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Architecture of an HIV-1 reverse transcriptase initiation complex.

Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV
Nature 557 118-122 (2018)
Cited: 32 times
EuropePMC logo PMID: 29695867

Abstract

Reverse transcription of the HIV-1 RNA genome into double-stranded DNA is a central step in viral infection 1 and a common target of antiretroviral drugs 2 . The reaction is catalysed by viral reverse transcriptase (RT)3,4 that is packaged in an infectious virion with two copies of viral genomic RNA 5 each bound to host lysine 3 transfer RNA (tRNALys3), which acts as a primer for initiation of reverse transcription6,7. Upon viral entry into cells, initiation is slow and non-processive compared to elongation8,9. Despite extensive efforts, the structural basis of RT function during initiation has remained a mystery. Here we use cryo-electron microscopy to determine a three-dimensional structure of an HIV-1 RT initiation complex. In our structure, RT is in an inactive polymerase conformation with open fingers and thumb and with the nucleic acid primer-template complex shifted away from the active site. The primer binding site (PBS) helix formed between tRNALys3 and HIV-1 RNA lies in the cleft of RT and is extended by additional pairing interactions. The 5' end of the tRNA refolds and stacks on the PBS to create a long helical structure, while the remaining viral RNA forms two helical stems positioned above the RT active site, with a linker that connects these helices to the RNase H region of the PBS. Our results illustrate how RNA structure in the initiation complex alters RT conformation to decrease activity, highlighting a potential target for drug action.

Reviews - 6b19 mentioned but not cited (3)

  1. Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance. Xavier Ruiz F, Arnold E. Curr Opin Struct Biol 61 113-123 (2020)
  2. Advances in understanding the initiation of HIV-1 reverse transcription. Krupkin M, Jackson LN, Ha B, Puglisi EV. Curr Opin Struct Biol 65 175-183 (2020)
  3. Structural and computational studies of HIV-1 RNA. Levintov L, Vashisth H. RNA Biol 21 1-32 (2024)

Articles - 6b19 mentioned but not cited (2)

  1. Architecture of an HIV-1 reverse transcriptase initiation complex. Larsen KP, Mathiharan YK, Kappel K, Coey AT, Chen DH, Barrero D, Madigan L, Puglisi JD, Skiniotis G, Puglisi EV. Nature 557 118-122 (2018)
  2. Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation. Das K, Martinez SE, DeStefano JJ, Arnold E. Proc Natl Acad Sci U S A 116 7308-7313 (2019)


Reviews citing this publication (10)

  1. Role of host tRNAs and aminoacyl-tRNA synthetases in retroviral replication. Jin D, Musier-Forsyth K. J Biol Chem 294 5352-5364 (2019)
  2. Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses. Li J, Boix E. Virulence 12 444-469 (2021)
  3. Relating Structure and Dynamics in RNA Biology. Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD. Cold Spring Harb Perspect Biol 11 a032474 (2019)
  4. Endogenous Retroviruses Walk a Fine Line between Priming and Silencing. Cullen H, Schorn AJ. Viruses 12 E792 (2020)
  5. Interplay between Host tRNAs and HIV-1: A Structural Perspective. Zhang J. Viruses 13 1819 (2021)
  6. Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions. Skeparnias I, Zhang J. Noncoding RNA 7 81 (2021)
  7. Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies. Singh AK, Das K. Viruses 14 1027 (2022)
  8. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Wood DM, Dobson RCJ, Horne CR. Biochem Soc Trans 49 2711-2726 (2021)
  9. Mechanistic Interplay between HIV-1 Reverse Transcriptase Enzyme Kinetics and Host SAMHD1 Protein: Viral Myeloid-Cell Tropism and Genomic Mutagenesis. Bowen NE, Oo A, Kim B. Viruses 14 1622 (2022)
  10. Recognition of the tRNA structure: Everything everywhere but not all at once. Zhang J. Cell Chem Biol 31 36-52 (2024)

