Ribosomal Frameshifting in Decoding Plant Viral RNAs

Miller, W. Allen; Giedroc, D.P.

doi:10.1007/978-0-387-89382-2_9

Cited by 24 publications

(15 citation statements)

References 94 publications

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“…In all studied poleroviruses, P2, which encodes the active site of the RdRp, is expressed only as a fusion with P1, as it is translated by frameshifting of ribosomes from ORF 1 to ORF 2 in the region of overlap (Prüfer et al, 1992; Kujawa et al, 1993; Miller and Giedroc, 2010). The CYDV/WYDV RdRp (P2) sequences clustered tightly in 100% of the replicates, but they all were strikingly distinct from RMV MTFE87 P2, which groups rather distantly with CtRLV (Figure 5A).…”

Section: Resultsmentioning

confidence: 99%

“…Base numbering (negative) is from the 3′ end of the genomes. (B) Predicted (BYDV-RMV) and known (PEMV1 and TuYV) (Su et al, 1999; Nixon et al, 2002; Miller and Giedroc, 2010) tertiary structures of pseudoknots downstream of the frameshift sites (boxed). Italics indicate base numbers in the genome.…”

Section: Discussionmentioning

confidence: 99%

“…In all Luteoviridae , ORF2 encoding the active site of the RdRp is translated via ribosomal frameshifting at a shifty heptanucleotide, fitting the motif XXXYYYZ (where X is any base, Y is A or U, and Z is any base except G), in the region of ORF1–ORF2 overlap. Seven nt downstream of this site, the polero- and enamovirus genomes fold into a small, compact pseudoknot that pauses the ribosome to facilitate frameshifting (Su et al, 1999; Nixon et al, 2002; Miller and Giedroc, 2010). Indeed, in the region of ORF1–ORF2 overlap in the RMV MTFE87 genome, we found the shifty heptanucleotide 1603 GGGAAAC 1609 , followed by a predicted pseudoknot that spans bases 1616–1643 (Figure 6B).…”

Section: Discussionmentioning

confidence: 99%

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The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses

Krueger¹,

Beckett²,

Gray³

et al. 2013

Front. Microbiol.

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The yellow dwarf viruses (YDVs) of the Luteoviridae family represent the most widespread group of cereal viruses worldwide. They include the Barley yellow dwarf viruses (BYDVs) of genus Luteovirus, the Cereal yellow dwarf viruses (CYDVs) and Wheat yellow dwarf virus (WYDV) of genus Polerovirus. All of these viruses are obligately aphid transmitted and phloem-limited. The first described YDVs (initially all called BYDV) were classified by their most efficient vector. One of these viruses, BYDV-RMV, is transmitted most efficiently by the corn leaf aphid, Rhopalosiphum maidis. Here we report the complete 5612 nucleotide sequence of the genomic RNA of a Montana isolate of BYDV-RMV (isolate RMV MTFE87, Genbank accession no. KC921392). The sequence revealed that BYDV-RMV is a polerovirus, but it is quite distantly related to the CYDVs or WYDV, which are very closely related to each other. Nor is BYDV-RMV closely related to any other particular polerovirus. Depending on the gene that is compared, different poleroviruses (none of them a YDV) share the most sequence similarity to BYDV-RMV. Because of its distant relationship to other YDVs, and because it commonly infects maize via its vector, R. maidis, we propose that BYDV-RMV be renamed Maize yellow dwarf virus-RMV (MYDV-RMV).

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses

Krueger¹,

Beckett²,

Gray³

et al. 2013

Front. Microbiol.

