Novel Victorivirus from a Pakistani Isolate of Alternaria alternata Lacking a Typical Translational Stop/Restart Sequence Signature.

Atif Jamal,Hideki Kondo,Yukiyo Sato,Nobuhiro Suzuki,Wajeeha Shamsi,Sabitree Shahi

doi:10.3390/v11060577

Atif Jamal, Hideki Kondo + Show 4 more

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https://doi.org/10.3390/v11060577

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Abstract

The family Totiviridae currently contains five genera Totivirus, Victorivirus, Leishmavirus, Trichomonasvirus, and Giardiavirus. Members in this family generally have a set of two-open reading frame (ORF) elements in their genome with the 5′-proximal ORF (ORF1) encoding a capsid protein (CP) and the 3′-proximal one (ORF2) for RNA-dependent RNA polymerase (RdRp). How the downstream open reading frames (ORFs) are expressed is genus-specific. All victoriviruses characterized thus far appear to use the stop/restart translation mechanism, allowing for the expression of two separate protein products from bicitronic genome-sized viral mRNA, while the totiviruses use a −1 ribosomal frame-shifting that leads to a fusion product of CP and RdRp. We report the biological and molecular characterization of a novel victorivirus termed Alternaria alternata victorivirus 1 (AalVV1) isolated from Alternaria alternata in Pakistan. The phylogenetic and molecular analyses showed AalVV1 to be distinct from previously reported victoriviruses. AalVV1 appears to have a sequence signature required for the −1 frame-shifting at the ORF1/2 junction region, rather than a stop/restart key mediator. By contrast, SDS–polyacrylamide gel electrophoresis and peptide mass fingerprinting analyses of purified virion preparations suggested the expression of two protein products, not a CP-RdRp fusion product. How these proteins are expressed is discussed in this study. Possible effects of infection by this virus were tested in two fungal species: A. alternata and RNA silencing proficient and deficient strains of Cryphonectria parasitica, a model filamentous fungus. AalVV1 showed symptomless infection in all of these fungal strains, even in the RNA silencing deficient C. parasitica strain.

Highlights

There are many double-stranded RNA viruses with a two-open reading frame (ORF), nonsegmented genome organization, one of the simplest genome types, reported from plants, fungi, protozoa, and insects, as exemplified by totiviruses and members of other genera in the Totiviridae [1], amalgaviruses [2,3], phlegiviruses [4], fusagraviruses [5], megatotiviruses [6], and many unclassified viruses
A local BLAST analysis showed the presence of a virus-like contig (A1-19), with an average coverage of 2680, and a size of 5159 bp in length (Figure 1C), which corresponded well to the length of the double-stranded RNA (dsRNA) purified from A-16
A number of RNA viruses have been reported from Alternaria spp., including dsRNA viruses: an alternavirus [51], a partitivirus [52], botybirnaviruses [43,53,54], chrysoviruses [55], and victoriviruses

Summary

Introduction

There are many double-stranded RNA (dsRNA) viruses with a two-open reading frame (ORF), nonsegmented genome organization, one of the simplest genome types, reported from plants, fungi, protozoa, and insects, as exemplified by totiviruses (members of the genus Totivirus) and members of other genera in the Totiviridae [1], amalgaviruses [2,3], phlegiviruses [4], fusagraviruses [5], megatotiviruses [6], and many unclassified viruses. The 30 proximal ORFs of these viruses are expressed by noncanonical translation mechanisms such as stop/restart translation [7,8] and ribosomal frame-shifting [9,10,11], though not substantiated, for many of these viruses. These viruses are expected have icosahedral T = 1 capsids as shown for totiviruses [12,13]. The rate of the frame-shifting ribosomes was estimated as 1.9% of ribosomes that have translated CP [11]

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