Analysis of sequence variability and protein domain architectures for bovine peptidoglycan recognition protein 1 and Toll-like receptors 2 and 6

A haplotype-like, chromosome-level assembled and annotated genome of Biomphalaria glabrata, an important intermediate host of schistosomiasis and the best studied model of schistosomiasis vector snails

Schistosomiasis is one of the world's most devastating parasitic diseases, afflicting 251 million people globally. The Neotropical snail Biomphalaria glabrata is an important intermediate host of the human blood fluke Schistosoma mansoni and a predominant model for schistosomiasis research. To fully exploit this model snail for biomedical research, here we report a haplotype-like, chromosome-level assembled and annotated genome of the homozygous iM line of B. glabrata that we developed at the University of New Mexico. Using multiple sequencing platforms, including Illumina, PacBio, and Omni-C sequencing, 18 sequence contact matrices representing 18 haploid chromosomes (2n = 36) were generated (337x genome coverage), and 96.5% of the scaffold sequences were anchored to the 18 chromosomes. Protein-coding genes (n = 34,559), non-coding RNAs (n = 2,406), and repetitive elements (42.52% of the genome) were predicted for the whole genome, and detailed annotations for individual chromosomes were also provided. Using this genomic resource, we have investigated the genomic structure and organization of the Toll-like receptor (TLR) and fibrinogen-domain containing protein (FReD) genes, the two important immune-related gene families. Notably, TLR-like genes are scattered on 13 chromosomes. In contrast, almost all (39 of 40) fibrinogen-related genes (FREPs) (immunoglobulin superfamily (IgSF) + fibrinogen (FBG)) are clustered within a 5-million nucleotide region on chromosome 13, yielding insight into mechanisms involved in the diversification of FREPs. This is the first genome of schistosomiasis vector snails that has been assembled at the chromosome level, annotated, and analyzed. It serves as a valuable resource for a deeper understanding of the biology of vector snails, especially Biomphalaria snails.

Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites

Proteins are under selection to maintain central functions and to accommodate needs that arise in ever-changing environments. The positive selection and neutral drift that preserve functions result in a diversity of protein variants. The amount of diversity differs between proteins: multifunctional or disease-related proteins tend to have fewer variants than proteins involved in some aspects of immunity. Our work focuses on the extensively studied protein Vitellogenin (Vg), which in honey bees (Apis mellifera) is multifunctional and highly expressed and plays roles in immunity. Yet, almost nothing is known about the natural variation in the coding sequences of this protein or how amino acid-altering variants might impact structure-function relationships. Here, we map out allelic variation in honey bee Vg using biological samples from 15 countries. The successful barcoded amplicon Nanopore sequencing of 543 bees revealed 121 protein variants, indicating a high level of diversity in Vg. We find that the distribution of non-synonymous single nucleotide polymorphisms (nsSNPs) differs between protein regions with different functions; domains involved in DNA and protein-protein interactions contain fewer nsSNPs than the protein's lipid binding cavities. We outline how the central functions of the protein can be maintained in different variants and how the variation pattern may inform about selection from pathogens and nutrition.

Relationship between polymorphism within Peptidoglycan Recognition Protein 1 gene (PGLYRP1) and somatic cell counts in milk of Holstein cows

Bovine peptidoglycan recognition protein 1 (PGLYRP1) is an important receptor that binds to murein peptidoglycans (PGN) of Gram-positive and Gram-negative bacteria and is, therefore, involved in innate immunity. The SNP T>C rs68268284 located in the 1st exon of the PGLYRP1 gene was identified by the PCR-RFLP method in a population of 319 Holstein cows. Somatic cell count (SCC) was measured 7–10 times in each of three completed lactations to investigate whether the PGLYRP1 polymorphism is associated with SCC. Using the GLM model, it was found that cows with the TT genotype showed significantly lower somatic cell counts than those with the CC genotype during the first lactation (P = 0.023). Moreover, during lactations 1–2 and 1–3, cows with the TT genotype reveal significantly lower SCC than CT heterozygotes, at P = 0.025 and P = 0.006, respectively. Computer-aided analysis showed that rs68268284 polymorphism could modify the PGLYRP1 functions because the mutated residue is located in a domain that is important for the binding of other molecules.

