of DNA polymerization activity catalyzed by wild-type and variant reverse transcriptases. Template-associated deficits in kinetics and fidelity suggest that even highly conservative template modifications give rise to error-prone DNA polymerase activity. Enzymatic copying of NP-DNA sequences is nevertheless an important step toward the future study and engineering of this synthetic genetic polymer.
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Affiliation(s)
- Victor S Lelyveld
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Enver Cagri Izgu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
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2
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Potapov V, Fu X, Dai N, Corrêa IR, Tanner NA, Ong JL. Base modifications affecting RNA polymerase and reverse transcriptase fidelity. Nucleic Acids Res 2019; 46:5753-5763. [PMID: 29750267 PMCID: PMC6009661 DOI: 10.1093/nar/gky341] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/18/2018] [Indexed: 01/28/2023] Open
Abstract
Ribonucleic acid (RNA) is capable of hosting a variety of chemically diverse modifications, in both naturally-occurring post-transcriptional modifications and artificial chemical modifications used to expand the functionality of RNA. However, few studies have addressed how base modifications affect RNA polymerase and reverse transcriptase activity and fidelity. Here, we describe the fidelity of RNA synthesis and reverse transcription of modified ribonucleotides using an assay based on Pacific Biosciences Single Molecule Real-Time sequencing. Several modified bases, including methylated (m6A, m5C and m5U), hydroxymethylated (hm5U) and isomeric bases (pseudouridine), were examined. By comparing each modified base to the equivalent unmodified RNA base, we can determine how the modification affected cumulative RNA polymerase and reverse transcriptase fidelity. 5-hydroxymethyluridine and N6-methyladenosine both increased the combined error rate of T7 RNA polymerase and reverse transcriptases, while pseudouridine specifically increased the error rate of RNA synthesis by T7 RNA polymerase. In addition, we examined the frequency, mutational spectrum and sequence context of reverse transcription errors on DNA templates from an analysis of second strand DNA synthesis.
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Affiliation(s)
| | - Xiaoqing Fu
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
- Dalian University of Technology, School of Life Science and Biotechnology, Dalian, Liaoning 116021, China
| | - Nan Dai
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Nathan A Tanner
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
| | - Jennifer L Ong
- New England Biolabs, Inc, Ipswich, Massachusetts, 01938, USA
- To whom correspondence should be addressed. Tel: +1 978 380 7448; Fax: +1 978 921 1350;
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3
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Cui J, Gizzi A, Stivers JT. Deoxyuridine in DNA has an inhibitory and promutagenic effect on RNA transcription by diverse RNA polymerases. Nucleic Acids Res 2019; 47:4153-4168. [PMID: 30892639 PMCID: PMC6486633 DOI: 10.1093/nar/gkz183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/04/2019] [Accepted: 03/09/2019] [Indexed: 12/16/2022] Open
Abstract
dUTP is a close structural congener of dTTP and can be readily incorporated into DNA opposite to adenine during DNA replication leading to non-mutagenic dU/A base pairs ('uracilation'). We find that dU/A pairs located within DNA transcriptional templates optimized for either T7 RNA polymerase (T7 RNAP) or human RNA polymerase II (pol II) have inhibitory and mutagenic effects on transcription. The data for T7 RNAP establishes that even a single dU/A pair can inhibit promoter binding and transcription initiation up to 30-fold, and that inhibitory effects on transcription elongation are also possible. Sequencing of the mRNA transcribed from uniformly uracilated DNA templates by T7 RNAP indicated an increased frequency of transversion and insertion mutations compared to all T/A templates. Strong effects of dU/A pairs on cellular transcription activity and fidelity were also observed with RNA pol II using uracil base excision repair (UBER)-deficient human cells. At the highest levels of template uracilation, transcription by RNA pol II was completely blocked. We propose that these effects arise from the decreased thermodynamic stability and increased dynamics of dU/A pairs in DNA. The potential implications of these findings on gene regulation and disease are discussed.
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Affiliation(s)
- Junru Cui
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Anthony Gizzi
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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4
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Palikša S, Alzbutas G, Skirgaila R. Decreased Km to dNTPs is an essential M-MuLV reverse transcriptase adoption required to perform efficient cDNA synthesis in One-Step RT-PCR assay. Protein Eng Des Sel 2019; 31:79-89. [PMID: 29608777 DOI: 10.1093/protein/gzy003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/05/2018] [Indexed: 01/27/2023] Open
Abstract
Personalized medicine and advanced diagnostic tools based on RNA analysis are focusing on fast and direct One-Step RT-PCR assays. First strand complementary DNA (cDNA) synthesized by the reverse transcriptase (RT) is exponentially amplified in the end-point or real-time PCR. Even a minor discrepancy in PCR conditions would result in big deviations during the data analysis. Thus, One-Step RT-PCR composition is typically based on the PCR buffer. In this study, we have used compartmentalized ribosome display technique for in vitro evolution of the Moloney Murine Leukemia Virus reverse transcriptase (M-MuLV RT) that would be able to perform efficient full-length cDNA synthesis in PCR buffer optimized for Thermus aquaticus DNA polymerase. The most frequent mutations found in a selected library were analyzed. Aside from the mutations, which switch off RNase H activity of RT and are beneficial for the full-length cDNA synthesis, we have identified several mutations in the active center of the enzyme (Q221R and V223A/M), which result in 4-5-fold decrease of Km for dNTPs (<0.2 mM). The selected mutations are in surprising agreement with the natural evolution process because they transformed the active center from the oncoretroviral M-MuLV RT-type to the lenitiviral enzyme-type. We believe that this was the major and essential phenotypic adjustment required to perform fast and efficient cDNA synthesis in PCR buffer at 0.2-mM concentration of each dNTP.
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Affiliation(s)
- S Palikša
- Thermo Fisher Scientific Baltics, UAB, LT-02241 Vilnius, Lithuania.,JSC Diagnolita, LT-10257 Vilnius, Lithuania
| | - G Alzbutas
- Thermo Fisher Scientific Baltics, UAB, LT-02241 Vilnius, Lithuania
| | - R Skirgaila
- Thermo Fisher Scientific Baltics, UAB, LT-02241 Vilnius, Lithuania
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5
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Cantão NM, Fogaça de Almeida L, Rodrigo Wolf I, Oliveira Almeida R, Alves de Almeida Cruz A, Nunes C, Barbosa AN, Valente GT, de Moura Campos Pardini MI, Grotto RMT. HIV Reverse Transcriptase and Protease Genes Variability Can Be a Biomarker Associated with HIV and Hepatitis B or C Coinfection. Sci Rep 2018; 8:8280. [PMID: 29844604 PMCID: PMC5974300 DOI: 10.1038/s41598-018-26675-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/10/2018] [Indexed: 11/09/2022] Open
Abstract
Variability of the HIV reverse transcriptase (RT) and protease (PR) genes has been used as indicators of drug resistance and as a mean to evaluate phylogenetic relationships among circulating virus. However, these studies have been carried in HIV mono-infected populations. The goal of this study was to evaluate, for the first time, the HIV PR and RT sequences from HIV/HBV and HIV/HCV co-infected patients. HIV PR and RT genes were amplificated and sequenced to resistance analysis. The bioinformatics analysis was performed to infer about sequences clustering and molecular evolution. The results showed that the most frequent amino acid substitutions in RT were L214F (67.6%), I135T (55.9%), and in PR was V15I (41.2%). The molecular clock analysis showed that the HIV circulating in co-infected patients were separated in two clusters in the years 1999-2000. Some patients included as HIV mono-infected according patients' medical records and inside the co-infected cluster were, in fact, co-infected by PCR analysis. Analysis of the decision trees showed susceptibility to lamivudine and emtricitabine were important attribute to characterize co-infected patients. In conclusion, the results obtained in this study suggest, for the first time, that HIV RT and PR genes variability could be a genetic biomarker to coinfection.
