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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
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Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells
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Novel 3' Proximal Replication Elements in Umbravirus Genomes.

Philip Z Johnson1, Hannah M Reuning1, Sayanta Bera1

  • 1Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.

Viruses
|December 23, 2022
PubMed
Summary
This summary is machine-generated.

A newly identified RNA structure, "Trio," is essential for umbravirus replication in plants. While not affecting translation, Trio hairpins are critical for viral RNA accumulation and replication, highlighting conserved replication mechanisms.

Keywords:
RNA structure/functionpea enation mosaic virus 2positive-strand RNA virus replication and translationumbravirus

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Area of Science:

  • Plant Virology
  • Molecular Biology
  • RNA Biology

Background:

  • 3' untranslated regions (UTRs) of positive-strand RNA viruses contain elements crucial for replication and translation.
  • Umbravirus pea enation mosaic virus 2 (PEMV2) possesses multiple 3' cap-independent translation enhancers (3'CITEs) and 3' terminal replication elements.

Purpose of the Study:

  • To identify and characterize novel RNA elements within the 3'UTR of umbraviruses.
  • To investigate the role of these elements in viral replication and translation.

Main Methods:

  • Bioinformatic identification of RNA structures (hairpins, pseudoknots) in umbravirus 3'UTRs.
  • Functional analysis using in vitro translation assays (wheat germ extracts) and in vivo reporter gene assays.
  • Assessment of viral RNA accumulation in *Arabidopsis thaliana* protoplasts.
  • Evaluation of viral replication using a trans-replication system in *Nicotiana benthamiana*.

Main Results:

  • A novel structure, termed "Trio" (three hairpins and a pseudoknot), was identified exclusively in a subset of umbraviruses, located upstream of the 3'TSS.
  • Trio modifications did not affect viral translation in vitro or in vivo.
  • Trio hairpins were essential for viral RNA accumulation in *Arabidopsis thaliana* protoplasts and for replication in *Nicotiana benthamiana*.

Conclusions:

  • The
  • Trio
  • RNA structure is a critical replication element in specific umbraviruses, independent of its role in translation.
  • Conserved 3' terminal replication elements suggest conserved replication strategies among umbraviruses, despite variations in translation enhancement mechanisms.