Identifying heat shock response systems from the genomic assembly of Ureibacillus thermophilus LM102 using protein-protein interaction networks

•U. thermophilus LM102 is a facultative thermophile with a growth range in 37 °C–60 °C.•The genome was sequenced and gaps were reduced manually, later validated using PCR.•Amino acid prevalence found mostly in thermophilic proteins is absent in LM102.•CshA, HemW identified in heat shock response using experimental protein interaction data. Ureibacillus thermophilus strain LM102 is a facultative thermophile with growth in range 37 °C–60 °C. Upon identification using the 16S rRNA marker, it showed highest similarity of 99.8% with U. thermophilus strain HC148. A phylogenetic analysis revealed U. suwonensis strain 6 T19 to be the closest species to strain LM102. Our aim was to determine the unique thermotolerant properties of LM102 by identifying thermostablity of its proteins and the interactions existing in its heat shock response systems (HSRS). The strain was sequenced, assembled and the draft genome (3,017,325 bp) was analyzed. Post-annotation, we randomly selected a set of hundred proteins and computed the percentage distribution of 12 amino acids which have been substantially studied for their role in thermostability. The protein homologues were searched and the residues of LM102 were compared with Bacillus subtilis and Thermus thermophilus, a mesophile and hyperthermophile respectively. Within the 95% confidence limit, a Z-score of −0.61 was observed between LM102 and B. subtilis. However, a significantly lower value of −8.84 was observed for the pair LM102 and T. thermophilus. The amino acid distribution did not appear to influence the protein thermostability. Further, we investigated the role of Protein-Protein interactions by building networks for heat shock responses, namely DNA repair, transcriptional regulation, and activation of heat shock proteins. Interaction data retrieved from the STRING database for more than 50 species were used to build these networks. Highly clustered MCODE results notably revealed RNA 3′-5′ exonuclease, CshA and HemW previously unreported, in association with other proteins. Additionally, these and other proteins estimated from the HSRS networks were found in both mesophiles and thermophiles, suggesting a crucial role of gene regulatory networks in the cellular viability of LM102 at high temperatures.