A novel chimeric RNA originating from BmCPV S4 and Bombyx mori HDAC11 transcripts regulates virus proliferation.

Polymerases encoded by segmented negative-strand RNA viruses cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching") to generate chimeric RNA, and trans-splicing occurs between viral and cellular transcripts. Bombyx mori cytoplasmic polyhedrosis virus (BmCPV), an RNA virus belonging to Reoviridae, is a major pathogen of silkworm (B. mori). The genome of BmCPV consists of 10 segmented double-stranded RNAs (S1-S10) from which viral RNAs encoding a protein are transcribed. In this study, chimeric silkworm-BmCPV RNAs, in which the sequence derived from the silkworm transcript could fuse with both the 5' end and the 3' end of viral RNA, were identified in the midgut of BmCPV-infected silkworms by RNA_seq and further confirmed by RT-PCR and Sanger sequencing. A novel chimeric RNA, HDAC11-S4 RNA 4, derived from silkworm histone deacetylase 11 (HDAC11) and the BmCPV S4 transcript encoding viral structural protein 4 (VP4), was selected for validation by in situ hybridization and Northern blotting. Interestingly, our results indicated that HDAC11-S4 RNA 4 was generated in a BmCPV RNA-dependent RNA polymerase (RdRp)-independent manner and could be translated into a truncated BmCPV VP4 with a silkworm HDAC11-derived N-terminal extension. Moreover, it was confirmed that HDAC11-S4 RNA 4 inhibited BmCPV proliferation, decreased the level of H3K9me3 and increased the level of H3K9ac. These results indicated that during infection with BmCPV, a novel mechanism, different from that described in previous reports, allows the genesis of chimeric silkworm-BmCPV RNAs with biological functions.

BmCPV replication is suppressed by the activation of the NF-κB/autophagy pathway through the interaction of vsp21 translated by vcircRNA_000048 with ubiquitin carboxyl-terminal hydrolase.

Bombyx mori cypovirus (BmCPV), a typical double-stranded RNA virus, was demonstrated to generate a viral circRNA, vcircRNA_000048, which encodes a vsp21 with 21 amino acid residues to suppress viral replication. However, the regulatory mechanism of vsp21 on virus infection remained unclear. This study discovered that vsp21 induces reactive oxygen species (ROS) generation, activates autophagy, and attenuates virus replication by inducing autophagy. Then we confirmed that the effect of vsp21-induced autophagy on viral replication was attributed to the activation of the NF-κB signaling pathway. Furthermore, we clarified that vsp21 interacted with ubiquitin carboxyl-terminal hydrolase (UCH) and that ubiquitination and degradation of phospho-IκB-α were enhanced by vsp21 via competitive binding to UCH. Finally, we validated that vsp21 activates the NF-κB/autophagy pathway to suppress viral replication by interacting with UCH. These findings provided new insights into regulating viral multiplication and reovirus-host interaction.

Identification and characterization of extrachromosomal circular DNA in the silk gland of Bombyx mori.

The silk gland cells of silkworm are special cells which only replicate DNA in the nucleus without cell division throughout the larval stage. The extrachromosomal circular DNAs (eccDNAs) have not yet been reported in the silk gland of silkworms. Herein, we have explored the characterization of eccDNAs in the posterior silk gland of silkworms. A total of 35 346 eccDNAs were identified with sizes ranging from 30 to 13 569 549 bp. Motif analysis revealed that dual direct repeats are flanking the 5' and 3' breaking points of eccDNA. The sequences exceeding 1 kb length in eccDNAs present palindromic sequence characteristics flanking the 5' and 3' breaking points of the eccDNA. These motifs might support possible models for eccDNA generation. Genomic annotation of the eccDNA population revealed that most eccDNAs (58.6%) were derived from intergenic regions, whereas full or partial genes were carried by 41.4% of eccDNAs. It was found that silk protein genes fib-H, fib-L, and P25, as well as the transcription factors SGF and sage, which play an important regulatory role in silk protein synthesis, could be carried by eccDNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses showed that the genes carried by eccDNAs were mainly associated with the development and metabolism-related signaling pathways. Moreover, it was found that eccDNAfib-L could promote the transcription of fib-L gene. Overall, the results of the present study not only provide a novel perspective on the mechanism of silk gland development and silk protein synthesis but also complement previously reported genome-scale eccDNA data supporting that eccDNAs are common in eukaryotes.

BmNPV circular RNA-encoded peptide VSP39 promotes viral replication.

