Plant and animal positive-sense single-stranded RNA viruses encode small proteins important for viral infection in their negative-sense strand

A novel peptide encoded by a rice circular RNA confers broad-spectrum disease resistance in rice plants

Circular RNAs (circRNAs) are a significant class of endogenous RNAs that exert crucial biological functions in human and animal systems, but little is currently understood regarding their roles in plants. Here, we identified a circRNA originating from the back-splicing of exon 4 and exon 5 of a rice gene, OsWRKY9, and named it circ-WRKY9. It is upregulated in rice stripe mosaic virus (RSMV)-infected rice plants. Notably, circ-WRKY9 contains two open reading frames with an internal ribosome entry site. We found that circ-WRKY9 encoded a peptide of 88 amino acids (aa) and named it WRKY9-88aa. Overexpression of WRKY9-88aa suppresses RSMV infection in rice plants, with increased reactive oxygen species production. Furthermore, WRKY9-88aa enhances resistance to blast disease and bacterial leaf blight, suggesting its potential to provide broad-spectrum disease resistance. Our findings provide the first evidence of a peptide encoded by a circRNA in planta and highlight its potential application to control a wide spectrum of plant diseases.

A conserved lysine/arginine-rich motif is essential for the autophagic degradation of potyviral 6K1 protein and virus infection

Potyviruses possess one positive-sense single-stranded RNA genome, mainly dependent on polyprotein processing as the expression strategy. The resulting polyproteins are proteolytically processed by three virus-encoded proteases into 11 or 12 mature proteins. One such factor, 6 kDa peptide 1 (6K1), is an understudied viral factor. Its function in viral infection remains largely mysterious. This study is to reveal part of its roles by using pepper veinal mottle virus (PVMV) as the model. Alanine substitution screening analysis revealed that 15 of 17 conserved residues across potyviral 6K1 sequences are essential for PVMV infection. However, 6K1 protein is less accumulated in virus-infected cells, although P3-6K1 and 6K1-CI junctions are efficiently processed by NIa-Pro for its release, indicating that 6K1 undergoes a self-degradation event. Mutating the cleavage site to prevent NIa-Pro processing abolishes viral infection, suggesting that the generation of 6K1 along with its degradation might be important for viral multiplication. We corroborated that cellular autophagy is engaged in 6K1's degradation. Individual engineering of the 15 6K1 variants into PVMV allows their expression along with viral infection. Five of such variants, D30A, V32A, K34A, L36A, and L39A, significantly interfere with viral infection. The five residues are enclosed in a conserved lysine/arginine-rich motif; four of them appear crucial in engaging autophagy-mediated self-degradation. Based on these data, we envisaged a scenario which potyviral 6K1s interact with an unknown anti-viral component to be co-degraded by autophagy to promote viral infection.IMPORTANCEPotyvirus is the largest genus of plant-infecting RNA viruses, which encompasses socio-economically important virus species, such as Potato virus Y, Plum pox virus, and Soybean mosaic virus. Like all picorna-like viruses, potyviruses express their factors mainly via polyprotein processing. Theoretically, viral factors P3 through CP, including 6K1, should share an equivalent number of molecules. The 6K1 is small in size (~6 kDa) and conserved across potyviruses but less accumulated in virus-infected cells. This study demonstrates that cellular autophagy is engaged in the degradation of 6K1 to promote viral infection. In particular, we found a conserved lysine/arginine-rich motif in 6K1s across potyviruses that is engaged in this degradation event. This finding reveals one facet of a small protein that helps understand the pro-viral role of cellular autophagy in viral infection.

Recognition of novel proteins encoded by an aquareovirus using mass spectrometry

AQUAREOVIRUS: a genus of within the family Spinareoviridae, order Reovirales, infects aquatic animals. Their genomes comprise 11 segments of double-stranded RNA, which function directly as mRNAs upon release into the cytoplasm of infected cells. Here, liquid chromatography-tandem mass spectrometry was employed to annotate small coding ORFs in the Aquareovirus-C genome. Its plus-strand RNA of segment 8 (S8) contains a novel protein-coding frame (NS15), and S5 seems to has an additional reading frame (NS18) with a putative non-AUG initiation codon. Among them, NS15 polypeptide has been proved by immunoblotting assay. Remarkably, the S4 and S11 minus-strand mRNAs may encode polypeptides, suggesting ambisense polarity of the two segmented RNAs. And the newly discovered NS12 ORF in 2019, from viral tricistronic S7 mRNA, was also confirmed by this mass-spectrometry data. Taken together, these identified new ORFs reveal the genome-coding complexity of Aquareovirus-C.

3C-like proteases at the interface of plant-virus-vector interactions: Focus on potyvirid NIa proteases and secovirid proteases

Plant viruses of the families Potyviridae and Secoviridae encode 3C-like proteases (3CLpro) that are related to picornavirus 3C proteases. This review discusses recent advances in deciphering the multifunctional activities of plant virus 3CLpro. These proteases regulate viral polyprotein processing and facilitate virus replication. They are also determinants of host range, virulence, symptomatology and super-infection exclusion in some plant-virus interactions and facilitate aphid transmission. Potyvirid NIa-Pro proteases interact with host factors to interfere with a variety of defense mechanisms: salicylic acid-dependent signaling, ethylene-dependent signaling, transcriptional gene silencing and RNA decay. Potyvirid NIa-Pro also cleave host proteins at signature cleavage sites, although the biological impact of these cleavage remains to be determined. Recently, a plant defense mechanism was uncovered that inhibits the proteolytic activity of a comovirus 3CLpro. Future perspectives are discussed including using proteomic and degradomic techniques to elucidate the network of interactions of plant virus 3CLpro with the host proteome.

