Page 17 - L. Genetics and genomics
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Bovine spongiform encephalopathy (BSE)-associated polymorphisms of shadow of prion
protein gene (SPRN) in Korean native cattle (Hanwoo) and Holstein cattle
Yong-Chan Kim, Byung-Hoon Jeong
Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Republic of Korea
Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
Abstract Introduction
Bovine spongiform encephalopathy (BSE) is a fatal infectious Transmissible spongiform encephalopathies (TSEs) are
neurodegenerative disease caused by the accumulation of pathogenic neurodegenerative diseases in humans and animals that are associated
Sc
prion protein (PrP ) in the central nervous system (CNS), particularly in with the accumulation of abnormal prion protein (PrPSc) in brain tissue.
the brain. In a recent study, the shadow of prion protein (Sho), encoded by Bovine spongiform encephalopathy (BSE) belongs to TSEs, which also
the shadow of prion protein (SPRN) gene, accelerates the progression of include scrapie in sheep and goats, chronic wasting disease (CWD) in deer,
prion diseases, and a 12-bp insertion/deletion polymorphism in the coding and Creutzfeldt–Jakob disease (CJD), in humans. The origin of BSE is
region of the SPRN gene is associated with susceptibility to atypical BSE- still unclear; however, it has been postulated that BSE-infected cattle are
affected Polish cattle. To date, the genetic study of the SPRN gene in sporadic or infected through the meat and bone meal from scrapie-
Korean cattle has not been performed. In this study, we investigated the Hanwoo Holstein affected sheep. Consumption of BSE-infected meat is a major cause of
genotype and allele frequencies of SPRN polymorphisms in 193 Hanwoo variant CJD in humans. In cattle, several polymorphisms of PRNP gene
and 168 Holstein cattle and analyzed the linkage disequilibrium (LD) and PrP c have been reported in association with the BSE susceptibility. However,
haplotypes of SPRN polymorphisms. In addition, we compared the SP HD β αA β αB αC Signal peptide although gene-regulated polymorphisms play pivotal role in several
Hydrophobic
Octapeptide CHO CHO GPI region diseases, the polymorphisms of the PRNP gene only modulate the
distribution of the 12-bp insertion/deletion polymorphism between repeat region α-helix
atypical BSE-diagnosed Polish cattle and Korean cattle to evaluate the Shadoo β-sheet expression level of the PRNP gene by mediating the binding ability of
transcription factors and they do not induce misfolding of the prion
susceptibility of atypical BSE. Furthermore, we estimated a deleterious SP HD protein. Thus, several studies have tried to find novel candidate
Basic
effect of polymorphisms on the Sho protein using PROVEAN. We found a repeat region CHO GPI transcription factors and it has been suggested that genetic susceptibility
total of 7 polymorphisms, including 1 novel single nucleotide Doppel to BSE is able to be controlled by genomic regions other than the PRNP
polymorphism (SNP), c.231G>A. We also found significantly different locus. Previous studies have reported that polymorphisms of the shadow
distributions of genotype, allele and haplotype frequencies of 7 SP β αA β α B/B’ αC
CHO CHO GPI of prion protein gene (SPRN) were associated with susceptibility to CJD,
polymorphisms between Hanwoo and Korean Holstein cattle. In addition, scrapie and BSE. Although the association of prion diseases with
except for the weak LD between the 12-bp insertion/deletion polymorphisms in the SPRN gene has apparently existed, genetic studies
polymorphism and the c.360G>A SNP, all other polymorphisms showed of the SPRN gene in Korean cattle have not been performed thus far.
strong LDs among the 7 polymorphisms. Interestingly, Hanwoo cattle In the present study, we investigated the genotype and allele frequencies
showed more potential susceptible distribution in the genotype and allele of SPRN polymorphisms in Korean cattle. In addition, we analyzed the
frequencies of the 12-bp insertion/deletion polymorphisms of the SPRN linkage disequilibrium (LD) and haplotypes of SPRN polymorphisms.
