The HIV plus-strand transfer reaction: determination of replication-competent intermediates and identification of a novel lentiviral element, the primer over-extension sequence

Muthuswami, Rohini; Chen, Joe; Burnett, Bruce; Thimmig, R L; Janjić, Nebojša; McHenry, Charles S.

doi:10.1006/jmbi.2001.5205

Cited by 16 publications

(15 citation statements)

References 46 publications

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“…The presence of Ψ54, if any, in Lys tRNAs could not be determined because Tm (2 ′ -O-methylribothymidine) commonly present at position 54 in these tRNAs inhibits primer extension for unknown reasons. This has also been observed by others (Muthuswami et al 2002). Most mammalian tRNAs contain m 1 A at position 58, which strongly inhibits primer extension.…”

Section: ψ Is Present At Position 54 In Certain Mammalian Trnassupporting

confidence: 79%

The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue

Deogharia

Mukhopadhyay

Joardar

et al. 2018

RNA

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The nearly conserved U54 of tRNA is mostly converted to a version of ribothymidine (T) in Bacteria and eukaryotes and to a version of pseudouridine (Ψ) in Archaea. Conserved U55 is nearly always modified to Ψ55 in all organisms. Orthologs of TrmA and TruB that produce T54 and Ψ55, respectively, in Bacteria and eukaryotes are absent in Archaea. Pus10 produces both Ψ54 and Ψ55 in Archaea. Pus10 orthologs are found in nearly all sequenced archaeal and most eukaryal genomes, but not in yeast and bacteria. This coincides with the presence of Ψ54 in most archaeal tRNAs and some animal tRNAs, but its absence from yeast and bacteria. Moreover, Ψ54 is found in several tRNAs that function as primers for retroviral DNA synthesis. Previously, no eukaryotic tRNA Ψ54 synthase had been identified. We show here that human Pus10 can produce Ψ54 in select tRNAs, including tRNA Lys3 , the primer for HIV reverse transcriptase. This synthase activity of Pus10 is restricted to the cytoplasm and is distinct from nuclear Pus10, which is known to be involved in apoptosis. The sequence GUUCAm 1 AAUC (m 1 A is 1-methyladenosine) at position 53-61 of tRNA along with a stable acceptor stem results in maximum Ψ54 synthase activity. This recognition sequence is unique for a Ψ synthase in that it contains another modification. In addition to Ψ54, SF9 cells-derived recombinant human Pus10 can also generate Ψ55, even in tRNAs that do not contain the Ψ54 synthase recognition sequence. This activity may be redundant with that of TruB.

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Section: ψ Is Present At Position 54 In Certain Mammalian Trnassupporting

confidence: 79%

The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue

Deogharia

Mukhopadhyay

Joardar

et al. 2018

RNA

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“…In reconstituted systems, termination also occurs at two other sites: a pseudouridine at position 55; and at a position in the anticodon loop of tRNA Lys 3 , which results in a dead-end product. [215][216][217] Termination at positions 55 and 58 was also observed in an HIV-1 ERT assay. 216 Interestingly, in some HIV-1 strains, e.g., NL4-3, 218 nt 56-58 in tRNA Lys 3 are complementary to the first three bases downstream of the PBS in vRNA, so that termination at position 55 in the tRNA does not interfere with subsequent plus-strand transfer.…”

Section: (See Ref 3 For Additional Citations)mentioning

confidence: 69%

Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription

et al. 2010

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The HIV-1 nucleocapsid protein (NC) is a nucleic acid chaperone, which remodels nucleic acid structures so that the most thermodynamically stable conformations are formed. This activity is essential for virus replication and has a critical role in mediating highly specific and efficient reverse transcription. NC's function in this process depends upon three properties: (1) ability to aggregate nucleic acids; (2) moderate duplex destabilization activity; and (3) rapid on-off binding kinetics. Here, we present a detailed molecular analysis of the individual events that occur during viral DNA synthesis and show how NC's properties are important for almost every step in the pathway. Finally, we also review biological aspects of reverse transcription during infection and the interplay between NC, reverse transcriptase, and human APOBEC3G, an HIV-1 restriction factor that inhibits reverse transcription and virus replication in the absence of the HIV-1 Vif protein.

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“…NC also serves as a chaperone, by promoting several annealing reactions in the reverse transcription process. For example, NC has been shown to facilitate the annealing of the tRNA primer onto the primer binding site (19)(20)(21), annealing of complementary sequences in plus-strand transfer (22)(23)(24)(25), and annealing of complementary repeat regions in minus-strand transfer (23,(26)(27)(28)(29)(30)(31)(32).…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule FRET Studies of Important Intermediates in the Nucleocapsid-Protein-Chaperoned Minus-Strand Transfer Step in HIV-1 Reverse Transcription

Liu

Cosa

Landes

et al. 2005

Biophysical Journal

137

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The minus-strand transfer step of HIV-1 reverse transcription is chaperoned by the nucleocapsid protein (NC), which has been shown to facilitate the annealing between the transactivation response element (TAR) RNA and complementary TAR DNA stem-loop structures. In this work, potential intermediates in the mechanism of NC-chaperoned TAR DNA/TAR RNA annealing have been examined using single-molecule fluorescence resonance energy transfer. The interaction between TAR DNA and various DNA oligonucleotides designed to mimic the initial annealing step was monitored to capture potential intermediates along the reaction pathway. Two possible mechanisms of annealing were examined, namely nucleation through the 3'/5' termini, termed the "zipper" complex, or nucleation through the hairpin loops in a "kissing" complex. Intermediates associated with both mechanisms were observed in the presence of NC, and the kinetics of formation of these intermediates were also measured. Thus, the single-molecule experiments support the notion that NC-assisted annealing of TAR DNA:TAR RNA may occur through multiple pathways.

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The HIV plus-strand transfer reaction: determination of replication-competent intermediates and identification of a novel lentiviral element, the primer over-extension sequence

Cited by 16 publications

References 46 publications

The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue

The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue

Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription

Single-Molecule FRET Studies of Important Intermediates in the Nucleocapsid-Protein-Chaperoned Minus-Strand Transfer Step in HIV-1 Reverse Transcription

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