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Affiliation(s)
- Natália Mirele Cantão
- São Paulo State University (Unesp), Medical School, Botucatu, Sao Paulo State, Brazil
| | - Lauana Fogaça de Almeida
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | - Ivan Rodrigo Wolf
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | - Rodrigo Oliveira Almeida
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | | | - Caroline Nunes
- São Paulo State University (Unesp), Medical School, Botucatu, Sao Paulo State, Brazil
| | | | - Guilherme Targino Valente
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil
| | | | - Rejane Maria Tommasini Grotto
- São Paulo State University (Unesp), Medical School, Botucatu, Sao Paulo State, Brazil.
- São Paulo State University (Unesp), School of Agriculture (FCA), Department of Bioprocess and Biotechnology, Botucatu, Sao Paulo State, Brazil.
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6
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Díaz-Martínez L, Brichette-Mieg I, Pineño-Ramos A, Domínguez-Huerta G, Grande-Pérez A. Lethal mutagenesis of an RNA plant virus via lethal defection. Sci Rep 2018; 8:1444. [PMID: 29362502 PMCID: PMC5780445 DOI: 10.1038/s41598-018-19829-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/09/2018] [Indexed: 01/28/2023] Open
Abstract
Lethal mutagenesis is an antiviral therapy that relies on increasing the viral mutation rate with mutagenic nucleoside or base analogues. Currently, the molecular mechanisms that lead to virus extinction through enhanced mutagenesis are not fully understood. Increasing experimental evidence supports the lethal defection model of lethal mutagenesis of RNA viruses, where replication-competent-defectors drive infective virus towards extinction. Here, we address lethal mutagenesis in vivo using 5-fluorouracil (5-FU) during the establishment of tobacco mosaic virus (TMV) systemic infections in N. tabacum. The results show that 5-FU decreased the infectivity of TMV without affecting its viral load. Analysis of molecular clones spanning two genomic regions showed an increase of the FU-related base transitions A → G and U → C. Although the mutation frequency or the number of mutations per molecule did not increase, the complexity of the mutant spectra and the distribution of the mutations were altered. Overall, our results suggest that 5-FU antiviral effect on TMV is associated with the perturbation of the mutation-selection balance in the genomic region of the RNA-dependent RNA polymerase (RdRp). Our work supports the lethal defection model for lethal mutagenesis in vivo in a plant RNA virus and opens the way to study lethal mutagens in plant-virus systems.
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Affiliation(s)
- Luis Díaz-Martínez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, 29071, Málaga, Spain
| | - Isabel Brichette-Mieg
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, 29071, Málaga, Spain
| | - Axier Pineño-Ramos
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, 29071, Málaga, Spain
| | - Guillermo Domínguez-Huerta
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, 29071, Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Estación Experimental "La Mayora", 29750, Algarrobo-Costa, Málaga, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Consejo Superior de Investigaciones Científicas-Universidad de Málaga, Área de Genética, Facultad de Ciencias, Campus de Teatinos, 29071, Málaga, Spain.
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7
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Sebastián-Martín A, Barrioluengo V, Menéndez-Arias L. Transcriptional inaccuracy threshold attenuates differences in RNA-dependent DNA synthesis fidelity between retroviral reverse transcriptases. Sci Rep 2018; 8:627. [PMID: 29330371 PMCID: PMC5766491 DOI: 10.1038/s41598-017-18974-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/18/2017] [Indexed: 01/01/2023] Open
Abstract
In M13mp2 lacZα forward mutation assays measuring intrinsic fidelity of DNA-dependent DNA synthesis, wild-type human immunodeficiency virus type 1 (HIV-1) RTs of group M/subtype B previously showed >10-fold higher error rates than murine leukaemia virus (MLV) and avian myeloblastosis virus (AMV) RTs. An adapted version of the assay was used to obtain error rates of RNA-dependent DNA synthesis for several RTs, including wild-type HIV-1BH10, HIV-1ESP49, AMV and MLV RTs, and the high-fidelity mutants of HIV-1ESP49 RT K65R and K65R/V75I. Our results showed that there were less than two-fold differences in fidelity between the studied RTs with error rates ranging within 2.5 × 10-5 and 3.5 × 10-5. These results were consistent with the existence of a transcriptional inaccuracy threshold, generated by the RNA polymerase while synthesizing the RNA template used in the assay. A modest but consistent reduction of the inaccuracy threshold was achieved by lowering the pH and Mg2+ concentration of the transcription reaction. Despite assay limitations, we conclude that HIV-1BH10 and HIV-1ESP49 RTs are less accurate when copying DNA templates than RNA templates. Analysis of the RNA-dependent mutational spectra revealed a higher tendency to introduce large deletions at the initiation of reverse transcription by all HIV-1 RTs except the double-mutant K65R/V75I.
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Affiliation(s)
- Alba Sebastián-Martín
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Verónica Barrioluengo
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049, Madrid, Spain
- DiaSorin Iberia S.A., Avenida de la Vega 1, 28108, Alcobendas (Madrid), Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas & Universidad Autónoma de Madrid), c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049, Madrid, Spain.
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8
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Yokomori M, Gotoh O, Murakami Y, Fujimoto K, Suyama A. A multiplex RNA quantification method to determine the absolute amounts of mRNA without reverse transcription. Anal Biochem 2017; 539:96-103. [PMID: 29029978 DOI: 10.1016/j.ab.2017.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 01/16/2023]
Abstract
We have developed a highly sensitive microarray-based method that determines the absolute amounts of mRNA in a total RNA sample in a multiplex manner without reverse transcription. This direct mRNA measurement promotes high-throughput testing and reduces bias in transcriptome analyses. Furthermore, quantification of the absolute amount of mRNA allows transcriptome analysis without common controls or additional, complicated normalization. The method, called Photo-DEAN, was validated using chemically synthesized RNAs of known quantities and mouse liver total RNA samples. We found that the absolute amounts of mRNA were successfully measured without the cDNA synthesis step, with a sensitivity of 15 zmol achieved in 7 h.
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Affiliation(s)
- Maasa Yokomori
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Osamu Gotoh
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yasufumi Murakami
- Department of Biological Science and Technology, Graduate School of Industrial Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kenzo Fujimoto
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | - Akira Suyama
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
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9
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Malik O, Khamis H, Rudnizky S, Marx A, Kaplan A. Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase. Nucleic Acids Res 2017; 45:10190-10205. [PMID: 28973474 PMCID: PMC5737391 DOI: 10.1093/nar/gkx720] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/08/2017] [Indexed: 12/20/2022] Open
Abstract
Reverse transcriptase (RT) catalyzes the conversion of the viral RNA into an integration-competent double-stranded DNA, with a variety of enzymatic activities that include the ability to displace a non-template strand concomitantly with polymerization. Here, using high-resolution optical tweezers to follow the activity of the murine leukemia Virus RT, we show that strand-displacement polymerization is frequently interrupted. Abundant pauses are modulated by the strength of the DNA duplex ∼8 bp ahead, indicating the existence of uncharacterized RT/DNA interactions, and correspond to backtracking of the enzyme, whose recovery is also modulated by the duplex strength. Dissociation and reinitiation events, which induce long periods of inactivity and are likely the rate-limiting step in the synthesis of the genome in vivo, are modulated by the template structure and the viral nucleocapsid protein. Our results emphasize the potential regulatory role of conserved structural motifs, and may provide useful information for the development of potent and specific inhibitors.
