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Choi DI, Zayed M, Jeong BH. Novel Single-Nucleotide Polymorphisms (SNPs) and Genetic Studies of the Shadow of Prion Protein ( SPRN) in Quails. Animals (Basel) 2024; 14:2481. [PMID: 39272266 PMCID: PMC11394228 DOI: 10.3390/ani14172481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/13/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Prion diseases are a group of deadly neurodegenerative disorders caused by the accumulation of the normal prion protein (PrPC) into misfolding pathological conformations (PrPSc). The PrP gene is essential for the development of prion diseases. Another candidate implicated in prion pathogenesis is the shadow of the prion protein (SPRN) gene. To date, genetic polymorphisms of the SPRN gene and the structure of the Sho protein have not been explored in quails. We used polymerase chain reaction (PCR) to amplify the SPRN gene sequence and then conducted Sanger DNA sequencing to identify the genetic polymorphisms in quail SPRN. Furthermore, we examined the genotype, allele, and haplotype frequencies, and assessed the linkage disequilibrium among the genetic polymorphisms of the SPRN gene in quails. Additionally, we used in silico programs such as MutPred2, SIFT, MUpro, AMYCO, and SODA to predict the pathogenicity of non-synonymous single-nucleotide polymorphisms (SNPs). Alphafold2 predicted the 3D structure of the Sho protein in quails. The results showed that a total of 13 novel polymorphisms were found in 106 quails, including 4 non-synonymous SNPs. Using SIFT and MUpro in silico programs, three out of the four non-synonymous SNPs (A68T, L74P, and M105I) were predicted to have deleterious effects on quail Sho. Furthermore, the 3D structure of quail Sho was predicted to be similar to that of chicken Sho. To our knowledge, this is the first report to investigate the genetic and structural properties of the quail SPRN gene.
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Affiliation(s)
- Da-In Choi
- Korea Zoonosis Research Institute, Jeonbuk National University, 820-120, Hana-ro, Iksan 54531, Republic of Korea
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Mohammed Zayed
- Korea Zoonosis Research Institute, Jeonbuk National University, 820-120, Hana-ro, Iksan 54531, Republic of Korea
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Surgery, College of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, 820-120, Hana-ro, Iksan 54531, Republic of Korea
- Department of Bioactive Material Sciences, Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Choi DI, Zayed M, Kim YC, Jeong BH. Novel polymorphisms and genetic studies of the shadow of prion protein gene ( SPRN) in pheasants. Front Vet Sci 2024; 11:1399548. [PMID: 38812560 PMCID: PMC11135176 DOI: 10.3389/fvets.2024.1399548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024] Open
Abstract
Background Prion 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. Methods Here, 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. Results In 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. Conclusion To 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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Affiliation(s)
- Da-In Choi
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
| | - Mohammed Zayed
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
- Department of Surgery, College of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Yong-Chan Kim
- Department of Biological Sciences, Andong National University, Andong, Republic of Korea
| | - Byung-Hoon Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
- Department of Bioactive Material Sciences and Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju, Republic of Korea
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Giráldez F, Santos N, Santos A, Valdés C, López S, Andrés S. Fattening lambs with divergent residual feed intakes and weight gains: Unravelling mechanisms driving feed efficiency. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.114821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Quach TT, Stratton HJ, Khanna R, Kolattukudy PE, Honnorat J, Meyer K, Duchemin AM. Intellectual disability: dendritic anomalies and emerging genetic perspectives. Acta Neuropathol 2021; 141:139-158. [PMID: 33226471 PMCID: PMC7855540 DOI: 10.1007/s00401-020-02244-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) corresponds to several neurodevelopmental disorders of heterogeneous origin in which cognitive deficits are commonly associated with abnormalities of dendrites and dendritic spines. These histological changes in the brain serve as a proxy for underlying deficits in neuronal network connectivity, mostly a result of