SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants.

Autor: Bayne CF; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Widawski ME; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Gao F; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA., Masab MH; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Chattopadhyay M; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA., Murawski AM; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Sansevere RM; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Lerner BD; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Castillo RJ; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Griesman T; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Fu J; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Hibben JK; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Garcia-Perez AD; Department of Biology, Dickinson College, Carlisle, PA 17013, USA., Simon AE; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA., Kushner DB; Department of Biology, Dickinson College, Carlisle, PA 17013, USA. Electronic address: kushnerd@dickinson.edu.
Jazyk: angličtina
Zdroj: Virology [Virology] 2018 Jul; Vol. 520, pp. 137-152. Date of Electronic Publication: 2018 Jun 01.
DOI: 10.1016/j.virol.2018.05.010
Abstrakt: Noncoding RNAs use their sequence and/or structure to mediate function(s). The 5' portion (166 nt) of the 356-nt noncoding satellite RNA C (satC) of Turnip crinkle virus (TCV) was previously modeled to contain a central region with two stem-loops (H6 and H7) and a large connecting hairpin (H2). We now report that in vivo functional selection (SELEX) experiments assessing sequence/structure requirements in H2, H6, and H7 reveal that H6 loop sequence motifs were recovered at nonrandom rates and only some residues are proposed to base-pair with accessible complementary sequences within the 5' central region. In vitro SHAPE of SELEX winners indicates that the central region is heavily base-paired, such that along with the lower stem and H2 region, one extensive hairpin exists composing the entire 5' region. As these SELEX winners are highly fit, these characteristics facilitate satRNA amplification in association with TCV in plants.
(Copyright © 2018 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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