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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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Exploration of Alternative Splicing (AS) Events in MDV-Infected Chicken Spleens. Genes (Basel) 2021; 12:genes12121857. [PMID: 34946806 PMCID: PMC8701255 DOI: 10.3390/genes12121857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Marek’s disease (MD) was an immunosuppression disease induced by Marek’s disease virus (MDV). MD caused huge economic loss to the global poultry industry, but it also provided an ideal model for studying diseases induced by the oncogenic virus. Alternative splicing (AS) simultaneously produced different isoform transcripts, which are involved in various diseases and individual development. To investigate AS events in MD, RNA-Seq was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and non-infected chicken spleens (NS). In this study, 32,703 and 25,217 AS events were identified in TS and SS groups with NS group as the control group, and 1198, 1204, and 348 differently expressed (DE) AS events (p-value < 0.05 and FDR < 0.05) were identified in TS vs. NS, TS vs. SS, SS vs. NS, respectively. Additionally, Function enrichment analysis showed that ubiquitin-mediated proteolysis, p53 signaling pathway, and phosphatidylinositol signaling system were significantly enriched (p-value < 0.05). Small structural variations including SNP and indel were analyzed based on RNA-Seq data, and it showed that the TS group possessed more variants on the splice site region than those in SS and NS groups, which might cause more AS events in the TS group. Combined with previous circRNA data, we found that 287 genes could produce both circular and linear RNAs, which suggested these genes were more active in MD lymphoma transformation. This study has expanded the understanding of the MDV infection process and provided new insights for further analysis of resistance/susceptibility mechanisms.
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Gallardo MJ, Delgado FO. Animal prion diseases: A review of intraspecies transmission. Open Vet J 2021; 11:707-723. [PMID: 35070868 PMCID: PMC8770171 DOI: 10.5455/ovj.2021.v11.i4.23] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Animal prion diseases are a group of neurodegenerative, transmissible, and fatal disorders that affect several animal species. The causative agent, prion, is a misfolded isoform of normal cellular prion protein, which is found in cells with higher concentration in the central nervous system. This review explored the sources of infection and different natural transmission routes of animal prion diseases in susceptible populations. Chronic wasting disease in cervids and scrapie in small ruminants are prion diseases capable of maintaining themselves in susceptible populations through horizontal and vertical transmission. The other prion animal diseases can only be transmitted through food contaminated with prions. Bovine spongiform encephalopathy (BSE) is the only animal prion disease considered zoonotic. However, due to its inability to transmit within a population, it could be controlled. The emergence of atypical cases of scrapie and BSE, even the recent report of prion disease in camels, demonstrates the importance of understanding the transmission routes of prion diseases to take measures to control them and to assess the risks to human and animal health.
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Affiliation(s)
- Mauro Julián Gallardo
- Instituto de Patobiología Veterinaria, IPVet, UEDD INTA-CONICET, Hurlingham, Argentina
- Cátedra de Enfermedades Infecciosas, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fernando Oscar Delgado
- Instituto de Patobiología Veterinaria, IPVet, UEDD INTA-CONICET, Hurlingham, Argentina
- Facultad de Cs. Agrarias y Veterinarias, Universidad del Salvador, Pilar, Argentina
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Kim YC, Won SY, Jeong MJ, Jeong BH. Absence of proteinase K-resistant PrP in Korean Holstein cattle carrying potential bovine spongiform encephalopathy-related E211K somatic mutation. Transbound Emerg Dis 2021; 69:805-812. [PMID: 33660931 DOI: 10.1111/tbed.14053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 10/22/2022]
