PRND Genes Research Articles

The first report of single nucleotide polymorphisms in the open reading frame of the prion-like protein gene in rabbits.

Natural cases of prion disease have not been reported in rabbits, and prior attempts to identify a prion conversion agent have been unsuccessful. However, recent applications of prion seed amplifying experimental techniques have sparked renewed interest in the potential susceptibility of rabbits to prion disease infections. Among several factors related to prion disease, polymorphisms within the prion-like protein gene (PRND), a member of the prion protein family, have been reported as significantly associated with disease susceptibility in various species. Therefore, our study aimed to investigate polymorphisms in the PRND gene of rabbits and analyze their genetic characteristics. Genomic DNA was extracted from 207 rabbit samples to investigate leporine PRND polymorphisms. Subsequently, amplicon sequencing targeting the coding region of the leporine PRND gene was conducted. Additionally, linkage disequilibrium (LD) analysis was employed to assess the connection within and between loci. The impact of non-synonymous single nucleotide polymorphisms (SNPs) on the Doppel protein was evaluated using PolyPhen-2. We found nine novel SNPs in the leporine PRND gene: c.18A > G, c.76G > C, c.128C > T, c.146C > T, c.315A > G, c.488G > A, c.525G > C, c.544G > A, and c.579A > G. Notably, seven of these PRND SNPs, excluding c.525G > C and c.579A > G, exhibited strong LD values exceeding 0.3. In addition, LD analysis confirmed a robust link between PRNP SNP c.234C > T and PRND SNPs at c.525G > C and c.579A > G. Furthermore, according to PolyPhen-2 and SIFT analyses, the four non-synonymous SNPs were predicted to have deleterious effects on the function or structure of the Doppel protein. However, PANTHER and Missense3D did not indicate such effects. In this paper, we have identified novel SNPs in the rabbit PRND gene and predicted their potential detrimental effects on protein function or structure through four non-synonymous SNPs. Additionally, we observed a genetic linkage between SNPs in the PRND and PRNP genes. These findings may provide insights into understanding the characteristics of rabbits as partially resistant species. To the best of our knowledge, this study is the first to genetically characterize PRND SNPs in rabbits.

Effect of arginine-induced motility and capacitation on RNA population in goat spermatozoa.

In vitro capacitation is essential in assisted reproductive technologies (ART) for embryo production. Recently, arginine has been proven to enhance capacitation in mammalian spermatozoa. However, the detailed mechanism of action of arginine remains elusive. This study investigated the effect of arginine-induced capacitation and motility enhancement on the spermatozoal RNA (spRNA) population in goats. Goat spermatozoa were treated with arginine for up to six hours and compared with non-treated or PHE (penicillamine, hypotaurine, and epinephrine)-treated spermatozoa at different intervals (0, 1, 2, 4, and 6 hours). Sperm parameters, including viability, individual motility, capacitation, acrosome reaction, and ROS production, were evaluated. The spRNA population was analyzed by short-read RNA sequencing (RNA-seq). The percentage of capacitated (73.21 ± 4.22%) and acrosome reacted (18.35 ± 0.56%) spermatozoa was highest in arginine treatment, while PHE treatment showed the highest percentage (79.82 ± 4.31%) of motile spermatozoa from 0 to 4 hours of incubation. RNA-seq analysis identified 1,321 differentially expressed genes (DEGs) in arginine-treated spermatozoa compared to the control. The PGK2, RNASE10, ODF1, and ROPN1L genes involved in sperm motility and ACR, DKKL1, KCNJ11, and PRND genes involved in the capacitation process were upregulated in arginine-treated spermatozoa. The DEGs regulate sperm capacitation-related cAMP-PKA, PI3-Akt, calcium, and MAPK signaling pathways. The arginine-induced capacitation and enhanced sperm motility were associated with the upregulation of several genes involved in sperm motility and capacitation pathways. The comparative study also suggests that arginine may be used in lieu of PHE for motility enhancement and in vitro capacitation of goat spermatozoa.

The First Report of Polymorphisms and Genetic Features of the prion-like Protein Gene (PRND) in a Prion Disease-Resistant Animal, Dog.

