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Genes 2018, 9(12), 591; https://doi.org/10.3390/genes9120591

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

1
Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan
2
Division of Chest Medicine, Department of Internal Medicine, Chang Bing Show Chwan Memorial Hospital, Changhua 505, Taiwan
3
Department of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, Pingtung 91201, Taiwan
4
Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
T.-L. Tsai, C.-C. Su and C.-C. Hsieh are co-first authors.
*
Author to whom correspondence should be addressed.
Received: 19 October 2018 / Revised: 20 November 2018 / Accepted: 26 November 2018 / Published: 29 November 2018
(This article belongs to the Special Issue Viral Genes and the Host: Evolution in Action)
PDF [1839 KB, uploaded 29 November 2018]

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.
Keywords: porcine epidemic diarrhea virus; cis-acting element; gene evolution; gene expression; nucleotide composition porcine epidemic diarrhea virus; cis-acting element; gene evolution; gene expression; nucleotide composition
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Tsai, T.-L.; Su, C.-C.; Hsieh, C.-C.; Lin, C.-N.; Chang, H.-W.; Lo, C.-Y.; Lin, C.-H.; Wu, H.-Y. Gene Variations in Cis-Acting Elements between the Taiwan and Prototype Strains of Porcine Epidemic Diarrhea Virus Alter Viral Gene Expression. Genes 2018, 9, 591.

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