genetic factors. Historically, chromosomal abnormalities have been reported by conventional karyotyping, targeted fluorescence in situ hybridization (FISH), and chromosomal microarray analysis. More recently, cytogenomic mapping, whole-exome sequencing, and bioinformatic mining have led to the identification of novel candidate genes, including genes involved in neuritogenesis, dendrite maintenance, and synaptic plasticity. Greater understanding of the roles of these putative ID genes and their functional interactions might boost investigations into determining the plausible link between cellular and behavioral alterations as well as the mechanisms contributing to the cognitive impairment observed in ID. Genetic data combined with histological abnormalities, clinical presentation, and transgenic animal models provide support for the primacy of dysregulation in dendrite structure and function as the basis for the cognitive deficits observed in ID. In this review, we highlight the importance of dendrite pathophysiology in the etiologies of four prototypical ID syndromes, namely Down Syndrome (DS), Rett Syndrome (RTT), Digeorge Syndrome (DGS) and Fragile X Syndrome (FXS). Clinical characteristics of ID have also been reported in individuals with deletions in the long arm of chromosome 10 (the q26.2/q26.3), a region containing the gene for the collapsin response mediator protein 3 (CRMP3), also known as dihydropyrimidinase-related protein-4 (DRP-4, DPYSL4), which is involved in dendritogenesis. Following a discussion of clinical and genetic findings in these syndromes and their preclinical animal models, we lionize CRMP3/DPYSL4 as a novel candidate gene for ID that may be ripe for therapeutic intervention.
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Affiliation(s)
- Tam T Quach
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Jérome Honnorat
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- SynatAc Team, Institut NeuroMyoGène, Lyon, France
| | - Kathrin Meyer
- The Research Institute of Nationwide Children Hospital, Columbus, OH, 43205, USA
- Department of Pediatric, The Ohio State University, Columbus, OH, 43210, USA
| | - Anne-Marie Duchemin
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH, 43210, USA.
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Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Fernández Escámez PS, Gironés R, Herman L, Koutsoumanis K, Lindqvist R, Nørrung B, Robertson L, Ru G, Sanaa M, Skandamis P, Speybroeck N, Simmons M, Kuile BT, Threlfall J, Wahlström H, Acutis PL, Andreoletti O, Goldmann W, Langeveld J, Windig JJ, Ortiz Pelaez A, Snary E. Genetic resistance to transmissible spongiform encephalopathies (TSE) in goats. EFSA J 2017; 15:e04962. [PMID: 32625625 PMCID: PMC7010077 DOI: 10.2903/j.efsa.2017.4962] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Breeding programmes to promote resistance to classical scrapie, similar to those for sheep in existing transmissible spongiform encephalopathies (TSE) regulations, have not been established in goats. The European Commission requested a scientific opinion from EFSA on the current knowledge of genetic resistance to TSE in goats. An evaluation tool, which considers both the weight of evidence and strength of resistance to classical scrapie of alleles in the goat PRNP gene, was developed and applied to nine selected alleles of interest. Using the tool, the quality and certainty of the field and experimental data are considered robust enough to conclude that the K222, D146 and S146 alleles both confer genetic resistance against classical scrapie strains known to occur naturally in the EU goat population, with which they have been challenged both experimentally and under field conditions. The weight of evidence for K222 is greater than that currently available for the D146 and S146 alleles and for the ARR allele in sheep in 2001. Breeding for resistance can be an effective tool for controlling classical scrapie in goats and it could be an option available to member states, both at herd and population levels. There is insufficient evidence to assess the impact of K222, D146 and S146 alleles on susceptibility to atypical scrapie and bovine spongiform encephalopathy (BSE), or on health and production traits. These alleles are heterogeneously distributed across the EU Member States and goat breeds, but often at low frequencies (< 10%). Given these low frequencies, high selection pressure may have an adverse effect on genetic diversity so any breeding for resistance programmes should be developed at Member States, rather than EU level and their impact monitored, with particular attention to the potential for any negative impact in rare or small population breeds.
