title: Rapid evolution of in vivo-selected sequences and structures replacing 20% of a subviral RNA.
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.
authors.affiliation: Department of Biology, Dickinson College, Carlisle, PA 17013, USA.
authors.forename: Allison M
authors.initials: AM
authors.lastname: Murawski
authors.affiliation: Department of Biology, Dickinson College, Carlisle, PA 17013, USA.
authors.forename: Johnathan L
authors.initials: JL
authors.lastname: Nieves
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
authors.forename: Maitreyi
authors.initials: M
authors.lastname: Chattopadhyay
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
authors.forename: Megan Y
authors.initials: MY
authors.lastname: Young
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Szarko
authors.affiliation: Department of Biology, Dickinson College, Carlisle, PA 17013, USA.
authors.forename: Holleh F
authors.initials: HF
authors.lastname: Tajalli
authors.affiliation: Department of Biology, Dickinson College, Carlisle, PA 17013, USA.
authors.forename: Tareq
authors.initials: T
authors.lastname: Azad
authors.affiliation: Department of Biology, Dickinson College, Carlisle, PA 17013, USA.
authors.forename: Nina B
authors.initials: NB
authors.lastname: Jean-Jacques
authors.affiliation: Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Simon
authors.affiliation: Department of Biology, Dickinson College, Carlisle, PA 17013, USA. Electronic address: kushnerd@dickinson.edu.
authors.forename: David B
authors.initials: DB
authors.lastname: Kushner
mesh_terms: D019184:Carmovirus / Q000235:genetics* / Q000254:growth & development; D019281:Dimerization; D019143:Evolution, Molecular; D009690:Nucleic Acid Conformation; D010944:Plants / Q000821:virology; D019244:RNA, Satellite / Q000737:chemistry / Q000235:genetics*; D052156:SELEX Aptamer Technique; D012641:Selection, Genetic; D013997:Time Factors
chemical_list: D019244:RNA, Satellite
keywords: SELEX; Satellite RNA; Turnip crinkle virus; Viral RNA evolution