Molecular and biological characterization of a novel botybirnavirus identified from a Pakistani isolate of Alternaria alternata

Shamsi, Wajeeha; Sato, Yukiyo; Jamal, Atif; Shahi, Sabitree; Kondō, Hideki; Suzuki, Nobuhiro; Bhatti, Muhammad Faraz

doi:10.1016/j.virusres.2019.01.006

Cited by 26 publications

(36 citation statements)

References 58 publications

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“…Viral genomic dsRNA sequences were determined using two approaches: conventional complimentary DNA (cDNA) library construction using purified viral dsRNA and subsequent Sanger sequencing (Chiba et al, 2016 ), and next-generation high-throughput sequencing (NGS) of total RNA from fractions obtained from infected mycelia (Shamsi et al, 2019 ). dsRNA was isolated from mycelia cultured in PDB media for 1 week as previously described (Chiba et al, 2013a ).…”

Section: Methodsmentioning

confidence: 99%

Diverse Partitiviruses From the Phytopathogenic Fungus, Rosellinia necatrix

et al. 2020

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Partitiviruses (dsRNA viruses, family Partitiviridae) are ubiquitously detected in plants and fungi. Although previous surveys suggested their omnipresence in the white root rot fungus, Rosellinia necatrix, only a few of them have been molecularly and biologically characterized thus far. We report the characterization of a total of 20 partitiviruses from 16 R. necatrix strains belonging to 15 new species, for which "Rosellinia necatrix partitivirus 11-Rosellinia necatrix partitivirus 25" were proposed, and 5 previously reported species. The newly identified partitiviruses have been taxonomically placed in two genera, Alphapartitivirus, and Betapartitivirus. Some partitiviruses were transfected into reference strains of the natural host, R. necatrix, and an experimental host, Cryphonectria parasitica, using purified virions. A comparative analysis of resultant transfectants revealed interesting differences and similarities between the RNA accumulation and symptom induction patterns of R. necatrix and C. parasitica. Other interesting findings include the identification of a probable reassortment event and a quintuple partitivirus infection of a single fungal strain. These combined results provide a foundation for further studies aimed at elucidating mechanisms that underly the differences observed.

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Section: Methodsmentioning

confidence: 99%

Diverse Partitiviruses From the Phytopathogenic Fungus, Rosellinia necatrix

et al. 2020

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“…Viral particles were purified as described by Shamsi et al [43]. This preparation was used for molecular analysis, transfection, and electron microscopy.…”

Section: Methodsmentioning

confidence: 99%

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

Jamal

Sato

Shahi

et al. 2019

Viruses

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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.

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“…The complete genome sequence of PjPmV1 was determined by next-generation sequencing (NGS) and Sanger sequencing. We performed NGS (HiSeq 2500, Illumina, Inc.) as previously described (Jamal et al, 2019;Shamsi et al, 2019). For NGS, we submitted a mixed dsRNA preparation (called "pool A1") from three fungal strains including P. janthinellum strain A58 and Alternaria alternata strain A16 (Jamal et al, 2019).…”

Section: Extraction Sequencing and Northern Hybridization Of Dsrnamentioning

confidence: 99%

“…A novel five-segmented polymycovirus, named Penicillium janthinellum polymycovirus 1 (PjPmV1), was discovered from one of fungal strains collected in Pakistan as previously described (Jamal et al, 2019;Shamsi et al, 2019;Sato et al, 2020). The host fungal strain A58 was identified as Penicillium species P. janthinellum based on the ITS sequence (see Materials and Methods).…”

Section: Molecular Characterization Of Pjpmv1mentioning

confidence: 99%

Molecular Characterization of a Novel Polymycovirus From Penicillium janthinellum With a Focus on Its Genome-Associated PASrp

et al. 2020

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The genus Polymycovirus of the family Polymycoviridae accommodates fungal RNA viruses with different genomic segment numbers (four, five, or eight). It is suggested that four members form no true capsids and one forms filamentous virus particles enclosing double-stranded RNA (dsRNA). In both cases, viral dsRNA is associated with a viral protein termed "proline-alanine-serine-rich protein" (PASrp). These forms are assumed to be the infectious entity. However, the detailed molecular characteristics of PASrps remain unclear. Here, we identified a novel five-segmented polymycovirus, Penicillium janthinellum polymycovirus 1 (PjPmV1), and characterized its purified fraction form in detail. The PjPmV1 had five dsRNA segments associated with PASrp. Density gradient ultracentrifugation of the PASrp-associated PjPmV1 dsRNA revealed its uneven structure and a broad fractionation profile distinct from that of typical encapsidated viruses. Moreover, PjPmV1-PASrp interacted in vitro with various nucleic acids in a sequence-non-specific manner. These PjPmV1 features are discussed in view of the diversification of genomic segment numbers of the genus Polymycovirus.

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Molecular and biological characterization of a novel botybirnavirus identified from a Pakistani isolate of Alternaria alternata

Cited by 26 publications

References 58 publications

Diverse Partitiviruses From the Phytopathogenic Fungus, Rosellinia necatrix

Diverse Partitiviruses From the Phytopathogenic Fungus, Rosellinia necatrix

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

Molecular Characterization of a Novel Polymycovirus From Penicillium janthinellum With a Focus on Its Genome-Associated PASrp

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