A complex pattern of microsatellite polymorphism within the bovine NRAMP1 gene

Microsatellite markers reveal polymorphisms at the 3′ untranslated region of the SLC11A1 gene in Zhongdian Yellow cattle (Bos taurus)

Solute carrier family 11-member A1 (SLC11A1) gene encodes natural macrophage resistance-associated protein which regulates activity of macrophages against intracellular pathogens. The objective of this study was to study the polymorphism in the microsatellites present at 3′ untranslated region (UTR) of the SLC11A1 gene in 113 Zhongdian Yellow cattle (Bos taurus). Using DNA bi-directional sequencing, we detected seven alleles (GT10–16) for the first microsatellite (MS1), five alleles (GT12–16) for MS2, and four alleles (GT4–7) for MS3. MS3 is studied for the first time and revealed four novel variants (alleles GT4–7). Alleles GT12 (45.1%), GT13 (59.3%), and GT5 (85.4%) were the most frequent alleles at MS1, MS2, and MS3, respectively, Genotypes G12/12, G13/13, and G5/5 had the highest frequency 0.239, 0.540, and 0.743 at MS1, MS2, and MS3, respectively. Haplotypic data revealed that GT12/GT13 was the most frequent haplotype observed followed by GT12/14 haplotype. Three nucleotide variations were observed in MS1 and MS2. Comparative analysis of GT12/GT12 and GT13/GT13 genotype with other bovine genotypes showed significant difference (P > 0.05). Our results suggest that the homozygous genotypes GT12/GT12 and GT13/GT13 in Zhongdian Yellow cattle might be related to disease resistance. The findings reported in this study would be helpful in cattle breeding programs.

Nitric oxide not apoptosis mediates differential killing of Mycobacterium bovis in bovine macrophages

To identify the resistance phenotype against Mycobacterium bovis in cattle, we used a bactericidal assay that has been considered a marker of this trait. Three of 24 cows (12.5%) were phenotyped as resistant and 21 as susceptible. Resistance of bovine macrophages (MΦ) to BCG challenge was evaluated for its association with SLC11A1 GT microsatellite polymorphisms within 3'UTR region. Twenty-three cows (95.8%) had a GT13 genotype, reported as resistant, consequently the SLC11A1 polymorphism was not in agreement with our bactericidal assay results. MΦ of cows with resistant or susceptible phenotype were challenged in vitro with virulent M. bovis field strain or BCG, and nitric oxide production, bacterial killing and apoptosis induction were measured in resting and LPS-primed states. M. bovis field strain induced more apoptosis than BCG, although the difference was not significant. Resistant MΦ controlled better the replication of M. bovis (P<0.01), produced more nitric oxide (P<0.05) and were slightly more prone to undergo apoptosis than susceptible cells. LPS pretreatment of MΦ enhanced all the functional parameters analyzed. Inhibition of nitric oxide production with n (G)-monomethyl-L-arginine monoacetate enhanced replication of M. bovis but did not modify apoptosis rates in both resistant and susceptible MΦ. We conclude that nitric oxide production not apoptosis is a major determinant of macrophage resistance to M. bovis infection in cattle and that the influence of SLC11A1 gene 3'UTR polymorphism is not associated with this event.

Genetic analysis of the 3' untranslated region of the bovine SLC11A1 gene reveals novel polymorphisms

Polymorphisms in microsatellites at the 3' untranslated region (3'UTR) of the SLC11A1 (solute carrier family 11 member A1) gene have been associated with natural resistance to Brucella abortus and Mycobacterium bovis infection in livestock species. Here, we carried out an individual genetic analysis of the two microsatellites present at the 3'UTR SLC11A1 gene in 254 Bos taurus purebred, 125 B. indicus purebred and 54 B. taurus × B. indicus crossbred cattle. The genotyping by capillary electrophoresis showed the presence of four alleles (157, 159, 161 and 163) for the first microsatellite (MS1) and six alleles (175, 177, 179, 181, 183 and 185) for the second microsatellite (MS2). The alleles 159 and 175 were the most frequent in all breeds analyzed. B. taurus showed the most homogeneous haplotype and genotype for both microsatellites, whereas B. indicus showed the most heterogeneous haplotype and genotype. Two novel variants (alleles 161 and 163) within the MS1 are reported as well as novel variants in MS2 in Holstein breed. The knowledge of the polymorphisms distribution in both microsatellites at the 3'UTR of the SLC11A1 gene in cattle breeds is useful for future experimental design to evaluate the association between reported genotypes and natural resistance to pathogens infection.

