1
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The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance. Viruses 2020; 12:v12030297. [PMID: 32182845 PMCID: PMC7150816 DOI: 10.3390/v12030297] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/31/2022] Open
Abstract
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic drugs. In addressing the crux of the issue, various attempts to estimate the mutation rate of HIV-1 resulted in a large range of 10−5–10−3 errors/bp/cycle due to the use of different types of investigation methods. In this review, we discuss the different assay methods, their findings on the mutation rates of HIV-1 and how the locations of mutations can be further analyzed for their allosteric effects to allow for new inhibitor designs. Given that HIV is one of the fastest mutating viruses, it serves as a good model for the comprehensive study of viral mutations that can give rise to a more horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.
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2
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Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF. Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage. Nucleic Acids Res 2017; 45:10143-10155. [PMID: 28973469 PMCID: PMC5737552 DOI: 10.1093/nar/gkx689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/24/2017] [Indexed: 01/03/2023] Open
Abstract
RNA dependent DNA-polymerases, reverse transcriptases, are key enzymes for retroviruses and retroelements. Their fidelity, including indel generation, is significant for their use as reagents including for deep sequencing. Here, we report that certain RNA template structures and G-rich sequences, ahead of diverse reverse transcriptases can be strong stimulators for slippage at slippage-prone template motif sequence 3′ of such ‘slippage-stimulatory’ structures. Where slippage is stimulated, the resulting products have one or more additional base(s) compared to the corresponding template motif. Such structures also inhibit slippage-mediated base omission which can be more frequent in the absence of a relevant stem–loop. Slippage directionality, base insertion and omission, is sensitive to the relative concentration ratio of dNTPs specified by the RNA template slippage-prone sequence and its 5′ adjacent base. The retrotransposon-derived enzyme TGIRT exhibits more slippage in vitro than the retroviral enzymes tested including that from HIV. Structure-mediated slippage may be exhibited by other polymerases and enrich gene expression. A cassette from Drosophila retrotransposon Dme1_chrX_2630566, a candidate for utilizing slippage for its GagPol synthesis, exhibits strong slippage in vitro. Given the widespread occurrence and importance of retrotransposons, systematic studies to reveal the extent of their functional utilization of RT slippage are merited.
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Affiliation(s)
- Christophe Penno
- School of Biochemistry, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Romika Kumari
- School of Biochemistry, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - John F Atkins
- School of Biochemistry, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
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3
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Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF. Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis. Nucleic Acids Res 2017; 45:10156-10167. [PMID: 28973470 PMCID: PMC5737442 DOI: 10.1093/nar/gkx690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/24/2017] [Indexed: 12/28/2022] Open
Abstract
Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels with their ratio being sensitive to the relative concentration ratio of dNTPs specified by the RNA template slippage-prone sequence and its 5' adjacent base. The GGG sequence 3' adjacent to the U6A shift/slippage site, which is important for ribosomal frameshifting, is shown here to limit reverse transcriptase base substitution and indel 'errors' in the run of A's in the product. The indels characterized here have either 1 more or less A, than the corresponding number of template U's. cDNA with 5 A's may yield novel Gag product(s), while cDNA with an extra base, 7 A's, may only be a minor contributor to GagPol polyprotein. Synthesis of a proportion of non-ribosomal frameshift derived GagPol would be relevant in efforts to identify therapeutically useful compounds that perturb the ratio of GagPol to Gag, and pertinent to the extent in which specific polymerase slippage is utilized in gene expression.