CircRNAs are covalently closed single-stranded circular RNA molecules, which are not easily degraded by endonucleases and play vital roles in many biological processes. Currently, most studies on circRNAs focus on endogenous circRNAs in cells, and there are few studies on virus-encoded circRNAs. In this study, a viral circRNA (circRNA-000010) derived from the region (-/bp: 114514-115,319) of the complementary strand of Bombyx mori Nucleopolyhedrovirus (BmNPV) genome was identified with the circRNA-sequencing. The authenticity of viral circRNA-000010 was further confirmed by reverse transcription PCR, reverse transcription-rolling circle amplification (TCA), in situ hybridization, immunofluorescent staining, and Northern blotting. The results of overexpression and knockdown experiments showed that circRNA-000010 promoted viral replication. Furthermore, a viral small peptide VSP39 with 39 amino acid residues translated by circRNA-000010 but not its linear molecule was confirmed. Finally, VSP39 was found to promote viral replication. Our findings indicated that a viral circRNA encoded by BmNPV promoted viral replication. These findings will provide new clues for further understanding coding information of the BmNPV genome and open a new insight for investigating host-virus interactions.

Interaction between Bombyx mori Cytoplasmic Polyhedrosis Virus NSP8 and BmAgo2 Inhibits RNA Interference and Enhances Virus Proliferation.

Some insect viruses encode suppressors of RNA interference (RNAi) to counteract the antiviral RNAi pathway. However, it is unknown whether Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) encodes an RNAi suppressor. In this study, the presence of viral small interfering RNA (vsiRNA) in BmN cells infected with BmCPV was confirmed by small RNA sequencing. The Dual-Luciferase reporter test demonstrated that BmCPV infection may prevent firefly luciferase (Luc) gene silencing caused by particular short RNA. It was also established that the inhibition relied on the nonstructural protein NSP8, which suggests that NSP8 was a possible RNAi suppressor. In cultured BmN cells, the expressions of viral structural protein 1 (vp1) and NSP9 were triggered by overexpression of nsp8, suggesting that BmCPV proliferation was enhanced by NSP8. A pulldown assay was conducted with BmCPV genomic double-stranded RNA (dsRNA) labeled with biotin. The mass spectral detection of NSP8 in the pulldown complex suggests that NSP8 is capable of direct binding to BmCPV genomic dsRNA. The colocalization of NSP8 and B. mori Argonaute 2 (BmAgo2) was detected by an immunofluorescence assay, leading to the hypothesis that NSP8 interacts with BmAgo2. Coimmunoprecipitation further supported the present investigation. Moreover, vasa intronic protein, a component of RNA-induced silencing complex (RISC), could be detected in the coprecipitation complex of NSP8 by mass spectrum analysis. NSP8 and the mRNA decapping protein (Dcp2) were also discovered to colocalize to processing bodies (P bodies) for RNAi-mediated gene silencing in Saccharomyces cerevisiae. These findings revealed that by interacting with BmAgo2 and suppressing RNAi, NSP8 promoted BmCPV growth. IMPORTANCE It has been reported that the RNAi pathway is inhibited by binding RNAi suppressors encoded by some insect-specific viruses belonging to Dicistroviridae, Nodaviridae, or Birnaviridae to dsRNAs to protect dsRNAs from being cut by Dicer-2. However, it is unknown whether BmCPV, belonging to Spinareoviridae, encodes an RNAi suppressor. In this study, we found that nonstructural protein NSP8 encoded by BmCPV inhibits small interfering RNA (siRNA)-induced RNAi and that NSP8, as an RNAi suppressor, can bind to viral dsRNAs and interact with BmAgo2. Moreover, vasa intronic protein, a component of RISC, was found to interact with NSP8. Heterologously expressed NSP8 and Dcp2 were colocalized to P bodies in yeast. These results indicated that NSP8 promoted BmCPV proliferation by binding itself to BmCPV genomic dsRNAs and interacting with BmAgo2 through suppression of siRNA-induced RNAi. Our findings deepen our understanding of the game between BmCPV and silkworm in regulating viral infection.

BmCPV-Derived Circular DNA vcDNA-S7 Mediated by Bombyx mori Reverse Transcriptase (RT) Regulates BmCPV Infection.

Circular DNAs derived from single-stranded RNA viruses play important roles in counteracting viral infection. However, whether double-stranded RNA viruses generate functional circular DNAs is still unknown. Using circDNA sequencing, divergent PCR, DNA in situ hybridization and rolling circular amplification, we presently confirmed that in silkworm, Bombyx mori cytoplasmic polyhedrosis virus (BmCPV), a double-stranded RNA virus belonging to cypovirus, is prone to produce a BmCPV-derived circular DNA termed as vcDNA-S7. We have also found that vcDNA-S7 formation is mediated by endogenous reverse transcriptase (RT), and the proliferation of BmCPV can be inhibited by vcDNA-S7 in vitro and in vivo. Moreover, we have discovered that the silkworm RNAi immune pathway is activated by vcDNA-S7, while viral small interfering RNAs (vsiRNAs) derived from transcribed RNA by vcDNA-S7 can be detected by small RNA deep sequencing. These results suggest that BmCPV-derived vcDNA-S7, mediated by RT, can serve as a template for the biogenesis of antiviral siRNAs, which may lead to the repression of BmCPV infection. To our knowledge, this is the first demonstration that a circular DNA, produced by double stranded RNA viruses, is capable of regulating virus infection.