Effect of polymorphisms in the Slc11a1 coding region on resistance to brucellosis by macrophages in vitro and after challenge in two Bos breeds (Blanco Orejinegro and Zebu)

The resistance/susceptibility of selected cattle breeds to brucellosis was evaluated in an F1 population generated by crossing animals classified as resistant (R) and susceptible (S) (R x R, R x S, S x R, S x S) based on challenges in vitro and in vivo. The association between single nucleotide polymorphisms identified in the coding region of the Slc11a1 gene and resistance/susceptibility was estimated. The trait resistance or susceptibility to brucellosis, evaluated by a challenge in vitro, showed a high heritable component in terms of additive genetic variance (h(2) = 0.54 ± 0.11). In addition, there was a significant association (p < 0.05) between the control of bacterial survival and two polymorphisms (a 3'UTR and SNP4 located in exon 10). The antibody response of animals classified as resistant to infection by Brucella abortus differed significantly (p < 0.05) from that of susceptible animals. However, there was no significant association between single nucleotide polymorphisms located in the Slc11a1 gene and the antibody response stimulated by a challenge in vivo.

Identification of single nucleotide polymorphisms in the bovine solute carrier family 11 member 1 (SLC11A1) gene and their association with infection by Mycobacterium avium subspecies paratuberculosis

Johne's disease is a chronic enteritis caused by Mycobacterium avium ssp. paratuberculosis (MAP) that causes substantial financial losses for the cattle industry. Susceptibility to MAP infection is reported to be determined in part by genetic factors, so marker-assisted selection could help to obtain bovine populations that are increasingly resistant to MAP infection. Solute carrier family 11 member 1 (SLC11A1) was adjudged to be a potential candidate gene because of its role in innate immunity, its involvement in susceptibility to numerous intracellular infections, and its previous association with bovine MAP infection. The objectives of this study were to carry out an exhaustive process of discovery and compilation of polymorphisms in SLC11A1 gene, and to perform a population-based genetic association study to test its implication in susceptibility to MAP infection in cattle. In all, 57 single nucleotide polymorphisms (SNP) were detected, 25 of which are newly described in Bos taurus. Twenty-four SNP and two 3'-untranslated region polymorphisms, previously analyzed, were selected for a subsequent association study in 558 European Holstein-Friesian animals. The SNP c.1067C>G and c.1157-91A>T and a haplotype formed by these 2 SNP yielded significant association with susceptibility to MAP infection. The c.1067C>G is a nonsynonymous SNP that causes an amino acid change in codon 356 from proline to alanine (P356A) that could alter SLC11A1 protein function. This association study supports the involvement of SLC11A1 gene in susceptibility to MAP infection in cattle. Our results suggest that SNP c.1067C>G may be a potential causal variant, although functional studies are needed to assure this point.

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.

SLC11A1 gene polymorphisms are not associated to somatic cell score and milk yield in Chinese Holstein

It has been well established that mutations of the solute carrier family 11 A1 (SLC11A1) gene are responsible for susceptibility to a number of intracellular pathogens. Mastitis is the most common and most costly disease of dairy cattle, commonly caused by bacteria. As SLC11A1 protein is involved in bacterial killing, we assumed SLC11A1 gene as a candidate gene for bovine mastitis resistance. In this study, polymorphisms in the SLC11A1 gene were identified in the Chinese Holstein population. Genotypes were constructed, and their associations with somatic cell score and milk yield were determined. Single-strand conformation polymorphisms and DNA sequencing were used to reveal polymorphisms in SLC11A1 gene. A SNP in coding region and a variation of GT repeats in 3'-untranslated region were detected. The SNP resulted in an amino acid variation of p.P356A in transmembrane 8 of SLC11A1 peptide, which is the most conserved consecutive region. However, no associations were observed between the detected polymorphisms and somatic cell scores and milk yield in the Chinese Holstein population.

NRAMP1 3' untranslated region polymorphisms are not associated with natural resistance to Brucella abortus in cattle

The NRAMP1 gene encodes a divalent cation transporter, located in the phagolysosomal membrane of macrophages, that has been associated with resistance to intracellular pathogens. In cattle, natural resistance against brucellosis has been associated with polymorphisms at the 3' untranslated region (3'UTR) of the NRAMP1 gene, which are detectable by single-strand conformational analysis (SSCA). This study aimed to evaluate the association between NRAMP1 3'UTR polymorphisms and resistance against bovine brucellosis in experimental and natural infections. In experimentally infected pregnant cows, abortion occurred in 42.1% of cows with a resistant genotype (SSCA(r); n = 19) and in 43.1% of those with a susceptible genotype (SSCA(s); n = 23). Furthermore, no association between intensity of pathological changes and genotype was detected. In a farm with a very high prevalence of bovine brucellosis, the percentages of strains of the SSCA(r) genotype were 86 and 84% in serologically positive (n = 64) and negative (n = 36) cows, respectively. Therefore, no association was found between the NRAMP1-resistant allele and the resistant phenotype in either experimental or naturally occurring brucellosis. To further support these results, bacterial intracellular survival was assessed in bovine monocyte-derived macrophages from cattle with either the resistant or susceptible genotype. In agreement with our previous results, no difference was observed in the rates of intracellular survival of B. abortus within macrophages from cattle with susceptible or resistant genotypes. Taken together, these results indicate that these polymorphisms at the NRAMP1 3'UTR do not affect resistance against B. abortus in cattle and that they are therefore not suitable markers of natural resistance against bovine brucellosis.