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Affiliation(s)
- Christophe Penno
- School of Biochemistry, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Romika Kumari
- School of Biochemistry, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - John F Atkins
- School of Biochemistry, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland.,Department of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
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4
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Kravatsky YV, Chechetkin VR, Fedoseeva DM, Gorbacheva MA, Kretova OV, Tchurikov NA. Mutation frequencies in HIV-1 subtype-A genome in regions containing efficient RNAi targets. Mol Biol 2016. [DOI: 10.1134/s0026893316020114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Kharytonchyk S, King SR, Ndongmo CB, Stilger KL, An W, Telesnitsky A. Resolution of Specific Nucleotide Mismatches by Wild-Type and AZT-Resistant Reverse Transcriptases during HIV-1 Replication. J Mol Biol 2016; 428:2275-2288. [PMID: 27075671 DOI: 10.1016/j.jmb.2016.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/16/2016] [Accepted: 04/04/2016] [Indexed: 12/14/2022]
Abstract
A key contributor to HIV-1 genetic variation is reverse transcriptase errors. Some mutations result because reverse transcriptase (RT) lacks 3' to 5' proofreading exonuclease and can extend mismatches. However, RT also excises terminal nucleotides to a limited extent, and this activity contributes to AZT resistance. Because HIV-1 mismatch resolution has been studied in vitro but only indirectly during replication, we developed a novel system to study mismatched base pair resolution during HIV-1 replication in cultured cells using vectors that force template switching at defined locations. These vectors generated mismatched reverse transcription intermediates, with proviral products diagnostic of mismatch resolution mechanisms. Outcomes for wild-type (WT) RT and an AZT-resistant (AZT(R)) RT containing a thymidine analog mutation set-D67N, K70R, D215F, and K219Q-were compared. AZT(R) RT did not excise terminal nucleotides more frequently than WT, and for the majority of tested mismatches, both WT and AZT(R) RTs extended mismatches in more than 90% of proviruses. However, striking enzyme-specific differences were observed for one mispair, with WT RT preferentially resolving dC-rC pairs either by excising the mismatched base or switching templates prematurely, while AZT(R) RT primarily misaligned the primer strand, causing deletions via dislocation mutagenesis. Overall, the results confirmed HIV-1 RT's high capacity for mismatch extension during virus replication and revealed dramatic differences in aberrant intermediate resolution repertoires between WT and AZT(R) RTs on one mismatched replication intermediate. Correlating mismatch extension frequencies observed here with reported viral mutation rates suggests a complex interplay of nucleotide discrimination and mismatch extension drives HIV-1 mutagenesis.
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Affiliation(s)
- Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Steven R King
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Clement B Ndongmo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Krista L Stilger
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Wenfeng An
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA.
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6
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Mutations in HIV-1 reverse transcriptase affect the errors made in a single cycle of viral replication. J Virol 2014; 88:7589-601. [PMID: 24760888 DOI: 10.1128/jvi.00302-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED The genetic variation in HIV-1 in patients is due to the high rate of viral replication, the high viral load, and the errors made during viral replication. Some of the mutations in reverse transcriptase (RT) that alter the deoxynucleoside triphosphate (dNTP)-binding pocket, including those that confer resistance to nucleoside/nucleotide analogs, affect dNTP selection during replication. The effects of mutations in RT on the spectrum (nature, position, and frequency) of errors made in vivo are poorly understood. We previously determined the mutation rate and the frequency of different types of mutations and identified hot spots for mutations in a lacZα (the α complementing region of lacZ) reporter gene carried by an HIV-1 vector that replicates using wild-type RT. We show here that four mutations (Y115F, M184V, M184I, and Q151M) in the dNTP-binding pocket of RT that had relatively small effects on the overall HIV-1 mutation rate (less than 3-fold compared to the wild type) significantly increased mutations at some specific positions in the lacZα reporter gene. We also show that changes in a sequence that flanks the reporter gene can affect the mutations that arise in the reporter. These data show that changes either in HIV-1 RT or in the sequence of the nucleic acid template can affect the spectrum of mutations made during viral replication. This could, by implication, affect the generation of drug-resistant mutants and immunological-escape mutants in patients. IMPORTANCE RT is the viral enzyme that converts the RNA genome of HIV into DNA. Errors made during replication allow the virus to escape from the host's immune system and to develop resistance to the available anti-HIV drugs. We show that four different mutations in RT which are known to be associated with resistance to anti-RT drugs modestly increased the overall frequency of errors made during viral replication. However, the increased errors were not uniformly distributed; the additional errors occurred at a small number of positions (hot spots). Moreover, some of the RT mutations preferentially affected the nature of the errors that were made (some RT mutations caused an increase in insertion and deletion errors; others caused an increase in substitution errors). We also show that sequence changes in a region adjacent to a target gene can affect the errors made within the target gene.
