Amino Acid Haplotypes Research Articles

Variation in the coding and 3′ untranslated regions of the porcine prolactin receptor short form modifies protein expression and function

The actions of prolactin (PRL) are mediated by both long (LF) and short isoforms (SF) of the PRL receptor (PRLR). Here, we report on a genetic and functional analysis of the porcine PRLR (pPRLR) SF. Three single nucleotide polymorphisms (SNPs) within exon 11 of the pPRLR-SF give rise to four amino acid haplotypes of the intracellular domain. We identified the dimorphic insertion of a short interspersed repetitive DNA element (PRE-1) along with 32 SNPs and four other insertion/deletion sites within the 3' untranslated region (UTR) of pPRLR-SF. The PRE-1 element reduced protein translation in vitro by 75%, whereas the combination of 10 SNPs and one insertion/deletion decreased translation by 50%. Full-length cDNAs for all four haplotypes of pPRLR-SF were cloned behind the elongation factor 1-alpha promoter and functionally analyzed in vitro. None of the haplotypes could initiate transcription from the ß-casein promoter, whereas all four were dominant negatives against PRL-activation of the pPRLR-LF. Two of the haplotypes completely inhibited pPRLR-LF activity at a four-fold excess, whereas the others required a six-fold excess to impart the same effect. The ligand binding affinities of the pPRLR-SF haplotypes did not differ. Expression of the pPRLR-SF increased linearly during gestation in the endometrium and was hormonally regulated in a tissue-specific manner in the mammary glands and uterus. In conclusion, we identified a PRE-1 and other SNPs in the pPRLR-SF 3' UTR that reduce protein expression and four haplotypes of the pPRLR-SF that suppress pPRLR-LF signaling and may differentially impact the phenotypic effects of PRL in vivo.

Detection and genetic characterization of ovine CSN1S2⁎B polymorphisms and their associations with milk production traits

CSN1S2 gene encodes the αS2-casein, one of the phosphoproteins (αS1, β, αS2 and κ) secreted in ruminants milk in form of stable calcium–phosphate micelles. CSN1S2⁎B variant contains the amino acid substitutions p.Asp75Tyr and p.Ile105Val in the mature protein. Recently, we have shown that two adjacent SNPs, [FN_601350: g.153G>T and 155C>T], located at exon 10, are causers of the p.Asp75Tyr substitution, while the non-synonymous mutation SNP [FN_601350: g.504A>G], in exon 11, led to codon exchange of p.Ile105Val. PCR-RFLP and RT-PCR analyses were used to detect and characterize the single nucleotide polymorphisms involved in the B variant of the CSN1S2 gene and to assess their effects on milk yield and composition traits. Four hundred and thirty samples from different breeds (Berrinchon du cher, Castellana, Ile de France and Merino) were analyzed and population genetic parameters were estimated for each locus and breed. Both polymorphic sites of the SNPs g.[153G>T and 155C>T] are conserved across analyzed breeds. Haplotype allele frequencies from the SNPs g.[153G>T and 155C>T]—GC, GT, TC and TT—varied among the breeds, being GC the most frequent allele in all populations (>0.5). Allele G from SNP g.504A>G had the minor allele frequency in all breeds analyzed (ranged from 0.225 to 0.333). The value of genetic differentiation (FST=0.0419) across breeds and loci indicates that there was no genetic divergence among the analyzed breeds. The haplotype frequencies, the deduced amino acid haplotypes and the occurrence of linkage disequilibrium were estimated in a large population (377 samples) of Merino sheep breed. The eight possible haplotypes of these two loci were identified, and substantial linkage disequilibrium was found. GCA was the haplotype most frequent (>70%) and Asp75–Ile105 the most frequent aminoacid haplotype (0.713). Recombinants haplotypes were observed in low frequencies (≤0.1). Association study between the ovine CSN1S2⁎B polymorphisms and the milk traits were estimated in 669 lactations from 218 Merino ewes. The CSN1S2 p.75 and CSN1S2 p.105 polymorphisms affected the non-fat solids and lactose percentages in milk, respectively. The CSN1S2 Tyr75Tyr ewes had the highest levels of non fat solids and the ewes carrying CSN1S2 Val105Val genotype had the smallest lactose percentage. Similar effects of the single markers have been observed for homozygous Tyr75–Val105 ewes on lactose percentage. This work provides the basis to study in further sheep breeds the CSN1S2⁎B polymorphisms and their effects on milk traits.