Articles citing this publication (17)

  1. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. Nat Methods 15 947-954 (2018)
  2. Intrinsic conformational dynamics of the HIV-1 genomic RNA 5'UTR. Brigham BS, Kitzrow JP, Reyes JC, Musier-Forsyth K, Munro JB. Proc Natl Acad Sci U S A 116 10372-10381 (2019)
  3. LC/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion. Šimonová A, Svojanovská B, Trylčová J, Hubálek M, Moravčík O, Zavřel M, Pávová M, Hodek J, Weber J, Cvačka J, Pačes J, Cahová H. Sci Rep 9 8697 (2019)
  4. High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs. Ha B, Larsen KP, Zhang J, Fu Z, Montabana E, Jackson LN, Chen DH, Puglisi EV. Nat Commun 12 2500 (2021)
  5. Dynamic Interplay of RNA and Protein in the Human Immunodeficiency Virus-1 Reverse Transcription Initiation Complex. Coey AT, Larsen KP, Choi J, Barrero DJ, Puglisi JD, Puglisi EV. J Mol Biol 430 5137-5150 (2018)
  6. Illuminating the virus life cycle with single-molecule FRET imaging. Lu M, Ma X, Mothes W. Adv Virus Res 105 239-273 (2019)
  7. Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR. Blakemore RJ, Burnett C, Swanson C, Kharytonchyk S, Telesnitsky A, Munro JB. Biophys J 120 4874-4890 (2021)
  8. Species-specific KRAB-ZFPs function as repressors of retroviruses by targeting PBS regions. Yang B, Fang L, Gao Q, Xu C, Xu J, Chen ZX, Wang Y, Yang P. Proc Natl Acad Sci U S A 119 e2119415119 (2022)
  9. Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening. Singh AK, Martinez SE, Gu W, Nguyen H, Schols D, Herdewijn P, De Jonghe S, Das K. Nat Commun 12 7127 (2021)
  10. Structural Insights to Human Immunodeficiency Virus (HIV-1) Targets and Their Inhibition. Vanangamudi M, Nair PC, Engels SEM, Palaniappan S, Namasivayam V. Adv Exp Med Biol 1322 63-95 (2021)
  11. Distinct Conformational States Underlie Pausing during Initiation of HIV-1 Reverse Transcription. Larsen KP, Choi J, Jackson LN, Kappel K, Zhang J, Ha B, Chen DH, Puglisi EV. J Mol Biol 432 4499-4522 (2020)
  12. Extended Interactions between HIV-1 Viral RNA and tRNALys3 Are Important to Maintain Viral RNA Integrity. Gremminger T, Song Z, Ji J, Foster A, Weng K, Heng X. Int J Mol Sci 22 E58 (2020)
  13. Post-Catalytic Complexes with Emtricitabine or Stavudine and HIV-1 Reverse Transcriptase Reveal New Mechanistic Insights for Nucleotide Incorporation and Drug Resistance. Bertoletti N, Chan AH, Schinazi RF, Anderson KS. Molecules 25 E4868 (2020)
  14. Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55Gag and its maturation products. Gilmer O, Mailler E, Paillart JC, Mouhand A, Tisné C, Mak J, Smyth RP, Marquet R, Vivet-Boudou V. RNA Biol 19 191-205 (2022)
  15. Reverse transcriptases prime DNA synthesis. Zabrady M, Zabrady K, Li AWH, Doherty AJ. Nucleic Acids Res 51 7125-7142 (2023)
  16. Human immunodeficiency virus 1 5'-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations. Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW. J Gen Virol 104 (2023)
  17. Pressure pushes tRNALys3 into excited conformational states. Wang J, Koduru T, Harish B, McCallum SA, Larsen KP, Patel KS, Peters EV, Gillilan RE, Puglisi EV, Puglisi JD, Makhatadze G, Royer CA. Proc Natl Acad Sci U S A 120 e2215556120 (2023)


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