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Nguyen TTD, Zayed M, Kim YC, Jeong BH. The First Genetic Characterization of the SPRN Gene in Pekin Ducks ( Anas platyrhynchos domesticus). Animals (Basel) 2024; 14:1588. [PMID: 38891635 PMCID: PMC11171214 DOI: 10.3390/ani14111588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Prion diseases are fatal neurodegenerative disorders characterized by an accumulation of misfolded prion protein (PrPSc) in brain tissues. The shadow of prion protein (Sho) encoded by the shadow of prion protein gene (SPRN) is involved in prion disease progress. The interaction between Sho and PrP accelerates the PrPSc conversion rate while the SPRN gene polymorphisms have been associated with prion disease susceptibility in several species. Until now, the SPRN gene has not been investigated in ducks. We identified the duck SPRN gene sequence and investigated the genetic polymorphisms of 184 Pekin ducks. We compared the duck SPRN nucleotide sequence and the duck Sho protein amino acid sequence with those of several other species. Finally, we predicted the duck Sho protein structure and the effects of non-synonymous single nucleotide polymorphisms (SNPs) using computational programs. We were the first to report the Pekin duck SPRN gene sequence. The duck Sho protein sequence showed 100% identity compared with the chicken Sho protein sequence. We found 27 novel SNPs in the duck SPRN gene. Four amino acid substitutions were predicted to affect the hydrogen bond distribution in the duck Sho protein structure. Although MutPred2 and SNPs&GO predicted that all non-synonymous polymorphisms were neutral or benign, SIFT predicted that four variants, A22T, G49D, A68T, and M105I, were deleterious. To the best of our knowledge, this is the first report about the genetic and structural characteristics of the duck SPRN gene.
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Affiliation(s)
- Thi-Thuy-Duong Nguyen
- Korea Zoonosis Research Institute, Jeonbuk National University, 820-120, Hana-ro, Iksan 54531, Republic of Korea (M.Z.)
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Mohammed Zayed
- Korea Zoonosis Research Institute, Jeonbuk National University, 820-120, Hana-ro, Iksan 54531, Republic of Korea (M.Z.)
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Surgery, College of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Yong-Chan Kim
- Department of Biological Sciences, Andong National University, Andong 36729, Republic of Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, 820-120, Hana-ro, Iksan 54531, Republic of Korea (M.Z.)
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Jeong MJ, Wang Z, Zou WQ, Kim YC, Jeong BH. The first report of polymorphisms of the prion protein gene ( PRNP) in Pekin ducks ( Anas platyrhynchos domestica). Front Vet Sci 2023; 10:1273050. [PMID: 38026621 PMCID: PMC10664711 DOI: 10.3389/fvets.2023.1273050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Background Prion diseases have been extensively reported in various mammalian species and are caused by a pathogenic prion protein (PrPSc), which is a misfolded version of cellular prion protein (PrPC). Notably, no cases of prion disease have been reported in birds. Single nucleotide polymorphisms (SNPs) of the prion protein gene (PRNP) that encodes PrP have been associated with susceptibility to prion diseases in several species. However, no studies on PRNP polymorphisms in domestic ducks have been reported thus far. Method To investigate PRNP polymorphisms in domestic ducks, we isolated genomic DNA from 214 Pekin duck samples and sequenced the coding region of the Pekin duck PRNP gene. We analyzed genotype, allele, and haplotype distributions and linkage disequilibrium (LD) among the SNPs of the Pekin duck PRNP gene. In addition, we evaluated the effects of the one non-synonymous SNP on the function and structure of PrP using the PROVEAN, PANTHER, SNPs & GO, SODA, and AMYCO in silico prediction programs. Results We found five novel SNPs, c.441 T > C, c.495 T > C, c.582A > G, c.710C > T(P237L), and c.729C > T, in the ORF region of the PRNP gene in 214 Pekin duck samples. We observed strong LD between c.441 T > C and c.582A > G (0.479), and interestingly, the link between c.495 T > C and c.729C > T was in perfect LD, with an r2 value of 1.0. In addition, we identified the five major haplotype frequencies: TTACC, CTGCC, CTACC, CCGCT, and CTATC. Furthermore, we found that the non-synonymous SNP, c.710C > T (P237L), had no detrimental effects on the function or structure of Pekin duck PrP. However, the non-synonymous SNP had deleterious effects on the aggregation propensity and solubility of Pekin duck PrP compared with wildtype Pekin duck PrP. Conclusion To the best of our knowledge, this study is the first report on the genetic characteristics of PRNP SNPs in Pekin ducks.
