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Jeong MJ, Kim YC, Jeong BH. The first report of single nucleotide polymorphisms in the open reading frame of the prion-like protein gene in rabbits. Front Vet Sci 2024; 11:1388339. [PMID: 38952802 PMCID: PMC11216025 DOI: 10.3389/fvets.2024.1388339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/29/2024] [Indexed: 07/03/2024] Open
Abstract
Background Natural cases of prion disease have not been reported in rabbits, and prior attempts to identify a prion conversion agent have been unsuccessful. However, recent applications of prion seed amplifying experimental techniques have sparked renewed interest in the potential susceptibility of rabbits to prion disease infections. Among several factors related to prion disease, polymorphisms within the prion-like protein gene (PRND), a member of the prion protein family, have been reported as significantly associated with disease susceptibility in various species. Therefore, our study aimed to investigate polymorphisms in the PRND gene of rabbits and analyze their genetic characteristics. Methods Genomic DNA was extracted from 207 rabbit samples to investigate leporine PRND polymorphisms. Subsequently, amplicon sequencing targeting the coding region of the leporine PRND gene was conducted. Additionally, linkage disequilibrium (LD) analysis was employed to assess the connection within and between loci. The impact of non-synonymous single nucleotide polymorphisms (SNPs) on the Doppel protein was evaluated using PolyPhen-2. Results We found nine novel SNPs in the leporine PRND gene: c.18A > G, c.76G > C, c.128C > T, c.146C > T, c.315A > G, c.488G > A, c.525G > C, c.544G > A, and c.579A > G. Notably, seven of these PRND SNPs, excluding c.525G > C and c.579A > G, exhibited strong LD values exceeding 0.3. In addition, LD analysis confirmed a robust link between PRNP SNP c.234C > T and PRND SNPs at c.525G > C and c.579A > G. Furthermore, according to PolyPhen-2 and SIFT analyses, the four non-synonymous SNPs were predicted to have deleterious effects on the function or structure of the Doppel protein. However, PANTHER and Missense3D did not indicate such effects. Conclusion In this paper, we have identified novel SNPs in the rabbit PRND gene and predicted their potential detrimental effects on protein function or structure through four non-synonymous SNPs. Additionally, we observed a genetic linkage between SNPs in the PRND and PRNP genes. These findings may provide insights into understanding the characteristics of rabbits as partially resistant species. To the best of our knowledge, this study is the first to genetically characterize PRND SNPs in rabbits.
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Affiliation(s)
- Min-Ju Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk, Republic of Korea
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeonbuk, Republic of Korea
| | - Yong-Chan Kim
- Department of Biological Sciences, Andong National University, Andong, Republic of Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk, Republic of Korea
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeonbuk, Republic of Korea
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Adeola AC, Bello SF, Abdussamad AM, Adedokun RAM, Olaogun SC, Abdullahi N, Mark AI, Onoja AB, Sanke OJ, Mangbon GF, Ibrahim J, Dawuda PM, Salako AE, Kdidi S, Yahyaoui MH. Single nucleotide polymorphisms (SNPs) in the open reading frame (ORF) of prion protein gene (PRNP) in Nigerian livestock species. BMC Genomics 2024; 25:177. [PMID: 38355406 PMCID: PMC10865551 DOI: 10.1186/s12864-024-10070-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Prion diseases, also known as transmissible spongiform encephalopathies (TSEs) remain one of the deleterious disorders, which have affected several animal species. Polymorphism of the prion protein (PRNP) gene majorly determines the susceptibility of animals to TSEs. However, only limited studies have examined the variation in PRNP gene in different Nigerian livestock species. Thus, this study aimed to identify the polymorphism of PRNP gene in Nigerian livestock species (including camel, dog, horse, goat, and sheep). We sequenced the open reading frame (ORF) of 65 camels, 31 village dogs and 12 horses from Nigeria and compared with PRNP sequences of 886 individuals retrieved from public databases. RESULTS All the 994 individuals were assigned into 162 haplotypes. The sheep had the highest number of haplotypes (n = 54), and the camel had the lowest (n = 7). Phylogenetic tree further confirmed clustering of Nigerian individuals into their various species. We detected five non-synonymous SNPs of PRNP comprising of G9A, G10A, C11G, G12C, and T669C shared by all Nigerian livestock species and were in Hardy-Weinberg Equilibrium (HWE). The amino acid changes in these five non-synonymous SNP were all "benign" via Polyphen-2 program. Three SNPs G34C, T699C, and C738G occurred only in Nigerian dogs while C16G, G502A, G503A, and C681A in Nigerian horse. In addition, C50T was detected only in goats and sheep. CONCLUSION Our study serves as the first to simultaneously investigate the polymorphism of PRNP gene in Nigerian livestock species and provides relevant information that could be adopted in programs targeted at breeding for prion diseases resistance.
