Abstract
Recent studies have identified a novel interkingdom signaling circuit, via plant signaling molecules, and a bacterial sub-family of LuxR proteins, bridging eukaryotes and prokaryotes. Indeed pivotal plant-bacteria interactions are regulated by the so called Plant Associated Bacteria (PAB) LuxR solo regulators that, although closely related to the quorum sensing (QS) LuxR family, do not bind or respond to canonical quorum sensing N-acyl homoserine lactones (AHLs), but only to specific host plant signal molecules. The large body of structural data available for several members of the QS LuxR family complexed with different classes of ligands (AHLs and other compounds), has been exploited to dissect the cartography of their regulatory domains through structure-based multiple sequence alignments, structural superimposition and a comparative analysis of the contact residues involved in ligand binding. In the absence of experimentally determined structures of members of the PAB LuxR solos subfamily, an homology model of its prototype OryR is presented, aiming to elucidate the architecture of its ligand-binding site. The obtained model, in combination with the cartography of the regulatory domains of the homologous QS LuxRs, provides novel insights into the 3D structure of its ligand-binding site and unveils the probable molecular determinants responsible for differences in selectivity towards specific host plant signal molecules, rather than to canonical QS compounds.
Highlights
Research over the last 15 years has evidenced that intercellular communication frequently occurs in bacteria regulating gene expression in a cell density-dependent signaling, referred to as “quorum sensing” (QS) [1]
Family [23,24,25,26,27,28,29,30] show a quite conserved overall folding, with the regulatory domain composed of five anti-parallel β-sheets flanked by three α-helixes on each side, our aim here is to: (i) validate and extend the previous analysis of LuxR-family, based on primary sequence alignment, in order to dissect the structural determinants involved in ligand recognition; and (ii) extend the outcomes of the detailed molecular cartography to the Plant Associated Bacteria (PAB) LuxR solos subfamily in order to identify the molecular determinants responsible for the different ligand selectivity of this subfamily
This finding supports the strategy to dissect the cartography of the ligand-binding sites of QS LuxRs in order to gain insight on the structural basis of PAB LuxR solos specificity
Summary
Research over the last 15 years has evidenced that intercellular communication frequently occurs in bacteria regulating gene expression in a cell density-dependent signaling, referred to as “quorum sensing” (QS) [1]. Conservation of primary structure among LuxR-family proteins is quite low (18%–25%), multiple sequence alignments performed have identified nine highly conserved residues (Figure 1): six of these residues delineate the cavity of the ligand-binding domain (W57, Y61, D70, P71, W85 and G113, according to TraR numbering) and the remaining three are located within the DNA-binding domain (E178, L182 G188) [19,20,21,22] On these bases in a recent review Gonzales and Venturi [4] pinpointed that members of PAB LuxR solos subfamily show substitutions in one or two of these highly conserved amino acids in the regulatory domain, namely, W57M and Y61W, suggesting an involvement of these residues in the different selectivity of this subfamily towards specific host plant signal molecules rather than to AHLs. Considering that the experimental three dimensional structures of several members of the LuxR family [23,24,25,26,27,28,29,30] show a quite conserved overall folding, with the regulatory domain composed of five anti-parallel β-sheets flanked by three α-helixes on each side, our aim here is to: (i) validate and extend the previous analysis of LuxR-family, based on primary sequence alignment, in order to dissect the structural determinants involved in ligand recognition; and (ii) extend the outcomes of the detailed molecular cartography to the PAB LuxR solos subfamily in order to identify the molecular determinants responsible for the different ligand selectivity of this subfamily. In the absence of experimentally determined structures of members of the PAB LuxR solos subfamily, the homology model of its prototype, OryR, is expected to provide us with sufficient information to gain insights into the architecture of its ligand-binding site, as well as to elucidate the likely structural basis of the reported different ligand selectivity between the PAB LuxR solos subfamily and the canonical QS LuxR receptors
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