Cloning, sequence analysis, and three-dimensional structure prediction of Universal stress protein A from Salmonella Typhimurium Isolated from the Poultry

Abstract Background Salmonella Typhimurium is a zoonotic pathogen responsible for food and waterborne gastroenteritis in humans. Salmonella Typhimurium expresses Universal stress proteins (USPs) when subjected to different biotic and abiotic stresses. This class of proteins is becoming widely recognizedfor its role in bacterial stress resistance and protracted growth arrest. USPs possesses versatile structures arising from the fusion of the USP domain with various other catalytic motifs; they are possibly involved in a variety of reactions and cellular activities under stressful conditions. Objective The aim of this study is to obtain the universal stress protein A (uspA) gene of Salmonella Typhimurium and clone it into the pET28C plasmid for nucleotide sequencing. And also 3D structure prediction of USPA protein and to evaluate its phylogenetic gene tree model. Methods In this study, we constructed a recombinant clone of the uspA (pET28c_uspA) gene from Salmonella Typhimurium, and various methods, including sequencing, did conformation to the clone. The sequence was subsequently submitted to the NCBI GenBank database. Besides, the Three-dimensional structure for USPA protein was predicted by comparative modeling. A phylogenetic gene tree was also constructed to trace the evolutionary history of the uspA gene of Salmonella Typhimurium. Results The uspA gene of 435 bp in length was successfully cloned. Comparing the uspA gene sequence with that reported in GenBank showed that identities were 100%. Furthermore, Sequence analysis also revealed the uspA gene is 435 bp long, encodes a protein of 144 amino acids with a calculated molecular mass of 16 kDa, and belongs to the USP family. Predicted 3D structure and sequence alignments of USPA showed that all residues’ sites are highly similar among the genome. The stereo-chemical property of the 3D structure of USPA was found to be of good quality. Conclusion A confirmed uspA gene from Salmonella Typhimurium was reported in this study. This study laid a solid foundation for recombination and research of genes. Moreover, the results of this study would help to detect the functional domains of the protein to elucidate their structural/functional characteristics.