A novel weevil-transmitted tymovirus found in mixed infection on hollyhock

Mahillon, Mathieu; Brodard, Justine; Kellenberger, Isabelle; Blouin, Arnaud; Schumpp, Olivier

doi:10.1186/s12985-023-01976-6

Cited by 6 publications

(5 citation statements)

References 65 publications

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“…The supernatant was then collected and placed on 5 ml of 20 % sucrose cushion (diluted in 0.1 M Tris, pH 8.2) followed by centrifugation at 150000 g using a Beckman Coulter 45Ti rotor for 1.5 h. The resulting pellet was incubated overnight at 4 °C in 1 ml of suspension buffer (0.02 M Tris, pH 7.0, 0.001 M MgCl 2 ). Enrichment in viral particles was verified by electron microscopy using 3 µl of particles as previously described [ 22 ], using the Tecnai G2 Spirit microscope (FEI, Eindhoven).…”

Section: Methodsmentioning

confidence: 99%

New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus

Jaccard

Dubuis

Kellenberger

et al. 2023

Journal of General Virology

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Despite the fact that Cladosporium sp. are ubiquitous fungi, their viromes have been little studied. By analysing a collection of Cladosporium fungi, two new partitiviruses named Cladosporium cladosporioides partitivirus 1 (CcPV1) and Cladosporium cladosporioides partitivirus 2 (CcPV2) co-infecting a strain of Cladosporium cladosporioides were identified. Their complete genome consists of two monocistronic dsRNA segments (RNA1 and RNA2) with a high percentage of pairwise identity on 5′ and 3′ end. The RNA directed RNA polymerase (RdRp) of both viruses and the capsid protein (CP) of CcPV1 display the classic characteristics required for their assignment to the Gammapartitivirus genus. In contrast, CcPV2 RNA2 encodes for a 41 KDa CP that is unusually smaller when aligned to CPs of other viruses classified in this genus. The structural role of this protein is confirmed by electrophoresis on acrylamide gel of purified viral particles. Despite the low percentage of identity between the capsid proteins of CcPV1 and CcPV2, their three-dimensional structures predicted by AlphaFold2 show strong similarities and confirm functional proximity. Fifteen similar viral sequences of unknown function were annotated using the CcPV2 CP sequence. The phylogeny of the CP was highly consistent with the phylogeny of their corresponding RdRp, supporting the organization of Gammapartitiviruses into three distinct clades despite stretching the current demarcation criteria. It is proposed that a new subgenus be created within the genus Gammapartitivirus for this new group.

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Section: Methodsmentioning

confidence: 99%

New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus

Jaccard

Dubuis

Kellenberger

et al. 2023

Journal of General Virology

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“…TYMV P69 has been shown to be essential for virus spread and affects symptom severity in infected plants but is dispensable for virus replication in single cells [51][52][53]. In MP proteins of viruses in the Tymovirus genus, the N-terminal region is more conserved than the C-terminal part and contains several conserved sequence motifs including blocks of positively charged amino acids [54].…”

Section: Family Tymoviridaementioning

confidence: 99%

Role of Plant Virus Movement Proteins in Suppression of Host RNAi Defense

Atabekova

Solovieva

Chergintsev

et al. 2023

IJMS

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One of the systems of plant defense against viral infection is RNA silencing, or RNA interference (RNAi), in which small RNAs derived from viral genomic RNAs and/or mRNAs serve as guides to target an Argonaute nuclease (AGO) to virus-specific RNAs. Complementary base pairing between the small interfering RNA incorporated into the AGO-based protein complex and viral RNA results in the target cleavage or translational repression. As a counter-defensive strategy, viruses have evolved to acquire viral silencing suppressors (VSRs) to inhibit the host plant RNAi pathway. Plant virus VSR proteins use multiple mechanisms to inhibit silencing. VSRs are often multifunctional proteins that perform additional functions in the virus infection cycle, particularly, cell-to-cell movement, genome encapsidation, or replication. This paper summarizes the available data on the proteins with dual VSR/movement protein activity used by plant viruses of nine orders to override the protective silencing response and reviews the different molecular mechanisms employed by these proteins to suppress RNAi.

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“…The pellet was resuspended in 50 µl of borate buffer. Particles were then observed by transmission electron microscopy (TEM) with the Tecnai G2 electron microscope, as previously described (Mahillon et al, 2023).…”

Section: Virions Semi-puri Cationmentioning

confidence: 99%

“…Reads coverages were determined using Bowtie2 (Langmead and Salzberg, 2012) and Samtools (Danecek et al, 2021). The viral termini were obtained by Sanger sequencing, as follows: the 5'-termini were ampli ed using the SMARTer RACE 5'/3' kit (Takara), and the 3'-termini were ampli ed using an oligo-dT in combination with speci c viral primers (Table S1), as previously described (Mahillon et al, 2023).…”

Section: Rna Isolation and Illumina Sequencingmentioning

confidence: 99%

A mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike

Mahillon,

Brodard,

Dubuis

et al. 2023

Preprint

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Background: In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues. Method: Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridaewere identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the newly-identified phytoviral ITPases were investigated. Results: While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinaegenus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. Strikingly, the endogenous ITPase of M. perennis is predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This particular subcellular localization is in line with the idea that the plant nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules. Conclusion: Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.

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A novel weevil-transmitted tymovirus found in mixed infection on hollyhock

Cited by 6 publications

References 65 publications

New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus

New viruses of Cladosporium sp. expand considerably the taxonomic structure of Gammapartitivirus genus

Role of Plant Virus Movement Proteins in Suppression of Host RNAi Defense

A mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike

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