Population genetic structure of the Plasmodium vivax circumsporozoite protein (Pvcsp) in Sri Lanka

Molecular methods elucidate evolutionary and ecological processes in parasites, where interaction between hosts and parasites enlighten the evolution of parasite lifestyles and host defenses. Population genetics of Plasmodium vivax parasites accurately describe transmission dynamics of the parasites and evaluation of malaria control measures. As a first generation vaccine candidate against malaria, the Circumsporozoite Protein (CSP) has demonstrated significant potential in P. falciparum. Extensive polymorphism hinders the development of a potent malaria vaccine. Hence, the genetic diversity of Pvcsp was investigated for the first time in 60 Sri Lankan clinical isolates by obtaining the nucleotide sequence of the central repeat (CR) domain and examining the polymorphism of the peptide repeat motifs (PRMs), the genetic diversity indices and phylogenetic relationships. PCR amplicons determined size polymorphism of 610, 700 and 710bp in Pvcsp of Sri Lanka where all amino acid sequences obtained were of the VK210 variant, consisting variable repeats of 4 different PRMs. The two most abundant PRMs of the CR domain, GDRADGQPA and GDRAAGQPA consisted ~2-4 repeats, while GNRAAGQPA was unique to the island. Though, different nucleotide sequences termed repeat allotypes (RATs) were observed for each PRM, these were synonymous contributing to a less polymorphic CR domain. The genetic diversity of Pvcsp in Sri Lanka was due to the number of repetitive peptide repeat motifs, point mutations, and intragenic recombination. The 19 amino acid haplotypes defined were exclusive to Sri Lanka, whereas the 194 Pvcsp sequences of global isolates generated 57 more distinct a.a. haplotypes of the VK210 variant. Strikingly, the CR domain of both VK210 and VK247 variants was under purifying selection interpreting the scarcity of CSP non-synonymous polymorphisms. Insights to the distribution of RATs in the CR region with geographic clustering of the P. vivax VK210 variant were revealed. The cladogram reiterated this unique geographic clustering of local (VK210) and global isolates (VK210 and VK247), which was further validated by the elevated fixation index values of the VK210 variant.

A combined DPA1∼DPB1 amino acid epitope is the primary unit of selection on the HLA-DP heterodimer

Here, we present results for DPA1 and DPB1 four-digit allele-level typing in a large (n = 5,944) sample of unrelated European American stem cell donors previously characterized for other class I and class II loci. Examination of genetic data for both chains of the DP heterodimer in the largest cohort to date, at the amino acid epitope, allele, genotype, and haplotype level, allows new insights into the functional units of selection and association for the DP heterodimer. The data in this study suggest that for the DPA1-DPB1 heterodimer, the unit of selection is the combined amino acid epitope contributed by both the DPA1 and DPB1 genes, rather than the allele, and that patterns of LD are driven primarily by dimer stability and conformation of the P1 pocket. This may help explain the differential pattern of allele frequency distribution observed for this locus relative to the other class II loci. These findings further support the notion that allele-level associations in disease and transplantation may not be the most important unit of analysis, and that they should be considered instead in the molecular context.Electronic supplementary materialThe online version of this article (doi:10.1007/s00251-012-0615-3) contains supplementary material, which is available to authorized users.