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Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.
| | - Semiu F Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China
| | - Abdussamad M Abdussamad
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, Bayero University, Kano, Nigeria
| | - Rahamon A M Adedokun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Nasiru Abdullahi
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Bayero University, Kano, Nigeria
| | - Akanbi I Mark
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Nigeria
| | - Anyebe B Onoja
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | | | - Jebi Ibrahim
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Philip M Dawuda
- Department of Animal Science, Faculty of Agriculture, National University of Lesotho, Maseru, South Africa
| | - Adebowale E Salako
- Department of Animal Science, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria
| | - Samia Kdidi
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Route El Djorf, Km 22.5, 4119, Medenine, Tunisia
| | - Mohamed Habib Yahyaoui
- Livestock and Wildlife Laboratory, Institut des Régions Arides, Université de Gabes, Route El Djorf, Km 22.5, 4119, Medenine, Tunisia
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Kim HH, Kim YC, Kim K, Kim AD, Jeong BH. Novel Polymorphisms and Genetic Features of the Prion Protein Gene ( PRNP) in Cats, Hosts of Feline Spongiform Encephalopathy. Genes (Basel) 2020; 12:genes12010013. [PMID: 33374431 PMCID: PMC7824082 DOI: 10.3390/genes12010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Prion diseases are fatal neurodegenerative disorders characterized by vacuolation and gliosis in the brain. Prion diseases have been reported in several mammals, and genetic polymorphisms of the prion protein gene (PRNP) play an essential role in the vulnerability of prion diseases. However, to date, investigations of PRNP polymorphisms are rare in cats, which are the major host of feline spongiform encephalopathy (FSE). Thus, we investigated the genetic polymorphisms of the cat PRNP gene and analyzed the structural characteristics of the PrP of cats compared to those of dog, prion disease-resistant animal. To investigate the genetic variations of the cat PRNP gene in 208 cats, we performed amplicon sequencing and examined the genotype, allele and haplotype frequencies of cat PRNP polymorphisms. We evaluated the influence of cat PRNP polymorphisms using PolyPhen-2, PANTHER, PROVEAN and AMYCO. In addition, we carried out structural analysis of cat PrP according to the allele of nonsynonymous single nucleotide polymorphism (SNP) (c.457G > A, Glu153Lys) using Swiss-PdbViewer. Finally, we compared the structural differences between cat and canine PrPs for SNPs associated with prion disease resistance in dogs. We identified a total of 15 polymorphisms, including 14 novel SNPs and one insertion/deletion polymorphism (InDel). Among them, Glu153Lys was predicted to affect the structural stability and amyloid propensity of cat PrP. In addition, asparagine at codon 166 of cat PrP was predicted to have longer hydrogen bond than aspartic acid at codon 163 of canine PrP. Furthermore, substitution to dog-specific amino acids in cat PrP showed an increase in structural stability. To the best of our knowledge, this is the first study regarding the structural characteristics of cat PRNP gene.
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Affiliation(s)
- Hyeon-Ho Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (H.-H.K.); (Y.-C.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (H.-H.K.); (Y.-C.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
| | - Kiwon Kim
- Haemalken Animal Hospital, Yangju, Gyeonggi 11492, Korea;
| | - An-Dang Kim
- Cool-Pet Animal Hospital, Anyang, Gyeonggi 14066, Korea;
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (H.-H.K.); (Y.-C.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
- Correspondence: ; Tel.: +82-63-900-4040; Fax: +82-63-900-4012
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Identification of the prion-related protein gene (PRNT) sequences in various species of the Cervidae family. Mol Biol Rep 2020; 47:6155-6164. [PMID: 32737828 DOI: 10.1007/s11033-020-05697-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/26/2020] [Indexed: 01/22/2023]
Abstract
Chronic wasting disease (CWD) is caused by abnormal deleterious prion protein (PrPSc), and transmissible spongiform encephalopathy occurs in the Cervidae family. In recent studies, the susceptibility of prion disease has been affected by polymorphisms of the prion gene family. However, the study of the prion-related protein gene (PRNT) is rare, and the DNA sequence of this gene was not fully reported in all Cervidae families. In the present study, we amplified and first identified PRNT DNA sequences in the Cervidae family, including red deer, elk, sika deer and Korean water deer, using polymerase chain reaction (PCR). We aligned nucleotide sequences of the PRNT gene and the amino acid sequences of prion-related protein (Prt) protein among several species. In addition, we performed phylogenetic analysis to measure the evolutionary relationships of the PRNT gene in the Cervidae family. Furthermore, we performed homology modeling of the Prt protein using SWISS-MODEL and compared the structure of Prt protein between sheep and the Cervidae family using the Swiss-PdbViewer program. We obtained much longer PRNT sequences of red deer compared to the PRNT gene sequence registered in GenBank. Korean water deer denoted more close evolutionary distances with goats and cattle than the Cervidae family. We found 6 Cervidae family-specific amino acids by the alignment of Prt amino acid sequences. There are significantly different distributions of hydrogen bonds and the atomic distance of the N-terminal tail and C-terminal tail between sheep and the Cervidae family. We also detected the mRNA expression of PRNT gene in 3 tissues investigated. To our knowledge, this report is the first genetic study of the PRNT gene in the Cervidae family.