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7
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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: 1.7] [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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8
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Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J. Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol 2012; 13:R67. [PMID: 22863408 PMCID: PMC4053741 DOI: 10.1186/gb-2012-13-8-r67] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 06/11/2012] [Accepted: 08/03/2012] [Indexed: 11/12/2022] Open
Abstract
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.
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Affiliation(s)
- Yoichiro Sugimoto
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Julian König
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Shobbir Hussain
- The Wellcome Trust Centre for Stem Cell Research, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Blaž Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Michaela Frye
- The Wellcome Trust Centre for Stem Cell Research, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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9
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Abstract
HIV-1 Reverse Transcriptase (HIV-1 RT) has been the target of numerous approved anti-AIDS drugs that are key components of Highly Active Anti-Retroviral Therapies (HAART). It remains the target of extensive structural studies that continue unabated for almost twenty years. The crystal structures of wild-type or drug-resistant mutant HIV RTs in the unliganded form or in complex with substrates and/or drugs have offered valuable glimpses into the enzyme’s folding and its interactions with DNA and dNTP substrates, as well as with nucleos(t)ide reverse transcriptase inhibitor (NRTI) and non-nucleoside reverse transcriptase inhibitor (NNRTIs) drugs. These studies have been used to interpret a large body of biochemical results and have paved the way for innovative biochemical experiments designed to elucidate the mechanisms of catalysis and drug inhibition of polymerase and RNase H functions of RT. In turn, the combined use of structural biology and biochemical approaches has led to the discovery of novel mechanisms of drug resistance and has contributed to the design of new drugs with improved potency and ability to suppress multi-drug resistant strains.
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10
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Transcript Slippage and Recoding. RECODING: EXPANSION OF DECODING RULES ENRICHES GENE EXPRESSION 2010. [DOI: 10.1007/978-0-387-89382-2_19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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11
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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: 87] [Impact Index Per Article: 5.8] [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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12
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de Villiers EM, Kimmel R, Leppik L, Gunst K. Intragenomic rearrangement in TT viruses: a possible role in the pathogenesis of disease. Curr Top Microbiol Immunol 2009; 331:91-107. [PMID: 19230559 DOI: 10.1007/978-3-540-70972-5_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A role for the ubiquitous Torque teno (TT) viruses in the pathogenesis of disease has not been resolved. In vivo and in vitro intragenomic rearrangement of TT virus genomes has been demonstrated. Replication in cell culture of a subviral molecule (411 bp) occurs through oligomerisation of RNA transcripts. Although the functions of the respective TT viral genes, as well as the newly formed genes in the rearranged subviral molecules, are largely unknown, certain similarities to genes of plant viruses of the family Geminiviridae will be described. A degree of similarity to certain cellular genes poses the question as to a role of molecular mimicry in the pathogenesis of autoimmune disease and diabetes.
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Affiliation(s)
- E M de Villiers
- E.-M. de Villiers Division for the Characterisation of Tumour Viruses, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
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13
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Chi LM, Lam SL. Nuclear magnetic resonance investigation of primer--template models: formation of a pyrimidine bulge upon misincorporation. Biochemistry 2008; 47:4469-76. [PMID: 18358004 DOI: 10.1021/bi8001456] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our previous studies have shown that misaligned structures can occur upon misincorporation of a dNTP opposite thymine templates. The formation of misaligned structures during DNA replication, if not repaired properly, can be bypassed and extended by low-fidelity polymerases and ultimately lead to mutations. In this study, the base pair structures at the replicating sites of a set of primer-template models which mimic the situation upon misincorporation of a dNTP opposite cytosine templates have been determined. High-resolution NMR structural results show that misaligned structures with a C-bulge can be formed upon incorporation of dCTP, dTTP, and dATP opposite 5'-GC, 5'-AC, and 5'-TC templates, respectively. The stabilities of misaligned structures depend on the types of terminal base pairs at the replicating sites. Together with the structural findings in thymine templates, we conclude that terminal G.C and C.G base pairs always contribute a larger stabilizing effect to the misaligned structures containing a pyrimidine bulge than terminal A.T and T.A base pairs. Misalignment and thus deletion mutation are more likely to occur if misincorporation of a nucleotide opposite a pyrimidine template can cause template slippage to form a terminal G.C or C.G base pair. Although misalignment also occurs when the newly formed terminal base pair is an A.T base pair or a T.A base pair, both misaligned and mismatched conformers coexist, which can lead to deletion and substitution mutations, respectively.