Prion disease has displayed large infection host ranges among several species; however, dogs have not been reported to be infected and are considered prion disease-resistant animals. Case-controlled studies in several species, including humans and cattle, indicated a potent association of prion protein gene (PRNP) polymorphisms in the progression of prion disease. Thus, because of the proximal location and similar structure of the PRNP gene among the prion gene family, the prion-like protein gene (PRND) was noted as a novel candidate gene that contributes to prion disease susceptibility. Several case-controlled studies have confirmed the relationship of the PRND gene with prion disease vulnerability, and strong genetic linkage disequilibrium blocks were identified in prion-susceptible species between the PRNP and PRND genes. However, to date, polymorphisms of the dog PRND gene have not been reported, and the genetic linkage between the PRNP and PRND genes has not been examined thus far. Here, we first investigated dog PRND polymorphisms in 207 dog DNA samples using direct DNA sequencing. A total of four novel single nucleotide polymorphisms (SNPs), including one nonsynonymous SNP (c.149G>A, R50H), were identified in this study. We also found two major haplotypes among the four novel SNPs. In addition, we compared the genotype and allele frequencies of the c.149G>A (R50H) SNP and found significantly different distributions among eight dog breeds. Furthermore, we annotated the c.149G>A (R50H) SNP of the dog PRND gene using in silico tools, PolyPhen-2, PROVEAN, and PANTHER. Finally, we examined linkage disequilibrium between the PRNP and PRND genes in dogs. Interestingly, we did not find a strong genetic linkage between these two genes. To the best of our knowledge, this was the first genetic study of the PRND gene in a prion disease-resistant animal, a dog.

The prion-related protein (testis-specific) gene (PRNT) is highly polymorphic in Portuguese sheep.

The objective of this study was to search for polymorphisms in the ovine prion-related protein (testis-specific) gene (PRNT). Sampling included 567 sheep from eight Portuguese breeds. The PRNT gene-coding region was analyzed by single-strand conformation polymorphism and sequencing, allowing the identification of the first ovine PRNT polymorphisms, in codons 6, 38, 43 and 48: c.17C>T (p.Ser6Phe, which disrupts a consensus arginine-X-X-serine/threonine motif); c.112G>C (p.Gly38>Arg); c.129T>C and c.144A>G (synonymous) respectively. Polymorphisms in codons 6, 38 and 48 occur simultaneously in 50.6% of the animals, 38.8% presenting as heterozygous. To study the distribution of the polymorphism in codon 43, a restriction fragment length polymorphism analysis was performed. Polymorphic variant c.129C, identified in 89.8% of the animals with 32.8% presented as heterozygous, was considered the wild genotype in Portuguese sheep. Eight different haplotypes which have comparable distribution in all breeds were identified for the PRNT gene. In conclusion, the PRNT coding region is highly polymorphic in sheep, unlike the prion protein 2 dublet gene (PRND), in which we previously found only one synonymous substitution (c.78G>A), in codon 26. The absence or reduced number of PRND heterozygotes (c.78G>A) was significantly associated with three PRNT haplotypes (17C-112G-129T-144A,17CT-112GC-129CT-144AG and 17T-112C-129C-144G), and the only three animals found homozygous at c.78A had the 17C-112G-129C-144A PRNT haplotype. These results constitute evidence of an association between polymorphic variation in PRND and PRNT genes, as has already been observed for PRND and prion protein gene (PRNP).

PRND 3′UTR polymorphism may be associated with behavioral disturbances in Alzheimer disease

The etiology of behavioral and psychological symptoms of dementia (BPSD) is complex, including putative biological, psychological, social and environmental factors. Recent years have witnessed accumulation of data on the association between genetic factors and behavioral abnormalities in Alzheimer disease (AD). In this research paper, our aim is to evaluate the association between the APOE, CYP46, PRNP and PRND genes and the profile of neuropsychiatric symptoms in Polish subjects with AD and mild cognitive impairment (MCI). We studied 99 patients with AD and 48 subjects with MCI. The presence and profile of BPSD were evaluated at baseline and prospectively with the Neuropsychiatric Inventory (NPI). Patients were dichotomized into those having ever experienced a particular symptom and those who did not over the whole disease period. Genotyping was performed using previously described standard protocols. The prevalence of comorbid behavioral symptoms and the overall level of behavioral burden were significantly greater in AD compared with the MCI group. In AD patients, carrier status of the T allele of the 3′UTR (untranslated region) PRND polymorphism was associated with an increased cumulative behavioral load and an elevated risk for delusions, anxiety, agitation/aggression, apathy and irritability/emotional ability. Among MCI subjects, APOE ε4 carriers demonstrated a reduced risk for nighttime behavior change. No other statistically significant genotype-phenotype correlations were observed, including the APOE, CYP46 and PRNP genes. A precise estimation of the exact significance of particular polymorphisms in BPSD etiology requires future studies on large populations.

