Biosecurity Research Articles

A short insert in the leader sequence of RNA 3L, a long variant of alfalfa mosaic virus RNA3, introduces two unidentified reading frames

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Publication Date


Journal Title

Virus Genes


Print: 0920-8569 Electronic: 1572-994X


Alfalfa mosaic virus-N20, RNA 3L, 5' leader URF1, URF2, 21aa peptides


Agronomy and Crop Sciences | Biosecurity


N20-RNA 3L, a large form of RNA 3 associated with Alfalfa mosaic virus (AMV) strain N20 comprises 2281nt and has approximately 97% overall sequence similarity to the longest previously described RNA 3 of AMV strain YSMV (YSMV-RNA 3; 2188nt). Compared with YSMV-RNA 3, N20-RNA 3L contains an additional 97nt in the 5' leader upstream of the open reading frames for movement protein (MP) and coat protein (CP). Two overlapping unidentified reading frames (URF1 and URF2) result from this modification, each of which code for putative translation products of 21 amino acids. The URF1 putative peptide has a hydrophilic N-terminus and a hydrophobic C-terminus, indicating a possible association with both host cell membrane and cytosol whereas the putative URF2 product is predominantly hydrophobic. A further structural modification found in N20-RNA 3L is a new tandem repeat of 243nts which overlaps with the MP open reading frame.



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