Protective effect of the Nramp1 BB genotype against Brucella abortus in the water buffalo (Bubalus bubalis)

We tested 413 water buffalo cows (142 cases and 271 controls) for the presence of anti-Brucella abortus antibodies (by the skin test, the agglutination test, and the complement fixation test) and the Nramp1 genotype (by capillary electrophoresis). Four alleles (Nramp1A, -B, -C, and -D) were detected in the 3' untranslated region of the Nramp1 gene. The BB genotype was represented among only controls, providing evidence that this genotype confers resistance to Brucella abortus. The monocytes from the BB (resistant) subjects displayed a higher basal level of Nramp1 mRNA and a lower number of viable intracellular bacteria than did the monocytes from AA (susceptible) subjects. The higher basal level of the antibacterial protein Nramp1 most probably provides the BB animals with the possibility of controlling bacteria immediately after their entry inside the cell.

Genetic resistance to Brucella abortus in the water buffalo (Bubalus bubalis)

Brucellosis is a costly disease of water buffaloes (Bubalus bubalis). Latent infections and prolonged incubation of the pathogen limit the efficacy of programs based on the eradication of infected animals. We exploited genetic selection for disease resistance as an approach to the control of water buffalo brucellosis. We tested 231 water buffalo cows for the presence of anti-Brucella abortus antibodies (by the agglutination and complement fixation tests) and the Nramp1 genotype (by PCR-denaturing gradient gel electrophoresis). When the 231 animals (58 cases and 173 controls) were divided into infected (seropositive) and noninfected (seronegative) groups and the Nramp1 genotypes were compared, the seropositive subjects were 52 out of 167 (31%) in the Nramp1A+ (Nramp1AA or Nramp1AB) group and 6 out of 64 (9.4%) in the Nramp1A- (Nramp1BB) group (odds ratio, 4.37; 95% confidence limits, 1.87 to 10.19; chi2, 11.65 for 1 degree of freedom). Monocytes from Nramp1BB subjects displayed significantly (P < 0.01) higher levels of Nramp1 mRNA than Nramp1AA subjects and also a significantly (P < 0.01) higher ability in controlling the intracellular replication of several Brucella species in vitro. Thus, selection for the Nramp1BB genotype can become a valuable tool for the control of water buffalo brucellosis in the areas where the disease is endemic.

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.

Frequency of bovine Nramp1 (Slc11a1) alleles in Holstein and Zebu breeds

Natural resistance against brucellosis in cattle is linked to the Nramp1 gene, which encodes a divalent cation transporter that localizes in the phagolysosome membrane in macrophages. Nramp1 gene in mouse plays a critical role in innate immunity favoring bacterial killing by macrophages in addition to its influence on adaptative immunity. Polymorphisms at the bovine Nramp1 3' untranslated region (3'UTR), detectable by Single Strand Conformational Analysis (SSCA), are associated with natural resistance against brucellosis. Such polymorphisms are associated with variation in the number of GT repeats. This study compared the frequency of Nramp1 3'UTR polymorphisms between Zebu and European bovine breeds. Eighty-one Holsteins (Bos taurus taurus) and 167 Zebu (Bos taurus indicus), including the following breeds: Nelore (n=95), Guzerá (n=37), and Gir (n=35), totaling 248 pure breed cattle studied. DNA extraction was performed using the guanidium protocol and genotyping was performed by SSCA. DNA from cattle considered genotypically resistant to brucellosis resulted in a single band (homozygous) with 175bp, corresponding to the 3'UTR with 13 GT pairs (GT13), whereas DNA from genotypically susceptible cattle generated one single band with 177bp (homozygous GT14) or double bands with both 175 and 177bp, or 175 and 179bp (heterozygous GT13/GT14 or GT13/GT15, respectively). A marked difference in the frequency of alleles was detected between the Zebu and Holstein cattle. Holsteins had an extremely homogeneous genotype, with 100% of the individuals with a GT13 genotype. In sharp contrast the Nelore breed had the most heterogeneous genotype with four allelic combinations, namely, homozygous GT13, homozygous GT14, heterozygous GT13/GT14, and heterozygous GT13/GT15. When the Zebu breeds were compared to each other, the only significant difference observed was the frequencies of the genotypes GT13 and GT14 between the Nelore and Guzerá breeds. The knowledge of allelic frequencies in different breeds of cattle may prove to be very useful in the future for planning breeding strategies for selection of resistant cattle.

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.

High-level expression of NRAMP1 in peripheral blood cells and tuberculous granulomas from Mycobacterium bovis-infected bovines

By Western blotting, we demonstrate high-level expression of NRAMP1 proteins in peripheral blood cells and granulomas of Mycobacterium bovis-infected bovines. Immunohistochemistry of granulomatous lesions showed heavily labeled epithelioid macrophages and Langhans cells. These data suggest that M. bovis infection enhances NRAMP1 expression and that active tuberculosis can occur despite this response.