Gene Variations in Cis-Acting Elements between the Taiwan and Prototype Strains of Porcine Epidemic Diarrhea Virus Alter Viral Gene Expression.

Tsung-Lin Tsai,Ching-Chi Hsieh,Hui-Wen Chang,Ching-Houng Lin,Chen-Chang Su,Hung-Yi Wu,Chao-Nan Lin,Chen-Yu Lo

doi:10.3390/genes9120591

Abstract

In 2013, the outbreak of porcine epidemic diarrhea (PED) in Taiwan caused serious economic losses. In this study, we examined whether the variations of the cis-acting elements between the porcine epidemic diarrhea virus (PEDV) Taiwan (TW) strain and the prototype strain CV777 alter gene expression. For this aim, we analyzed the variations of the cis-acting elements in the 5′ and 3′ untranslated regions (UTRs) between the PEDV TW, CV777, and other reference strains. We also determined the previously unidentified transcription regulatory sequence (TRS), a sequence motif required for coronavirus transcription, and found that a nucleotide deletion in the TW strain, in comparison with CV777 strain, immediately downstream of the leader core sequence alters the identity between the leader TRS and the body TRS. Functional analyses using coronavirus defective interfering (DI) RNA revealed that such variations in cis-acting elements for the TW strain compared with the CV777 strain have an influence on the efficiency of gene expression. The current data show for the first time the evolution of PEDV in terms of cis-acting elements and their effects on gene expression, and thus may contribute to our understanding of recent PED outbreaks worldwide.

Highlights

Porcine epidemic diarrhea virus (PEDV) belongs to the genus Alphacoronavirus of subfamilyCoronavirinae, which is in the family Coronaviridae, order Nidovirales [1,2]
To understand whether the sequences for the 50 terminal genome region of other porcine epidemic diarrhea virus (PEDV) strains are altered, the reference strains were selected from GenBank based on the viruses that have been circulating in different countries in recent years (2012–2015) and compared
We found variations in cis-acting elements in the 50 and 30 untranslated regions (UTRs) between the PEDV

Summary

Introduction

Porcine epidemic diarrhea virus (PEDV) belongs to the genus Alphacoronavirus of subfamilyCoronavirinae, which is in the family Coronaviridae, order Nidovirales [1,2]. RNA elements in the 50 and 30 untranslated regions (UTRs) that are important for coronaviral gene expression are collectively referred to as cis-acting RNA elements [4]. Analyses of Alphacoronavirus 50 UTRs have revealed four conserved RNA secondary structures, including stem-loops (SLs) 1, 2, 4, and 5, which are conserved for Betacoronavirus [4,7]. Studies in Betacoronavirus have determined a requirement of these 50 secondary structures for coronaviral RNA synthesis [8]. RNA structures and their functions in coronaviral RNA synthesis and pathogenesis have been identified in Betacoronavirus 30 UTRs, including the 50 -most bulged stem-loop (BSL) [9,10], hair-pin pseudoknot (PK) [11], and 30 -most hypervariable region (HVR) [12]

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Conclusion