Association of TLR gene variants in a Czech Red Pied cattle population with reproductive traits

The bovine genes TLR1, TLR2 and TLR6, which encode Toll-like receptors, key components of the innate immune system, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle, and the different variants present in the population were tested for association with reproductive and fitness traits. Diversity was investigated in a group of 164 bulls using hybrid resequencing of pooled amplicons with PacBio technology and of pooled genomic DNA using HiSeq X-Ten technology. The validated single nucleotide polymorphisms (SNPs) were genotyped in individual animals using the primer extension technique. The association of genotypic classes of 16 polymorphisms with six phenotypic traits were estimated with one-way analysis of variance (ANOVA) and with restricted maximum likelihood (REML) algorithm. The evaluated traits included the incidence of cystic ovaries, index of early reproductive disorders, paternal and maternal indicators of calving ease, production longevity and calf vitality index. The estimated breeding values were used for combined trait quantification. Early traits, namely, cystic ovaries and early reproductive disorders, were not associated with any of the tested polymorphisms according to the general ANOVA test. By contrast, five variants of all three genes were associated with calving ease, both paternal and maternal. The production longevity correlated with two variants of TLR1 and the calf vitality index correlated with the 1044 T > C (rs68268249) polymorphism in TLR2. The false discovery rate (FDR) according to Benjamini-Hochberg was favourable for the calving ease trait (0.221) and maternal calving ease (0.214), which allows to consider the observed associations real, regardless of the error arising from the multiple comparisons. These results were supported by REML only partially, probably in view of the additivity assumption. Two mechanisms of action on calving are conceivable, either via infection resistance or via the involvement of TLR2 in signalling in the myometrium. The known formation of heterodimers by the TLR1, -2 and -6 products might be responsible for the shared pattern of action in these genes. The association of the calf vitality index with TLR2 variation might reflect the increased role of infections in calves compared to adult animals.

Potential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencing

A production herd of Czech Simmental cattle (Czech Red Pied, CRP), the conserved subpopulation of this breed, and the ancient local breed Czech Red cattle (CR) were screened for diversity in the antibacterial toll-like receptors (TLRs), which are members of the innate immune system. Polymerase chain reaction (PCR) amplicons of TLR1, TLR2, TLR4, TLR5, and TLR6 from pooled DNA samples were sequenced with PacBio technology, with 3- 5 ×  coverage per gene per animal. To increase the reliability of variant detection, the gDNA pools were sequenced in parallel with the Illumina X-ten platform at low coverage ( 60 × per gene). The diversity in conserved CRP and CR was similar to the diversity in conserved and modern CRP, representing 76.4 % and 70.9 % of its variants, respectively. Sixty-eight (54.4 %) polymorphisms in the five TLR genes were shared by the two breeds, whereas 38 (30.4 %) were specific to the production herd of CRP; 4 (3.2 %) were specific to the broad CRP population; 7 (5.6 %) were present in both conserved populations; 5 (4.0 %) were present solely for the conserved CRP; and 3 (2.4 %) were restricted to CR. Consequently, gene pool erosion related to intensive breeding did not occur in Czech Simmental cattle. Similarly, no considerable consequences were found from known bottlenecks in the history of Czech Red cattle. On the other hand, the distinctness of the conserved populations and their potential for resistance breeding were only moderate. This relationship might be transferable to other non-abundant historical cattle breeds that are conserved as genetic resources. The estimates of polymorphism impact using Variant Effect Predictor and SIFT software tools allowed for the identification of candidate single-nucleotide polymorphisms (SNPs) for association studies related to infection resistance and targeted breeding. Knowledge of TLR-gene diversity present in Czech Simmental populations may aid in the potential transfer of variant characteristics from other breeds.

