Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles

Abstract

SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria. organisms [11,13]. The increase in ion-pair interactions is due to a higher composition of charged amino acids such as lysine (Lys), arginine (Arg), glutamic acid (Glu) and asparagine (Asn) in the proteins from thermophilic bacteria when compared to those from mesophilic bacteria [11,13]. Sequence and structural characteristics such as presence of insertions and deletions, proline substitutions, closer packing of water-accessible surface residues, and increase in helical contents and hydrogen bonds has also been suggested to contribute towards increase in the thermostability of thermophilic proteins [14][15][16]. Evidently, the characteristics providing thermostability to proteins can exist in various forms, and further understanding protein features and characteristics that likely contribute towards the thermostability of proteins is of much interest [13,17].Within the domain Bacteria, hyperthermophilic organisms are mainly present in three bacterial phyla viz. Aquificae, and Thermotogae [4,9,[18][19][20][21]. The members from these phyla, which contain some of the most hyperthermophilic organisms known (e.g., Thermotoga maritima, Thermus aquaticus, and Aquifex aeolicus), are notable for their thermostable enzymes [1,2,5,9,22]. However, of these three phyla, while the phylum Aquificae is primarily comprised of thermophilic-hyperthermophilic organisms [18,20], in the other two phyla, hy...

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Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera

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Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers

“…Lastly, the CSIs which are exclusively shared by a given group of organisms are the results of highly specific genetic/molecular changes (synapomorphies) [22,49,61]. Earlier work on these molecular markers show that the genetic changes represented by the CSIs are functionally important to the group of organisms, which contain them [62][63][64]. Hence, genetic and biochemical studies directed towards understanding the functional significance of these CSIs could provide information regarding novel biochemical and/or other characteristics of the specific groups of micro-organisms.…”