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. 2017 Apr 21;7:1017. doi: 10.1038/s41598-017-01243-z

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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SL1 and SLC of BPMV are interchangeable. (a) Sequences of the SL1 and SLC portions of BR1 and BR2G-AN, respectively, and their deletion/replacement mutants. SL1 and SLC sequences are in blue and black letters, respectively; with the conserved loop nts in red. The nts involved in stems are underlined with dots. The AUG start codon in SL1, and its mutated form (ACG), are underlined with solid lines. Note that the last fifteen and nine nts of SL1 were retained in BR1-ΔSL1 and BR1-SLC, respectively, to preserve the AUG translational start codon. In BR2G derivatives containing SL1 segments, the AUG within the SL1 stem was changed to ACG to avoid its potential translational conflict with the RNA2 start codon downstream. (b) Lima bean cotyledons bombarded with various mutants, along with IL and SL images of soybean infected with the corresponding viruses. (c) RT-PCR detection of BR1 and BR2G RNAs in lima bean cotyledons bombarded with the mutants. (d) The stem of SL1 needs to remain base-paired in order for SL1 to be functional. Top: the predicted structure of SL1 in BR2G backbone, along with the three mutations (mL, MR, and mLR) introduced into the shaded area of the stem. Both mL and mR were predicted to disrupt the stem, whereas mLR should restore the base pairs with different sequences. Bottom: lima bean cotyledons bombarded with the constructs indicated above showing the restoration of replicability by the mLR mutant.