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Wang S, Zhao H, Zhang Y. Advances in research on Shadoo, shadow of prion protein. CHINESE SCIENCE BULLETIN-CHINESE 2014. [DOI: 10.1007/s11434-014-0129-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zhao H, Liu LL, Du SH, Wang SQ, Zhang YP. Comparative analysis of the Shadoo gene between cattle and buffalo reveals significant differences. PLoS One 2012; 7:e46601. [PMID: 23071594 PMCID: PMC3468620 DOI: 10.1371/journal.pone.0046601] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 09/01/2012] [Indexed: 12/03/2022] Open
Abstract
Background While prions play a central role in the pathogenesis of transmissible spongiform encephalopathies, the biology of these proteins and the pathophysiology of these diseases remain largely unknown. Since no case of bovine spongiform encephalopathy (BSE) has ever been reported in buffalo despite their phylogenetic proximity to cattle, genetic differences may be driving the different susceptibilities of these two species to BSE. We thus hypothesized that differences in expression of the most recently identified member of the prion family or Shadoo (SPRN) gene may relate to these species-specific differences. Principal Findings We first analyzed and compared the polymorphisms of the SPRN gene (∼4.4 kb), including the putative promoter, coding and 3′ regions, and further verified the entire ORF and putative promoter. This yielded a total of 117 fixed differences, remarkably: 1) a 12-bp insertion/deletion polymorphism in the hydrophobic domain of the cattle but not buffalo gene, introducing a four amino acid expansion/contraction in a series of 5 tandem Ala/Gly-containing repeats; 2) two fixed missense mutations (102Ser→Gly and 119Thr→Ala), and three missense mutations (92Pro>Thr/Met, 122Thr>Ile and 139Arg>Trp) in the coding region presenting different (P<0.05) genotypic and allelic frequency distributions between cattle and buffalo; and, 3) functional luciferase-reporter experiments for the predicted promoter region, consistent with a significantly higher activity in buffalo than cattle. Supporting these findings, immunoblotting revealed higher relative expression levels of Sho protein in cerebrum from buffalo than from cattle. In addition, for cattle, highest Sho expression was detected in obex, as compared to cerebrum or cerebellum. Significance Our findings support Sho as a non-PrP specific marker for prion infections, with obex as the best tissue source for the detection of Sho in TSE rapid tests. Moreover, these discoveries may prove advantageous for further understanding the biology of prion diseases.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Binding Sites
- Brain/metabolism
- Buffaloes/genetics
- Cattle/genetics
- Encephalopathy, Bovine Spongiform/genetics
- Gene Components
- Gene Expression
- Gene Frequency
- Genes, Reporter
- INDEL Mutation
- Luciferases, Renilla/biosynthesis
- Luciferases, Renilla/genetics
- Mutation, Missense
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Organ Specificity
- Polymorphism, Genetic
- Protein Structure, Tertiary
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Hui Zhao
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, People’s Republic of China
| | - Lin-Lin Liu
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, People’s Republic of China
| | - Shou-Hui Du
- School of Life Science, Yunnan University, Kunming, People’s Republic of China
| | - Si-Qi Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, People’s Republic of China
| | - Ya-Ping Zhang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, People’s Republic of China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People’s Republic of China
- * E-mail:
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PRNP and SPRN genes polymorphism in atypical bovine spongiform encephalopathy cases diagnosed in Polish cattle. J Appl Genet 2012; 53:337-42. [PMID: 22723200 DOI: 10.1007/s13353-012-0102-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 05/21/2012] [Accepted: 05/31/2012] [Indexed: 10/28/2022]
Abstract
Polymorphisms in the coding region of the prion protein gene (PRNP) have been associated with the susceptibility and incubation period of prion diseases in humans and sheep. However, polymorphisms in this part of the bovine PRNP gene do not affect the classical bovine spongiform encephalopathy (BSE) susceptibility in cattle. Studies carried out in Germany have shown that insertion/deletion-type polymorphisms located in the promoter region of the bovine prion gene are possible genetic factors modulating BSE susceptibility by changing the level of PRNP expression. No such association was observed for atypical BSE cases; however, due to the rare nature of the disease, these results should be confirmed. Additionally, a single nonsynonymous mutation in PRNP codon 211 (E211K) was described in one H-type BSE case in the USA; however, it was not found in any other cases. Here, we performed genetic characterization of PRNP promoter indel variations and determined the polymorphism of open reading frames (ORFs) of PRNP and bovine prion-like Shadoo (SPRN) genes in six Polish atypical BSE cases and compared these results to the population of clinically healthy Polish Holstein cattle. No potentially pathogenic mutations were found in the PRNP ORF in atypical BSE-affected cattle, but our study showed a high frequency of deletions at the indel loci of PRNP promoter in these animals. Additionally, a rare sequence variation in the SPRN protein-coding sequence was found in one L-type atypical BSE-affected animal.