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Affiliation(s)
- Omri Malik
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hadeel Khamis
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Faculty of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ailie Marx
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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10
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Menéndez-Arias L, Sebastián-Martín A, Álvarez M. Viral reverse transcriptases. Virus Res 2017; 234:153-176. [PMID: 28043823 DOI: 10.1016/j.virusres.2016.12.019] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/19/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
Reverse transcriptases (RTs) play a major role in the replication of Retroviridae, Metaviridae, Pseudoviridae, Hepadnaviridae and Caulimoviridae. RTs are enzymes that are able to synthesize DNA using RNA or DNA as templates (DNA polymerase activity), and degrade RNA when forming RNA/DNA hybrids (ribonuclease H activity). In retroviruses and LTR retrotransposons (Metaviridae and Pseudoviridae), the coordinated action of both enzymatic activities converts single-stranded RNA into a double-stranded DNA that is flanked by identical sequences known as long terminal repeats (LTRs). RTs of retroviruses and LTR retrotransposons are active as monomers (e.g. murine leukemia virus RT), homodimers (e.g. Ty3 RT) or heterodimers (e.g. human immunodeficiency virus type 1 (HIV-1) RT). RTs lack proofreading activity and display high intrinsic error rates. Besides, high recombination rates observed in retroviruses are promoted by poor processivity that causes template switching, a hallmark of reverse transcription. HIV-1 RT inhibitors acting on its polymerase activity constitute the backbone of current antiretroviral therapies, although novel drugs, including ribonuclease H inhibitors, are still necessary to fight HIV infections. In Hepadnaviridae and Caulimoviridae, reverse transcription leads to the formation of nicked circular DNAs that will be converted into episomal DNA in the host cell nucleus. Structural and biochemical information on their polymerases is limited, although several drugs inhibiting HIV-1 RT are known to be effective against the human hepatitis B virus polymerase. In this review, we summarize current knowledge on reverse transcription in the five virus families and discuss available biochemical and structural information on RTs, including their biosynthesis, enzymatic activities, and potential inhibition.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain.
| | - Alba Sebastián-Martín
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mar Álvarez
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, c/Nicolás Cabrera, 1, Campus de Cantoblanco, 28049 Madrid, Spain
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11
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Harjanto D, Papamarkou T, Oates CJ, Rayon-Estrada V, Papavasiliou FN, Papavasiliou A. RNA editing generates cellular subsets with diverse sequence within populations. Nat Commun 2016; 7:12145. [PMID: 27418407 PMCID: PMC4947178 DOI: 10.1038/ncomms12145] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 06/06/2016] [Indexed: 12/20/2022] Open
Abstract
RNA editing is a mutational mechanism that specifically alters the nucleotide content in transcribed RNA. However, editing rates vary widely, and could result from equivalent editing amongst individual cells, or represent an average of variable editing within a population. Here we present a hierarchical Bayesian model that quantifies the variance of editing rates at specific sites using RNA-seq data from both single cells, and a cognate bulk sample to distinguish between these two possibilities. The model predicts high variance for specific edited sites in murine macrophages and dendritic cells, findings that we validated experimentally by using targeted amplification of specific editable transcripts from single cells. The model also predicts changes in variance in editing rates for specific sites in dendritic cells during the course of LPS stimulation. Our data demonstrate substantial variance in editing signatures amongst single cells, supporting the notion that RNA editing generates diversity within cellular populations. RNA editing rate detected from bulk RNA-seq data can vary widely. Here, by constructing a hierarchical Bayesian model, the authors report substantial variance in editing signatures detected by RNA-seq data from both single cells and a cognate bulk sample.
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Affiliation(s)
- Dewi Harjanto
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York 10065, USA
| | - Theodore Papamarkou
- School of Mathematics and Statistics, University of Glasgow, Glasgow G12 8QW, UK
| | - Chris J Oates
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Violeta Rayon-Estrada
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York 10065, USA
| | - F Nina Papavasiliou
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York 10065, USA
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12
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Hameed A, Abdullah MI, Ahmed E, Sharif A, Irfan A, Masood S. Anti-HIV cytotoxicity enzyme inhibition and molecular docking studies of quinoline based chalcones as potential non-nucleoside reverse transcriptase inhibitors (NNRT). Bioorg Chem 2016; 65:175-82. [PMID: 26964017 DOI: 10.1016/j.bioorg.2016.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/20/2022]
Abstract
A series of fourteen (A1 - A14) qunioline based chalcones were screened for reverse transcriptase inhibitors (RT) and found potentially active against RT. Bioassay, theoretical and dockings studies with RT (the enzyme required for reverse transcription of viral RNA) results showed that the type and positions of the substituents seemed to be critical for their inhibition against RT. The bromo and chloro substituted chalcone displayed high degree of inhibition against RT. The A4 andA6 showed high interaction with RT, contributing high free binding energy (ΔG -9.30 and -9.13kcal) and RT inhibition value (IC50 0.10μg/ml and 0.11μg/ml).
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Affiliation(s)
- Asima Hameed
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan
| | | | - Ejaz Ahmed
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan.
| | - Ahsan Sharif
- Institute of Chemistry, University of the Punjab, Lahore, P.O 54590, Pakistan
| | - Ahmad Irfan
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia; Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Sara Masood
- Sheikh Zayed Madical College & Hospital Rahim Yar Khan, Pakistan
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Bartels M, French R, Graybosch RA, Tatineni S. Triticum mosaic virus exhibits limited population variation yet shows evidence of parallel evolution after replicated serial passage in wheat. Virology 2016; 492:92-100. [PMID: 26914507 DOI: 10.1016/j.virol.2016.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
Abstract
An infectious cDNA clone of Triticum mosaic virus (TriMV) (genus Poacevirus; family Potyviridae) was used to establish three independent lineages in wheat to examine intra-host population diversity levels within protein 1 (P1) and coat protein (CP) cistrons over time. Genetic variation was assessed at passages 9, 18 and 24 by single-strand conformation polymorphism, followed by nucleotide sequencing. The founding P1 region genotype was retained at high frequencies in most lineage/passage populations, while the founding CP genotype disappeared after passage 18 in two lineages. We found that rare TriMV genotypes were present only transiently and lineages followed independent evolutionary trajectories, suggesting that genetic drift dominates TriMV evolution. These results further suggest that experimental populations of TriMV exhibit lower mutant frequencies than that of Wheat streak mosaic virus (genus Tritimovirus; family Potyviridae) in wheat. Nevertheless, there was evidence for parallel evolution at a synonymous site in the TriMV CP cistron.
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Affiliation(s)
- Melissa Bartels
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Roy French
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Robert A Graybosch
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Satyanarayana Tatineni
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
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14
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Nazar MF, Abdullah MI, Badshah A, Mahmood A, Rana UA, Khan SUD. Synthesis, structure–activity relationship and molecular docking of cyclohexenone based analogous as potent non-nucleoside reverse-transcriptase inhibitors. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.12.090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Iyidogan P, Anderson KS. Current perspectives on HIV-1 antiretroviral drug resistance. Viruses 2014; 6:4095-139. [PMID: 25341668 PMCID: PMC4213579 DOI: 10.3390/v6104095] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/08/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
Current advancements in antiretroviral therapy (ART) have turned HIV-1 infection into a chronic and manageable disease. However, treatment is only effective until HIV-1 develops resistance against the administered drugs. The most recent antiretroviral drugs have become superior at delaying the evolution of acquired drug resistance. In this review, the viral fitness and its correlation to HIV-1 mutation rates and drug resistance are discussed while emphasizing the concept of lethal mutagenesis as an alternative therapy. The development of resistance to the different classes of approved drugs and the importance of monitoring antiretroviral drug resistance are also summarized briefly.
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Affiliation(s)
- Pinar Iyidogan
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA.
| | - Karen S Anderson
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA.
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16
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Analysis of genome integrity of influenza virus in formaldehyde-inactivated split vaccines. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0200-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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18
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Álvarez M, Menéndez-Arias L. Temperature effects on the fidelity of a thermostable HIV-1 reverse transcriptase. FEBS J 2013; 281:342-51. [PMID: 24279450 DOI: 10.1111/febs.12605] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/04/2013] [Accepted: 11/01/2013] [Indexed: 11/30/2022]
Abstract
Transcriptomics and gene expression analysis are largely dependent of the availability of efficient thermostable reverse transcriptases (RTs). However, the intrinsic fidelity of DNA synthesis catalyzed by retroviral RTs is low. Reported error rates are in the range 1.2 × 10(-5)-6.7 × 10(-4), with oncoretroviral RTs being the most faithful enzymes. Wild-type HIV-1 group O (HIV-1O) RT is a thermostable polymerase that is able to synthesize cDNA at temperatures as high as 70 °C. At 37 °C, its error rate has been estimated at 5.8 × 10(-5) in M13mp2 lacZ-based forward mutation assays. However, at higher temperatures (e.g. 50 and 55 °C), the accuracy of HIV-1O RT is increased by approximately two- to five-fold. At 55 °C, the HIV-1O RT error rate (1.3 × 10(-5)) was similar to that shown by the AffinityScript (Agilent Technologies Inc., La Jolla, CA, USA) RT, a commercially available thermostable murine leukaemia virus RT. At higher temperatures, the increased accuracy of the HIV-1 enzyme results from a lower base substitution error rate, although it shows a higher tendency to introduce frameshifts. Kinetic studies carried out with model template-primers suggest minor differences in nucleotide discrimination, although, at higher temperatures, HIV-1O RT showed a reduced ability to extend mispaired template-primers.