gene than Holstein cattle. Finally, using PROVEAN, we found 1 novel Furthermore, we compared the distributions of the indel polymorphism
deleterious nonsynonymous SNP to Sho protein, c.110G>C (G37A). To the between atypical BSE-diagnosed Polish cattle and Korean cattle. Finally,
Shadoo protein of cattle predicted Shadoo protein of cattle predicted
best of our knowledge, this is the first study of the SPRN gene in Korean by the Swiss-PdbViewer by the Swiss model program we evaluated a deleterious effect of polymorphisms causing protein
cattle. sequence changes in the shadow of prion protein (Sho) using PROVEAN.
Results Conclusions
(A) (B) ◆ First, we investigated the genotype, allele and haplotype frequencies
of bovine SPRN polymorphisms in Korean cattle and the
significantly different distributions of genotype, allele and haplotype
frequencies of bovine SPRN polymorphisms between Hanwoo and
Holstein cattle.
◆ Second, we also found that Hanwoo cattle showed more potential
susceptible genetic features of the SPRN gene than Holstein cattle
using comparisons of genotype and allele distributions of a 12-bp
insertion/deletion polymorphism found in atypical BSE-infected
Polish cattle.
◆ Third, we estimated the impact of polymorphisms on the Sho protein
using an in silico analysis and found a novel candidate SNP, G37A,
which can induce structural or functional effects on the Sho protein.
To the best of our knowledge, this is the first report of the SPRN
Figure 1 (A) Gene map and polymorphisms identified in the shadow of prion protein gene (SPRN) on chromosome 26 in Korean cattle. The open reading frame (ORF) within exon 2 is
marked by a shaded block, and the 5’ and 3’ untranslated regions (UTRs) are indicated by a white block. The arrows indicate the 7 polymorphisms found in this study. The edged horizontal gene in Korean cattle.
bar indicates the region sequenced. Asterisks denote novel single nucleotide polymorphisms (SNPs). (B) Electropherogram of novel SNPs in the SPRN gene. colors indicate individual bases
References
of the DNA sequence using an ABI 3730 automatic sequencer (blue: cytosine; red: thymine; black: guanine; and green: adenine).
(A) (B)
◆ Beck, J. A. et al. Association of a null allele of SPRN with variant
Creutzfeldt-Jakob disease. J Med Genet 45, 813-817 (2008).
◆ Lampo, E. et al. Identification of polymorphisms in the ovine
Shadow of prion protein (SPRN) gene and assessment of their effect
on promoter activity and susceptibility for classical scrapie. Anim
Genet 41, 169-178 (2010).
◆ Peletto, S. et al. Association of an indel polymorphism in the 3'UTR
of the caprine SPRN gene with scrapie positivity in the central
nervous system. J Gen Virol 93, 1620-1623 (2012).
◆ Jeong, B. H., Jin, H. T., Carp, R. I., Kim, Y. S. Bovine spongiform
encephalopathy (BSE)-associated polymorphisms of the prion
protein (PRNP) gene in Korean native cattle. Anim Genet 44, 356-357
(2013).
◆ Kim, Y. C., Kim, S. K., Jeong, B. H. Scrapie susceptibility-associated
Figure 2 (A) Comparison of genotype frequencies on the c.199_210delGCCGCGGCGGGG (67_70AAAG) insertion/deletion polymorphism of the shadow of prion protein (SPRN) gene in
atypical BSE-affected Polish cattle and Korean cattle. (B) The comparison of allele frequencies on the c.199_210delGCCGCGGCGGGG (67_70AAAG) insertion/deletion polymorphism of indel polymorphism of shadow of prion protein gene (SPRN) in
the shadow of prion protein (SPRN) gene in atypical BSE-affected Polish cattle and Korean cattle. Parentheses indicate the number of cattle. Korean native black goats. Sci Rep 9, 15261 (2019).
Table 1. Genotype and allele frequencies of SPRN polymorphisms in Korean cattle. Table 3. Haplotype analysis of SPRN polymorphisms in Korean cattle.
