title: Sequence based structural characterization and genetic diversity analysis across coding and promoter regions of goat Toll-like receptor 5 gene.
abstract: The exploration of candidate immune response genes in goat may be vital in improving further our understanding about the species specific response to pathogens specifically among the ruminants. In this study, approximately 3.7 kb long genomic sequence of Toll-like receptor 5 (TLR5) covering the entire coding and 5'upstream regions of the gene, was characterized in the Indian goat breeds. Sequence analysis revealed a 2577-nucleotide long open reading frame (ORF) of goat TLR5, encoding 858 amino acids from single exon, similar to other ruminants. The domain structure analysis of goat TLR5 showed the presence of 13 leucine rich repeats (LRRs) in extracellular domain (amino acid position 1-634), single transmembrane domain (position 644-666), and a Toll/interleukin-1 receptor (position 692-837) in cytoplasmic domain, similar to other species. A total of 87 putative transcription factor binding sites were observed within the 5' upstream region of TLR5 gene in goat, 106 in cattle, and 103 in buffalo. Sixteen polymorphic sites were observed in goat TLR5 gene, out of which 10 non-synonymous SNPs were in the functionally important regions. However, none of the amino acid substitutions was found to be potentially damaging to the structure and function of the receptor protein. Further, one of the SNPs in the transmembrane region was genotyped by a TETRA-ARMS PCR in 444 goats of nine breeds from different geographical regions and having different utilities. A significant variation in allelic frequencies was observed across the milch and other types of goat breeds. The comparative modeling of goat TLR5 followed by molecular dynamics simulation gave an insight into its 3D structural arrangements. The molecular docking of Salmonella flagellin and TLR5 dimer elucidated LRRNT (N-terminal) to LRR4 as the key flagellin binding domains region in goat TLR5. The study shows that, although being highly conserved among the ruminants, comparatively high variations in goat TLR5 might give an opportunity to host for recognizing the wider spectrum of pathogens.
authors: National Bureau of Animal Genetic Resources, G.T. Road By-Pass, Karnal, Haryana 132001 India.
authors: Shubham
authors: S
authors: Goyal
authors: National Bureau of Animal Genetic Resources, G.T. Road By-Pass, Karnal, Haryana 132001 India.
authors: P K
authors: PK
authors: Dubey
authors: Laboratory of Molecular Biophysics, Institute of Protein Research, Osaka University, Osaka Prefecture 5650871, Japan.
authors: B R
authors: BR
authors: Sahoo
authors: National Bureau of Animal Genetic Resources, G.T. Road By-Pass, Karnal, Haryana 132001 India.
authors: S K
authors: SK
authors: Mishra
authors: National Bureau of Animal Genetic Resources, G.T. Road By-Pass, Karnal, Haryana 132001 India.
authors: S K
authors: SK
authors: Niranjan
authors: National Bureau of Animal Genetic Resources, G.T. Road By-Pass, Karnal, Haryana 132001 India.
authors: Sanjeev
authors: S
authors: Singh
authors: Department of Biotechnology, Kurukshetra University, Kurukshetra, Haryana, India.
authors: Ritu
authors: R
authors: Mahajan
authors: Department of Biotechnology, Kurukshetra University, Kurukshetra, Haryana, India. Electronic address: katariaranji@yahoo.co.in.
authors: R S
authors: RS
authors: Kataria
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D005787:Gene Frequency; D006041:Goats / Q000235:genetics*; D056004:Molecular Dynamics Simulation; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D017422:Sequence Analysis, DNA; D051198:Toll-Like Receptor 5 / Q000737:chemistry / Q000235:genetics*
chemical_list: D051198:Toll-Like Receptor 5
keywords: Goat, Toll-like receptor 5; Leucine-rich repeats (LRR); Molecular docking; Molecular dynamics simulation; Polymorphism; Toll/IL-1 receptor (TIR) domain; Transcription factor binding sites