Abstract
Bovine spongiform encephalopathy (BSE) is a kind of prion disease caused by proteinase K-resistant prion protein (PrPSc ) in cattle. Although BSE has been reported worldwide, BSE-infected cases have never been reported in Korea. In a previous study, we identified BSE-related somatic mutation E211K in 3 Korean Holstein cattle. In Korea, the BSE surveillance system has been established. However, several genetic factors have not been controlled simultaneously thus far. In the present study, we performed enhanced surveillance of prion disease-related factors in Korean cattle, including Holstein cattle and Hanwoo (Korean native cattle), which is widely raised for meat. We investigated the germline mutation E211K at codon 211 of the PRNP gene and analysed genotype, allele and haplotype frequencies of the 23- and 12-bp insertion/deletion polymorphisms of the PRNP gene using direct DNA sequencing. In addition, we investigated linkage disequilibrium (LD) and compared haplotype distributions of polymorphisms among cattle breeds. Furthermore, we carried out BSE diagnosis in the medulla oblongata (MO) of Korean cattle including 3 Korean Holstein cattle carrying somatic mutation E211K using Western blotting analysis. We did not find the E211K mutation in the PRNP gene in any of the Korean cattle and found significantly different genotype, allele and haplotype distributions of the 23- and 12-bp insertion/deletion polymorphisms of the PRNP gene in male Holstein compared with male Hanwoo, female Hanwoo and total Hanwoo. In addition, only male Holstein showed weak LD between 23- and 12-bp insertion/deletion polymorphisms. Furthermore, the PrPSc bands were not detected in all Korean cattle tested. To the best of our knowledge, the enhanced surveillance system of BSE was conducted for the first time in Korean cattle.
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Affiliation(s)
- Yong-Chan Kim
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Korea
| | - Sae-Young Won
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Korea
| | - Min-Ju Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Korea.,Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Korea
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Potential scrapie-associated polymorphisms of the prion protein gene (PRNP) in Korean native black goats. Sci Rep 2019; 9:15293. [PMID: 31653880 PMCID: PMC6814802 DOI: 10.1038/s41598-019-51621-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022] Open
Abstract
Small ruminants, including sheep and goats are natural hosts of scrapie, and the progression of scrapie pathogenesis is strongly influenced by polymorphisms in the prion protein gene (PRNP). Although Korean native goats have been consumed as meat and health food, the evaluation of the susceptibility to scrapie in these goats has not been performed thus far. Therefore, we investigated the genotype and allele frequencies of PRNP polymorphisms in 211 Korean native goats and compared them with those in scrapie-affected animals from previous studies. We found a total of 12 single nucleotide polymorphisms (SNPs) including 10 nonsynonymous and 2 synonymous SNPs in Korean native goats. Significant differences in allele frequencies of PRNP codons 143 and 146 were found between scrapie-affected goats and Korean native goats (p < 0.01). By contrast, in PRNP codons 168, 211 and 222, there were no significant differences in the genotype and allele frequencies between scrapie-affected animals and Korean native goats. To evaluate structural changes caused by nonsynonymous SNPs, PolyPhen-2, PROVEAN and AMYCO analyses were performed. PolyPhen-2 predicted “possibly damaging” for W102G and R154H, “probably damaging” for G127S. AMYCO predicted relatively low for amyloid propensity of prion protein in Korean native black goats. This is the first study to evaluate the scrapie sensitivity and the first in silico evaluation of nonsynonymous SNPs in Korean native black goats.