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Piestrzyńska-Kajtoch A, Gurgul A, Polak MP, Smołucha G, Zmudziński JF, Rejduch B. Characterization of PRNP and SPRN coding regions from atypical scrapie cases diagnosed in Poland. Mol Biol Rep 2011; 39:2575-83. [PMID: 21674189 DOI: 10.1007/s11033-011-1010-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 06/02/2011] [Indexed: 10/18/2022]
Abstract
Scrapie, a fatal transmissible spongiform encephalopathy (TSE) occurs in two phenotypes: classical and atypical. Many authors point out that the polymorphism of three codons (136, 154, 171) of the PRNP (PrP gene) is associated with a sheep susceptibility to classical scrapie. Until now, only one PRNP gene variant coding phenylalanine at codon 141 has been found to be associated with atypical scrapie. Another recently identified and interesting candidate gene for scrapie susceptibility in sheep is an SPRN gene coding for Shadoo protein (Sho). Sho is a highly interspecies conserved protein and an insertion/deletion (indel) found in a sheep Sho gene was associated with classical scrapie occurrence. Here we determined the polymorphism of PRNP and SPRN genes in nine atypical scrapie cases (six in native born sheep and three in imported sheep) and compared these results with a control group of healthy animals comprising six corresponding Polish sheep breeds. In atypical scrapie cases five PRNP diplotypes were identified: A(136)R(154)Q(171)/ARQ, AHQ/ARQ, ARR/ARQ, ARR/AHQ and AHQ/AHQ. The ARR/AHQ diplotype was found only in imported sheep. A previously unobserved SNP in PRNP (E224K) was also found in both atypical scrapie and in a few control animals. In the ORF of the SPRN gene, six SNPs and one indel were identified. None of these variations was exclusive for scrapie animals and they were probably, naturally occurring polymorphisms. Special attention was given to the 6-bp indel SPRN polymorphism which was previously associated with classical scrapie occurrence.
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Affiliation(s)
- Agata Piestrzyńska-Kajtoch
- Department of Animal Immuno- and Cytogenetics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice n Krakow, Poland
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Westaway D, Daude N, Wohlgemuth S, Harrison P. The PrP-Like Proteins Shadoo and Doppel. Top Curr Chem (Cham) 2011; 305:225-56. [DOI: 10.1007/128_2011_190] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Lampo E, Van den Broeck W, Willemarck N, Van Poucke M, Casteleyn CR, De Spiegelaere W, Van Zeveren A, Peelman LJ. Distribution of the Shadoo protein in the ovine brain assessed by immunohistochemistry. Res Vet Sci 2010; 90:372-8. [PMID: 20667569 DOI: 10.1016/j.rvsc.2010.06.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 06/14/2010] [Accepted: 06/28/2010] [Indexed: 11/18/2022]
Abstract
Shadow of prion protein is a gene potentially involved in the pathogenesis of prion diseases. However, the Shadoo protein encoded by this gene has not yet been studied in sheep, an important species in prion matters. Therefore, we developed a polyclonal antibody against ovine Shadoo and assessed the presence and distribution of this protein in the ovine brain by immunohistochemistry. The strongest staining level was found in the cerebellum (especially in the Purkinje cells) and in the pons, but cerebrum, hippocampus, pituitary gland, medulla oblongata, thalamus and hypothalamus were also immunopositive. Remarkably, a typical granular pattern was seen in most of the tested brain tissues, which might indicate that Shadoo is primarily expressed at synapses. The results of this study and the availability of an ovine anti-Shadoo antibody can contribute to future research on the function of Shadoo and on its potential involvement in prion diseases.
