Quorum sensing in Mycobacteria: understanding the recognition machinery conundrum through an in-silico approach

Abstract

Bacteria employ a cell-to-cell communication process called quorum sensing (QS) to orchestrate group behaviors like exo-factors and host-adapted traits. The QS machinery in gram negative bacteria comprises of LuxR proteins (and their homologs) that are transcription factors which recognize and bind to the classical signaling molecules acyl homoserine lactones (AHLs). On the other hand, QS in gram positive bacteria is mediated through autoinducer peptides recognized by two-component systems (TCS). However, in acid-fast bacteria, the very process of QS and the underlying molecular machinery remains elusive. In the present work, we have investigated the proteins annotated as LuxR family proteins of the clinically important genera of the acid-fast bacteria, mycobacteria through computational analysis. We have chosen Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis and a most widely used model system for Mycobacterial studies, Mycobacterium smegmatis. A total of 17 genes annotated as LuxR homologs (7 from Mtb and 10 from M. smegmatis) were analyzed. We found that only 14 of these proteins (5 from Mtb and 9 from M. smegmatis) harbor the HTH motif typical to the LuxR/FixJ superfamily of transcriptional regulators affirming their belonging to LuxR family. Rv0894 and MSMEG_0545 both annotated as LuxR homologs, do not harbor HTH motif and RegX (also annotated as LuxR homolog) does not have the tetra helical HTH which is the characteristic of LuxR/FixJ superfamily and hence are not LuxR family proteins. Interestingly, most of the LuxR family proteins (2 in Mtb and 6 in M. smegmatis) are response regulators (RRs) that harbor REC domain that is involved in phosphotransfer from the histidine kinases (HK) thus forming a TCS involved in physiological processes. Few of them have their cognate HKs while few are orphan regulators. The remaining of the proteins harbor various sensory domains that include MalT, PAS, GAF, AcyC, ATPase, TPR, TOMM, and HchA which are either enzymes or bind to small ligand or proteins. STITCH-an online protein-chemical interaction server in deed revealed various small molecules including c-di-GMP (QS molecule in M. smegmatis), and 3-oxo-C12-HSL (a QS signal in P. aeruginosa) binding to the ligand-harboring LuxR proteins. Our study not only confirms the authenticity of Mycobacterial LuxRs but also reveals the diversity of domains in the proteins annotated as LuxR family members in mycobacteria. This type of domain organization is strikingly different from the classical quorum sensing machinery of other bacteria, which might have evolved for a hitherto unknown multifunctionality including QS. IMPORTANCEThough QS is an important biological process regulating various traits in most other bacteria, the workings of it remain elusive in Mycobacteria. Hence, in the present study, we have attempted to unearth the nature of proteins annotated as LuxR family proteins (which participate in quorum sensing in other bacteria) in mycobacteria through in silico analysis. We show that LuxRs of mycobacteria fall into four different families of LuxR/FixJ group of proteins, based on the presence and nature of the sensory domains. Our results provide an understanding of how diverse LuxR proteins could be in terms of domain composition and hence function. This also hints towards the ligands of varied nature such as second messengers and aromatic compounds that might potentially bind to some of these LuxRs harboring the GAF/PAS domains and thus participate in QS or in stress-response phenomena suggesting that these mycobacterial proteins might have in other physiological processes important for survival of the bacteria as an individual or as a community in various.