Abstract
LuxR solo transcriptional regulators contain both an autoinducer binding domain (ABD; N-terminal) and a DNA binding Helix-Turn-Helix domain (HTH; C-terminal), but are not associated with a cognate N-acyl homoserine lactone (AHL) synthase coding gene in the same genome. Although a few LuxR solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. In this study we have carried out a systematic survey of distribution of all ABD containing LuxR transcriptional regulators (QS domain LuxRs) available in the InterPro database (IPR005143), and identified those lacking a cognate AHL synthase. These LuxR solos were then analyzed regarding their taxonomical distribution, predicted functions of neighboring genes and the presence of complete AHL-QS systems in the genomes that carry them. Our analyses reveal the presence of one or multiple predicted LuxR solos in many proteobacterial genomes carrying QS domain LuxRs, some of them harboring genes for one or more AHL-QS circuits. The presence of LuxR solos in bacteria occupying diverse environments suggests potential ecological functions for these proteins beyond AHL and interkingdom signaling. Based on gene context and the conservation levels of invariant amino acids of ABD, we have classified LuxR solos into functionally meaningful groups or putative orthologs. Surprisingly, putative LuxR solos were also found in a few non-proteobacterial genomes which are not known to carry AHL-QS systems. Multiple predicted LuxR solos in the same genome appeared to have different levels of conservation of invariant amino acid residues of ABD questioning their binding to AHLs. In summary, this study provides a detailed overview of distribution of LuxR solos and their probable roles in bacteria with genome sequence information.
Highlights
Bacteria sense and respond to changes in external environments through signal transduction systems that include transcriptional regulators for modulating gene expression
The protein entries obtained from Interpro were classified as LuxR solos (1) if no gene coding for a LuxI homolog was found in the genome, (2) if no gene was found in the genomic locus near the gene coding for quorum sensing (QS) domain LuxR protein, or (3) if no unpaired or extra genes coding for LuxI homolog were present in the genome
DISTRIBUTION OF LuxR SOLOS IN SEQUENCED BACTERIAL GENOMES The complete collection of QS domain LuxR proteins were sourced from Interpro database (IPR005143) and analyzed to identify LuxR solos or orphans according to the criteria outlined in materials and methods
Summary
Bacteria sense and respond to changes in external environments through signal transduction systems that include transcriptional regulators for modulating gene expression. A sub-group of LuxR transcriptional regulators with N-terminal autoinducer binding domains (ABD) and C-terminal Helix-Turn-Helix (HTH) DNA binding domains are known to be involved in quorum sensing (QS) signaling in many proteobacteria (the presence of both domains is referred to as QS domain here on) (Choi and Greenberg, 1991; Hanzelka and Greenberg, 1995; Luo and Farrand, 1999). Genes coding for these LuxR regulators usually occur together with a gene coding for the synthesis of Nacyl homoserine lactone (AHL) signaling molecules, the LuxI homolog. They are thought to be important for bacterial signal perception in inter-bacterial and host–bacterial interactions (Soares and Ahmer, 2011; Venturi and Fuqua, 2013)
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