title: Sequence characterization of S100A8 gene reveals structural differences of protein and transcriptional factor binding sites in water buffalo and yak.
abstract: The present study was undertaken to characterize the structure of S100A8 gene and its promoter in water buffalo and yak. Sequence data of 2.067 kb, 2.071 kb, and 2.052 kb with respect to complete S100A8 gene including 5' flanking region was generated in river buffalo, swamp buffalo, and yak, respectively. BLAST analysis of coding DNA sequences (CDS) of S100A8 gene revealed 95% homology of buffalo sequence with cattle, 85% with pig and horse, 83% with dog, 72-73% with murines, and around 79% with primates and humans. Phylogenetic analysis of predicted CDS revealed distinct clustering of murines, primates, and domestic animals with bovines and bubalines forming a subcluster among farm animals. In silico translation of predicted CDS revealed a sequence of 89 amino acids with 7 amino acid changes between cattle and buffalo and 2 changes between cattle and yak. The search for Pfam family revealed the N-terminal calcium binding domain and the noncanonical EF hand domain in the carboxy terminus, with more variations being observed in the N-terminal domain among different species. Two amino acid changes observed in carboxy terminal EF hand domain resulted in altered secondary structure of yak S100A8 protein. Analysis of S100A8 gene promoter revealed 14 putative motifs for transcriptional factor binding sites. Two putative motifs viz. C/EBP and v-Myb were found to be absent in swamp buffalo as compared to river buffalo and cattle. Differences in the structure of S100A8 protein and the transcriptional factor binding sites identified in the present study need to be analyzed further for their functional significance in yak and swamp buffalo respectively.
authors.affiliation: Buffalo Genomics Laboratory, National Bureau of Animal Genetic Resources, Karnal, Haryana, India. kathirvet@yahoo.co.in
authors.forename: P
authors.initials: P
authors.lastname: Kathiravan
authors.forename: S
authors.initials: S
authors.lastname: Goyal
authors.forename: R S
authors.initials: RS
authors.lastname: Kataria
authors.forename: B P
authors.initials: BP
authors.lastname: Mishra
authors.forename: S
authors.initials: S
authors.lastname: Jayakumar
authors.forename: B K
authors.initials: BK
authors.lastname: Joshi
mesh_terms: D000818:Animals; D001665:Binding Sites; D002020:Buffaloes / Q000235:genetics*; D040501:Calgranulin A / Q000737:chemistry / Q000235:genetics*; D002417:Cattle / Q000235:genetics*; D002874:Chromosome Mapping; D003198:Computer Simulation; D010802:Phylogeny; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics*
chemical_list: D040501:Calgranulin A; D014157:Transcription Factors