The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7

Abstract

Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3Ј PBS for primer tRNA i Met annealing to the genomic RNA, and the 5Ј PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNA i Met bound to the PBS was found to direct dimerization of Ty3 RNAtRNA i Met . Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs.

The Prion Protein Has RNA Binding and Chaperoning Properties Characteristic of Nucleocapsid Protein NCp7 of HIV-1

“…The ovine PrP (ovPrP) was found to be as effective as huPrP and HIV-1 NCp7 in directing the specific annealing reaction (lanes 9 -11). These data demonstrate that PrP of human or ovine origin has nucleic acid annealing activity characteristic of HIV-1 NCp7 and retroviral NC proteins in general (16,18,19,(27)(28)(29)(30).…”

Variability, Recombination, and Mosaic Evolution of the Barley BARE-1 Retrotransposon

“…Hence, it appears that this BARE-2 is a mosaic or chimeric element generated by stand switching during replication. Retrotransposons (Gabus et al 1998;Feng et al 2000) and retroviruses (Hu and Temin 1990) are known to package two RNA templates. In yeast, 14 of the 32 elements previously identified as Ty1 are actually Ty1/Ty2 hybrid elements McDonald 1998, 1999); template switching between packaged Ty1 RNAs occurs with a high frequency (Wilhelm et al 1999).…”

Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate

“…For instance, retroviruses form noncovalent dimers of their mRNA to facilitate strand transfer in trans (Paillart et al 1996). In the yeast retrotransposon Ty3, an extended, basepaired structure encompassing two mRNAs and two tRNAs has been identified (Gabus et al 1998). RNA of yeast Ty1 also displays base-pairing interactions, both between 5 0 -and 3 0 -sequences, and within the 5 0 -region, whose likely effect is to align sequences for reverse transcription and strand transfer (Cristofari et al 2002;Bolton et al 2005).…”