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: 9.67). 09/2002; 99(17):11133-8. DOI: 10.1073/pnas.162223099
Source: PubMed


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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    • "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 certain cases, an additional long-range RNA–RNA interaction between the shift-proximal higher-order structure and a sequence far downstream in the genome is needed for frameshifting to occur (Fig. 2A). This latter requirement is true for both luteoviruses and dianthoviruses, and the communication may help to coordinate frameshifting with minus-strand RNA synthesis (Barry and Miller, 2002; Tajima et al., 2011). The less typical þ1 frameshifting has been proposed to occur in Citrus tristeza virus (CTV) and Beet yellows virus (BYV), members of the family Closteroviridae (Miller and Giedroc, 2010), but this process and its associated RNA elements are less well characterized. "
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    • "The box shows CIRV-fs PRTE-DRTE compensatory mutants with substitutions in red. (C) Predicted RNA secondary structure for BYDV showing its SL-PRTE-like and DRTE-like elements in green (Barry and Miller, 2002 "
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