Lnc557 promotes Bombyx mori nucleopolyhedrovirus replication by interacting with BmELAVL1 to enhance its stability and expression

Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen that threatens the growth and sustainability of the sericultural industry. Currently, accumulated studies showed that long non-coding RNAs (lncRNAs) play important roles in the genesis and progression of various viruses and host-pathogens interactions. However, the functions and regulatory mechanisms of lncRNAs in insect-virus interaction are still limited. In this study, transcriptome sequencing and ribosome profiling sequencing (Ribo-seq) were performed in the BmNPV-infected midgut and control tissue, and a total of 9 differentially expressed (DE) lncRNAs and 27 small ORFs (sORFs) with micropeptide coding potential were identified. Among them, lncRNA XR_001139971.3 (lnc557) is verified to be significantly up-regulated upon BmNPV infection and may have the potential to encode a small peptide (ORF-674). The subcellular localization experiment showed that lnc557 was expressed in the cytoplasm. Overexpression of lnc557 promotes BmNPV replication and vice versa. By combining RNA pull-down, mass spectrometry, protein truncation and RNA immunoprecipitation (RIP) assays, we confirmed that lnc557 can bind to the RRM-5 domain of BmELAVL1 protein. Subsequently, we found that lnc557 could promote the expression of BmELAVL1 by enhancing the stability of BmELAVL1. Further, enhancing the expression of BmELAVL1 can promote the proliferation of BmNPV, while knockdown shows the opposite effect. Our data suggest that lnc557-mediated BmELAVL1 expression enhancement could play a positive role in BmNPV replication, which will provide a new insight into the molecular mechanism of interaction between Bombyx mori and virus. The speculated mechanism diagram of lnc557 function in BmNPV proliferation. The speculated mechanism diagram of lnc557 function in BmNPV proliferation. During BmNPV infection, lnc557 expression was increased and it interacted with the RRM-5 domain of BmELAVL1, which stablized the expression of BmELAVL1. BmELAVL1 can promote the proliferation of BmNPV. [Display omitted] •51 differentially expressed sORF in BmNPV-infected midgut of silkworm were identified by Ribo-seq.•3 DE sORFs in silkworm were identified to be have coding potential.•Both lnc557 and BmELAVL1 can promote the proliferation of BmNPV.•Lnc557 could bind to the RRM-5 domain of BmELAVL1 and promoted BmELAVL1 expression by enhancing the stability of BmELAVL1.•Lnc557 promotes BmNPV replication by interacting with BmELAVL1.