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Affiliation(s)
- Lai Man Chi
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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14
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Matamoros T, Kim B, Menéndez-Arias L. Mechanistic insights into the role of Val75 of HIV-1 reverse transcriptase in misinsertion and mispair extension fidelity of DNA synthesis. J Mol Biol 2007; 375:1234-48. [PMID: 18155043 DOI: 10.1016/j.jmb.2007.11.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Revised: 11/06/2007] [Accepted: 11/07/2007] [Indexed: 10/22/2022]
Abstract
The side chain of Val75 stabilizes the fingers subdomain of the human immunodeficiency virus type 1 reverse transcriptase (RT), while its peptide backbone interacts with the single-stranded DNA template (at nucleotide +1) and with the peptide backbone of Gln151. Specific DNA polymerase activities of mutant RTs bearing amino acid substitutions at position 75 (i.e., V75A, V75F, V75I, V75L, V75M, V75S and V75T) were relatively high. Primer extension experiments carried out in the absence of one deoxyribonucleoside-triphosphate suggested that mutations did not affect the accuracy of the RT, except for V75A, V75F, V75I, and to a lesser extent V75T. The fidelity of RTs bearing mutations V75F and V75I increased 1.8- and 3-fold, respectively, as measured by the M13 lacZ alpha forward mutation assay, while V75A showed 1.4-fold decreased accuracy. Steady- and pre-steady-state kinetics demonstrated that the increased fidelity of V75I and V75F was related to their decreased ability to extend mismatched template-primers, while misincorporation efficiencies were not significantly affected by mutations. The increased mispair extension fidelity of mutant V75I RT could be attributed to the nucleotide affinity loss, observed in reactions with mismatched template-primers. Altogether, these data suggest that Val75 interactions with the 5' template overhang are important determinants of fidelity.
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Affiliation(s)
- Tania Matamoros
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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15
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Chi LM, Lam SL. NMR investigation of primer-template models: structural effect of sequence downstream of a thymine template on mutagenesis in DNA replication. Biochemistry 2007; 46:9292-300. [PMID: 17658896 DOI: 10.1021/bi700865e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misaligned structures can occur in primer-templates during DNA replication, which can be bypassed and extended by low-fidelity polymerases and ultimately lead to mutations. In this study, we have investigated how the nucleotide downstream of a thymine template affects the primer-template structures upon misincorporation of dNTPs. The base pair structures at the replicating sites of a set of primer-template models containing either a G or an A downstream of the thymine template have been determined using NMR spectroscopy. Incorporation of dCTP and dTTP opposite 5'-GT and 5'-AT templates, respectively, can result in misaligned structures with a T-bulge. Depending on the downstream sequence, subsequent extension of the primers may stabilize the misaligned structures or cause the formation of mismatched structures. These results provide alternative pathways for base substitution and deletion errors during DNA replication by low-fidelity polymerases.
