Cloning, sequencing and linkage mapping of the NRAMP1 gene of sheep and deer

Chromosomal localisation and genetic variation of the SLC11A1 gene in goats (Capra hircus)

The solute carrier family 11 member A1 (SLC11A1) gene is associated with resistance to infectious diseases. Chromosomal localisation, genomic regions corresponding to functional domains and the genetic variability of microsatellites in the 3' untranslated region (3'-UTR) of this gene were investigated in 427 goats (Capra hircus) of six breeds. Using dual colour fluorescence in situ hybridisation, SLC11A1 was localised to goat chromosome 2. Single strand conformation polymorphism was used to screen for polymorphisms in SLC11A1 exons 2, 10 and 15. There was no variation among goat breeds in the sarcoma homology 3 (SH3) binding motif, the protein kinase C phosphorylation site or the two N-linked glycosylation sites. Exon 15 exhibited variability due to the presence of two polymorphic microsatellites. Genotyping of the upstream guanine-thymine repeat (GTn) at 3'-UTR revealed eight alleles (GT11, GT12, GT14-GT19) in goats, whereas GT13 (present in cattle) was absent. Most goats carried the GT16 allele and no allele was found to be exclusive to only one breed. The coefficient of genetic differentiation value (G(ST)) was 0.084. This microsatellite appears to be an informative DNA marker for genetic linkage analysis in goats.

Molecular cloning and characterization of SLC11A1 cDNA in Japanese Quail (Coturnix Coturnix Japonica)

SLC11A1 is one of the most potent candidate genes conferring host's genetic resistance/susceptibility to various antigenically different intracellular pathogens. In this manuscript, we report the cloning and characterization of the complete coding sequence of SLC11A1 cDNA in Japanese quail. The 1680bp of cloned SLC11A1 cDNA consisted of an open reading frame of 1665bp which coded for a complete protein of 555 amino acid residues. At nucleotide and amino acid sequence levels, Japanese quail SLC11A1 exhibited 95.1 and 96.9% identity with that of chicken, respectively. However, when compared with the mammalian homologues, it exhibited 64.8-66.4% and 64.5-66.9% identity, respectively. Phylogram constructed on the basis of both nucleotide and deduced amino acid sequences revealed similar pattern with the placement of Japanese quail and chicken SLC11A1 in the same clad.

Genomic organization and polymorphisms detected by denaturing high-performance liquid chromatography of porcine SLC11A1 gene

SLC11A1 (also known as Natural Resistance Associated Macrophage Protein1, NRAMP1) plays a crucial role in resistance of inbred mice to infection with several intracellular pathogens such as Mycobacterium, Leishmania and Salmonella. In this study, PCR amplification and sequencing were performed to obtain the genomic organization and sequence of porcine SLC11A1 gene by comparative genomic analysis. Results showed that porcine SLC11A1 gene consists of 15 exons and 14 introns, which is consistent with that of mice and human. All introns were sequenced and their nucleotide sequences were submitted to GenBank. The exon/intron boundaries were determined by comparing cDNA sequence with amplified genomic DNA sequences. Mutational analysis was performed on exonic and neighboring intronic region by denaturing high-performance liquid chromatography (DHPLC) and sequencing confirmation. Forty polymorphisms were identified; six are located in exons and thirty-four in introns. Two exonic polymorphisms are nonsynonymous changes (D6H and V175I), three are synonymous changes (S23, G33 and I155), and one is in 3' UTR. The availability of the fine genomic organization and identification of the polymorphisms will facilitate the evaluation of porcine SLC11A1 functional role in diseases resistance or susceptibility.

Lack of association of brucellosis resistance with (GT)13 microsatellite allele at 3′UTR of NRAMP1 gene in Indian zebu (Bos indicus) and crossbred (Bos indicus×Bos taurus) cattle