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Affiliation(s)
- E Lampo
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
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Van den Broeke A, Van Poucke M, Marcos-Carcavilla A, Hugot K, Hayes H, Bertaud M, Van Zeveren A, Peelman LJ. Characterization of the ovine ribosomal protein SA gene and its pseudogenes. BMC Genomics 2010; 11:179. [PMID: 20233419 PMCID: PMC2850357 DOI: 10.1186/1471-2164-11-179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 03/16/2010] [Indexed: 12/15/2022] Open
Abstract
Background The ribosomal protein SA (RPSA), previously named 37-kDa laminin receptor precursor/67-kDa laminin receptor (LRP/LR) is a multifunctional protein that plays a role in a number of pathological processes, such as cancer and prion diseases. In all investigated species, RPSA is a member of a multicopy gene family consisting of one full length functional gene and several pseudogenes. Therefore, for studies on RPSA related pathways/pathologies, it is important to characterize the whole family and to address the possible function of the other RPSA family members. The present work aims at deciphering the RPSA family in sheep. Results In addition to the full length functional ovine RPSA gene, 11 other members of this multicopy gene family, all processed pseudogenes, were identified. Comparison between the RPSA transcript and these pseudogenes shows a large variety in sequence identities ranging from 99% to 74%. Only one of the 11 pseudogenes, i.e. RPSAP7, shares the same open reading frame (ORF) of 295 amino acids with the RPSA gene, differing in only one amino acid. All members of the RPSA family were annotated by comparative mapping and fluorescence in situ hybridization (FISH) localization. Transcription was investigated in the cerebrum, cerebellum, spleen, muscle, lymph node, duodenum and blood, and transcripts were detected for 6 of the 11 pseudogenes in some of these tissues. Conclusions In the present work we have characterized the ovine RPSA family. Our results have revealed the existence of 11 ovine RPSA pseudogenes and provide new data on their structure and sequence. Such information will facilitate molecular studies of the functional RPSA gene taking into account the existence of these pseudogenes in the design of experiments. It remains to be investigated if the transcribed members are functional as regulatory non-coding RNA or as functional proteins.
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Affiliation(s)
- Alice Van den Broeke
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
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13
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Lampo E, Duchateau L, Schepens B, Van Poucke M, Saelens X, Erkens T, Van Zeveren A, Peelman LJ. 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 2009; 41:169-78. [PMID: 19917049 DOI: 10.1111/j.1365-2052.2009.01984.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Shadow of prion protein (SPRN) is an interesting candidate gene thought to be involved in prion pathogenesis. In humans, an association has already been discovered between mutations in SPRN and the incidence of variant and sporadic Creutzfeldt-Jakob disease. However, in sheep, the effect of mutations in SPRN is largely unknown. Therefore, we analysed the presence of mutations in the entire ovine SPRN gene, their association with scrapie susceptibility and their effect on SPRN promoter activity. In total, 26 mutations were found: seven in the promoter region, four in intron 1, seven in the coding sequence and eight in the 3' untranslated region. The mutations detected in the coding sequence and the promoter region were subsequently analysed in more detail. In the coding sequence, a polymorphism causing a deletion of two alanines was found to be associated with susceptibility for classical scrapie in sheep. Furthermore, a functional analysis of deletion constructs of the ovine SPRN promoter revealed that the region 464 to 230 bp upstream of exon 1 (containing a putative AP-2 and putative Sp1 binding sites) is of functional importance for SPRN transcription. Six mutations in the SPRN promoter were also found to alter the promoter activity in vitro. However, no association between any of these promoter mutations and susceptibility for classical scrapie was found.