Allele frequency,
Polymorphisms Breeds Total, n Genotype frequency, n (%) P value P value HWE Frequency
n (%) Haplotypes P value
c.110G>C (G37A) G/G G/C C/C G C Hanwoo (n=386) Holstein (n=336)
Hanwoo 193 192 (99.5) 1 (0.5) 0 (0) 1.0 385 (99.7) 1 (0.3) 1.0 0.971
Holstein 168 168 (100) 0 (0) 0 (0) 336 (100) 0 (0) - GCGWtGAG 206 (0.534) 212 (0.632) -
c.125C>T (A42V) C/C C/T T/T C T
Hanwoo 193 193 (100) 0 (0) 0 (0) 386 (100) 0 (0) -
Holstein 168 166 (98.8) 2 (1.2) 0 (0) 0.216 334 (99.4) 2 (0.6) 0.216 0.938 GCGWtGGG 139 (0.359) 77 (0.228) 0.0003
c.128G>A (R43K) G/G G/A A/A G A
Hanwoo 193 193 (100) 0 (0) 0 (0) 386 (100) 0 (0) -
Holstein 168 166 (98.8) 2 (1.2) 0 (0) 0.216 334 (99.4) 2 (0.6) 0.216 0.938 GCGWtGGA 19 (0.049) 40 (0.12) 0.0174
c.199_210delGC WT/WT WT/Del Del/Del WT Del
CGCGGCGGGG
(67_70delAAAG) Hanwoo 193 176 (91.2) 17 (8.8) 0 (0) < 0.0001 369 (95.6) 17 (4.4) < 0.0001 0.522 GCGDelGGG 15 (0.040) 0 (0.000) < 0.001
Holstein 168 168 (100) 0 (0) 0 (0) 336 (100) 0 (0) -
c.231G>A (A77A) G/G G/A A/A G A
Hanwoo 193 189 (97.9) 4 (2.1) 0 (0) 0.127 382 (99.0) 4 (1.0) 0.128 0.884 GCGWtAGG 4 (0.010) 0 (0.000) 0.06
Holstein 168 168 (100) 0 (0) 0 (0) 336 (100) 0 (0) -
c.288A>G (E96E) A/A A/G G/G A G
Hanwoo 193 52 (26.9) 101 (52.3) 40 (20.7) 205 (53.1) 181 (46.9) 0.481 GCGWtGAA 0 (0.000) 5 (0.014) 0.061
Holstein 168 73 (43.5) 71 (42.3) 24 (14.3) 0.004 217 (64.6) 119 (35.4) 0.0019 0.324
c.360G>A (G120G) G/G G/A A/A G A
Hanwoo 193 174 (90.2) 19 (9.8) 0 (0) 0.0004 367 (95.1) 19 (4.9) 0.0001 0.472 Others 3 (0.08) 2 (0.006) -
Holstein 168 133 (79.2) 26 (15.5) 9 (5.4) 292 (86.9) 44 (13.1) < 0.001
Table 2. Linkage disequilibrium (LD) analysis of SPRN polymorphisms in Korean cattle. Table 4. In silico evaluation of the impact of SPRN polymorphisms on the Sho protein.
c.110G>C c.125C>T c.128G>A c.199_210del c.231G>A c.288A>G c.360G>A Variants Score Prediction (cutoff= -2.5)
c.110G>C - 1.0 1.0 1.0 1.0 1.0 1.0
c.110G>C G37A -4.635 Deleterious
c.125C>T - - 1.0 1.0 1.0 1.0 1.0
c.128G>A - - - 1.0 1.0 1.0 1.0 c.125C>T A42V -1.890 Neutral
c.199_210del - - - - 1.0 0.832 0.77
c.231G>A - - - - - 1.0 1.0 c.128G>A R43K -2.377 Neutral
c.288A>G - - - - - - 0.864
c.199_210delGCCGCGGCGGGG 67_70delAAAG -11.067 Deleterious
c.360G>A - - - - - - -