Natural resistance associated macrophage protein 1 (NRAMP1), an integral transmembrane protein, is reported to influence the intraphagosomal microbial replication and thereby confer resistance to several intracellular pathogens in mice. In bovine, a significant association of (GT)(13) allelic variant of polymorphic microsatellite at 3' untranslated region (UTR) of NRAMP1 gene with natural resistance to brucellosis has been established. The present study was aimed to detect polymorphism at 3'UTR of NRAMP1 gene in Hariana breed of Bos indicus cattle and Holstein Friesian crossbred (B. indicusxBos taurus) cattle, and to determine the association of this polymorphism with resistance/susceptibility to brucellosis. The (GT)(n) polymorphism at 3'UTR in terms of variation in fragment length was determined using denaturing polyacrylamide gel analysis of radioisotope incorporated amplicon of 174 bp. Screening of a total of 100 samples (comprising 50 random samples of each breed) revealed that animals were of same genotype, i.e., homozygous (GT)(13)/(GT)(13). Sequencing of amplicons from representative animals confirmed the presence of (GT)(13) repeat. For association study, the animals that were positive in all three serological tests (viz., RBPT, STAT and ELISA) and had history of abortion were grouped as "affected"; whereas the animals that were negative in all these tests and completed third lactation without any history of abortion were grouped as "non-affected". Since, all animals belonging to either group were homozygous (GT)(13), association could not be established. However, the present study demonstrated that the presence of (GT)(13) allele even in homozygous condition could not provide enough resistance to brucellosis in a naturally infected herd.

Sequence analysis of the NRAMP1 genes from different bovine and buffalo breeds

The natural resistance associated macrophage protein 1 (Nramp1) has been reported to confer resistance or susceptibility to Mycobacterium bovis, Salmonella typhimurium, and Leishmania donovani in the mouse, Mus musculus. A Gly and Asp substitution at position 169 of the mouse Nramp protein is invariably associated with the resistant and susceptible phenotypes, respectively. The present study aimed to detect polymorphisms in the NRAMP1 gene from different cattle and buffalo breeds. Genomic DNAs from five breeds of cattle and four breeds of buffalo were used in the study. Sequencing showed two nucleotide substitutions found in intron 4, three in exon V, and ten in intron 5. An amino acid substitution was observed at nucleotide position 1202 in exon V of the Japanese black, Angus, Philippine and Bangladesh swamp-type buffaloes which coded for Thr, while the Korean cattle, Holstein, African N'dama, Indonesian swamp-type buffalo and the Bangladesh river-type buffalo had Ile. All the breeds of cattle and buffaloes tested in this study coded for Gly at the position in exon VI which corresponds to the same amino acid of the murine Nramp1-resistant phenotype at position 169. The phylogenetic relationship among the different breeds showed a cluster comprised mainly of cattle and another one mainly of buffaloes.

Mapping and sequencing of the canine NRAMP1 gene and identification of mutations in leishmaniasis-susceptible dogs

The NRAMP1 gene (Slc11a1) encodes an ion transporter protein involved in the control of intraphagosomal replication of parasites and in macrophage activation. It has been described in mice as the determinant of natural resistance or susceptibility to infection with antigenically unrelated pathogens, including Leishmania. Our aims were to sequence and map the canine Slc11a1 gene and to identify mutations that may be associated with resistance or susceptibility to Leishmania infection. The canine Slc11a1 gene has been mapped to dog chromosome CFA37 and covers 9 kb, including a 700-bp promoter region, 15 exons, and a polymorphic microsatellite in intron 1. It encodes a 547-amino-acid protein that has over 87% identity with the Slc11a1 proteins of different mammalian species. A case-control study with 33 resistant and 84 susceptible dogs showed an association between allele 145 of the microsatellite and susceptible dogs. Sequence variant analysis was performed by direct sequencing of the cDNA and the promoter region of four unrelated beagles experimentally infected with Leishmania infantum to search for possible functional mutations. Two of the dogs were classified as susceptible and the other two were classified as resistant based on their immune responses. Two important mutations were found in susceptible dogs: a G-rich region in the promoter that was common to both animals and a complete deletion of exon 11, which encodes the consensus transport motif of the protein, in the unique susceptible dog that needed an additional and prolonged treatment to avoid continuous relapses. A study with a larger dog population would be required to prove the association of these sequence variants with disease susceptibility.

Genetic control of disease resistance and immunoresponsiveness

A great deal of evidence points to substantial genetic control over at least some of the immune responses, although genetic parameters for clinical disease have been less favorable. The past two decades have illustrated that single genes with a large impact on food animal health do exist and can be used to improve the health of domestic populations. The current focus on molecular genetics within food animal species will likely unveil numerous other examples of single genes with large effects, although the use of animals possessing favorable genotypes for disease resistance may represent a compromise in selection for increased production of raw product. Moreover, it is also clear that genetic control over the immune system is not limited to a few genes but is more likely influenced by many genes, each with small effects. The use of this information in animal improvement programs is not straightforward because of factors complicating the identification of superior individuals within the population. The scarcity of information dealing with phenotypic and genetic relationships between measures of disease resistance and aspects of immune response complicates the situation even further. Despite these potential hurdles, the potential for permanent improvement of disease resistance within food animal species in the future is tantalizing and merits intensified future study.