Distribution of single nucleotide polymorphisms and protein domain architecture of toll-like receptor-2 in Pahari cattle (Indian non-descript indigenous breed)

Distribution of polymorphism in TLR2 gene was studied in Pahari (Indian non-descript indigenous breed) cattle of Himachal Pradesh. The complete sequence of TLR2 gene consisted of 136bp 5'-UTR, 2355bp CDS and 1316bp 3'UTR. The phylogenetic analysis revealed clustering of Indian Zebu with Bos taurus as the nearest neighbour. The nucleotide sequences of TLR2 revealed the occurrence of 19 SNPs including 47% non-synonymous and 53% synonymous SNPs within TLR domain among all bovines. The dS/dN ratio (ω)<1 at polymorphic sites revealed purifying selection and thus, indicating the presence of highly conserved domains. Two SNPs in the extracellular domain of TLR2 were predicted to have damaging effect whereas the rest have benign effect. The amino acid sequence of the coding region corresponds to a protein of 784 amino acids long with predicted molecular weight 104kDa and 6.97 pI value. The amino acid sequence analysis showed extracellular domain composed of leucine rich repeats (LRR), trans- membrane domain and Toll-IL receptor domain in the protein. The 3D structure of TLR2 is a solenoid-like having active sites buried in the concave side and forming a pocket for ligand binding. The substitution of G with T in nucleotide sequence leads to the replacement of amino acid W↔L at position 119 which has not been reported so far. These findings indicate that polymorphism may be associated with PAMPs mediated differential TLR signaling of bovine immunity and could determine the outcome of infection.

Functional polymorphisms in Toll-like receptor genes for innate immunity in farm animals

The exploitation of the genetic factors affecting the health status of farm animals represents an alternative approach to controlling the diseases caused by microbial pathogens. The determination of innate immunity based on the genotype of the germplasm cells is a constraint for specificity but becomes an advantage in breeding schemes. The structural deviations among Toll-like receptors (TLRs), as the most frequently studied innate immunity components, have been documented at all levels, i.e., interspecific, inter- and intravarietal, in the main farm species. The current computational methods facilitate the prediction of the functional consequences of the observed mutations. Subsequently, these predictions can be verified through immunological responsiveness and population-wide association studies. The frequency and haplotype grouping of individual polymorphisms are used to track the origin and selection coefficient as independent indicators of functional changes. The Toll-like receptor variants associated with mastitis and mycobacterial infection have been identified in cattle, consequently, the targeting of these proteins in breeding could contribute to disease control. The range of infections affected by TLR polymorphisms suggests that the improvement of innate resistance is feasible in more species. Thus, the traditional breeds and wild populations should be regarded as the resources of genetic variability accessible for these purposes.

Sequence characterization of river buffalo Toll-like receptor genes 1-10 reveals distinct relationship with cattle and sheep

The present study was undertaken to characterize the full-length transcripts of Toll-like receptor (TLR) genes 1-10 of river buffalo. The conceptualized amino acid identity of bubaline TLRs ranged between 86% to 100% with ruminants, while it ranged between 45% to 91% with other vertebrate species. Simple modular architecture tool (SMART) analysis revealed the presence of TIR domains and varying numbers of leucine-rich repeat motifs in all the buffalo TLRs. With respect to TIR domains, TLRs 1, 2 and 3 of river buffalo were found to have 99.3% identity with cattle and 100% identity of TLRs 4, 6 and 10 with sheep. Phylogenetic analysis of TLRs of buffalo and different vertebrate species revealed the clustering of major TLR gene subfamilies with high bootstrap values. The evolutionary relationship between buffalo and other ruminant species was found to vary among different TLRs. In order to understand the relationship between TLRs of different ruminant species, multidimensional scaling (MDS) analysis of pairwise amino acid differences between different species within each TLR was performed. Buffalo and cattle were found to be closely related only with respect to TLRs 1, 2 and 7, while buffalo and sheep were found to be clustering together with respect to TLRs 3, 6, 8 and 10. The distinct relationship of bubaline TLRs with cattle and sheep revealed the possible differences in the pathogen recognition receptor systems in these animals and consequently the differences in their susceptibility/resistance to various invading organisms.

