Two mutually exclusive evolutionary scenarios for allexiviruses that overcome host RNA silencing and autophagy by regulating viral CRP expression

Abstract

The genus Allexivirus currently includes eight virus species that infect allium plants. Previously, we showed that there are two distinct groups of allexiviruses (deletion [D]-type and insertion [I]-type) based on the presence or absence of a 10- to 20-base insert (IS) between the coat protein (CP) and cysteine rich protein (CRP) genes. In the present study of CRPs to analyze their functions, we postulated that evolution of allexiviruses may have been largely directed by CRPs and thus proposed two evolutionary scenarios for allexiviruses based mainly on the presence or absence of IS and determined by how the allexiviruses challenge host resistance mechanisms (RNA silencing and autophagy). We found that both CP and CRP are RNA silencing suppressors (RSS), that they can inhibit each other’s RSS activity in the cytoplasm, and that CRP becomes a target of host autophagy in the cytoplasm but not CP. To mitigate CRP interference with CP, and to increase the CP’s RSS activity, allexiviruses developed two strategies: confinement of D-type CRP in the nucleus and degradation of I-type CRP by autophagy in the cytoplasm. Here, we demonstrate that viruses of the same genus achieve two completely different evolutionary scenarios by controlling expression and subcellular localization of CRP.

Mutation of the allexivirus-specific P40 gene of Wineberry latent virus, an isolate of Blackberry virus E, greatly reduces virus multiplication

“…WLV, and other allexiviruses including Papaya virus A, Alfalfa virus S and Arachis pintoi virus, encode similar ORFs 1 to 5 but do not encode the ORF6 (CRP). Using a recently described infectious cDNA clone of Garlic virus C both the CRP and CP were shown to act as competing suppressors of RNA silencing (Kim et al, 2023). The only previously documented study of the allexivirus-specific P40 protein in WLV) used an infectious clone of Shallot virus X, a CRPencoding allexivirus, in sugar beet protoplasts (Vishnishenko et al, 2000;2002).…”

Selective autophagy receptor‐encoding sequences in shallot transcriptome: In silico identification and expression patterns in response to asymptomatic shallot virus X infection

“…In garlic (Allexi)virus X (GarVX) infection, selective autophagic degradation in the cytoplasm occurs with one of the two viral RNA silencing suppressors (RSS) identified in this pathosystem, namely, the cysteine‐rich protein (CRP), but not the capsid protein (CP) (Kim et al., 2023). SARs that determine the selectivity of autophagic degradation of different allexiviral proteins were not identified in this study.…”

An Inexpensive System for Rapid and Accurate On-site Detection of Garlic-Infected Viruses by Agarose Gel Electrophoresis Followed by Array Assay

“…In particular, monitoring for allexiviruses that infect garlic plants in the field is difficult. Seven species of allexiviruses have been currently reported and are characterized by relatively low homology even among isolates of the same species ( Kim et al, 2023 ). In the laboratory, these garlic viruses are mainly diagnosed using an enzyme-linked immunosorbent assay or reverse transcription polymerase chain reaction (RT-PCR) for each virus; for simultaneous detection of the three viruses (LYSV, OYDV, and allexiviruses), multiplex RT-PCR has been reported ( Hu et al, 2015 ; Majumder and Baranwal, 2014 ; Nam et al, 2015 ; Park et al, 2005 ).…”

“…In the laboratory, these garlic viruses are mainly diagnosed using an enzyme-linked immunosorbent assay or reverse transcription polymerase chain reaction (RT-PCR) for each virus; for simultaneous detection of the three viruses (LYSV, OYDV, and allexiviruses), multiplex RT-PCR has been reported ( Hu et al, 2015 ; Majumder and Baranwal, 2014 ; Nam et al, 2015 ; Park et al, 2005 ). However, the nucleotide sequence diversity of the viruses infecting garlic in different regions is considerable ( Kawakubo et al, 2023 ; Kim et al, 2023 ). Although allexiviruses have been detected by RT-PCR in some reports ( Chen et al, 2004 ), often they cannot be similarly detected in garlic plants in other countries using the conditions described ( Kim et al, 2023 ).…”

“…However, the nucleotide sequence diversity of the viruses infecting garlic in different regions is considerable ( Kawakubo et al, 2023 ; Kim et al, 2023 ). Although allexiviruses have been detected by RT-PCR in some reports ( Chen et al, 2004 ), often they cannot be similarly detected in garlic plants in other countries using the conditions described ( Kim et al, 2023 ). Consequently, the nucleotide sequences of isolates in the region need to be checked, and the conditions for the multiplex RT-PCR designed for each isolate should be determined.…”