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Ruiz-De-La-Cruz G, Sifuentes-Rincón AM, Paredes-Sánchez FA, Parra-Bracamonte GM, Casas E, Riley DG, Perry GA, Welsh TH, Randel RD. Analysis of nonsynonymous SNPs in candidate genes that influence bovine temperament and evaluation of their effect in Brahman cattle. Mol Biol Rep 2024; 51:285. [PMID: 38324050 PMCID: PMC10850011 DOI: 10.1007/s11033-024-09264-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/17/2024] [Indexed: 02/08/2024]
Abstract
BACKGROUND Temperament is an important production trait in cattle and multiple strategies had been developed to generate molecular markers to assist animal selection. As nonsynonymous single nucleotide polymorphisms are markers with the potential to affect gene functions, they could be useful to predict phenotypic effects. Genetic selection of less stress-responsive, temperamental animals is desirable from an economic and welfare point of view. METHODS AND RESULTS Two nonsynonymous single nucleotide polymorphisms identified in HTR1B and SLC18A2 candidate genes for temperament were analyzed in silico to determine their effects on protein structure. Those nsSNPs allowing changes in proteins were selected for a temperament association analysis in a Brahman population. Transversion effects on protein structure were evaluated in silico for each amino acid change model, revealing structural changes in the proteins of the HTR1B and SLC18A2 genes. The selected nsSNPs were genotyped in a Brahman population (n = 138), and their genotypic effects on three temperament traits were analyzed: exit velocity, pen score, and temperament score. Only the SNP rs209984404-HTR1B (C/A) showed a significant association (P = 0.0144) with pen score. The heterozygous genotype showed a pen score value 1.17 points lower than that of the homozygous CC genotype. CONCLUSION The results showed that in silico analysis could direct the selection of nsSNPs with the potential to change the protein. Non-synonymous single nucleotide polymorphisms causing structural changes and reduced protein stability were identified. Only rs209984404-HTR1B shows that the allele affecting protein stability was associated with the genotype linked to docility in cattle.
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Affiliation(s)
- Gilberto Ruiz-De-La-Cruz
- Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, 88710, México
| | - Ana María Sifuentes-Rincón
- Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, 88710, México.
| | | | - Gaspar Manuel Parra-Bracamonte
- Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, 88710, México
| | - Eduardo Casas
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, 50010, USA
| | - David G Riley
- Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA
| | | | - Thomas H Welsh
- Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA
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Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls. Genet Res (Camb) 2022; 2022:9452234. [PMID: 35356752 PMCID: PMC8941572 DOI: 10.1155/2022/9452234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/03/2021] [Accepted: 02/16/2022] [Indexed: 11/29/2022] Open
Abstract
Transition nuclear proteins (TNPs), the principal proteins identified in the condensing spermatids chromatin, have been found to play a key role in histone displacement and chromatin condensation during mammalian spermatogenesis. One such gene belonging to the TNP family called TNP1 gene is abundantly expressed in the regulation of spermatogenesis, and its sequence is remarkably well conserved among mammals. Genomic analysis, by sequencing and computational approach, was used to identify the novel polymorphisms and to evaluate the molecular regulation of TNP1 gene expression in Sahiwal cattle breeding bulls. DNA samples were sequenced to identify novel single nucleotide polymorphisms (SNPs) in the TNP1 gene. Modern computational tools were used to predict putative transcription factor binding in the TNP1 promoter and CpG islands in the TNP1 promoter region. In the TNP1 gene, four SNPs, three TATA boxes, and one CAAT box were identified. One CAAT box was discovered at 89 bp upstream of start site ATG. The computational analyses indicated that the polymorphisms inside the promoter sequence results in an added HNF-1 transcription factor binding site. In contrast, the other variations may remove the naturally occurring SRF transcription factor binding site. The CpG islands in the TNP1 promoter region were predicted to be absent by the MethPrimer program before and after SNP site mutations. These findings pave the way for more research into the TNP1 gene's promoter activity and the links between these SNPs and reproductive attributes in the Sahiwal breeding bulls.
