3′-End Stem-Loops of the Subviral RNAs Associated with Turnip Crinkle Virus Are Involved in Symptom Modulation and Coat Protein Binding

Abstract

Many plant RNA viruses are associated with one or more subviral RNAs. Two subviral RNAs, satellite RNA C (satC) and defective interfering RNA G (diG) intensify the symptoms of their helper, turnip crinkle virus (TCV). However, when the coat protein (CP) of TCV was replaced with that of the related Cardamine chlorotic fleck virus (CCFV), both subviral RNAs attenuated symptoms of the hybrid virus TCV-CP CCFV . In contrast, when the translation initiation codon of the TCV CP was altered to ACG and reduced levels of CP were synthesized, satC attenuated symptoms while diG neither intensified nor attenuated symptoms. The determinants for this differential symptom modulation were previously localized to the 3-terminal 100 bases of the subviral RNAs, which contain six positional differences (Q. Kong, J.-W. Oh, C. D. Carpenter, and A. E. Simon, Virology 238:478-485, 1997). In the current study, we have determined that certain sequences within the 3-terminal stem-loop structures of satC and diG, which also serve as promoters for complementary strand synthesis, are critical for symptom modulation. Furthermore, the ability to attenuate symptoms was correlated with weakened binding of TCV CP to the hairpin structure.Many plant RNA viruses are associated with one or more nonessential subviral RNAs, including defective interfering RNAs (DI RNAs) and satellite RNAs (satRNAs), which depend on a helper virus for replication, encapsidation, and movement in plants (26). DI RNAs are fairly ubiquitous in animal virus systems and relatively rare among plant viruses (34, 57). On the other hand, satRNAs are almost exclusively associated with plant viruses (33). DI RNAs are generated as a consequence of errors in viral genome replication, and interference with the replication of the helper virus frequently results in substantial symptom attenuation (6,9,14,35). However, some DI RNAs increase the symptom severity of their helper viruses, such as the DI RNA of broad bean mottle virus (32), DI RNA G (diG) of turnip crinkle virus (TCV) (19) and the DI RNA of bovine diarrhea virus (50). Unlike DI RNAs, which are shortened versions of viral genomic RNAs, satRNAs usually share little sequence similarity with their helper virus. As molecular parasites of their helper viruses, satRNAs can have dramatic effects on symptoms, ranging from amelioration to severe exacerbation (33).There are several mechanisms that satRNAs can use to attenuate symptoms. In many hosts, disease attenuation by cucumber mosaic virus (CMV) satRNAs is accompanied by a reduction in virus accumulation (12, 13). In contrast, CMV satRNA symptom attenuation of the closely related tomato aspermy virus is not always accompanied by a noticeable decrease in the level of viral RNA (25). Symptom modulation by satRNAs is thought to involve a trilateral interaction among the host plant, satRNA, and helper virus. The involvement of the host was demonstrated when particular subspecies of tobacco determined whether the Y-satellite RNA of CMV produced yellow or green mosaic symptoms (22). Th...

Secondary Structural Elements within the 3′ Untranslated Region of Mouse Hepatitis Virus Strain JHM Genomic RNA

“…The conserved stem-loop structures in HIV type 1 (HIV-1) RNA regulate RNA splicing and mRNA translation (24). The functions of conserved secondary structures in plant viruses have also been studied (3,13,30,35). The structural elements in the 3Ј UTR of the barley yellow dwarf virus genome are required for cap-independent translation and communication with the 5Ј end of the mRNA (6).…”

Effects on the local symptoms of subgenomic RNAs expressions and their translational products of Tobacco necrosis virus A Chinese isolate

“…In Turnip crinkle virus (TCV) of the family Tombusviridae, as is TNV, the coat protein was responsible for symptom modulation of virus infection [28] , and showed function as an elicitor for the hypersensitive response (HR) to virus infection in Arabidopsis [29] , in which alteration of the amino acids at N-terminal position of 4 and 85 led to breaking of virus resistance in Arabidopsis ecotype Di-17. Also, function as a RNA silencing suppressor was reported for the TCV coat protein [30,31] , while the coding sequence for coat protein of Cymbidium ringspot tombusvirus (CymRSV) was recognized as an avirulence factor in very rapid HR-like response of Datura stramonium to virus infection [32] .…”

Evolution of a helper virus-derived, ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus

“…In satC, these hairpins are thought to be present in the replication-active structure (Zhang et al, 2006a; Zhang et al, 2006b), and it is currently not known which hairpins (if any) are also present in the pre-active conformation. Despite sequence conservation in the 3’ region of the satRNA and helper virus, satC with the 3' 100 bases of TCV, and TCV with satC 3' 100 bases accumulate very poorly in plants and protoplasts (Wang and Simon, 2000). The residues most responsible for the sequence-specific effects were mapped to the 3' terminal Pr hairpin (Song and Simon, 1995; Sun and Simon, 2006; Zhang et al, 2006c), which in TCV interacts with upstream sequences that are not present in the satRNA (Yuan et al, 2009; Yuan et al, 2010).…”