In silico Comparative Analysis of DNA and Amino Acid Sequences for Prion Protein Gene

Prion diseases are fatal neurodegenerative diseases characterised by the accumulation of an abnormal prion protein isoform (PrPSc), which is converted from the normal prion protein (PrPC). Prion diseases have been reported in an extensive number of species but not in horses up to now; therefore, horses are known to be a species resistant to prion diseases. The prion-like protein gene (PRND) is closely located downstream of the prion protein gene (PRNP) and the prion-like protein (Doppel) is a homologue with PrP. Previous studies have shown that an association between prion diseases and polymorphisms of the PRND gene is reported in the main hosts of prion diseases. Hence, we examined the genetic variations of the PRND gene in Thoroughbred horses. Interestingly, polymorphisms of the PRND gene were not detected. In addition, we conducted a comparative analysis of the amino acid sequences of the PRND gene to identify the differences between horses and other species. The amino acid sequence of the horse PRND gene showed the highest identity to that of sheep (83.7%), followed by that of goats, cattle and humans. To the best of our knowledge, this is the first genetic study of the PRND gene in horses.

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Prion protein gene polymorphisms in natural goat scrapie

Journal of General Virology ◽

10.1099/0022-1317-83-3-713 ◽

2002 ◽

Vol 83 (3) ◽

pp. 713-721 ◽

Cited By ~ 83

Author(s):

Charalambos Billinis ◽

Cynthia H. Panagiotidis ◽

Vassilios Psychas ◽

Stamatis Argyroudis ◽

Anna Nicolaou ◽

...

Keyword(s):

Amino Acid ◽

Prion Protein ◽

Gene Polymorphisms ◽

Protein Gene ◽

Clinical Signs ◽

Amino Acid Sequences ◽

Prion Protein Gene ◽

Gene Encoding ◽

Histopathological Lesions ◽

The Brain

A total of 51 goats, including seven clinical cases, from the first herd in Greece reported to have scrapie was examined to discern an association between scrapie susceptibility and polymorphisms of the gene encoding the prion protein (PrP). Each animal was evaluated for clinical signs of the disease, histopathological lesions associated with scrapie, the presence of detectable protease-resistant PrP in the brain and PrP genotype. Eleven different PrP genotypes encoding at least five unique predicted mature PrP amino acid sequences were found. These genotypes included the amino acid polymorphisms at codons 143 (H→R) and 240 (S→P) and ‘silent’ nucleotide alterations at codons 42 (a→g) and 138 (c→t). Additionally, novel caprine amino acid polymorphisms were detected at codons 21 (V→A), 23 (L→P), 49 (G→S), 154 (R→H), 168 (P→Q) and 220 (Q→H) and new silent mutations were found at codons 107 (g→a) and 207 (g→a). The following variants were found in scrapie-affected goats: VV21, LL23, GG49, SS49, HH143, HR143, RR154, PP168, PP240, SP240 and SS240. All scrapie-affected animals carried the HH143RR154 genotype, with the exception of two goats (HR143), both of which had detectable protease-resistant PrP but showed no clinical signs or histopathological lesions characteristic of scrapie.

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First Report of the Potential Bovine Spongiform Encephalopathy (BSE)-Related Somatic Mutation E211K of the Prion Protein Gene (PRNP) in Cattle

International Journal of Molecular Sciences ◽

10.3390/ijms21124246 ◽

2020 ◽

Vol 21 (12) ◽

pp. 4246 ◽

Cited By ~ 2

Author(s):

Sae-Young Won ◽

Yong-Chan Kim ◽

Byung-Hoon Jeong

Keyword(s):

Bovine Spongiform Encephalopathy ◽

Prion Protein ◽

Somatic Mutation ◽

Prion Disease ◽

In Silico ◽

Somatic Mutations ◽

Protein Gene ◽

Prnp Gene ◽

Spongiform Encephalopathy ◽

Prion Protein Gene

Bovine spongiform encephalopathy (BSE) is a prion disease characterized by spongiform degeneration and astrocytosis in the brain. Unlike classical BSE, which is caused by prion-disease-contaminated meat and bone meal, the cause of atypical BSE has not been determined. Since previous studies have reported that the somatic mutation in the human prion protein gene (PRNP) has been linked to human prion disease, the somatic mutation of the PRNP gene was presumed to be one cause of prion disease. However, to the best of our knowledge, the somatic mutation of this gene in cattle has not been investigated to date. We investigated somatic mutations in a total of 58 samples, including peripheral blood; brain tissue including the medulla oblongata, cerebellum, cortex, and thalamus; and skin tissue in 20 individuals from each breed using pyrosequencing. In addition, we estimated the deleterious effect of the K211 somatic mutation on bovine prion protein by in silico evaluation tools, including PolyPhen-2 and PANTHER. We found a high rate of K211 somatic mutations of the bovine PRNP gene in the medulla oblongata of three Holsteins (10% ± 4.4%, 28% ± 2%, and 19.55% ± 3.1%). In addition, in silico programs showed that the K211 somatic mutation was damaging. To the best of our knowledge, this study is the first to investigate K211 somatic mutations of the bovine PRNP gene that are associated with potential BSE progression.