Divalent-metal transport by NRAMP proteins at the interface of host-pathogen interactions

The NRAMP family of divalent-metal transporters plays a key role in the homeostasis of iron and other metals. NRAMP2 (DMT1) acts as an iron-uptake protein in both the duodenum and in peripheral tissues. NRAMP1 functions as a divalent-metal efflux pump at the phagosomal membrane of macrophages and neutrophils, and mutations in NRAMP1 cause susceptibility to several intracellular pathogens. NRAMP homologues have been identified in bacteria and are involved in acquiring divalent metals from the extracellular environment. Interestingly, bacterial and mammalian NRAMP proteins would compete for the same essential substrates within the microenvironment of the phagosome, at the interface of host-pathogen interactions.

Genetic resistance to experimental infection with Mycobacterium bovis in red deer (Cervus elaphus)

Tuberculosis (Tb) caused by Mycobacterium bovis is a worldwide threat to livestock and humans. One control strategy is to breed livestock that are more resistant to Mycobacterium bovis. In a 3-year heritability study 6 farmed red deer stags were selected from 39 on the basis of their differing responses to experimental challenge via the tonsillar sac with approximately 500 CFU of M. bovis. Two stags remained uninfected, two were moderately affected, and two developed serious spreading Tb. Seventy offspring, bred from these six stags by artificial insemination using stored semen, were similarly challenged with M. bovis. The offspring showed patterns of response to M. bovis challenge similar to those of their sires, providing evidence for a strong genetic basis to resistance to Tb, with an estimated heritability of 0.48 (standard error, 0.096; P < 0. 01). This is the first time the heritability of Tb resistance in domestic livestock has been measured. The breeding of selection lines of resistant and susceptible deer will provide an ideal model to study the mechanisms of Tb resistance in a ruminant and could provide an additional strategy for reducing the number and severity of outbreaks of Tb in farmed deer herds. Laboratory studies to identify genetic and immunological markers for resistance to Tb are under way. Preliminary studies showed no associations between NRAMP or DRB genes and resistance to Tb in deer. Patterns of immune responses seen in resistant animals suggest that both innate and acquired pathways of immunity are necessary to produce the resistant phenotype.

Comparative analysis of two Nramp loci from rainbow trout

Innate resistance to intracellular parasites is controlled in part by Nramp1 (Natural resistance-associated macrophage protein 1) in mammals and birds. To isolate Nramp homologs from rainbow trout, a combination of library screening and rapid amplification of cDNA ends was performed. Two closely related Nramp loci, designated OmNramp alpha and OmNramp beta, were cloned and characterized. OmNramp alpha and OmNramp beta encode two highly conserved proteins of 585 and 558 amino acids, respectively. Deduced amino acid seqences showed that the OmNramp alpha and OmNramp beta proteins share 90% of their residues and contain all of the signature features of the Nramp family of proteins: 12 transmembrane domains, two N-linked glycosylation sites, and a conserved transport motif. Phylogenetic analysis supported a close relation to Nramp2 proteins, a related member of the Nramp family. Despite this relation, juvenile trout expressed OmNramp alpha in a manner consistent with an Nramp1 homolog and OmNramp beta similar to an Nramp2 locus. Both trout loci were expressed at relatively high amounts in the ovaries of juveniles, a finding not reported in the investigations of previously characterized mammalian and avian homologs. These results suggest a role for Nramp loci in the follicular development of teleost fishes, as well as in mammals. Because salmonid fishes are ancestral tetraploids, fragments of OmNramp alpha and OmNramp beta were isolated from smelt, a diploid relative, to determine whether the trout loci represent duplicates of a single gene. Homologous sequences for both loci were found in smelt, supporting the hypothesis that OmNramp alpha and OmNramp beta are indeed independent loci that were present before the chromosomal duplication of salmonids. The isolation of Nramp loci from rainbow trout may eventually produce a genetic tool for the control of disease in aquaculture operations. Determining the involvement of trout homologs in innate immunity may also provide insight regarding the evolution of host resistance to pathogens.