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A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and

Tamanash Bhattacharya1, Eva M Alleman1, Alexander C Noyola1,2

  • 1Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Biorxiv : the Preprint Server for Biology
|September 4, 2024
PubMed
Summary

Alphaviruses use a specific stop codon (opal) in nsP3 for optimal replication at 37°C. This codon balances viral polymerase production and protein processing, crucial for Sindbis virus (SINV) fitness in dual hosts.

Keywords:
Sindbis Virusalphaviruseshost-switchingopal codonprotease cleavagetemperature-dependencetranslational readthrough

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Area of Science:

  • Virology
  • Molecular Biology
  • Genetics

Background:

  • Alphaviruses are RNA viruses with dual-host lifecycles.
  • A conserved opal (UGA) stop codon in nsP3 is critical for alphavirus propagation.
  • The evolutionary pressures on this opal codon remain unclear.

Purpose of the Study:

  • To investigate the role and selective pressure on the nsP3 opal codon in Sindbis virus (SINV).
  • To determine the impact of temperature and host cells on opal codon selection.
  • To understand how this codon influences viral fitness and replication.

Main Methods:

  • Extensive mutational analysis of the nsP3 opal codon in SINV.
  • Experiments conducted in primate and mosquito cell lines.
  • Comparative analysis of viral fitness at different temperatures (37°C and lower).

Main Results:

  • The opal codon is highly favored in primate cells at 37°C, with preference decreasing at lower temperatures.
  • Opal codon selection is driven by temperature, not host genetics.
  • Substituting opal with sense codons impairs viral fitness by disrupting protein processing and RNA replication transitions.

Conclusions:

  • The nsP3 opal stop codon is essential for optimal alphavirus replication at 37°C.
  • This codon represents a finely tuned strategy to balance viral polymerase production and processing.
  • The findings reveal a sophisticated mechanism for optimizing dual-host alphavirus fitness at the codon level.