Novel Single Nucleotide Polymorphisms (SNPs) and Genetic Features of the Prion Protein Gene (PRNP) in Quail (Coturnix japonica)

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.

A Review of Fifteen Years Developing Computational Tools to Study Protein Aggregation

“…At that time, its performance was better than previous state-of-the-art predictors. Since its publication, AMYCO implementation has been used to gain insights into prion evolution, especially the appearance and conservation of prion-protective or -enhancing mutations in different mammals [103][104][105][106] and birds [107]. It has also been used to identify prion disease-related somatic mutation in the prion gene from cancer patients [108] or to rationalize the effect of point mutations in the hnRNPDL gene on the onset of a rare type of muscular atrophy [109].…”

The first report of polymorphisms of the prion protein gene (PRNP) in Pekin ducks (Anas platyrhynchos domestica)

“…Of them, c.163_180delAACCCAGGGTACCCCCAT is a hexapeptide deletion polymorphism in unit (U) 2 of the tandem repeat spanning U1 to U7 (32). Interestingly, a substantial number of polymorphisms, consisting of 33 SNPs in quails and 28 SNPs along with six insertion/deletion polymorphisms in pheasants, were identified within their PRNP gene (41,42). Moreover, when compared to chickens, the structure of the hexapeptide repeat region in both quails and pheasants remains highly conserved.…”

“…In addition, when a substitution to incorporate a specific amino acid from chicken PrP occurred in the PrP sequence of domestic ducks, the amyloid propensity was observed to decrease, compared with that of wildtype duck (33). Furthermore, polymorphisms of the PRNP gene have been identified in many animals (10,31,32,(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44). However, no studies on PRNP polymorphisms in domestic ducks have yet been reported.…”