Genetic diversity of transmission-blocking vaccine candidates Pvs25 and Pvs28 in Plasmodium vivax isolates from Yunnan Province, China

BackgroundTransmission-blocking vaccines (TBVs) have been considered an important strategy for disrupting the malaria transmission cycle, especially for Plasmodium vivax malaria, which undergoes gametocytogenesis earlier during infection. Pvs25 and Pvs28 are transmission-blocking vaccine candidates for P. vivax malaria. Assessment of genetic diversity of the vaccine candidates will provide necessary information for predicting the performance of vaccines, which will guide us during the development of malaria vaccines.ResultsWe sequenced the coding regions of pvs25 and pvs28 from 30 P. vivax isolates from Yunnan Province, identifying five amino acid haplotypes of Pvs25 and seven amino acid haplotypes of Pvs28. Among a total of four mutant residues, the predominant haplotype of Pvs25 only had the I130T substitution. For Pvs28, a total of eight amino acid substitutions were identified. The predominant haplotype of Pvs28 had two substitution at positions 52 (M52L) and 140 (T140S) with 5-6 GSGGE/D tandem repeats at the end of fourth EGF-like domain. Most amino acid substitutions were common with previous reports from South Asian isolates. Although the nucleotide diversity of pvs28 (π = 0.0034 ± 0.0012) was significantly higher than pvs25 (π = 0.0013 ± 0.0009), it was still conserved when compared with the blood stage vaccine candidates.ConclusionsGenetic analysis revealed limited genetic diversity of pvs25 and pvs28, suggesting antigenic diversity may not be a particular problem for Sal I based TBVs in most P. vivax-endemic areas of China.

Genetic diversity and the ensuing strain specific immunity to asexual erythrocytic stage vaccine candidate antigens, MSP-1, AMA-1 and DBP, of Plasmodium vivax in Sri Lanka

Characterization of genetic diversity among locally prevalent parasite strains and the ensuing strain-specific immunity will be particularly important in a specific geographical setting for development of vaccine constructs and for planning future vaccination strategies. The present study characterized the prevailing genetic diversity of three major asexual stage putative vaccine antigens of Plasmodium vivax, 42 kDa fragment of the Merozoite Surface Protein -1 (MSP-142), Apical Membrane Antigen-1 domain II (AMA-1 DII) and the Duffy Binding Protein region II (PvDBPII), in patients infected with P. vivax malaria from two endemic areas, Anuradhapura and Kataragama, in Sri Lanka, where unstable malaria prevails with low transmission, and from a malaria non-endemic area, Colombo, where the patients contracted the infections while visiting areas endemic to vivax malaria. Based on nucleotide sequences, extensive allelic polymorphism was evident in the N-terminal region of MSP-142(Pvmsp-133), Pvama- 1dII and PvdbpII, due to recombination, mutations, natural selection and genetic differentiation. Nucleotide sequences of Pvmsp-142(N=95), Pvama-1dII (64) and PvdbpII (100), generated 27, 21 and 33 amino acid (a.a) haplotypes, respectively. Clinical isolates with amino acid haplotypes available for all three antigens (N=24) revealed uniquely different haplotype combinations in each isolate. Conversely, PvMSP-119, domain II loop of PvAMA-1 and the six a.a. in the critical binding domain of PvDBPII responsible for direct binding with the Duffy antigen on human RBC, showed 100% conservation of the amino acid sequences. In order to evaluate whether sequence differences among each antigen was indicative of strain-specific immunity, amino acid sequences of PvMSP-142, PvAMA-1DII and PvDBPII were aligned with the homologous total (IgM + IgG) antibody responses assayed by ELISA against the recombinant protein of each antigen, and the seven (P01-P07) PvAMA-1DII peptides. Though Anti-PvMSP-119 and anti-P04 antibody prevalence precludes strain-specific immune responses against the highly conserved PvMSP-119 and the P04 peptide on domain II loop of PvAMA-1, a protective immune response was clearly elicited to these two regions by the marked isotype switch from IgM to IgG with increasing exposure in areas of endemicity. Further, the presence of strain transcending (cross reactive) PvDBPII specific functionally active binding inhibitory antibodies were demonstrated among locally exposed P. vivax patients. Thus this study may support the inclusion of PvMSP-119, P04 region of PvAMA-1 domain II and region II of PvDBP as veritable vaccine components for a multi component cocktail asexual stage vaccine against P. vivax malaria in Sri Lanka.

