A -1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA

Plant Pathology Department, Iowa State University, Ames, IA 50011, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 09/2002; 99(17):11133-8. DOI: 10.1073/pnas.162223099
Source: PubMed

ABSTRACT Programmed -1 ribosomal frameshifting is necessary for translation of the polymerase genes of many viruses. In addition to the consensus elements in the mRNA around the frameshift site, we found previously that frameshifting on Barley yellow dwarf virus RNA requires viral sequence located four kilobases downstream. By using dual luciferase reporter constructs, we now show that a predicted loop in the far downstream frameshift element must base pair to a bulge in a bulged stem loop adjacent to the frameshift site. Introduction of either two or six base mismatches in either the bulge or the far downstream loop abolished frameshifting, whereas mutations in both sites that restored base pairing reestablished frameshifting. Likewise, disruption of this base pairing abolished viral RNA replication in plant cells, and restoration of base pairing completely reestablished virus replication. We propose a model in which Barley yellow dwarf virus uses this and another long-distance base-pairing event required for cap-independent translation to allow the replicase copying from the 3' end to shut off translation of upstream ORFs and free the RNA of ribosomes to allow unimpeded replication. This would be a means of solving the "problem," common to positive strand RNA viruses, of competition between ribosomes and replicase for the same RNA template.

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Available from: Wyatt Allen Miller, Jul 08, 2015
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    • "Thus translation must be stopped and ribosomes removed from the RNA before it can be replicated . As proposed previously ( Barry and Miller , 2002 ; Miller and White , 2006 ) , this may be achieved as follows . After the long - distance base pairing allows cap - independent trans - lation and ribosomal frameshifting to produce the viral RdRp , the viral RdRp then proceeds to initiate negative strand syn - thesis at the 3 end . "
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    • "In addition to these RNA elements, Barley yellow dwarf virus (BYDV) requires a third RNA element that is located in the 3′ untranslated region (UTR) (Paul et al., 2001). This far-downstream element is thought to base-pair with a bulge-loop in a stem-loop adjacent to the shifty site, where it facilitates frameshifting (Barry and Miller, 2002). "
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    • "Black boxes on genome indicate predicted cis-acting structures (left to right): BTE complementary loop of genomic RNA (gBCL, Fig. 3), shifty heptanucleotide and bulged stem–loop at frameshift site (FS, Fig. 4), BTE complementary loop at predicted 5′ end of sgRNA1 (sg1BCL, Fig. 3), BYDV-like cap-independent translation element (BTE, Fig. 5) and long-distance frameshift element that interacts with the frameshift site (LDFE, Fig. 4). long-distance interaction (Fig. 4) is essential for frameshifting on BYDV RNA (Barry and Miller, 2002). Viruses in the Luteovirus, Necrovirus and Dianthovirus genera harbor a BTE in the 3′ UTR (Guo et al., 2001; Mizumoto et al., 2003; Shen and Miller, 2004b) "
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