Earlier Onset of Alzheimer's Disease: Risk Polymorphisms Within PRNP, PRND, CYP46, and APOE Genes

We studied eight polymorphisms within APOE, PRNP, PRND, and CYP46 genes in 213 Polish late-onset patients with Alzheimer's disease (AD) and 171 non-demented elderly controls. A latent classification approach, grade-of-membership analysis, was taken to identify three extreme pure type risk sets defined by the probabilities of being affected with AD and for genotypes found at the examined genes. Sets I and II represented high intrinsic risk, having a higher density of various genotypes compared to set III, at low intrinsic risk. A gradient of onset age depending on membership in the risk sets was also observed. Logistic regression analysis showed that the highest risk for AD was found for individuals who co-inherited APOE epsilon4 allele, PRNP codon 129 homozygosity, PRND codon 174 Thr allele, and CYP46 rs754203 g allele. AD can be influenced by genetic profiles leading to appearance of the disease, composed of genes which separately evoke a little or unnoticeable effect. Moreover, there may be multiple sufficient risk sets for AD. Looking at multiple genes together rather than analyzing them individually, may improve identification of risk alleles.

Doppel Induces Degeneration of Cerebellar Purkinje Cells Independently of Bax

Doppel (Dpl) is a prion protein paralog that causes neurodegeneration when expressed ectopically in the brain. To investigate the cellular mechanism underlying this effect, we analyzed Dpl-expressing transgenic mice in which the gene for the proapoptotic protein Bax had been deleted. We found that Bax deletion does not alter either clinical symptoms or Purkinje cell degeneration in Dpl transgenic mice. In addition, we observed that degenerating Purkinje cells in these animals do not display DNA fragmentation or caspase-3 activation. Our results suggest that non-Bax-dependent pathways mediate the toxic effects of Dpl in Purkinje cells, highlighting a possible role for nonapoptotic mechanisms in the death of these neurons.

Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments

The prevalence of antibiotic production loci in soil is a key issue of current research aimed to unravel the mechanisms underlying the suppressiveness of soil to plant pathogens. Pyrrolnitrin (PRN) is a key antibiotic involved in the suppression of a range of phytopathogenic fungi. Therefore, field soils from different agricultural regimes, including permanent grassland, arable land under common agricultural rotation and arable land under maize monoculture, were investigated in respect of the prevalence of pyrrolnitrin biosynthetic loci. Primers for detection of the prnD gene were used for initial PCR/hybridisation-based assessments. By this method, evidence was obtained for the contention that PRN production loci were most prevalent in grasslands, however, robust quantitative data were not achieved. To quantify the prevalence of PRN biosynthetic loci, we designed a TaqMan PCR system based on the prnD gene for the real-time quantitative detection of this production locus in soil. The system was found to be specific for prnD sequences from Pseudomonas, Serratia and Burkholderia species. Using pure culture DNA, the prnD gene was detectable down to a level of 60 fg, or approximately 10 gene copies, per amplification reaction. Application of the system to soil DNA spiked with different levels of the target DNA indicated that, in a soil DNA background, specific amplification could be obtained to about the same level of sensitivity. Field soil samples obtained from the different agricultural regimes were then screened for the prevalence of prnD with the real-time PCR system. The quantitative data obtained suggested a strongly enhanced presence of prnD genes in grassland or grassland-derived plots, as compared to the prevalence of this biosynthetic locus in the arable land plots. The implications of these findings are placed in the context of the suppressiveness of soil to phytopathogens, notably Rhizoctonia solani AG3.

Sequence determination and expression of the ovine doppel-encoding gene in transgenic mice

The ovine Doppel-encoding gene transcription unit (TU) and proximal flanking regions were cloned from a bacterial artificial chromosome (BAC) and sequenced. The 4586 bp TU is composed of two exons and one intron. When compared with its human counterpart, beside the open reading frame and part of the 3′ untranslated sequence, significant regions of homology were found within the intron and the proximal 5′ flanking regions. Sequence analysis of the BAC clone revealed that the ovine Prnd gene is located around 52 kb downstream of the Prnp locus. Expression of the sheep and murine Prnd genes was observed in all tissues analyzed of transgenic mice bearing the BAC insert, with a noticeable highest expression level observed in the testis, with no associated noticeable phenotype. The present data suggest that, in contrast to ovine Prnp, ovine Prnd expression in transgenic mice has no obvious influence on conferred susceptibility to scrapie.

