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

Bijendra Khadka,Dhillon Persaud,Radhey S Gupta

doi:10.3390/microorganisms8010059

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.

Highlights

Thermophilic organisms are of great scientific interest due to their ability to grow at temperatures well above 60 ◦C [1,2,3,4,5]
The present study focuses on our identification of two large conserved signature inserts (CSIs) in the SecA protein, which are uniquely found in different homologs from the thermophilic–hyperthermophilic phyla of bacteria
It should be noted in this regard, that within the phylum Thermotogae, the order Thermotogales encompasses all of the thermophilic–hyperthermophilic organisms, whereas the other two orders lacking this CSI are comprised of mesophilic organisms [4,23,26,64]

Summary

Introduction

Thermophilic organisms (bacteria) are of great scientific interest due to their ability to grow at temperatures well above 60 ◦C [1,2,3,4,5]. Within industrial settings, the higher temperature stability of these protein catalysts allows for reactions at higher temperatures resulting in decreased contamination concerns and overall faster reaction speeds [9]. An example in this regard includes widespread use of enzyme Thermus aquaticus (Taq) polymerase in the technique of polymerase chain reaction (PCR) [10]. One prevalent characteristic is the increase in the presence of ion-pair interactions in thermophilic organisms [11,13]. 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]

Methods

Results

Conclusion