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Won SY, Kim YC, Do K, Jeong BH. Absence of Strong Genetic Linkage Disequilibrium between Single Nucleotide Polymorphisms (SNPs) in the Prion Protein Gene ( PRNP) and the Prion-Like Protein Gene ( PRND) in the Horse, a Prion-Resistant Species. Genes (Basel) 2020; 11:genes11050518. [PMID: 32392732 PMCID: PMC7290373 DOI: 10.3390/genes11050518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 01/19/2023] Open
Abstract
Prion disease is a fatal neurodegenerative disorder caused by a deleterious prion protein (PrPSc). However, prion disease has not been reported in horses during outbreaks of transmissible spongiform encephalopathies (TSEs) in various animals in the UK. In previous studies, single nucleotide polymorphisms (SNPs) in the prion protein gene (PRNP) have been significantly associated with susceptibility to prion disease, and strong linkage disequilibrium (LD) between PRNP and prion-like protein gene (PRND) SNPs has been identified in prion disease-susceptible species. On the other hand, weak LD values have been reported in dogs, a prion disease-resistant species. In this study, we investigated SNPs in the PRND gene and measured the LD values between the PRNP and PRND SNPs and the impact of a nonsynonymous SNP found in the horse PRND gene. To identify SNPs in the PRND gene, we performed direct sequencing of the PRND gene. In addition, to assess whether the weak LD value between the PRNP and PRND SNPs is a characteristic of prion disease-resistant animals, we measured the LD value between the PRNP and PRND SNPs using D’ and r2 values. Furthermore, we evaluated the impact of a nonsynonymous SNP in the Doppel protein with PolyPhen-2, PROVEAN, and PANTHER. We observed two novel SNPs, c.331G > A (A111T) and c.411G > C. The genotype and allele frequencies of the c.331G > A (A111T) and c.411G > C SNPs were significantly different between Jeju, Halla, and Thoroughbred horses. In addition, we found a total of three haplotypes: GG, AG, and GC. The GG haplotype was the most frequently observed in Jeju and Halla horses. Furthermore, the impact of A111T on the Doppel protein was predicted to be benign by PolyPhen-2, PROVEAN, and PANTHER. Interestingly, a weak LD value between the PRNP and PRND SNPs was found in the horse, a prion disease-resistant animal. To the best of our knowledge, these results suggest that a weak LD value could be one feature of prion disease-resistant animals.
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Affiliation(s)
- Sae-Young Won
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (S.-Y.W.); (Y.-C.K.)
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (S.-Y.W.); (Y.-C.K.)
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
| | - Kyoungtag Do
- Lab of Equine Science, Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 63243, Korea;
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (S.-Y.W.); (Y.-C.K.)
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
- Correspondence: ; Tel.: +82-63-900-4040; Fax: +82-63-900-4012
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Won SY, Kim YC, Kim SK, Jeong BH. The First Report of Genetic and Structural Diversities in the SPRN Gene in the Horse, an Animal Resistant to Prion Disease. Genes (Basel) 2019; 11:genes11010039. [PMID: 31905681 PMCID: PMC7016944 DOI: 10.3390/genes11010039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/29/2019] [Accepted: 12/25/2019] [Indexed: 01/20/2023] Open
Abstract
Prion diseases are fatal neurodegenerative diseases and are characterized by the accumulation of abnormal prion protein (PrPSc) in the brain. During the outbreak of the bovine spongiform encephalopathy (BSE) epidemic in the United Kingdom, prion diseases in several species were reported; however, horse prion disease has not been reported thus far. In previous studies, the shadow of prion protein (Sho) has contributed to an acceleration of conversion from normal prion protein (PrPC) to PrPSc, and the shadow of prion protein gene (SPRN) polymorphisms have been significantly associated with the susceptibility of prion diseases. We investigated the genotype, allele and haplotype frequencies of the SPRN gene using direct sequencing. In addition, we analyzed linkage disequilibrium (LD) and haplotypes among polymorphisms. We also investigated LD between PRNP and SPRN single nucleotide polymorphisms (SNPs). We compared the amino acid sequences of Sho protein between the horse and several prion disease-susceptible species using ClustalW2. To perform Sho protein modeling, we utilized SWISS-MODEL and Swiss-PdbViewer programs. We found a total of four polymorphisms in the equine SPRN gene; however, we did not observe an in/del polymorphism, which is correlated with the susceptibility of prion disease in prion disease-susceptible animals. The SPRN SNPs showed weak LD value with PRNP SNP. In addition, we found 12 horse-specific amino acids of Sho protein that can induce significantly distributional differences in the secondary structure and hydrogen bonds between the horse and several prion disease-susceptible species. To the best of our knowledge, this is the first report regarding the genetic and structural characteristics of the equine SPRN gene.
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Affiliation(s)
- Sae-Young Won
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (S.-Y.W.); (Y.-C.K.); (S.-K.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (S.-Y.W.); (Y.-C.K.); (S.-K.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
| | - Seon-Kwan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (S.-Y.W.); (Y.-C.K.); (S.-K.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Jeonbuk 54531, Korea; (S.-Y.W.); (Y.-C.K.); (S.-K.K.)
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Jeonbuk 54896, Korea
- Correspondence: ; Tel.: +82-63-900-4040; Fax: +82-63-900-4012
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