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Kim YC, Jeong BH. First report of prion-related protein gene (PRNT
) polymorphisms in cattle. Vet Rec 2018; 182:717. [DOI: 10.1136/vr.104123] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/16/2017] [Accepted: 04/04/2018] [Indexed: 11/03/2022]
Affiliation(s)
- Yong-Chan Kim
- Department of Bioactive Material Sciences; Chonbuk National University; Jeonju Jeonbuk Republic of Korea
- Korea Zoonosis Research Institute, ChonbukNational University; Iksan Jeonbuk Republic of Korea
| | - Byung-Hoon Jeong
- Department of Bioactive Material Sciences; Chonbuk National University; Jeonju Jeonbuk Republic of Korea
- Korea Zoonosis Research Institute, ChonbukNational University; Iksan Jeonbuk Republic of Korea
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Sorbolini S, Gaspa G, Steri R, Dimauro C, Cellesi M, Stella A, Marras G, Marsan PA, Valentini A, Macciotta NPP. Use of canonical discriminant analysis to study signatures of selection in cattle. Genet Sel Evol 2016; 48:58. [PMID: 27521154 PMCID: PMC4983034 DOI: 10.1186/s12711-016-0236-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 08/01/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Cattle include a large number of breeds that are characterized by marked phenotypic differences and thus constitute a valuable model to study genome evolution in response to processes such as selection and domestication. Detection of "signatures of selection" is a useful approach to study the evolutionary pressures experienced throughout history. In the present study, signatures of selection were investigated in five cattle breeds farmed in Italy using a multivariate approach. METHODS A total of 4094 bulls from five breeds with different production aptitudes (two dairy breeds: Italian Holstein and Italian Brown Swiss; two beef breeds: Piemontese and Marchigiana; and one dual purpose breed: Italian Simmental) were genotyped using the Illumina BovineSNP50 v.1 beadchip. Canonical discriminant analysis was carried out on the matrix of single nucleotide polymorphisms (SNP) genotyping data, separately for each chromosome. Scores for each canonical variable were calculated and then plotted in the canonical space to quantify the distance between breeds. SNPs for which the correlation with the canonical variable was in the 99th percentile for a specific chromosome were considered to be significantly associated with that variable. Results were compared with those obtained using an FST-based approach. RESULTS Based on the results of the canonical discriminant analysis, a large number of signatures of selection were detected, among which several had strong signals in genomic regions that harbour genes known to have an impact on production and morphological bovine traits, including MSTN, LCT, GHR, SCD, NCAPG, KIT, and ASIP. Moreover, new putative candidate genes were identified, such as GCK, B3GALNT1, MGAT1, GALNTL1, PRNP, and PRND. Similar results were obtained with the FST-based approach. CONCLUSIONS The use of canonical discriminant analysis on 50 K SNP genotypes allowed the extraction of new variables that maximize the separation between breeds. This approach is quite straightforward, it can compare more than two groups simultaneously, and relative distances between breeds can be visualized. The genes that were highlighted in the canonical discriminant analysis were in concordance with those obtained using the FST index.
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Affiliation(s)
- Silvia Sorbolini
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Giustino Gaspa
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Roberto Steri
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, via Salaria 31, 00015, Monterotondo, Italy
| | - Corrado Dimauro
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | - Massimo Cellesi
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy
| | | | | | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Alessio Valentini
- Dipartimento per l'Innovazione dei Sistemi Biologici Agroalimentari e Forestali DIBAF, Università della Tuscia, Viterbo, Italy
| | - Nicolò Pietro Paolo Macciotta
- Dipartimento di Agraria, Sezione di Scienze Zootecniche, Università degli Studi di Sassari, V. le Italia, 9, 07100, Sassari, Italy.
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Murdoch BM, Murdoch GK. Genetics of Prion Disease in Cattle. Bioinform Biol Insights 2015; 9:1-10. [PMID: 26462233 PMCID: PMC4589088 DOI: 10.4137/bbi.s29678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 12/03/2022] Open
Abstract
Bovine spongiform encephalopathy (BSE) is a prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. As a transmissible disease of livestock, it has impacted food safety, production practices, global trade, and profitability. Genetic polymorphisms that alter the prion protein in humans and sheep are associated with transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that nonsynonymous mutations in the bovine prion gene (PRNP) are associated with classical BSE (C-BSE) disease susceptibility, though two bovine PRNP insertion/deletion polymorphisms, in the putative region, are associated with susceptibility to C-BSE. However, these associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. This article provides a review of the current state of genetic knowledge regarding prion diseases in cattle.
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Affiliation(s)
- Brenda M Murdoch
- Animal and Veterinary Science, University of Idaho, Moscow, ID, USA
| | - Gordon K Murdoch
- Animal and Veterinary Science, University of Idaho, Moscow, ID, USA
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