Requirement for Host RNA-Silencing Components and the Virus-Silencing Suppressor when Second-Site Mutations Compensate for Structural Defects in the 3′ Untranslated Region
| Autor: | Anne E. Simon, Vera A. Stupina, Feng Gao, Kerong Shi, Maitreyi Chattopadhyay, Christine Szarko, Xuefeng Yuan, Micki M. Kuhlmann |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
RNA Folding
RNA-induced transcriptional silencing RNA-induced silencing complex Immunology Arabidopsis RNA-dependent RNA polymerase Biology Microbiology Open Reading Frames Virology Tobacco RNA Small Interfering 3' Untranslated Regions Suppressor mutation RNA Double-Stranded Genetics Arabidopsis Proteins Turnip crinkle virus RNA Argonaute biology.organism_classification Genome Replication and Regulation of Viral Gene Expression RNA silencing Insect Science Argonaute Proteins Host-Pathogen Interactions Mutation RNA Viral Capsid Proteins Carmovirus RNA Interference |
| Popis: | Turnip crinkle virus (TCV) contains a structured 3′ region with hairpins and pseudoknots that form a complex network of noncanonical RNA:RNA interactions supporting higher-order structure critical for translation and replication. We investigated several second-site mutations in the p38 coat protein open reading frame (ORF) that arose in response to a mutation in the asymmetric loop of a critical 3′ untranslated region (UTR) hairpin that disrupts local higher-order structure. All tested second-site mutations improved accumulation of TCV in conjunction with a partial reversion of the primary mutation (TCV-rev1) but had neutral or a negative effect on wild-type (wt) TCV or TCV with the primary mutation. SHAPE ( s elective 2′- h ydroxyl a cylation analyzed by p rimer e xtension) structure probing indicated that these second-site mutations reside in an RNA domain that includes most of p38 (domain 2), and evidence for RNA:RNA interactions between domain 2 and 3′UTR-containing domain 1 was found. However, second-site mutations were not compensatory in the absence of p38, which is also the TCV silencing suppressor, or in dcl-2/dcl4 or ago1/ago2 backgrounds. One second-site mutation reduced silencing suppressor activity of p38 by altering one of two GW motifs that are required for p38 binding to double-stranded RNAs (dsRNAs) and interaction with RNA-induced silencing complex (RISC)-associated AGO1/AGO2. Another second-site mutation substantially reduced accumulation of TCV-rev1 in the absence of p38 or DCL2/DCL4. We suggest that the second-site mutations in the p38 ORF exert positive effects through a similar downstream mechanism, either by enhancing accumulation of beneficial DCL-produced viral small RNAs that positively regulate the accumulation of TCV-rev1 or by affecting the susceptibility of TCV-rev1 to RISC loaded with viral small RNAs. IMPORTANCE Genomes of positive-strand RNA viruses fold into high-order RNA structures. Viruses with mutations in regions critical for translation and replication often acquire second-site mutations that exert a positive compensatory effect through reestablishment of canonical base pairing with the altered region. In this study, two distal second-site mutations that individually arose in response to a primary mutation in a critical 3′ UTR hairpin in the genomic RNA of turnip crinkle virus did not directly interact with the primary mutation. Although different second-site changes had different attributes, compensation was dependent on the production of the viral p38 silencing suppressor and on the presence of silencing-required DCL and AGO proteins. Our results provide an unexpected connection between a 3′ UTR primary-site mutation proposed to disrupt higher-order structure and the RNA-silencing machinery. |
| Databáze: | OpenAIRE |
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