Rapid evolution of in vivo-selected sequences and structures replacing 20% of a subviral RNA

Virology. 2015 Sep:483:149-62. doi: 10.1016/j.virol.2015.04.002. Epub 2015 May 15.

Abstract

The 356 nt noncoding satellite RNA C (satC) of Turnip crinkle virus (TCV) is composed of 5' sequences from a second TCV satRNA (satD) and 3' sequences derived from TCV. SHAPE structure mapping revealed that 76 nt in the poorly-characterized satD-derived region form an extended hairpin (H2). Pools of satC in which H2 was replaced with 76, 38, or 19 random nt were co-inoculated with TCV helper virus onto plants and satC fitness assessed using in vivo functional selection (SELEX). The most functional progeny satCs, including one as fit as wild-type, contained a 38-39 nt H2 region that adopted a hairpin structure and exhibited an increased ratio of dimeric to monomeric molecules. Some progeny of satC with H2 deleted featured a duplication of 38 nt, partially rebuilding the deletion. Therefore, H2 can be replaced by a 38-39 nt hairpin, sufficient for overall structural stability of the 5' end of satC.

Keywords: SELEX; Satellite RNA; Turnip crinkle virus; Viral RNA evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carmovirus / genetics*
  • Carmovirus / growth & development
  • Dimerization
  • Evolution, Molecular*
  • Nucleic Acid Conformation
  • Plants / virology
  • RNA, Satellite / chemistry
  • RNA, Satellite / genetics*
  • SELEX Aptamer Technique
  • Selection, Genetic*
  • Time Factors

Substances

  • RNA, Satellite