Spontaneous Mutations in the Plasmodium falciparum Sarcoplasmic/ Endoplasmic Reticulum Ca 2+ -ATPase (PfATP6) Gene among Geographically Widespread Parasite Populations Unexposed to Artemisinin-Based Combination Therapies

Recent reports on the decline of the efficacy of artemisinin-based combination therapies (ACTs) indicate a serious threat to malaria control. The endoplasmic/sarcoplasmic reticulum Ca(2+)-ATPase ortholog of Plasmodium falciparum (PfSERCA) has been suggested to be the target of artemisinin and its derivatives. It is assumed that continuous artemisinin pressure will affect polymorphism of the PfSERCA gene (serca) if the protein is the target. Here, we investigated the polymorphism of serca in parasite populations unexposed to ACTs to obtain baseline information for the study of potential artemisinin-driven selection of resistant parasites. Analysis of 656 full-length sequences from 13 parasite populations in Africa, Asia, Oceania, and South America revealed 64 single nucleotide polymorphisms (SNPs), of which 43 were newly identified and 38 resulted in amino acid substitutions. No isolates showed L263E and S769N substitutions, which were reportedly associated with artemisinin resistance. Among the four continents, the number of SNPs was highest in Africa. In Africa, Asia, and Oceania, common SNPs, or those with a minor allele frequency of ≥0.05, were less prevalent, with most SNPs noted to be continent specific, whereas in South America, common SNPs were highly prevalent and often shared with those in Africa. Of 50 amino acid haplotypes observed, only one haplotype (3D7 sequence) was seen in all four continents (64%). Forty-eight haplotypes had frequencies of less than 5%, and 40 haplotypes were continent specific. The geographical difference in the diversity and distribution of serca SNPs and haplotypes lays the groundwork for assessing whether some artemisinin resistance-associated mutations and haplotypes are selected by ACTs.

Genetic and functional analysis of common MRC1 exon 7 polymorphisms in leprosy susceptibility

The chromosomal region 10p13 has been linked to paucibacillary leprosy in two independent studies. The MRC1 gene, encoding the human mannose receptor (MR), is located in the 10p13 region and non-synonymous SNPs in exon 7 of the gene have been suggested as leprosy susceptibility factors. We determined that G396S is the only non-synonymous exon 7-encoded polymorphism in 396 unrelated Vietnamese subjects. This SNP was genotyped in 490 simplex and 90 multiplex leprosy families comprising 704 patients (47% paucibacillary; 53% multibacillary). We observed significant under-transmission of the serine allele of the G396S polymorphism with leprosy per se (P = 0.036) and multibacillary leprosy (P = 0.034). In a sample of 384 Brazilian leprosy cases (51% paucibacillary; 49% multibacillary) and 399 healthy controls, we observed significant association of the glycine allele of the G396S polymorphism with leprosy per se (P = 0.016) and multibacillary leprosy (P = 0.023). In addition, we observed a significant association of exon 7 encoded amino acid haplotypes with leprosy per se (P = 0.012) and multibacillary leprosy (P = 0.004). Next, we tested HEK293 cells over-expressing MR constructs (293-MR) with three exon 7 haplotypes of MRC1 for their ability to bind and internalize ovalbumin and zymosan, two classical MR ligands. No difference in uptake was measured between the variants. In addition, 293-MR failed to bind and internalize viable Mycobacterium leprae and BCG. We propose that the MR-M. leprae interaction is modulated by an accessory host molecule of unknown identity.

SnTox3 Acts in Effector Triggered Susceptibility to Induce Disease on Wheat Carrying the Snn3 Gene