Biology of the prion gene complex

The prion protein gene Prnp encodes PrPSc, the major structural component of prions, infectious pathogens causing a number of disorders including scrapie and bovine spongiform encephalopathy (BSE). Missense mutations in the human Prnp gene, PRNP, cause inherited prion diseases such as familial Creutzfeldt-Jakob Disease. In uninfected animals, Prnp encodes a GPI-anchored protein denoted PrPC, and in prion infections, PrPC is converted to PrPSc by templated refolding. Although Prnp is conserved in mammalian species, attempts to verify interactions of putative PrP-binding proteins by genetic means have proven frustrating in that two independent lines of Prnp gene ablated mice (Prnp0/0 mice: ZrchI and Npu) lacking PrPC remain healthy throughout development. This indicates that PrPC serves a function that is not apparent in a laboratory setting or that other molecules have overlapping functions. Shuttling or sequestration of synaptic Cu(II) via binding to N-terminal octapeptide residues and (or) signal transduction involving the fyn kinase are possibilities currently under consideration. A new point of entry into the issue of prion protein function has emerged from identification of a paralog, Prnd, with 25% coding sequence identity to Prnp. Prnd lies downstream of Prnp and encodes the Dpl protein. Like PrPC, Dpl is presented on the cell surface via a GPI anchor and has three alpha-helices: however, it lacks the conformationally plastic and octapeptide repeat domains present in its well-known relative. Interestingly, Dpl is overexpressed in two other lines of Prnp0/0 mice (Ngsk and Rcm0) via intergenic splicing events. These lines of Prnp0/0 mice exhibit ataxia and apoptosis of cerebellar cells, indicating that ectopic synthesis of Dpl protein is toxic to CNS neurons: this inference has now been confirmed by the construction of transgenic mice expressing Dpl under the direct control of the PrP promoter. Remarkably, Dpl-programmed ataxia is rescued by wt Prnp transgenes. The interaction between the Prnp and Prnd genes in mouse cerebellar neurons may have a physical correlate in competition between Dpl and PrPC within a common biochemical pathway that, when misregulated, leads to apoptosis.

Metabolite repression and inducer exclusion in the proline utilization gene cluster of Aspergillus nidulans.

The clustered prnB, prnC, and prnD genes are repressed by the simultaneous presence of glucose and ammonium. A derepressed mutation inactivating a CreA-binding site acts in cis only on the permease gene (prnB) while derepression of prnD and prnC is largely the result of reversal of inducer exclusion.

Ataxia in prion protein (PrP)-deficient mice is associated with upregulation of the novel PrP-like protein doppel

The novel locus Prnd is 16 kb downstream of the mouse prion protein (PrP) gene Prnp and encodes a 179 residue PrP-like protein designated doppel (Dpl). Prnd generates major transcripts of 1.7 and 2.7 kb as well as some unusual chimeric transcripts generated by intergenic splicing with Prnp. Like PrP, Dpl mRNA is expressed during embryogenesis but, in contrast to PrP, it is expressed minimally in the CNS. Unexpectedly, Dpl is upregulated in the CNS of two PrP-deficient ( Prnp 0/0) lines of mice, both of which develop late-onset ataxia, suggesting that Dpl may provoke neurodegeneration. Dpl is the first PrP-like protein to be described in mammals, and since Dpl seems to cause neurodegeneration similar to PrP, the linked expression of the Prnp and Prnd genes may play a previously unrecognized role in the pathogenesis of prion diseases or other illnesses.

Regulation of Proline Transport in Aspergillus nidulans

Aspergillus nidulans has at least two permeases for l-proline. The prnB gene of the prn gene cluster specifies the major proline permease, which is inducible by proline. Synthesis of the prnB permease is subject to repression by ammonium at 37 °C but not at 25 °C. A genetically unidentified minor proline permease(s) does not respond to proline induction or ammonium repression but is inhibited by ammonium. areAr mutants are unable to utilize nitrogen sources other than ammonium because they lack a positive-acting regulatory product required for expression of ammonium-repressible activities. However, there are very few cases in which the lack of growth of areAr mutants on a particular nitrogen source can be attributed to a reduction in the level of a particular enzyme activity or permease. Reduced expression of the prnB permease can account for the inability of areAr mutants to utilize proline. This is demonstrated by the ability of cis-acting regulatory mutations designated prnd , which derepress synthesis of the prnB permease, to suppress areAr mutations for proline utilization. The apparent ability of prnd mutations to derepress synthesis of proline oxidase and l-pyrroline-5-carboxylate dehydrogenase is probably an indirect consequence of their ability to derepress synthesis of the prnB permease, preventing inducer exclusion. There is presently no evidence that prnd mutations directly affect expression of the prnA, prnC or prnD genes, but this possibility has not been definitively eliminated.