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Affiliation(s)
- Mar Álvarez
- Centro de Biología Molecular 'Severo Ochoa', Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Spain
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19
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Johnson KC, Yongky A, Vishwanathan N, Jacob NM, Jayapal KP, Goudar CT, Karypis G, Hu WS. Exploring the transcriptome space of a recombinant BHK cell line through next generation sequencing. Biotechnol Bioeng 2013; 111:770-81. [DOI: 10.1002/bit.25135] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/05/2013] [Accepted: 10/07/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Kathryn C. Johnson
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota
| | - Andrew Yongky
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota
| | - Nandita Vishwanathan
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota
| | - Nitya M. Jacob
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota
| | | | - Chetan T. Goudar
- Global Biologic Development; Bayer HealthCare; Berkeley California
| | - George Karypis
- Department of Computer Science and Engineering; University of Minnesota; Minneapolis Minnesota
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota
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20
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Walsh SR, Linnerth-Petrik NM, Yu DL, Foster RA, Menzies PI, Diaz-Méndez A, Chalmers HJ, Wootton SK. Experimental transmission of enzootic nasal adenocarcinoma in sheep. Vet Res 2013; 44:66. [PMID: 23899161 PMCID: PMC3734154 DOI: 10.1186/1297-9716-44-66] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 07/26/2013] [Indexed: 12/21/2022] Open
Abstract
Enzootic nasal adenocarcinoma (ENA) is a contagious neoplasm of the secretory epithelial cells of the nasal mucosa of sheep and goats. It is associated with the betaretrovirus, enzootic nasal tumor virus (ENTV), but a causative relationship has yet to be demonstrated. In this study, 14-day-old lambs were experimentally infected via nebulization with cell-free tumor filtrates derived from naturally occurring cases of ENA. At 12 weeks post-infection (wpi), one of the five infected lambs developed clinical signs, including continuous nasal discharge and open mouth breathing, and was euthanized. Necropsy revealed the presence of a large bilateral tumor occupying the nasal cavity. At 45 wpi, when the study was terminated, none of the remaining infected sheep showed evidence of tumors either by computed tomography or post-mortem examination. ENTV-1 proviral DNA was detected in the nose, lung, spleen, liver and kidney of the animal with experimentally induced ENA, however there was no evidence of viral protein expression in tissues other than the nose. Density gradient analysis of virus particles purified from the experimentally induced nasal tumor revealed a peak reverse transcriptase (RT) activity at a buoyant density of 1.22 g/mL which was higher than the 1.18 g/mL density of peak RT activity of virus purified from naturally induced ENA. While the 1.22 g/mL fraction contained primarily immature unprocessed virus particles, mature virus particles with a similar morphology to naturally occurring ENA could be identified by electron microscopy. Full-length sequence analysis of the ENTV-1 genome from the experimentally induced tumor revealed very few nucleotide changes relative to the original inoculum with only one conservative amino acid change. Taken together, these results demonstrate that ENTV-1 is associated with transmissible ENA in sheep and that under experimental conditions, lethal tumors are capable of developing in as little as 12 wpi demonstrating the acutely oncogenic nature of this ovine betaretrovirus.
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21
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Álvarez M, Barrioluengo V, Afonso-Lehmann RN, Menéndez-Arias L. Altered error specificity of RNase H-deficient HIV-1 reverse transcriptases during DNA-dependent DNA synthesis. Nucleic Acids Res 2013; 41:4601-12. [PMID: 23444139 PMCID: PMC3632107 DOI: 10.1093/nar/gkt109] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Asp(443) and Glu(478) are essential active site residues in the RNase H domain of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). We have investigated the effects of substituting Asn for Asp(443) or Gln for Glu(478) on the fidelity of DNA-dependent DNA synthesis of phylogenetically diverse HIV-1 RTs. In M13mp2 lacZα-based forward mutation assays, HIV-1 group M (BH10) and group O RTs bearing substitutions D443N, E478Q, V75I/D443N or V75I/E478Q showed 2.0- to 6.6-fold increased accuracy in comparison with the corresponding wild-type enzymes. This was a consequence of their lower base substitution error rates. One-nucleotide deletions and insertions represented between 30 and 68% of all errors identified in the mutational spectra of RNase H-deficient HIV-1 group O RTs. In comparison with the wild-type RT, these enzymes showed higher frameshift error rates and higher dissociation rate constants (koff) for DNA/DNA template-primers. The effects on frameshift fidelity were similar to those reported for mutation E89G and suggest that in HIV-1 group O RT, RNase H inactivation could affect template/primer slippage. Our results support a role for the RNase H domain during plus-strand DNA polymerization and suggest that mutations affecting RNase H function could also contribute to retrovirus variability during the later steps of reverse transcription.
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Affiliation(s)
- Mar Álvarez
- Centro de Biología Molecular Severo Ochoa Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049 Madrid, Spain
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22
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Liu Z, Wang Y, Yedidi RS, Dewdney TG, Reiter SJ, Brunzelle JS, Kovari IA, Kovari LC. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes. Biochem Biophys Res Commun 2012; 430:1022-7. [PMID: 23261453 DOI: 10.1016/j.bbrc.2012.12.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 11/18/2022]
Abstract
The success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. In addition, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.
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Affiliation(s)
- Zhigang Liu
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine Detroit, MI 48201, USA
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23
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Lindén J, Ranta J, Pohjanvirta R. Bayesian modeling of reproducibility and robustness of RNA reverse transcription and quantitative real-time polymerase chain reaction. Anal Biochem 2012; 428:81-91. [DOI: 10.1016/j.ab.2012.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 06/08/2012] [Indexed: 10/28/2022]
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24
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Carvalhais LC, Dennis PG, Tyson GW, Schenk PM. Application of metatranscriptomics to soil environments. J Microbiol Methods 2012; 91:246-51. [PMID: 22963791 DOI: 10.1016/j.mimet.2012.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 08/10/2012] [Accepted: 08/22/2012] [Indexed: 01/24/2023]
Abstract
The activities of soil microbial communities are of critical importance to terrestrial ecosystem functioning. The mechanisms that determine the interactions between soil microorganisms, their environment and neighbouring organisms, however, are poorly understood. Due to advances in sequencing technologies, an increasing number of metagenomics studies are being conducted on samples from diverse environments including soils. This information has not only increased our awareness of the functional potential of soil microbial communities, but also constitutes powerful reference material for soil metatranscriptomics studies. Metatranscriptomics provides a snapshot of transcriptional profiles that correspond to discrete populations within a microbial community at the time of sampling. This information can indicate the potential activities of complex microbial communities and the mechanisms that regulate them. Here we summarise the technical challenges for metatranscriptomics applied to soil environments and discuss approaches for gaining biologically meaningful insight into these datasets.