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Affiliation(s)
- Lai Man Chi
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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16
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Boyer PL, Stenbak CR, Hoberman D, Linial ML, Hughes SH. In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT. Virology 2007; 367:253-64. [PMID: 17631930 PMCID: PMC2720797 DOI: 10.1016/j.virol.2007.05.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 01/22/2007] [Accepted: 05/14/2007] [Indexed: 01/30/2023]
Abstract
We compared the in vitro fidelity of wild-type human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) and the prototype foamy virus (PFV) RT. Both enzymes had similar error rates for single nucleotide substitutions; however, PFV RT did not appear to make errors at specific hotspots, like HIV-1 RT. In addition, PFV RT made more deletions and insertions than HIV-1 RT. Although the majority of the missense errors made by HIV-1 RT and PFV RT are different, relatively few of the mutations caused by either enzyme can be explained by a misalignment/slippage mechanism. We suggest that the higher polymerase activity of PFV RT could contribute to the ability of the enzyme to jump to the same or a different template.
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Affiliation(s)
- Paul L. Boyer
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | | | - David Hoberman
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | - Maxine L. Linial
- Division of Basic Sciences A3-015, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Stephen H. Hughes
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702
- Corresponding author. Fax: +1 301 846-6966. E-mail address:
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17
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Leppik L, Gunst K, Lehtinen M, Dillner J, Streker K, de Villiers EM. In vivo and in vitro intragenomic rearrangement of TT viruses. J Virol 2007; 81:9346-56. [PMID: 17596318 PMCID: PMC1951432 DOI: 10.1128/jvi.00781-07] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The in vitro replication of the Torque teno virus (TT virus) tth8 full-length genome and particle formation in a Hodgkin's lymphoma-derived cell line after transfection with cloned viral DNA were demonstrated. Analyses of the transcription patterns of tth8 and tth7 TT virus isolates in a number of lymphoma and T-cell leukemia cell lines indicated differential additional splicing events and intragenomic rearrangement generating open reading frames which could not be deducted from the genomic sequence. We also demonstrated the presence of rearranged TT virus genomes in vivo in sera taken from pregnant mothers whose children later developed childhood leukemia, as well as sera from control mothers. Control experiments using religated cloned genomic tth8 DNA mixed with cellular DNA did not result in such subviral molecules. These subviral isolates ranged from 172 bp to full-length TT virus genomes. Possible in vivo selection for specific rearranged molecules was indicated by the presence of one isolate (561 bp) in 11 serum samples. It remains to be clarified whether selected rearranged subviral components resulting from specific TT virus types may contribute to the initiation of disease. These data demonstrate new features of TT viruses suggesting possible similarities to plant viruses of the family Geminiviridae, as well as raise questions about the documented plurality and diversity of anelloviruses.
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MESH Headings
- Cell Line, Tumor
- Child
- DNA Virus Infections/virology
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Female
- Genome, Viral
- Humans
- Infant
- Molecular Sequence Data
- Mothers
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Viral/biosynthesis
- RNA, Viral/genetics
- Recombination, Genetic
- Sequence Analysis, DNA
- Serum/virology
- Torque teno virus/genetics
- Torque teno virus/isolation & purification
- Torque teno virus/physiology
- Transcription, Genetic
- Virus Replication
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Affiliation(s)
- Ludmila Leppik
- Division for the Characterization of Tumor Viruses, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
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Chi LM, Lam SL. NMR investigation of DNA primer-template models: structural insights into dislocation mutagenesis in DNA replication. FEBS Lett 2006; 580:6496-500. [PMID: 17107673 DOI: 10.1016/j.febslet.2006.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2006] [Revised: 10/28/2006] [Accepted: 11/01/2006] [Indexed: 11/20/2022]
Abstract
Slipped frameshift intermediates can occur when DNA polymerase slows or stalls at sites of DNA lesions. However, this phenomenon is much less common when unmodified DNA is replicated. In order to study the effect of templating bases on the alignment of primer-templates, NMR structural investigation has been performed on primer-template oligonucleotide models which mimic the situation that dNTP has just been incorporated opposite template. NMR evidence reveals the occurrence of misalignment when dGTP is incorporated opposite template T with a downstream nucleotide C. Depending on the template sequence, further extension of the primer can lead to realignment.
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Affiliation(s)
- Lai Man Chi
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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