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Whitney J, Haase B, Beatty J, Barrs VR. Breed-specific variations in the coding region of toll-like receptor 4 in the domestic cat. Vet Immunol Immunopathol 2019; 209:61-69. [PMID: 30885307 PMCID: PMC7126157 DOI: 10.1016/j.vetimm.2019.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/01/2019] [Accepted: 02/25/2019] [Indexed: 12/15/2022]
Abstract
Specific point mutations in the human toll-like receptor 4 (TLR4) confer altered risk for diverse diseases including sepsis, aspergillosis and inflammatory bowel disease. Some of these TLR4 polymorphisms are racially specific. We hypothesised that feline TLR4 polymorphisms might underlie an observed increased risk to infectious and inflammatory diseases in some cat breeds. The aim of this study was to identify breed-specific variations in the coding region of feline TLR4 and to model the effect of mutations on protein structure and function in silico. The entire coding region of TLR4 was sequenced in 8 groups (7 pure-bred, 1 crossbred) of domestic cats (Felis catus) comprising 158 individuals. Twenty-two single nucleotide polymorphisms (SNPs) were identified in TLR4, with 16 located in the coding region (11 non-synonymous) and four in the 3′UTR. Comparison of breed specific allelic frequencies indicated that Burmese and British shorthairs most commonly differed from other breeds. In silico analyses to predict the impact of the 11 non-synonymous variants indicated a deleterious effect on protein structure for one SNP (c.869 G > A), which was not associated with a specific breed. Overall, findings from this study do not support a role of TLR4 dysfunction in breed-predispositions to infectious diseases in domestic cats in Australia.
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Affiliation(s)
- J Whitney
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW 2006, Australia.
| | - B Haase
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW 2006, Australia.
| | - J Beatty
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW 2006, Australia; Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, NSW 2006, Australia.
| | - V R Barrs
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW 2006, Australia; Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, NSW 2006, Australia.
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Gurung AB, Bhattacharjee A. Impact of a non-synonymous Q281R polymorphism on structure of human Lipoprotein-Associated Phospholipase A 2 (Lp-PLA 2 ). J Cell Biochem 2018; 119:7009-7021. [PMID: 29737567 DOI: 10.1002/jcb.26909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/28/2018] [Indexed: 01/27/2023]
Abstract
Non-synonymous single nucleotide polymorphisms (nsSNPs) are genetic variations at single base resulting in an amino acid change which have been associated with various complex human diseases. The human Lipoprotein-associated phospholipase A2 (Lp-PLA2 ) gene harbours a rare Q281R polymorphism which was previously reported to cause loss of enzymatic function. Lp-PLA2 is an important enzyme which catalyzes the hydrolysis of polar phospholipids releasing pro-atherogenic and pro-inflammatory mediators involved in the pathogenesis of atherosclerosis. Our current study is aimed at elucidating the structural and functional consequences of Q281R polymorphism on Lp-PLA2 . The Q281R mutation is classified as deleterious and causes protein instability as deduced from evolutionary, folding free energy changes and Support vector machine (SVM)-based methods. A Q281R mutant structure was deciphered using homology modelling approach and was validated using phi and psi dihedral angles distribution, ERRAT, Verify_3D scores, Protein Structure Analysis (ProSA) energ,y and Z-score. A decreased hydrophobic interactions and weaker substrate binding affinity was observed in the mutant compared to the wild- type (WT) using molecular docking. Further, the mutant displayed enhanced structural flexibility particularly in the low density lipoprotein (LDL) binding domain, decreased solvent accessibility of catalytic residues-Phe274 and Ser273 and increased Cɑ distance between Phe274 and Leu153 and large conformational entropy change as inferred from all-atom molecular dynamics (MD) simulation and essential dynamics (ED) studies. Our results corroborate well with previous experimental studies and thus these aberrations in the Q281R mutant structure may help explain the molecular basis of loss of enzyme activity.
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Affiliation(s)
- Arun B Gurung
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Atanu Bhattacharjee
- Computational Biology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, India.,Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
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