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Affiliation(s)
- Lilia C Carvalhais
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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25
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Moser MJ, DiFrancesco RA, Gowda K, Klingele AJ, Sugar DR, Stocki S, Mead DA, Schoenfeld TW. Thermostable DNA polymerase from a viral metagenome is a potent RT-PCR enzyme. PLoS One 2012; 7:e38371. [PMID: 22675552 PMCID: PMC3366922 DOI: 10.1371/journal.pone.0038371] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 05/04/2012] [Indexed: 02/03/2023] Open
Abstract
Viral metagenomic libraries are a promising but previously untapped source of new reagent enzymes. Deep sequencing and functional screening of viral metagenomic DNA from a near-boiling thermal pool identified clones expressing thermostable DNA polymerase (Pol) activity. Among these, 3173 Pol demonstrated both high thermostability and innate reverse transcriptase (RT) activity. We describe the biochemistry of 3173 Pol and report its use in single-enzyme reverse transcription PCR (RT-PCR). Wild-type 3173 Pol contains a proofreading 3′-5′ exonuclease domain that confers high fidelity in PCR. An easier-to-use exonuclease-deficient derivative was incorporated into a PyroScript RT-PCR master mix and compared to one-enzyme (Tth) and two-enzyme (MMLV RT/Taq) RT-PCR systems for quantitative detection of MS2 RNA, influenza A RNA, and mRNA targets. Specificity and sensitivity of 3173 Pol-based RT-PCR were higher than Tth Pol and comparable to three common two-enzyme systems. The performance and simplified set-up make this enzyme a potential alternative for research and molecular diagnostics.
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26
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Barrioluengo V, Wang Y, Le Grice SFJ, Menéndez-Arias L. Intrinsic DNA synthesis fidelity of xenotropic murine leukemia virus-related virus reverse transcriptase. FEBS J 2012; 279:1433-44. [PMID: 22340433 DOI: 10.1111/j.1742-4658.2012.08532.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Although recent reports have provided strong evidence to suggest that xenotropic murine leukemia virus-related virus (XMRV) is unlikely to be the causative agent of prostate cancer and chronic fatigue syndrome, this recombinant retrovirus can nonetheless infect human cells in vitro and induce a chronic infection in macaques. In the present study, we determined the accuracy of DNA synthesis of the reverse transcriptases (RTs) of XMRV and Moloney murine leukemia virus (MoMLV) using a combination of pre-steady-state kinetics of nucleotide incorporation and an M13mp2-based forward mutation assay. The results obtained were compared with those previously reported for the HIV type 1 BH10 strain (HIV-1(BH10)) RT. MoMLV and XMRV RTs were 13.9 and 110 times less efficient [as determined by the catalytic rate constant of the nucleotide incorporation reaction ((pol))/equilibrium constant (K(d))] than the HIV-1(BH10) RT in incorporating correct nucleotides. Misinsertion and mispair extension kinetic studies demonstrated that MoMLV RT was more accurate than the HIV-1(BH10) RT. In comparison with the MoMLV RT, the XMRV RT showed decreased mispair extension fidelity and was less faithful when misincorporating C or A opposite A. However, the XMRV RT showed stronger selectivity against G in misinsertion fidelity assays. Forward mutation assays revealed that XMRV and MoMLV RTs had similar accuracy of DNA-dependent DNA synthesis, but were > 13 times more faithful than the HIV-1(BH10) enzyme. The mutational spectra of XMRV and MoMLV RTs were similar in having a relatively higher proportion of frameshifts and transversions compared with the HIV-1(BH10) RT. However, the XMRV polymerase was less prone to introduce large deletions and one-nucleotide insertions.
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Affiliation(s)
- Verónica Barrioluengo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
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27
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Kumar S, Banks TW, Cloutier S. SNP Discovery through Next-Generation Sequencing and Its Applications. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:831460. [PMID: 23227038 PMCID: PMC3512287 DOI: 10.1155/2012/831460] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/08/2012] [Indexed: 05/08/2023]
Abstract
The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
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Affiliation(s)
- Santosh Kumar
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
| | - Travis W. Banks
- Department of Applied Genomics, Vineland Research and Innovation Centre, Vineland Station, ON, Canada L0R 2E0
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada R3T 2M9
- *Sylvie Cloutier:
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Abstract
Under drug selection pressure, emerging mutations render HIV-1 protease drug resistant, leading to the therapy failure in anti-HIV treatment. It is known that nine substrate cleavage site peptides bind to wild type (WT) HIV-1 protease in a conserved pattern. However, how the multidrug-resistant (MDR) HIV-1 protease binds to the substrate cleavage site peptides is yet to be determined. MDR769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, and 90) was selected for present study to understand the binding to its natural substrates. MDR769 HIV-1 protease was co-crystallized with nine substrate cleavage site hepta-peptides. Crystallographic studies show that MDR769 HIV-1 protease has an expanded substrate envelope with wide open flaps. Furthermore, ligand binding energy calculations indicate weaker binding in MDR769 HIV-1 protease-substrate complexes. These results help in designing the next generation of HIV-1 protease inhibitors by targeting the MDR HIV-1 protease.
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Thermostable HIV-1 group O reverse transcriptase variants with the same fidelity as murine leukaemia virus reverse transcriptase. Biochem J 2011; 436:599-607. [DOI: 10.1042/bj20101852] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Wild-type HIV-1 group O RT (reverse transcriptase) shows increased thermostability in comparison with HIV-1 group M subtype B RT and MLV (murine leukaemia virus) RT. However, its utility in the amplification of RNA targets is limited by the reduced accuracy of lentiviral RTs compared with oncoretroviral RTs (i.e. MLV RT). The effects of the mutations K65R, R78A and K65R/V75I on the fidelity of HIV-1 group O RTs were studied using gel-based and M13mp2 lacZ forward-mutation fidelity assays. Forward-mutation assays demonstrated that mutant RTs K65R, R78A and K65R/V75I showed >9-fold increased accuracy in comparison with the wild-type enzyme and were approximately two times more faithful than the MLV RT. Compared with MLV RT, all of the tested HIV-1 group O RT variants showed decreased frameshift fidelity. However, K65R RT showed a higher tendency to introduce one-nucleotide deletions in comparison with other HIV-1 group O RT variants. R78A had a destabilizing effect on the RT, either in the presence or absence of V75I. At temperatures above 52 °C, K65R and K65R/V75I retained similar levels of DNA polymerase activity to the wild-type HIV-1 group O RT, but were more efficient than HIV-1 group M subtype B and MLV RTs. K65R, K65R/V75I and R78A RTs showed decreased misinsertion and mispair extension fidelity in comparison with the wild-type enzyme for most base pairs studied. These assays revealed that nucleotide selection is mainly governed by kpol (pol is polymerization) in the case of K65R, whereas both kpol and Kd affect nucleotide discrimination in the case of K65R/V75I.
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Ozsolak F, Milos PM. Single-molecule direct RNA sequencing without cDNA synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:565-70. [PMID: 21957044 DOI: 10.1002/wrna.84] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Methods for in-depth genome-wide characterization of transcriptomes and quantification of transcript levels using various microarray and next-generation sequencing technologies have emerged as valuable tools for understanding cellular physiology and human disease biology and have begun to be utilized in various clinical diagnostic applications. Current methods, however, typically require RNA to be converted to complementary DNA prior to measurements. This step has been shown to introduce many biases and artifacts. In order to best characterize the 'true' transcriptome, the single-molecule direct RNA sequencing (DRS) technology was developed. This review focuses on the underlying principles behind the DRS, sample preparation steps, and the current and novel avenues of research and applications DRS offers.
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Affiliation(s)
- Fatih Ozsolak
- Helicos BioSciences Corporation, Cambridge, MA, USA.
