Scrapie susceptibility-associated indel polymorphism of shadow of prion protein gene (SPRN) in Korean native black goats

Yong-Chan Kim,Seon-Kwan Kim,Byung-Hoon Jeong

doi:10.1038/s41598-019-51625-8

Abstract

Prion diseases in sheep and goats are called scrapie and belong to a group of transmissible spongiform encephalopathies (TSEs) caused by the abnormal misfolding of the prion protein encoded by the prion protein gene (PRNP). The shadow of the prion protein gene (SPRN) is the only prion gene family member that shows a protein expression profile similar to that of the PRNP gene in the central nervous system. In addition, genetic susceptibility of the SPRN gene has been reported in variant Creutzfeldt–Jakob disease (CJD), bovine spongiform encephalopathy (BSE) and scrapie. However, genetic studies of the SPRN gene have not been carried out in Korean native black goats. Here, we investigated the genotype and allele frequencies of SPRN polymorphisms in 213 Korean native black goats and compared these polymorphisms with those previously reported for scrapie-affected animals. We found a total of 6 polymorphisms including 1 nonsynonymous single nucleotide polymorphism (SNP) and 1 synonymous SNP in the open reading frame (ORF) region and 3 SNPs and 1 indel polymorphism (c.495_496insCTCCC) in the 3′ untranslated region (UTR) by direct DNA sequencing. A significant difference in the allele frequency of the c.495_496insCTCCC indel polymorphism was found between the Italian scrapie-affected goats and the Korean native black goats (P < 0.001). Furthermore, there was a significant difference in the allele frequencies of the c.495_496insCTCCC indel polymorphism between Italian healthy goats and Korean native black goats (P < 0.001). To evaluate the biological impact of the novel nonsynonymous SNP c.416G > A (Arg139Gln), we carried out PROVEAN analysis. PROVEAN predicted the SNP as ‘Neutral’ with a score of −0.297. To the best of our knowledge, this is the first genetic study of the SPRN gene in Korean native black goats.

Highlights

Prion diseases, known as transmissible spongiform encephalopathies (TSEs), are fatal neurodegenerative disorders caused by pathogenic forms of the prion protein (PrPSc), which is induced by structural changes of the normal prion protein (PrPC) in the central nervous system[1]
We investigated, for the first time, caprine shadow of prion protein gene (SPRN) polymorphisms in 213 Korean native black goats and found a total of 6 polymorphisms of the SPRN gene, including one novel nonsynonymous single nucleotide polymorphism (SNP), R139Q
The prion gene family consists of four members, the prion protein gene (PRNP) gene, prion-like protein gene (PRND), prion-related protein gene (PRNT) and SPRN gene[30,31,32,33,34,35,36]

Summary

Introduction

Known as transmissible spongiform encephalopathies (TSEs), are fatal neurodegenerative disorders caused by pathogenic forms of the prion protein (PrPSc), which is induced by structural changes of the normal prion protein (PrPC) in the central nervous system[1]. Variants of the PRNP gene have a strong impact on the development of prion diseases, inbred mouse lines that contain identical DNA sequences to these prion proteins had varying incubation periods for prion disease. Genetic polymorphisms of the SPRN gene showed significant associations with the susceptibility to prion diseases[20,23,24,25,26,27]. We investigated genetic polymorphisms of the SPRN gene by using direct DNA sequencing and genotyping with SPRN gene-specific primers in 213 healthy Korean native black goats. We compared the genetic distribution of an insertion polymorphism of the SPRN gene in healthy Korean native black goats with that of scrapie-affected goats from previous studies. We evaluated the biological impact of nonsynonymous single nucleotide polymorphisms (SNPs) of the SPRN gene using PROVEAN28,29

Methods

Results

Conclusion