Characterizing the impact of CPSF30 gene disruption on TuMV infection in Arabidopsis thaliana

CPSF30, a key polyadenylation factor, also serves as an m6A reader, playing a crucial role in determining RNA fate post-transcription. While its homologs mammals are known to be vital for viral replication and immune evasion, the full scope of CPSF30 in plant, particular in viral regulation, remains less explored. Our study demonstrates that CPSF30 significantly facilitates the infection of turnip mosaic virus (TuMV) in Arabidopsis thaliana, as evidenced by infection experiments on the engineered cpsf30 mutant. Among the two isoforms, CPSF30-L, which were characterized with m6A binding activity, emerged as the primary isoform responding to TuMV infection. Analysis of m6A components revealed potential involvement of the m6A machinery in regulating TuMV infection. In contrast, CPSF30-S exhibited distinct subcellular localization, coalescing with P-body markers (AtDCP1 and AtDCP2) in cytoplasmic granules, suggesting divergent regulatory mechanisms between the isoforms. Furthermore, comprehensive mRNA-Seq and miRNA-Seq analysis of Col-0 and cpsf30 mutants revealed global transcriptional reprogramming, highlighting CPSF30's role in selectively modulating gene expression during TuMV infection. In conclusion, this research underscores CPSF30's critical role in the TuMV lifecycle and sets the stage for further exploration of its function in plant viral regulation.

The Molecular Maze of Potyviral and Host Protein Interactions

The negative effects of potyvirus diseases on the agricultural industry are extensive and global. Understanding how protein-protein interactions contribute to potyviral infections is imperative to developing resistant varieties that help counter the threat potyviruses pose. While many protein-protein interactions have been reported, only a fraction are essential for potyviral infection. Accumulating evidence demonstrates that potyviral infection processes are interconnected. For instance, the interaction between the eukaryotic initiation factor 4E (eIF4E) and viral protein genome-linked (VPg) is crucial for both viral translation and protecting viral RNA (vRNA). Additionally, recent evidence for open reading frames on the reverse-sense vRNA and for nonequimolar expression of viral proteins has challenged the previous polyprotein expression model. These discoveries will surely reveal more about the potyviral protein interactome. In this review, we present a synthesis of the potyviral infection cycle and discuss influential past discoveries and recent work on protein-protein interactions in various infection processes.

Unveiling the viroporin arsenal in plant viruses: Implications for the future

Viroporins are small, hydrophobic viral proteins that modify cellular membranes to form tiny pores for influx of ions and small molecules. Previously, viroporins were identified exclusively in vertebrate viruses. Recent studies have shown that both plant-infecting positive-sense single-stranded (+ss) and negative-sense single-stranded (-ss) RNA viruses also encode functional viroporins. These seminal discoveries not only advance our understanding of the distribution and evolution of viroporins, but also open up a new field of plant virus research.

The 6-kilodalton peptide 1 in plant viruses of the family Potyviridae is a viroporin

Potyviridae, the largest family of plant RNA viruses, includes many important pathogens that significantly reduce the yields of many crops worldwide. In this study, we report that the 6-kilodalton peptide 1 (6K1), one of the least characterized potyviral proteins, is an endoplasmic reticulum-localized protein. AI-assisted structure modeling and biochemical assays suggest that 6K1 forms pentamers with a central hydrophobic tunnel, can increase the cell membrane permeability of Escherichia coli and Nicotiana benthamiana, and can conduct potassium in Saccharomyces cerevisiae. An infectivity assay showed that viral proliferation is inhibited by mutations that affect 6K1 multimerization. Moreover, the 6K1 or its homologous 7K proteins from other viruses of the Potyviridae family also have the ability to increase cell membrane permeability and transmembrane potassium conductance. Taken together, these data reveal that 6K1 and its homologous 7K proteins function as viroporins in viral infected cells.

Plant virology in the 21st century in China: Recent advances and future directions

Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.

The minus strand of positive-sense RNA viruses encodes small proteins

It is widely accepted that the minus strands of positive single-strand RNA (+ssRNA) viruses function as replication templates only. Gong et al. revealed that the minus strand of two unrelated +ssRNA viruses encodes proteins. This textbook-changing discovery calls for the reconsideration of the molecular mechanisms underlying the infection cycle of +ssRNA viruses.

ORF3c is expressed in SARS-CoV-2-infected cells and inhibits innate sensing by targeting MAVS

Most SARS-CoV-2 proteins are translated from subgenomic RNAs (sgRNAs). While the majority of these sgRNAs are monocistronic, some viral mRNAs encode more than one protein. One example is the ORF3a sgRNA that also encodes ORF3c, an enigmatic 41-amino-acid peptide. Here, we show that ORF3c is expressed in SARS-CoV-2-infected cells and suppresses RIG-I- and MDA5-mediated IFN-β induction. ORF3c interacts with the signaling adaptor MAVS, induces its C-terminal cleavage, and inhibits the interaction of RIG-I with MAVS. The immunosuppressive activity of ORF3c is conserved among members of the subgenus sarbecovirus, including SARS-CoV and coronaviruses isolated from bats. Notably, however, the SARS-CoV-2 delta and kappa variants harbor premature stop codons in ORF3c, demonstrating that this reading frame is not essential for efficient viral replication in vivo and is likely compensated by other viral proteins. In agreement with this, disruption of ORF3c does not significantly affect SARS-CoV-2 replication in CaCo-2, CaLu-3, or Rhinolophus alcyone cells. In summary, we here identify ORF3c as an immune evasion factor of SARS-CoV-2 that suppresses innate sensing in infected cells.