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31
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The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1. J Mol Biol 2011; 407:661-72. [PMID: 21320510 DOI: 10.1016/j.jmb.2011.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 11/20/2022]
Abstract
Reverse transcriptases (RTs) encoded by a wide range of mobile retroelements have had a major impact on the structure and function of genomes. Among the most abundant elements in eukaryotes are the non long terminal repeat (LTR) retrotransposons. Here we compare the dNTP concentration requirements and error rates of the RT encoded by the non-LTR retrotransposon R2 of Bombyx mori with the well-characterized RTs of retroviruses. Surprisingly, R2 was found to have properties more similar to those of lentiviral RTs, such as human immunodeficiency virus type 1 (HIV-1), than to those of oncoretroviral RTs, such as murine leukemia virus. Like HIV-1 RT, R2 RT was able to synthesize DNA at low dNTP concentrations, suggesting that R2 is able to retrotranspose in nondividing cells. R2 RT also showed levels of misincorporation in biased dNTP pools and replication error rates in M13 lacZα forward mutation assays, similar to HIV-1 RT. Most of the R2 base substitutions in the forward mutation assay were caused by the misincorporation of dTMP. Analogous to HIV-1, the high error rate of R2 RT appears to be a result of its ability to extend mismatches once generated. We suggest that the low fidelity of R2 RT is a by-product of the flexibility of its active site/dNTP binding pocket required for the target-primed reverse transcription reaction used by R2 for retrotransposition. Finally, we discuss that in spite of the high R2 RT error rate, the long-term nucleotide substitution rate for R2 is not significantly above that associated with cellular DNA replication, based on the frequency of R2 retrotranspositions determined in natural populations.
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32
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Abstract
In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.
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Affiliation(s)
- Fatih Ozsolak
- Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA.
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33
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Abstract
In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.
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Affiliation(s)
- Fatih Ozsolak
- Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA.
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Yu WH, Høvik H, Olsen I, Chen T. Strand-specific transcriptome profiling with directly labeled RNA on genomic tiling microarrays. BMC Mol Biol 2011; 12:3. [PMID: 21235785 PMCID: PMC3031212 DOI: 10.1186/1471-2199-12-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 01/14/2011] [Indexed: 01/08/2023] Open
Abstract
Background With lower manufacturing cost, high spot density, and flexible probe design, genomic tiling microarrays are ideal for comprehensive transcriptome studies. Typically, transcriptome profiling using microarrays involves reverse transcription, which converts RNA to cDNA. The cDNA is then labeled and hybridized to the probes on the arrays, thus the RNA signals are detected indirectly. Reverse transcription is known to generate artifactual cDNA, in particular the synthesis of second-strand cDNA, leading to false discovery of antisense RNA. To address this issue, we have developed an effective method using RNA that is directly labeled, thus by-passing the cDNA generation. This paper describes this method and its application to the mapping of transcriptome profiles. Results RNA extracted from laboratory cultures of Porphyromonas gingivalis was fluorescently labeled with an alkylation reagent and hybridized directly to probes on genomic tiling microarrays specifically designed for this periodontal pathogen. The generated transcriptome profile was strand-specific and produced signals close to background level in most antisense regions of the genome. In contrast, high levels of signal were detected in the antisense regions when the hybridization was done with cDNA. Five antisense areas were tested with independent strand-specific RT-PCR and none to negligible amplification was detected, indicating that the strong antisense cDNA signals were experimental artifacts. Conclusions An efficient method was developed for mapping transcriptome profiles specific to both coding strands of a bacterial genome. This method chemically labels and uses extracted RNA directly in microarray hybridization. The generated transcriptome profile was free of cDNA artifactual signals. In addition, this method requires fewer processing steps and is potentially more sensitive in detecting small amount of RNA compared to conventional end-labeling methods due to the incorporation of more fluorescent molecules per RNA fragment.
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Affiliation(s)
- Wen-Han Yu
- Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA
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35
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Abstract
Methods for in-depth characterization of transcriptomes and quantification of transcript levels have emerged as valuable tools for understanding cellular physiology and human disease biology, and have begun to be utilized in various clinical diagnostic applications. Today, current methods utilized by the scientific community typically require RNA to be converted to cDNA prior to comprehensive measurements. However, this cDNA conversion process has been shown to introduce many biases and artifacts that interfere with the proper characterization and quantitation of transcripts. We have developed a direct RNA sequencing (DRS) approach, in which, unlike other technologies, RNA is sequenced directly without prior conversion to cDNA. The benefits of DRS include the ability to use minute quantities (e.g. on the order of several femtomoles) of RNA with minimal sample preparation, the ability to analyze short RNAs which pose unique challenges for analysis using cDNA-based approaches, and the ability to perform these analyses in a low-cost and high-throughput manner. Here, we describe the strategies and procedures we employ to prepare various RNA species for analysis with DRS.
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36
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Ubol S, Suksatu A, Modhiran N, Sangma C, Thitithanyanont A, Fukuda M, Juthayothin T. Intra-host diversities of the receptor-binding domain of stork faeces-derived avian H5N1 viruses and its significance as predicted by molecular dynamic simulation. J Gen Virol 2010; 92:307-14. [PMID: 20980529 PMCID: PMC3081079 DOI: 10.1099/vir.0.025973-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Virus evolution facilitates the emergence of viruses with unpredictable impacts on human health. This study investigated intra-host variations of the receptor-binding domain (RBD) of the haemagglutinin (HA) gene of the avian H5N1 viruses obtained from the 2004 and 2005 epidemics. The results showed that the mutation frequency of the RBD ranged from 0.3 to 0.6 %. The mutations generated one consensus and several minor populations. The consensus population of the 2004 epidemic was transmitted to the 2005 outbreak with increased frequency (39 and 45 %, respectively). Molecular dynamics simulation was applied to predict the significance of the variants. The results revealed that the consensus sequence (E218K/V248I) interacted unstably with sialic acid (SA) with an α2,6 linkage (SAα2,6Gal). Although the mutated K140R/E218K/V248I and Y191C/E218K/V248I sequences decreased the HA binding capacity to α2,3-linked SA, they were shown to bind α2,6-linked SA with increased affinity. Moreover, the substitutions at aa 140 and 191 were positive-selection sites. These data suggest that the K140R and Y191C mutations may represent a step towards human adaptation of the avian H5N1 virus.
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Affiliation(s)
- Sukathida Ubol
- Department of Microbiology, Faculty of Science, Mahidol University, 272 Rama 6 Road, Ratchatewee, Bangkok 10400, Thailand.
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37
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Menéndez-Arias L. Mutation rates and intrinsic fidelity of retroviral reverse transcriptases. Viruses 2009; 1:1137-65. [PMID: 21994586 PMCID: PMC3185545 DOI: 10.3390/v1031137] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 12/03/2009] [Accepted: 12/03/2009] [Indexed: 11/27/2022] Open
Abstract
Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that affect the accuracy of the viral polymerase have been identified by in vitro analysis of the fidelity of DNA synthesis, by using enzymological (gel-based) and genetic assays (e.g., M13mp2 lacZ forward mutation assays). For several amino acid substitutions, these observations have been confirmed in cell culture using viral vectors. This review provides an update on studies leading to the identification of the major components of the fidelity center in retroviral RTs.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" [Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid], Campus de Cantoblanco, 28049 Madrid, Spain; E-Mail: ; Tel.: +34 91 196 4494
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38
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Increased Thermostability and Fidelity of DNA Synthesis of Wild-Type and Mutant HIV-1 Group O Reverse Transcriptases. J Mol Biol 2009; 392:872-84. [DOI: 10.1016/j.jmb.2009.07.081] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/24/2009] [Accepted: 07/28/2009] [Indexed: 11/18/2022]
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Domingo-Calap P, Sentandreu V, Bracho MA, González-Candelas F, Moya A, Sanjuán R. Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virus. J Virol Methods 2009; 161:136-140. [PMID: 19523983 DOI: 10.1016/j.jviromet.2009.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 05/28/2009] [Accepted: 06/02/2009] [Indexed: 02/07/2023]
Abstract
Although viral variability studies have focused traditionally on consensus sequences, the relevance of molecular clone sequences for studying viral evolution at the intra-host level is being increasingly recognized. However, for this approach to be reliable, RT-PCR artifacts do not have to contribute excessively to the observed variability. Molecular clone sequences were obtained from an in vitro transcript to estimate the maximum error rate associated to RT-PCR for the Hepatitis C virus (HCV) E1-E2 region. On average, the frequency of RT-PCR errors was one order of magnitude lower than the level of intra-host genetic variability observed in samples from an HCV outbreak. However, RT-PCR errors were not distributed evenly along the E1-E2 region and were concentrated heavily in the hypervariable region 2 (HVR 2). Although it is concluded that RT-PCR molecular clone sequences are reliable, these results warn against extrapolation of RT-PCR error rates to different genome regions. The data suggest that the RNA sequence context or secondary structure can determine the fidelity of in vitro transcription or reverse transcription. Potentially, these factors might also modify the fidelity of the viral polymerase.