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“…Eukaryotic − 1 frameshift sites typically consist of a slippery heptanucleotide fitting the consensus motif X XXY YYZ, where XXX represents any three identical nucleotides, YYY represents AAA or UUU, and Z represents any nucleotide except G. The shift site is followed by a 'spacer' region of 5-9 nt, and then a highly structured region, often an RNA pseudoknot or hairpin. 1,2 To date, nearly all known − 1 frameshift sites in virus genomes have a long downstream − 1 frame open reading frame (ORF). One example is the Gag-Pol gene in human immunodeficiency virus (HIV), where Pol is expressed as a − 1 frameshift fusion product with Gag.…”

Section: Introductionmentioning

confidence: 99%

Frameshifting in Alphaviruses: A Diversity of 3′ Stimulatory Structures

Chung

Firth

Atkins

2010

Journal of Molecular Biology

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“…Interestingly, antisense oligonucleotides or guanine-rich sequences that can fold into four-stranded structures of stacked guaninetetrads, so-called G-quadruplexes, can also stimulate À1PRF, reaching efficiencies up to 40% [20,21]. In addition, in some cases a Shine-Dalgarno-like element 11-14 nt upstream of the first slippery codon [22] or even longdistance base-pairing appear to stimulate frameshifting [23].…”

Section: Prevalence Of Ribosomal Frameshiftingmentioning

confidence: 99%

Changed in translation: mRNA recoding by −1 programmed ribosomal frameshifting

Caliskan

Peske

Rodnina

2015

Trends in Biochemical Sciences

116

118

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Programmed S1 ribosomal frameshifting (S1PRF) is an mRNA recoding event commonly utilized by viruses and bacteria to increase the information content of their genomes. Recent results have implicated S1PRF in quality control of mRNA and DNA stability in eukaryotes. Biophysical experiments demonstrated that the ribosome changes the reading frame while attempting to move over a slippery sequence of the mRNA -when a roadblock formed by a folded downstream segment in the mRNA stalls the ribosome in a metastable conformational state. The efficiency of S1PRF is modulated not only by cis-regulatory elements in the mRNA but also by transacting factors such as proteins, miRNAs, and antibiotics. These recent results suggest a molecular mechanism and new important cellular roles for S1PRF.Accurate decoding versus programmed recoding Ribosomes (see Glossary) are cellular factories that produce proteins in all cells using the nucleotide sequence of mRNAs as a blueprint. Nucleotide triplets of an mRNAthe codons -are translated into an amino acid sequence of a protein. The selection of the translation start and the reading frame on an mRNA is tightly controlled during the initiation phase of protein synthesis. The subsequent elongation phase entails repeated cycles of codon decoding by aminoacyl-tRNA, peptide bond formation, and tRNAmRNA translocation. Elongation cycles continue until the ribosome reaches a stop codon, on which translation is terminated. It is intuitively clear that translation of an mRNA sequence into a protein must be colinear and highly accurate. Errors can lead to the formation of toxic or misfolded proteins, increase the energetic cost of translation, and cause additional load on the cellular clean-up and quality-control machineries [1]. To avoid this burden, cells have evolved sophisticated control mechanisms that ensure the fidelity of decoding and reading frame maintenance. However, in special cases, the ribosomes, guided by signals encoded in the mRNA, abandon the principle of mRNAprotein colinearity and read the message in an alternative way, which results in mRNA recoding (Box 1) [2][3][4].Programmed frameshifting is a recoding event that can occur in the + or À direction relative to the normal 0-frame mRNA translation by shifting the ribosome by one or two nucleotides, thereby producing two (or even three) different proteins from one mRNA. In contrast to spontaneous frameshifting, which is infrequent, the efficiency of programmed frameshifting may be as high as 80%, although in many cases it is only a few percent [5]. Programmed frameshifting increases the coding potential of the genome and is often used to expand the variability of cellular proteomes, adapt to changing environments, or ensure a defined stoichiometry of protein products. The mechanisms of +1 and À1 frameshifting appear to be different, and particularly the mechanism of À1 programmed ribosome frameshifting (À1PRF), its abundance, and physiological significance have remained unclear for a long time. The advances of biophysical techniqu...

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Ribosomal Frameshifting in Decoding Plant Viral RNAs

Cited by 24 publications

References 94 publications

The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses

The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new Polerovirus distantly related to other yellow dwarf viruses

Frameshifting in Alphaviruses: A Diversity of 3′ Stimulatory Structures

Changed in translation: mRNA recoding by −1 programmed ribosomal frameshifting

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