Evolution of the bovine TLR gene family and member associations with Mycobacterium avium subspecies paratuberculosis infection

Members of the Toll-like receptor (TLR) gene family occupy key roles in the mammalian innate immune system by functioning as sentries for the detection of invading pathogens, thereafter provoking host innate immune responses. We utilized a custom next-generation sequencing approach and allele-specific genotyping assays to detect and validate 280 biallelic variants across all 10 bovine TLR genes, including 71 nonsynonymous single nucleotide polymorphisms (SNPs) and one putative nonsense SNP. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and specialized beef and dairy breeds could not be differentiated despite an average polymorphism density of 1 marker/158 bp. Collectively, 160 tagSNPs and two tag insertion-deletion mutations (indels) were sufficient to predict 100% of the variation at 280 variable sites for both Bos subspecies and their hybrids, whereas 118 tagSNPs and 1 tagIndel predictively captured 100% of the variation at 235 variable sites for B. t. taurus. Polyphen and SIFT analyses of amino acid (AA) replacements encoded by bovine TLR SNPs indicated that up to 32% of the AA substitutions were expected to impact protein function. Classical and newly developed tests of diversity provide strong support for balancing selection operating on TLR3 and TLR8, and purifying selection acting on TLR10. An investigation of the persistence and continuity of linkage disequilibrium (r²≥0.50) between adjacent variable sites also supported the presence of selection acting on TLR3 and TLR8. A case-control study employing validated variants from bovine TLR genes recognizing bacterial ligands revealed six SNPs potentially eliciting small effects on susceptibility to Mycobacterium avium spp paratuberculosis infection in dairy cattle. The results of this study will broadly impact domestic cattle research by providing the necessary foundation to explore several avenues of bovine translational genomics, and the potential for marker-assisted vaccination.

Sequence analysis of Toll-like receptor genes 1-10 of goat (Capra hircus)

This study involved cloning and sequencing of the coding regions of all 10 Toll-like receptor (TLR) genes of goat. Goat TLR 1-10 gene sequences revealed a high degree of nucleotide identity with sheep and cattle sequences (>90%) and 75-85% with pig, mouse and human sequences. At the amino acid level, 85-99% similarity was observed with sheep and cattle and 60-85% with pig, mouse and human. TLR9c DNA of goat showed the highest amino acid identity to that of sheep (99%) while TLR8 cDNA showed the lowest identity of 88.7% to that of sheep. Variations were seen in the number of leucine rich repeats (LRRs) of goat TLRs as compared to other ruminant species with maximum differences in the TLR3 gene. Phylogenetic analysis through molecular evolution and genetic analysis (MEGA) software and multi dimensional scaling revealed a high degree of conservation of goat TLRs with those from other species. However when the TIR domain of all the TLRs were compared, goat TLR7 TIR alone showed a high divergence of 19.3 as compared to sheep sequences. This is the first report of the full-length cDNA sequences of all the 10 TLR genes of goats which would be a useful tool for the study of evolutionary lineages and for phylogenetic analysis.

Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle

The Toll-like receptor (TLR) and peptidoglycan recognition protein 1 (PGLYRP1) genes play key roles in the innate immune systems of mammals. While the TLRs recognize a variety of invading pathogens and induce innate immune responses, PGLYRP1 is directly microbicidal. We used custom allele-specific assays to genotype and validate 220 diallelic variants, including 54 nonsynonymous SNPs in 11 bovine innate immune genes (TLR1-TLR10, PGLYRP1) for 37 cattle breeds. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and we were unable to differentiate between the specialized B. t. taurus beef and dairy breeds, despite an average polymorphism density of one locus per 219 bp. Ninety-nine tagSNPs and one tag insertion-deletion polymorphism were sufficient to predict 100% of the variation at all 11 innate immune loci in both subspecies and their hybrids, whereas 58 tagSNPs captured 100% of the variation at 172 loci in B. t. taurus. PolyPhen and SIFT analyses of nonsynonymous SNPs encoding amino acid replacements indicated that the majority of these substitutions were benign, but up to 31% were expected to potentially impact protein function. Several diversity-based tests provided support for strong purifying selection acting on TLR10 in B. t. taurus cattle. These results will broadly impact efforts related to bovine translational genomics.