The necrotrophic fungus Stagonospora nodorum produces multiple proteinaceous host-selective toxins (HSTs) which act in effector triggered susceptibility. Here, we report the molecular cloning and functional characterization of the SnTox3-encoding gene, designated SnTox3, as well as the initial characterization of the SnTox3 protein. SnTox3 is a 693 bp intron-free gene with little obvious homology to other known genes. The predicted immature SnTox3 protein is 25.8 kDa in size. A 20 amino acid signal sequence as well as a possible pro sequence are predicted. Six cysteine residues are predicted to form disulfide bonds and are shown to be important for SnTox3 activity. Using heterologous expression in Pichia pastoris and transformation into an avirulent S. nodorum isolate, we show that SnTox3 encodes the SnTox3 protein and that SnTox3 interacts with the wheat susceptibility gene Snn3. In addition, the avirulent S. nodorum isolate transformed with SnTox3 was virulent on host lines expressing the Snn3 gene. SnTox3-disrupted mutants were deficient in the production of SnTox3 and avirulent on the Snn3 differential wheat line BG220. An analysis of genetic diversity revealed that SnTox3 is present in 60.1% of a worldwide collection of 923 isolates and occurs as eleven nucleotide haplotypes resulting in four amino acid haplotypes. The cloning of SnTox3 provides a fundamental tool for the investigation of the S. nodorum–wheat interaction, as well as vital information for the general characterization of necrotroph–plant interactions.

DNA Sequence Variation in the Tetranychus kanzawai Complex in Northern Hokkaido, Japan

DNA sequences of the internal transcribed spacer 1 (ITS1) of the nuclear ribosomal RNA gene and of mitochondrial cytochrome oxidase subunit I (COI) were analyzed for 13 Tetranychus kanzawai populations collected in northern Hokkaido, Japan. Five and 13 DNA haplotypes were found for ITS1 and COI, respectively, and the COI haplotypes were classified into 5 amino acid haplotypes. Monophyly of all haplotypes found in this study was strongly supported by bootstrap analysis, confirming that all analyzed individuals belonged to the T. kanzawai complex. The geographic distributions of these haplotypes overlapped, showing that populations had differentiated genetically from each other. However, some hybrid individuals were detected, indicating that genetic differentiation was not complete. Large genetic variation in the DNA sequences in the study area and the discovery of ancestral haplotypes strongly suggest that the complex originated in Northeast Asia.

Single and interacting QTLs for cholesterol gallstones revealed in an intercross between mouse strains NZB and SM

Quantitative trait locus (QTL) mapping was employed to investigate the genetic determinants of cholesterol gallstone formation in a large intercross between mouse strains SM/J (resistant) and NZB/B1NJ (susceptible). Animals consumed a gallstone-promoting diet for 18 weeks. QTL analyses were performed using gallstone weight and gallstone absence/presence as phenotypes; various models were explored for genome scans. We detected seven single QTLs: three new, significant QTLs were named Lith17 [chromosome (Chr) 5, peak=60 cM, LOD=5.4], Lith18 (Chr 5, 76 cM, LOD=4.3), and Lith19 (Chr 8, 0 cM, LOD=5.3); two confirmed QTLs identified previously and were named Lith20 (Chr 9, 44 cM, LOD=2.7) and Lith21 (Chr 10, 24 cM, LOD=2.9); one new, suggestive QTL (Chr 17) remains unnamed. Upon searching for epistatic interactions that contributed to gallstone susceptibility, the final suggestive QTL on Chr 7 was determined to interact significantly with Lith18 and, therefore, was named Lith22 (65 cM). A second interaction was identified between Lith19 and a locus on Chr 11; this QTL was named Lith23 (13 cM). mRNA expression analyses and amino acid haplotype analyses likely eliminated Slc10a2 as a candidate gene for Lith19. The QTLs identified herein largely contributed to gallstone formation rather than gallstone severity. Cloning the genes underlying these murine QTLs should facilitate prediction and cloning of the orthologous human genes.

Influence of polymorphisms within the CX3CR1 and MDR-1 genes on initial antiretroviral therapy response.

