PMID: 8609616Feb 16, 1996Paper

Secondary structure model for the first three domains of Q beta RNA. Control of A-protein synthesis

Journal of Molecular Biology
J BeekwilderJ van Duin

Abstract

We present a secondary structure model for the first 860 nucleotides of Q beta RNA. The model is supported by phylogenetic comparison, nuclease S1 structure probing and computer prediction using energy minimization and a Monte Carlo approach. To provide the necessary data for the comparative analysis we have sequenced the single-stranded RNA coliphages MX1, M11 and NL95. Together with the known sequences of Q beta and SP, this yields five sequences with sufficient sequence diversity to be useful for the analysis. The part of the Q beta genome examined contains the 60 nucleotide 5' untranslated region and the first 800 nucleotide of the maturation protein gene. The RNA adopts a highly ordered structure in which all hairpins are held in place by a network of long-distance interactions, which form three-way and four-way junctions. Only the 5'-terminal hairpin is unrestrained, while connected by a few single-stranded nucleotides to the body of the RNA. The start region of the A-protein gene, which is part of the network of long-distance interactions, is base-paired to three non-contiguous downstream sequences. As a result, translation is expected to be progressively quenched when the length of the nascent chains increases. This fea...Continue Reading

Citations

Oct 23, 1997·Nucleic Acids Research·J KlovinsR C Olsthoorn
Jun 27, 1998·Molecular Microbiology·J J BullI J Molineux
Jan 19, 2013·Microbiology·Catrina A ReedRy Young
Jun 14, 2013·Open Biology·Libertad García-Villada, John W Drake
Mar 10, 2015·RNA Biology·Jing Yun A Zhu, Irmtraud M Meyer
Sep 28, 2016·Proceedings of the National Academy of Sciences of the United States of America·Karl V GorzelnikJunjie Zhang
May 25, 2002·The Journal of General Virology·J KlovinsJ van Duin
Sep 14, 2010·Journal of Evolutionary Biology·P Domingo-CalapR Sanjuán
Jul 25, 2018·Viruses·Julie CallananColin Hill
Feb 21, 2013·RNA Biology·Alexander BorodavkaPeter G Stockley
Oct 6, 2004·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·Tohru NishiharaYukinobu Nishimura
Feb 8, 2006·Applied and Environmental Microbiology·Jill R StewartMark D Sobsey

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