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Affiliation(s)
- Pilar Domingo-Calap
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Spain
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40
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Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, McInerney P, Thompson JF, Bowers J, Jarosz M, Milos PM. Direct RNA sequencing. Nature 2009; 461:814-8. [PMID: 19776739 DOI: 10.1038/nature08390] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 08/05/2009] [Indexed: 01/24/2023]
Abstract
Our understanding of human biology and disease is ultimately dependent on a complete understanding of the genome and its functions. The recent application of microarray and sequencing technologies to transcriptomics has changed the simplistic view of transcriptomes to a more complicated view of genome-wide transcription where a large fraction of transcripts emanates from unannotated parts of genomes, and underlined our limited knowledge of the dynamic state of transcription. Most of this broad body of knowledge was obtained indirectly because current transcriptome analysis methods typically require RNA to be converted to complementary DNA (cDNA) before measurements, even though the cDNA synthesis step introduces multiple biases and artefacts that interfere with both the proper characterization and quantification of transcripts. Furthermore, cDNA synthesis is not particularly suitable for the analysis of short, degraded and/or small quantity RNA samples. Here we report direct single molecule RNA sequencing without prior conversion of RNA to cDNA. We applied this technology to sequence femtomole quantities of poly(A)(+) Saccharomyces cerevisiae RNA using a surface coated with poly(dT) oligonucleotides to capture the RNAs at their natural poly(A) tails and initiate sequencing by synthesis. We observed transcript 3' end heterogeneity and polyadenylated small nucleolar RNAs. This study provides a path to high-throughput and low-cost direct RNA sequencing and achieving the ultimate goal of a comprehensive and bias-free understanding of transcriptomes.
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Affiliation(s)
- Fatih Ozsolak
- Helicos BioSciences Corporation, One Kendall Square, Cambridge, Massachusetts 02139, USA.
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41
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Abstract
Reverse transcriptases (RTs) are multifunctional enzymes, but are mainly used as RNA-directed DNA polymerases in first-strand cDNA synthesis. Specifically, oligodeoxynucleotides are used as primers for extension on RNA templates. The DNA synthesized from an RNA template is referred to as complementary DNA (cDNA) and is often used as a template for PCR or converted to dsDNA for cloning. This unit describes appropriate reaction conditions for RTs from Moloney murine leukemia virus (MMLV) and avian myeloblastosis virus (AMV), along with applications such as synthesizing cDNA, 3' fill-in reactions, and labeling the 3' terminus of DNA fragments with 5' protruding ends, and DNA sequencing.
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42
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Wang X, Olszewska M, Capacio V, Stefanski J, Przybylowski M, Samakoglu S, Chang AH, Sadelain M, Rivière I. Quantitative analysis of clinically relevant mutations occurring in lymphoid cells harboring gamma-retrovirus-encoded hsvtk suicide genes. Gene Ther 2008; 15:1454-9. [PMID: 18563185 PMCID: PMC4528371 DOI: 10.1038/gt.2008.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 05/14/2008] [Accepted: 05/14/2008] [Indexed: 12/20/2022]
Abstract
The in vivo regulation of T lymphocyte activity by the activation of a suicide mechanism is an essential paradigm for the safety of adoptive cell therapies. In light of reports showing that gamma-retroviral vector-encoded herpes simplex virus thymidine kinase (hsvtk) undergoes recombination, we undertook a thorough investigation of the genomic stability of SFG-based vectors using two variants of the wild-type hsvtk gene. In a large panel of independent clones, we demonstrate that both hsvtk genes undergo recombination with molecular signatures indicative of template switching in GC-rich regions displaying homology at the deletion junctions or RNA splicing. In the absence of ganciclovir selection, the frequency of recombination is 3% per retroviral replication cycle. Our results underscore the importance of the five nucleotide difference between the two hsvtk genes that account for the presence of recombinogenic hot spots in one variant and not the other, indicating that the probability of RNA splicing is influenced by minute nucleotide changes in sequences adjacent to the splice donor and acceptor sites. Furthermore, our mutational analysis in an unbiased panel of human lymphoid cells (that is, without immune or ganciclovir-mediated selective pressure) provides a robust in vitro assay to predict and quantify clinically relevant mutations in hsvtk suicide genes, which can be applied to studying and improving the stability of any transgene expressed in gamma-retroviral or lentiviral vectors.
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Affiliation(s)
- X Wang
- Gene Transfer and Somatic Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - M Olszewska
- Gene Transfer and Somatic Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - V Capacio
- Gene Transfer and Somatic Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - J Stefanski
- Gene Transfer and Somatic Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - M Przybylowski
- Gene Transfer and Somatic Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - S Samakoglu
- Gene Transfer and Gene Expression Laboratory, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - AH Chang
- Gene Transfer and Gene Expression Laboratory, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - M Sadelain
- Gene Transfer and Somatic Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Gene Transfer and Gene Expression Laboratory, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - I Rivière
- Gene Transfer and Somatic Cell Engineering Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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Nalam MNL, Schiffer CA. New approaches to HIV protease inhibitor drug design II: testing the substrate envelope hypothesis to avoid drug resistance and discover robust inhibitors. Curr Opin HIV AIDS 2008; 3:642-6. [PMID: 19373036 PMCID: PMC2710804 DOI: 10.1097/coh.0b013e3283136cee] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Drug resistance results when the balance between the binding of inhibitors and the turnover of substrates is perturbed in favor of the substrates. Resistance is quite widespread to the HIV-1 protease inhibitors permitting the protease to process its 10 different substrates. This processing of the substrates permits the virus HIV-1 to mature and become infectious. The design of HIV-1 protease inhibitors that closely fit within the substrate-binding region is proposed to be a strategy to avoid drug resistance. RECENT FINDINGS Cocrystal structures of HIV-1 protease with its substrates define an overlapping substrate-binding region or substrate envelope. Novel HIV-1 protease inhibitors that were designed to fit within this substrate envelope were found to retain high binding affinity and have a flat binding profile against a panel of drug-resistant HIV-1 proteases. SUMMARY The avoidance of drug resistance needs to be considered in the initial design of inhibitors to quickly evolving targets such as HIV-1 protease. Using a detailed knowledge of substrate binding appears to be a promising strategy for achieving this goal to obtain robust HIV-1 protease inhibitors.
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Affiliation(s)
- Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA, , 508-856-8008 phone, 508-856-6464 FAX
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA, , 508-856-8008 phone, 508-856-6464 FAX
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44
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Hizi A, Herschhorn A. Retroviral reverse transcriptases (other than those of HIV-1 and murine leukemia virus): a comparison of their molecular and biochemical properties. Virus Res 2008; 134:203-20. [PMID: 18291546 DOI: 10.1016/j.virusres.2007.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 12/16/2007] [Accepted: 12/17/2007] [Indexed: 10/22/2022]
Abstract
This chapter reviews most of the biochemical data on reverse transcriptases (RTs) of retroviruses, other than those of HIV-1 and murine leukemia virus (MLV) that are covered in detail in other reviews of this special edition devoted to reverse transcriptases. The various RTs mentioned are grouped according to their retroviral origins and include the RTs of the alpharetroviruses, lentiviruses (both primate, other than HIV-1, and non-primate lentiviruses), betaretroviruses, deltaretroviruses and spumaretroviruses. For each RT group, the processing, molecular organization as well as the enzymatic activities and biochemical properties are described. Several RTs function as dimers, primarily as heterodimers, while the others are active as monomeric proteins. The comparisons between the diverse properties of the various RTs show the common traits that characterize the RTs from all retroviral subfamilies. In addition, the unique features of the specific RTs groups are also discussed.