Single nucleotide polymorphisms (SNP) in the genes encoding the human CX3CR1 chemokine receptor and the P-glycoprotein multidrug transporter have been associated with accelerated disease progression in untreated individuals and implicated in therapeutic response, respectively. This retrospective study assessed the influence of SNP in the CX3CR1 and MDR-1 genes on initial virological and immunological response in 461 HIV-infected, antiretroviral-naive individuals initiating antiretroviral therapy in British Columbia, Canada. CX3CR1 and MDR-1 SNP were determined by PCR amplification of human DNA from plasma, followed by DNA sequencing. Time to virological success [time to HIV plasma viral load (pVL) < or = 500 copies/ml], virological failure (subsequent time to the second of two consecutive pVL > or = 500) and immunological failure (time to the second consecutive CD4 cell count below baseline) were analyzed by Kaplan-Meier methods. Frequencies of CX3CR1 amino acid haplotypes were 249V 280T (0.75), 249I 280M (0.15), and 249I 280T (0.1). Frequencies of MDR-1 nucleotide polymorphisms were 3435C (0.47) and 3435T (0.53). There was no effect detected for SNP in CX3CR1 or MDR-1 on time to virological success, nor of CX3CR1 and MDR-1 SNP on time to virological and immunological failure, respectively ( P > 0.1). There was a trend to earlier virological failure in the MDR-1 3435C/C genotype group ( P = 0.07), and a statistically significant trend to earlier immunological failure in individuals with the CX3CR1 249I polymorphism ( P = 0.02). These remained significant after correcting for baseline age, sex, pVL, CD4 cell count, type of therapy, and adherence ( P < or = 0.05). Polymorphisms in MDR-1 and CX3CR1 may be associated with accelerated virological and immunological therapy failure, respectively.

Evolution of a unique Plasmodium falciparum chloroquine-resistance phenotype in association with pfcrt polymorphism in Papua New Guinea and South America.

The mechanistic basis for chloroquine resistance (CQR) in Plasmodium falciparum recently has been linked to the polymorphic gene pfcrt. Alleles associated with CQR in natural parasite isolates harbor threonine (T), as opposed to lysine (K) at amino acid 76. P. falciparum CQR strains of African and Southeast Asian origin carry pfcrt alleles encoding an amino acid haplotype of CVIET (residues 72-76), whereas most South American CQR strains studied carry an allele encoding an SVMNT haplotype; chloroquine-sensitive strains from malarious regions around the world carry a CVMNK haplotype. Upon investigating the origin of pfcrt alleles in Papua New Guinean (PNG) P. falciparum we found either the chloroquine-sensitive-associated CVMNK or CQR-associated SVMNT haplotypes previously seen in Brazilian isolates. Remarkably we did not find the CVIET haplotype observed in CQR strains from Southeast Asian regions more proximal to PNG. Further we found a previously undescribed CQR phenotype to be associated with the SVMNT haplotype from PNG and South America. This CQR phenotype is significantly less responsive to verapamil chemosensitization compared with the effect associated with the CVIET haplotype. Consistent with this, we observed that verapamil treatment of P. falciparum isolates carrying pfcrt SVMNT is associated with an attenuated increase in digestive vacuole pH relative to CVIET pfcrt-carrying isolates. These data suggest a key role for pH-dependent changes in hematin receptor concentration in the P. falciparum CQR mechanism. Our findings also suggest that P. falciparum CQR has arisen through multiple evolutionary pathways associated with pfcrt K76T.

Amino acid polymorphisms for esterase-6 in Drosophila melanogaster.

High-resolution electrophoresis has revealed 10 allozymes of esterase-6 (EC 3.1.1.1) in Drosophila melanogaster. The sequences of 13 isolates of the Est6 gene covering all 10 allozymes were obtained and 52 nucleotide differences were found. Sixteen of these cause amino acid replacements, of which three result in charge differences whose size and direction are consistent with the electrophoretic mobilities of the allozymes in which they occur. The smeared electrophoretic phenotype of one allozyme can be explained by the loss of a cysteine residue involved in a disulfide bridge. Several minor mobility variants within the major F and S electrophoretic phenotypes differ by amino acid substitutions that are generally conservative for charge but not for some other properties (size, polarity, or hydrophobicity). Four amino acid differences are found among different isolates of the same allozymes and, overall, 12 amino acid haplotypes occur among the 13 isolates sequenced. Nevertheless, the most common variants within F and S are distinguished by only two amino acids (Asn/Asp at 237 and Thr/Ala at 247), and these are the most likely targets for the selection underlying complementary latitudinal clines in F and S frequencies.