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Affiliation(s)
- Min-Ju Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
| | - Zerui Wang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Wen-Quan Zou
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - 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, Republic of Korea
- Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, United States
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Kim KH, Kim YC, Jeong BH. Novel Polymorphisms and Genetic Characteristics of the Prion Protein Gene in Pheasants. Front Vet Sci 2022; 9:935476. [PMID: 35903139 PMCID: PMC9322948 DOI: 10.3389/fvets.2022.935476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) also known as prion diseases, are fatal neurodegenerative diseases. Prion diseases are caused by abnormal prion protein (PrPSc) derived from normal prion protein (PrPC), which is encoded by the prion protein gene (PRNP). Prion diseases have been reported in several mammals. Notably, chickens, one species of bird, have not been reported to develop prion diseases and showed resistance to bovine spongiform encephalopathy (BSE) infection. However, genetic polymorphisms of the PRNP gene and protein structure of the prion protein (PrP) related to vulnerability to prion diseases have not been investigated in pheasants, another species of bird. We performed amplicon sequencing of the pheasant PRNP gene to identify genetic polymorphisms in 148 pheasants. We analyzed the genotype, allele and haplotype frequencies of the pheasant PRNP polymorphisms. In addition, we evaluated the effect of genetic polymorphisms of the pheasant PRNP gene on pheasant PrP by the AMYCO, PROVEAN, PolyPhen-2 and PANTHER softwares. Furthermore, we compared the amino acid sequences of tandem repeat domains and secondary and tertiary structures of prion proteins (PrPs) among several animals. Finally, we investigated the impact of non-synonymous single nucleotide polymorphisms (SNPs) on hydrogen bonds and tertiary structures of pheasant PrP by Swiss PDB viewer software. We identified 34 novel genetic polymorphisms of the pheasant PRNP gene including 8 non-synonymous SNPs and 6 insertion/deletion polymorphisms. Among the non-synonymous SNPs, the L23F, G33C and R177Q SNPs showed that they could have a deleterious effect on pheasant PrP. In addition, the R177Q SNP was predicted to show an increase in amyloid propensity and a reduction in hydrogen bonds of pheasant PrP. Among the insertion/deletion polymorphisms, c.163_180delAACCCGGGGTATCCCCAC showed that it could have a detrimental effect on pheasant PrP. Furthermore, secondary and tertiary structures of pheasant PrP were predicted to have structures similar to those of chicken PrP. To the best of our knowledge, this is the first study on genetic polymorphisms of the pheasant PRNP gene.
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Affiliation(s)
- Kyung Han Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Jeonju, South Korea
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, South Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Jeonju, South Korea
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, South Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Jeonju, South Korea
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, South Korea
- *Correspondence: Byung-Hoon Jeong
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Kim Y, Kim YC, Jeong BH. Novel Single Nucleotide Polymorphisms (SNPs) and Genetic Features of the Prion Protein Gene (PRNP) in Quail (Coturnix japonica). Front Vet Sci 2022; 9:870735. [PMID: 35692300 PMCID: PMC9174905 DOI: 10.3389/fvets.2022.870735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Prion diseases are fatal infectious diseases caused by conformational changes of a prion protein (PrPSc) derived from a normal prion protein (PrPC). Prion diseases have been reported in several mammalian hosts but not in any birds, including the most popular poultry species, of which chickens showed some resistance to experimental prion infection. To identify the genetic polymorphisms in the quail prion protein gene (PRNP), polymerase chain reaction and DNA sequencing were performed with gene-specific primers in 164 quails. Four in silico programs, including PROVEAN, PANTHER, SIFT, and AMYCO, were used to investigate the effect of non-synonymous single nucleotide polymorphisms (SNPs) on quail PrP. Furthermore, to investigate the genetic relationship of avian PrPs, phylogenetic analysis and multiple sequence alignments were performed using MEGA X program. Finally, the secondary and tertiary structures of avian PrPs were analyzed by SWISS-MODEL. We identified 33 novel SNPs in the quail PRNP gene, including three non-synonymous SNPs, c.56C>T (T19I), c.60C>T (V21I), and c.61G>A (A22S). Although V21I was predicted to have deleterious effects by SIFT, the substitutions of all three amino acids did not affect the amyloid propensity, 3D structure, or hydrogen bonds of quail PrP. Quail PrP showed a close evolutionary relationship and similar secondary and tertiary structures to chicken PrP compared to duck PrP. To our knowledge, this is the first report on the genetic and structural properties of the quail PRNP gene.
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Affiliation(s)
- Yoonhee Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, South Korea
| | - Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, South Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, South Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, South Korea
- *Correspondence: Byung-Hoon Jeong
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Kim YC, Park KJ, Hwang JY, Park HC, Kang HE, Sohn HJ, Jeong BH. In-depth examination of PrP Sc in Holstein cattle carrying the E211K somatic mutation of the bovine prion protein gene (PRNP). Transbound Emerg Dis 2021; 69:e356-e361. [PMID: 34470082 DOI: 10.1111/tbed.14309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022]
Abstract
Prion diseases are transmissible spongiform encephalopathies caused by deleterious prion protein (PrPSc ) derived from normal prion protein (PrPC ), which is encoded by the prion protein gene (PRNP). We performed an in-depth examination to detect PrPSc by using enzyme immunoassay (EIA), real-time quaking-induced conversion reactions (RT-QuIC) and protein misfolding cyclic amplification (PMCA) in nine brain tissues derived from three Holstein cattle carrying the E211K somatic mutation of the bovine PRNP gene. The EIA, RT-QuIC and PMCA analyses were not able to detect the PrPSc band in any tested samples. To the best of our knowledge, this report is the first to describe an in-depth examination of PrPSc in cattle carrying the E211K somatic mutation of the bovine PRNP gene.
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Affiliation(s)
- Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyung-Je Park
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Ji-Yong Hwang
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hoo-Chang Park
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hae-Eun Kang
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Hyun-Joo Sohn
- Reference Laboratory for CWD, Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
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