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Affiliation(s)
- Amnon Hizi
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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45
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Bakkour S, Sha WC. Mapping of the ICOS binding surface of murine B7h using an unbiased, cellular library of B7h mutants created by cyclical packaging rescue. J Immunol Methods 2008; 332:151-61. [PMID: 18294651 DOI: 10.1016/j.jim.2008.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 01/12/2008] [Accepted: 01/17/2008] [Indexed: 11/28/2022]
Abstract
Functional studies of immunologically relevant molecules often involve time-consuming generation and cloning of gene mutations prior to introduction into mammalian cells. We describe here an alternative mutagenesis approach that relies solely on transfer of helper-free retroviral supernatants to rapidly create in virtually any cell line of interest a large cellular library that retrovirally expresses a defined number of independent point mutations in a gene of interest. Using this rapid non-cloning approach, we generated a 3T3 cellular library retrovirally expressing 2 x 10(5) mutants of the murine costimulatory B7h gene. Screening of this unbiased cellular library identified six residues of murine B7h that are critical for binding to the ICOS receptor. These residues are located on the same strands of human B7h that were identified by targeted mutagenesis [Chattopadhyay, K., Bhatia, S., Fiser, A., Almo, S.C., Nathenson, S.G. (2006). Structural basis of inducible costimulator ligand costimulatory function: determination of the cell surface oligomeric state and functional mapping of the receptor-binding site of the protein. J. Immunol. 177, 3920], indicating that the ICOS receptor-binding interface is similar in mouse and human B7h. Based on this proof-of-principle study, CPR-based mutagenesis is applicable to studies of gene function in a variety of mammalian cells.
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Affiliation(s)
- Sonia Bakkour
- Cancer Research Laboratory, 441 LSA, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200 United States
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46
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Küpfer PA, Crey-Desbiolles C, Leumann CJ. Trans-lesion synthesis and RNaseH activity by reverse transcriptases on a true abasic RNA template. Nucleic Acids Res 2007; 35:6846-53. [PMID: 17932068 PMCID: PMC2175328 DOI: 10.1093/nar/gkm767] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While much is known about abasic DNA, the biological impact of abasic RNA is largely unexplored. To test the mutagenic potential of this RNA lesion in the context of retroviruses, we synthesized a 31-mer oligoribonucleotide containing an abasic (rAS) site and used it as a template for studying DNA primer extension by HIV-1, avian myeloblastosis virus (AMV) and moloney murine leukemia virus (MMLV) reversed transcriptases (RT). We found that trans-lesion synthesis readily takes place with HIV-1 RT and to a lesser extent with AMV RT while MMLV RT aborts DNA synthesis. The preference of dNTP incorporation follows the order A∼G > C∼T and thus obeys to the ‘A-rule’. In the case of HIV-1 RT, we measured the kinetic data of dNTP incorporation and compared it to abasic DNA. We found that A-incorporation is only 2-fold slower relative to a matched (undamaged) RNA template while it is 7-fold slower in the case of DNA. Furthermore, there is less discrimination in incorporation between the four dNTPs in the case of abasic RNA compared to abasic DNA. These experiments clearly point to a higher promiscuity of lesion bypass on abasic RNA. Given their known higher chemical stability, such rAS sites can clearly contribute to (retro)viral evolution.
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Affiliation(s)
- Pascal A Küpfer
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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47
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Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH. Improved repeat identification and masking in Dipterans. Gene 2006; 389:1-9. [PMID: 17137733 PMCID: PMC1945102 DOI: 10.1016/j.gene.2006.09.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 09/08/2006] [Accepted: 09/09/2006] [Indexed: 12/23/2022]
Abstract
Repetitive sequences are a major constituent of many eukaryote genomes and play roles in gene regulation, chromosome inheritance, nuclear architecture, and genome stability. The identification of repetitive elements has traditionally relied on in-depth, manual curation and computational determination of close relatives based on DNA identity. However, the rapid divergence of repetitive sequence has made identification of repeats by DNA identity difficult even in closely related species. Hence, the presence of unidentified repeats in genome sequences affects the quality of gene annotations and annotation-dependent analyses (e.g. microarray analyses). We have developed an enhanced repeat identification pipeline using two approaches. First, the de novo repeat finding program PILER-DF was used to identify interspersed repetitive elements in several recently finished Dipteran genomes. Repeats were classified, when possible, according to their similarity to known elements described in Repbase and GenBank, and also screened against annotated genes as one means of eliminating false positives. Second, we used a new program called RepeatRunner, which integrates results from both RepeatMasker nucleotide searches and protein searches using BLASTX. Using RepeatRunner with PILER-DF predictions, we masked repeats in thirteen Dipteran genomes and conclude that combining PILER-DF and RepeatRunner greatly enhances repeat identification in both well-characterized and un-annotated genomes.
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Affiliation(s)
- Christopher D Smith
- Department of Biology, San Francisco State University, San Francisco, CA, United States.
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48
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Kulpa DA, Moran JV. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 2006; 13:655-60. [PMID: 16783376 DOI: 10.1038/nsmb1107] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 05/11/2006] [Indexed: 11/09/2022]
Abstract
LINE-1 retrotransposons (L1s) constitute approximately 17% of human DNA, and their activity continues to affect genome evolution. Retrotransposition-competent human L1s encode two proteins required for their mobility (ORF1p and ORF2p); however, biochemical activities associated with ORF2p have been difficult to detect in cells. Here, we show for the first time the colocalization of L1 RNA, ORF1p and ORF2p to a putative ribonucleoprotein retrotransposition intermediate. We further demonstrate that ORF2p preferentially uses its encoding RNA as a template for reverse transcription. Thus, our data provide the first biochemical evidence supporting the cis-preferential action of the L1 reverse transcriptase.
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Affiliation(s)
- Deanna A Kulpa
- Department of Human Genetics 1241 E. Catherine St., University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA.
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Sato H, Yokoyama M. [RNA viruses and mutations]. Uirusu 2006; 55:221-9. [PMID: 16557007 DOI: 10.2222/jsv.55.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Actively replicating RNA viruses in nature are continually changing their genetic information by spontaneous mutations. These changes often result in alterations in immune-sensitivity, drug-sensitivity, cell-tropism, and host-range, causing uncontrollability of the pathogen and emerging/re-emerging infections. To better understand the virus changes and develop effective methods to control the moving targets, it is essential to obtain information on changes in viral genomes and proteins. Although information on genetic changes is being accumulated very rapidly, assessment of changes in protein structure and function still requires time-consuming works. In this review, we will overview mutation studies of human immunodeficiency virus and other RNA viruses. In addition, we will introduce recent advances in the computational science and its application on mutation studies and drug development.
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Affiliation(s)
- Hironori Sato
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo, Japan.
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Operario DJ, Reynolds HM, Kim B. Comparison of DNA polymerase activities between recombinant feline immunodeficiency and leukemia virus reverse transcriptases. Virology 2005; 335:106-21. [PMID: 15823610 DOI: 10.1016/j.virol.2005.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2004] [Revised: 12/22/2004] [Accepted: 02/11/2005] [Indexed: 11/29/2022]
Abstract
In this study, we present enzymatic differences found between recombinant RTs derived from feline leukemia virus and feline immunodeficiency virus. Firstly, FIV RT showed low steady state K(m) values for dNTPs compared to FeLV RT. Consistent with this, FIV RT synthesized DNA more efficiently than FeLV RT at low dNTP concentrations. We observed similar concentration-dependent activity differences between other lentiviral (HIV-1 and SIV) and non-lentiviral (MuLV and AMV) RTs. Second, FeLV RT showed less efficient misincorporation with biased dNTP pools and mismatch primer extension capabilities, compared to FIV RT. In M13mp2 lacZalpha forward mutation assays, FeLV RT displayed approximately 11-fold higher fidelity than FIV RT. Finally, FeLV RT was less sensitive to 3TCTP and ddATP than FIV RT. This study represents the comprehensive enzymatic characterization of RTs from a lentivirus and a non-lentivirus retrovirus from the same host species. The data presented here support enzymatic divergences seen among retroviral RTs.
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Affiliation(s)
- Darwin J Operario
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 672, Rochester, NY 14642, USA
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