Abstract

Pseudorabies virus (PRV) belongs to the Alphaherpesvirinae subfamily of Herpesviridae. PRV-induced pseudorabies is a highly contagious disease that has caused huge economic losses to the global swine industry. The PRV gE/gI gene deletion vaccine strain (Fa ΔgE/gI strain) constructed from the PRV Fa wild-type strain was shown to have a protective effect against infection. However, the interaction between PRV gE/gI genes and host miRNA needs further exploration, and little is known about the regulatory mechanisms of non-coding RNAs during PRV infection. miRNAs play a key regulatory role in viral infection and immune responses, so we analyzed the differential expression of miRNAs induced by the PRV Fa ΔgE/gI strain and Fa wild-type strain in the PK15 cell line. High-throughput sequencing reads were aligned to known Sus scrofa pre-miRNAs in the miRBase database. Target genes of differentially expressed miRNAs were predicted using the miRGen 3.0 database, then filtered miRNA target genes were subjected to Gene Ontology (GO) analysis and Search Tool for the Retrieval of Interacting Genes/ Proteins (STRING) analysis. Stem-loop quantitative real-time PCR was performed to confirm the accuracy of high-throughput sequencing data. In total, 387, 472, and 490 annotated and novel mature miRNAs were identified from PRV Fa ΔgE/gI strain-infected, Fa wild-type strain-infected, and non-infected PK-15 cells, respectively. Five PRV-encoded miRNAs were also identified. GO analysis showed that target genes of differentially expressed miRNAs in PRV Fa ΔgE/gI strain-infected and Fa wild-type strain-infected PK-15 cells were mainly involved in biological regulation and metabolic processes. STRING analysis showed that immune-related target genes of differentially expressed miRNAs in the Toll-like receptor signaling pathway, B cell receptor signaling pathway, T cell receptor signaling pathway, nuclear factor-κB signaling pathway, and transforming growth factor-β signaling pathway were interrelated. This is the first report of the small RNA transcriptome in PRV mutant wild-type strain-infected and Fa ΔgE/gI strain-infected porcine cell lines. Our findings will contribute to the prevention and treatment of PRV mutant strains.

Highlights

  • Pseudorabies virus (PRV) is a member of the Alphaherpesvirinae subfamily of the Herpesviridae family

  • The analysis of adapter-trimmed reads in small (s) RNAsequencing libraries showed that the lengths of sRNAs were concentrated around 21–24 nt (Fig. 1, Fig. S1), miRNA expression was significantly suppressed under PRV infection (Table 2)

  • We found that 2.6% (10/387) of miRNAs accounted for 72.5% of total miRNA expression in PRV Fa wild-type strain-infected PK-15 cells, while 2.1% (10/472) of miRNAs accounted for 75.5% of total miRNA expression in PRV Fa ΔgE/gI strain-infected PK-15 cells

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Summary

Introduction

Pseudorabies virus (PRV) is a member of the Alphaherpesvirinae subfamily of the Herpesviridae family. It is a double-stranded linear DNA virus with a 150 kb genome that encodes approximately 100 proteins. All strains and ages of pigs are susceptible to PRV, as well as a variety of domestic and wild animals. PRV spreads throughout the respiratory and reproductive systems, and PRV-infected pigs and mice are the main sources of infection [6]. PRV mutant strains cause severe respiratory symptoms in adult pigs, and cause reproductive failure in boar [7,8,9,10,11,12,13]

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