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Comparative analysis of the prion protein gene sequences in African lion

Virus Genes ◽

10.1007/s11262-005-0058-0 ◽

2006 ◽

Vol 33 (2) ◽

pp. 213-214 ◽

Cited By ~ 1

Author(s):

Chang-De Wu ◽

Wan-Yong Pang ◽

De-Ming Zhao

Keyword(s):

Comparative Analysis ◽

Prion Protein ◽

Protein Gene ◽

Prion Protein Gene ◽

Gene Sequences ◽

African Lion

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Amino acid sequence of the Pekingese dog prion protein gene

Xenotransplantation ◽

10.1111/j.1399-3089.2006.00325.x ◽

2006 ◽

Vol 13 (5) ◽

pp. 471-474 ◽

Cited By ~ 2

Author(s):

Changde Wu ◽

Wanyong Pang ◽

Jianmin Yang ◽

Xiangmei Zhou ◽

Deming Zhao

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Prion Protein ◽

Protein Gene ◽

Prion Protein Gene

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CHARACTERISTICS OF ALLELE POOL OF THE ROMANOV SHEEP BREED FOR THE PRION PROTEIN GENE ASSOCIATED WITH GENETIC SUSTAINABILITY TO SCRAPIE

Sel skokhozyaistvennaya Biologiya ◽

10.15389/agrobiology.2017.6.1157eng ◽

2017 ◽

Vol 52 (6) ◽

pp. 1157-1165

Author(s):

E.A. Gladyr ◽

◽

T.E. Deniskova ◽

V.A. Bagirov ◽

O.V. Kostyunina ◽

...

Keyword(s):

Prion Protein ◽

Protein Gene ◽

Sheep Breed ◽

Prion Protein Gene ◽

Allele Pool

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Faculty Opinions recommendation of Balancing selection at the prion protein gene consistent with prehistoric kurulike epidemics.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1013616.191427 ◽

2003 ◽

Author(s):

Deborah Charlesworth

Keyword(s):

Prion Protein ◽

Protein Gene ◽

Balancing Selection ◽

Prion Protein Gene

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The First Report of the Prion Protein Gene (PRNP) Sequence in Pekin Ducks (Anas platyrhynchos domestica): The Potential Prion Disease Susceptibility in Ducks

Genes ◽

10.3390/genes12020193 ◽

2021 ◽

Vol 12 (2) ◽

pp. 193

Author(s):

Min-Ju Jeong ◽

Yong-Chan Kim ◽

Byung-Hoon Jeong

Keyword(s):

Prion Protein ◽

Dna Sequence ◽

Prion Disease ◽

Protein Gene ◽

Prnp Gene ◽

Pekin Duck ◽

Prion Protein Gene ◽

First Report ◽

Aggregation Propensity ◽

Pekin Ducks

Pathogenic prion protein (PrPSc), converted from normal prion protein (PrPC), causes prion disease. Although prion disease has been reported in several mammalian species, chickens are known to show strong resistance to prion diseases. In addition to chickens, the domestic duck occupies a large proportion in the poultry industry and may be regarded as a potential resistant host against prion disease. However, the DNA sequence of the prion protein gene (PRNP) has not been reported in domestic ducks. Here, we performed amplicon sequencing targeting the duck PRNP gene with the genomic DNA of Pekin ducks. In addition, we aligned the PrP sequence of the Pekin duck with that of various species using ClustalW2 and carried out phylogenetic analysis using Molecular Evolutionary Genetics Analysis X (MEGA X). We also constructed the structural modeling of the tertiary and secondary structures in avian PrP using SWISS-MODEL. Last, we investigated the aggregation propensity on Pekin duck PrP using AMYCO. We first reported the DNA sequence of the PRNP gene in Pekin ducks and found that the PrP sequence of Pekin ducks is more similar to that of geese than to that of chickens and mallards (wild ducks). Interestingly, Pekin duck PrP showed a high proportion of β-sheets compared to that of chicken PrP, and a high aggregation propensity compared to that of avian PrPs. However, Pekin duck PrP with substitutions of chicken-specific amino acids showed reduced aggregation propensities. To the best of our knowledge, this is the first report on the genetic characteristics of the PRNP sequence in Pekin ducks.

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