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Affiliation(s)
- E Lampo
- Department of Nutrition, Genetics and Ethology, Ghent University, Merelbeke, Belgium
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14
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Young R, Passet B, Vilotte M, Cribiu EP, Béringue V, Le Provost F, Laude H, Vilotte JL. The prion or the related Shadoo protein is required for early mouse embryogenesis. FEBS Lett 2009; 583:3296-300. [PMID: 19766638 DOI: 10.1016/j.febslet.2009.09.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 09/14/2009] [Indexed: 10/25/2022]
Abstract
The prion protein PrP has a key role in transmissible spongiform encephalopathies but its biological function remains largely unknown. Recently, a related protein, Shadoo, was discovered. Its biological properties and brain distribution partially overlap that of PrP. We report that the Shadoo-encoding gene knockdown in PrP-knockout mouse embryos results in a lethal phenotype, occurring between E8 and E11, not observed on the wild-type genetic background. It reveals that these two proteins play a shared, crucial role in mammalian embryogenesis, explaining the lack of severe phenotype in PrP-knockout mammals, an appreciable step towards deciphering the biological role of this protein family.
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Affiliation(s)
- Rachel Young
- INRA-UMR1313, Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, 78350 Jouy-en-Josas, France
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15
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Daude N, Wohlgemuth S, Rogaeva E, Farid AH, Heaton M, Westaway D. Frequent missense and insertion/deletion polymorphisms in the ovine Shadoo gene parallel species-specific variation in PrP. PLoS One 2009; 4:e6538. [PMID: 19657386 PMCID: PMC2716538 DOI: 10.1371/journal.pone.0006538] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 07/15/2009] [Indexed: 11/18/2022] Open
Abstract
Background The cellular prion protein PrPC is encoded by the Prnp gene. This protein is expressed in the central nervous system (CNS) and serves as a precursor to the misfolded PrPSc isoform in prion diseases. The prototype prion disease is scrapie in sheep, and whereas Prnp exhibits common missense polymorphisms for V136A, R154H and Q171R in ovine populations, genetic variation in mouse Prnp is limited. Recently the CNS glycoprotein Shadoo (Sho) has been shown to resemble PrPC both in a central hydrophobic domain and in activity in a toxicity assay performed in cerebellar neurons. Sho protein levels are reduced in prion infections in rodents. Prompted by these properties of the Sho protein we investigated the extent of natural variation in SPRN. Principal Findings Paralleling the case for ovine versus human and murine PRNP, we failed to detect significant coding polymorphisms that alter the mature Sho protein in a sample of neurologically normal humans, or in diverse strains of mice. However, ovine SPRN exhibited 4 missense mutations and expansion/contraction in a series of 5 tandem Ala/Gly-containing repeats R1-R5 encoding Sho's hydrophobic domain. A Val71Ala polymorphism and polymorphic expansion of wt 67(Ala)3Gly70 to 67(Ala)5Gly72 reached frequencies of 20%, with other alleles including Δ67–70 and a 67(Ala)6Gly73 expansion. Sheep V71, A71, Δ67–70 and 67(Ala)6Gly73 SPRN alleles encoded proteins with similar stability and posttranslational processing in transfected neuroblastoma cells. Significance Frequent coding polymorphisms are a hallmark of the sheep PRNP gene and our data indicate a similar situation applies to ovine SPRN. Whether a common selection pressure balances diversity at both loci remains to be established.
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Affiliation(s)
- Nathalie Daude
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Serene Wohlgemuth
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
| | - Ekaterina Rogaeva
- Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - A. Hossein Farid
- Department of Animal Science, Nova Scotia Agricultural College, Truro, Nova Scotia, Canada
| | - Mike Heaton
- United States Department of Agriculture, U. S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - David Westaway
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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16
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Stewart P, Shen C, Zhao D, Goldmann W. Genetic analysis of the SPRN gene in ruminants reveals polymorphisms in the alanine-rich segment of shadoo protein. J Gen Virol 2009; 90:2575-2580. [PMID: 19515828 DOI: 10.1099/vir.0.011494-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Prion diseases in ruminants, especially sheep scrapie, cannot be fully explained by PRNP genetics, suggesting the influence of a second modulator gene. The SPRN gene is a good candidate for this role. The SPRN gene encodes the shadoo protein (Sho) which has homology to the PRNP gene encoding prion protein (PrP). Murine Sho has a similar neuroprotective activity to PrP and SPRN gene variants are associated with human prion disease susceptibility. SPRN gene sequences were obtained from 14 species in the orders Artiodactyla and Rodentia. We report here the sequences of more than 20 different Sho proteins that have arisen due to single amino acid substitutions and amino acid deletions or insertions. All Sho sequences contained an alanine-rich sequence homologous to a hydrophobic region with amyloidogenic characteristics in PrP. In contrast with PrP, the Sho sequence showed variability in the number of alanine residues.
