The First Report of Polymorphisms and Genetic Characteristics of the Shadow of Prion Protein (SPRN) in Prion Disease-Resistant Animal, Chickens

Kim, Yongchan; Kim, Hyeon-Ho; Jeong, Byung‐Hoon

doi:10.3389/fvets.2022.904305

Cited by 6 publications

(10 citation statements)

References 22 publications

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“…The Sho proteins of pheasants and chickens were the shortest among the eight species (117 amino acids). As in a previous study, although the Sho-PrP interaction regions (red box) and the NXT glycosylation motif (black box) were conserved among every species ( 14 ), the N-terminal and C-terminal regions exhibited significantly low sequence homology between mammals and pheasants.…”

Section: Resultssupporting

confidence: 60%

“…Previous studies have reported that prion disease-susceptible species, including cattle, goats, and sheep, have highly polymorphic SPRN genes ( 12 , 13 , 38 , 39 ). In contrast, a prion disease-resistant species, horses and chickens have one polymorphism of the SPRN gene ( 9 , 14 , 40 ). Dogs, a prion disease-resistant animal, have one insertion/deletion polymorphism in SPRN gene ( 10 ).…”

Section: Discussionmentioning

confidence: 99%

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Novel polymorphisms and genetic studies of the shadow of prion protein gene (SPRN) in pheasants

Choi,

Zayed,

Kim

et al. 2024

Front. Vet. Sci.

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BackgroundPrion diseases in mammals are caused by the structural conversion of the natural prion protein (PrPC) to a pathogenic isoform, the “scrapie form of prion protein (PrPSc).” Several studies reported that the shadow of prion protein (Sho), encoded by the shadow of prion protein gene (SPRN), is involved in prion disease development by accelerating the conformational conversion of PrPC to PrPSc. Until now, genetic polymorphisms of the SPRN gene and the protein structure of Sho related to fragility to prion disease have not been investigated in pheasants, which are a species of poultry.MethodsHere, we identified the SPRN gene sequence by polymerase chain reaction (PCR) and compared the SPRN gene and Sho protein sequences among various prion disease-susceptible and -resistant species to identify the distinctive genetic features of pheasant Sho using Clustal Omega. In addition, we investigated genetic polymorphisms of the SPRN gene in pheasants and analyzed genotype, allele, and haplotype frequencies, as well as linkage disequilibrium among the genetic polymorphisms. Furthermore, we used in silico programs, namely Mutpred2, MUpro and AMYCO, to investigate the effect of non-synonymous single nucleotide polymorphisms (SNPs). Finally, the predicted secondary and tertiary structures of Sho proteins from various species were analyzed by Alphafold2.ResultsIn the present study, we reported pheasant SPRN gene sequences for the first time and identified a total of 14 novel SNPs, including 7 non-synonymous and 4 synonymous SNPs. In addition, the pheasant Sho protein sequence showed 100% identity with the chicken Sho protein sequence. Furthermore, amino acid substitutions were predicted to affect the hydrogen bond distribution in the 3D structure of the pheasant Sho protein.ConclusionTo the best of our knowledge, this is the first report of the genetic and structural features of the pheasant SPRN gene.

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Section: Resultssupporting

confidence: 60%

Section: Discussionmentioning

confidence: 99%

Novel polymorphisms and genetic studies of the shadow of prion protein gene (SPRN) in pheasants

Choi,

Zayed,

Kim

et al. 2024

Front. Vet. Sci.

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“…We noticed that various SNPs were found in the ORF of the prion diseasesusceptible group, whereas, in the prion disease-resistant group, except for ducks, only one SNP was found in the ORF of the SPRN gene. in humans [26,42], cattle [15,[43][44][45], goats [27,44,46], sheep [28,42,44], dogs [47], horses [48,49], chickens [50], and ducks (this study). The edged horizontal bar indicates the number of amino acids in the SPRN gene.…”

Section: Distribution Of Snps In the Orf Of The Sprn Gene In Several ...mentioning

confidence: 67%

“…In this work, we identified 27 novel SNPs. Notably, four of them, c.183G>A, c.354+33G>A, c.354+69C>A, and c.354+94A>G, are homologous to four SNPs identified in the chicken SPRN gene in a previous study [ 50 ], suggesting conservation among birds’ SPRN genes.…”

Section: Discussionmentioning

confidence: 83%

“…We collected reported genetic polymorphisms in the ORF of the SPRN gene in prion disease-susceptible animals (humans [ 26 , 42 ], cattle [ 15 , 43 , 44 , 45 ], sheep [ 28 , 42 , 44 ], goats [ 27 , 44 , 46 ]), and prion disease-resistant animals (dogs [ 47 ], horses [ 48 , 49 ], chickens [ 50 ], and ducks (this study) to compare the distribution of SNPs between these two groups ( Figure 6 ). We noticed that various SNPs were found in the ORF of the prion disease-susceptible group, whereas, in the prion disease-resistant group, except for ducks, only one SNP was found in the ORF of the SPRN gene.…”

Section: Resultsmentioning

confidence: 99%

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The First Genetic Characterization of the SPRN Gene in Pekin Ducks (Anas platyrhynchos domesticus)

Nguyen,

Zayed,

Kim

et al. 2024

Animals

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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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The first report of single nucleotide polymorphisms in the open reading frame of the prion-like protein gene in rabbits

Jeong,

Kim,

Jeong

2024

Front. Vet. Sci.

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BackgroundNatural 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.MethodsGenomic 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.ResultsWe 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.ConclusionIn 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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The First Report of Polymorphisms and Genetic Characteristics of the Shadow of Prion Protein (SPRN) in Prion Disease-Resistant Animal, Chickens

Cited by 6 publications

References 22 publications

Novel polymorphisms and genetic studies of the shadow of prion protein gene (SPRN) in pheasants

Novel polymorphisms and genetic studies of the shadow of prion protein gene (SPRN) in pheasants

The First Genetic Characterization of the SPRN Gene in Pekin Ducks (Anas platyrhynchos domesticus)

The first report of single nucleotide polymorphisms in the open reading frame of the prion-like protein gene in rabbits

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