Comparative genomics of Toll-like receptor signalling in five species

BACKGROUND

Over the last decade, several studies have identified quantitative trait loci (QTL) affecting variation of immune related traits in mammals. Recent studies in humans and mice suggest that part of this variation may be caused by polymorphisms in genes involved in Toll-like receptor (TLR) signalling. In this project, we used a comparative approach to investigate the importance of TLR-related genes in comparison with other immunologically relevant genes for resistance traits in five species by associating their genomic location with previously published immune-related QTL regions.

RESULTS

We report the genomic localisation of TLR1-10 and ten associated signalling molecules in sheep and pig using in-silico and/or radiation hybrid (RH) mapping techniques and compare their positions with their annotated homologues in the human, cattle and mouse whole genome sequences. We also report medium-density RH maps for porcine chromosomes 8 and 13. A comparative analysis of the positions of previously published relevant QTLs allowed the identification of homologous regions that are associated with similar health traits in several species and which contain TLR related and other immunologically relevant genes. Additional evidence was gathered by examining relevant gene expression and association studies.

CONCLUSION

This comparative genomic approach identified eight genes as potentially causative genes for variations of health related traits. These include susceptibility to clinical mastitis in dairy cattle, general disease resistance in sheep, cattle, humans and mice, and tolerance to protozoan infection in cattle and mice. Four TLR-related genes (TLR1, 6, MyD88, IRF3) appear to be the most likely candidate genes underlying QTL regions which control the resistance to the same or similar pathogens in several species. Further studies are required to investigate the potential role of polymorphisms within these genes.

Microbial antigens mediate HLA-B27 diseases via TLRs

HLA-B27 positive individuals are predisposed to reactive arthritis developing 1-3 weeks after urogenital and gastrointestinal infections. Also ankylosing spondylitis (AS) associates strongly to HLA-B27, but no specific infection, Klebsiella pneumoniae excluded, has been linked to it. Before the discovery of its HLA-B27 association there were many reports suggesting a link between chronic prostatitis in men or pelvic inflammatory disease in women and AS. They have since been forgotten although HLA-B27 did not help to understand, why this disease has an axial and ascending nature. It is proposed that the urogenital organs form a source of damage (or danger)-associated molecular patterns (DAMPs), either exogenous pathogen-associated molecular patterns (PAMPs) from microbes or endogenous alarmins, such as uric acid, released from necrotic cells or urate deposits. DAMPs are slowly seeded from low-down upwards via the pelvic and spinal lymphatic pathways. They reach Toll-like receptors (TLRs) in their target mesenchymal stem cells, which are stimulated to ectopic enchondral bone formation leading to syndesmophytes and bamboo spine. At the same time inflammatory cytokines induce secondary osteoporosis of the spine. This new paradigm places microbes, HLA-B27 and TLRs in the pathogenic centre stage, but without pinpointing any (one) specific pathogen; instead, shared microbial patterns are indicated.

Sequence analysis and polymorphism discovery in 4 members of the bovine cathelicidin gene family

Cathelicidins (CATHLs) are small, cationic antimicrobial peptides that establish an early innate immune defense against infections in mammals. Beyond their wide spectrum of antimicrobial activity, these peptides play important roles in wound repair, chemotactic activity, and apoptosis. Thus, polymorphisms present in bovine CATHLs 2, 5, 6, and 7 could potentially underlie inherited differences in innate immunity and disease resistance. The purpose of the present study was to characterize single nucleotide polymorphisms (SNPs) and insertion-deletion (indel) polymorphisms within the bovine CATHL gene family. Comparative sequence analysis for 10 domestic cattle breeds representing both Bos taurus and Bos indicus revealed 60 SNPs, 7 of which were nonsynonymous and 5 indel mutations. Characterization of these novel polymorphisms is central to developing a firm understanding regarding what effects, if any, nonsynonymous CATHL variation has with respect to bovine innate immunity.