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Affiliation(s)
- Paula Stewart
- Roslin Institute and R(D)SVS, University of Edinburgh, Neuropathogenesis Division, Roslin, Midlothian, UK
| | - Cuicui Shen
- National TSE Laboratory, College of Veterinary Medicine, China Agriculture University, Beijing, PR China.,Roslin Institute and R(D)SVS, University of Edinburgh, Neuropathogenesis Division, Roslin, Midlothian, UK
| | - Deming Zhao
- National TSE Laboratory, College of Veterinary Medicine, China Agriculture University, Beijing, PR China
| | - Wilfred Goldmann
- Roslin Institute and R(D)SVS, University of Edinburgh, Neuropathogenesis Division, Roslin, Midlothian, UK
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17
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Gossner AG, Bennet N, Hunter N, Hopkins J. Differential expression of Prnp and Sprn in scrapie infected sheep also reveals Prnp genotype specific differences. Biochem Biophys Res Commun 2008; 378:862-6. [PMID: 19070601 DOI: 10.1016/j.bbrc.2008.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 12/02/2008] [Indexed: 01/25/2023]
Abstract
The central role for PrP in the pathogenesis of the transmissible spongiform encephalopathies (TSEs) is illustrated by the resistance of Prnp(0/0) mice to disease and by the inverse association of Prnp gene dosage with incubation period. Understanding the role of PrP(C) in TSEs necessitates knowledge of expression levels of the Prnp gene during the development of disease. SSBP/1 scrapie shows a defined pattern of disease progression and here we show that Prnp and shadow of PrP (Sprn) are differentially expressed in different brain areas and lymphoid tissues. Counter-intuitively we found that there is no positive correlation between expression of Prnp or Sprn and patterns of disease progression. Prnp and Sprn expression levels are both influenced by Prnp genotype; although the scrapie-sensitive VRQ/VRQ sheep did not express the highest level of either. In addition, infection with SSBP/1 scrapie seems to have little effect on either PrP or Shadoo expression levels.
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Affiliation(s)
- A G Gossner
- Division of Infection & Immunity, The Roslin Institute, Royal Dick School of Veterinary Studies, University of Edinburgh, Summerhall, Edinburgh, UK
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18
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Lampo E, Van Poucke M, Vandesompele J, Erkens T, Van Zeveren A, Peelman LJ. Positive correlation between relative mRNA expression of PRNP and SPRN in cerebral and cerebellar cortex of sheep. Mol Cell Probes 2008; 23:60-4. [PMID: 19059475 DOI: 10.1016/j.mcp.2008.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 11/12/2008] [Accepted: 11/13/2008] [Indexed: 10/21/2022]
Abstract
SPRN is an interesting new member of the PRNP family because of its sequence homology with the hydrophobic region of PRNP, its expression in brain tissue and its PrP-like properties in functional experiments on Prnp(0/0) mice. In this study, we investigated by quantitative real-time PCR the relative mRNA expression levels of SPRN and PRNP in sheep cerebrum and cerebellum and the mutual relationship between these expression levels. Analysis of PRNP and SPRN mRNA expression levels in 45 cerebral cortex and 47 cerebellar cortex samples showed that the PRNP expression level was significantly higher (p<0.05) in cerebellum than in cerebrum, while no significant difference was detected for SPRN between these tissues. The expression level varied clearly more in cerebrum than in cerebellum for both genes tested, and the variation was larger for SPRN than for PRNP in both types of brain tissue. Remarkably, the mRNA expression levels of PRNP and SPRN showed a highly significant positive correlation in both cerebrum (p<0.0001) and cerebellum (p<0.001). This positive correlation might indicate co-regulation between these genes. Further investigation on the causal nature of this correlation may provide new insights into prion pathogenesis.
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Affiliation(s)
- Evelyne Lampo
- Department of Nutrition, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
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