title: Census of solo LuxR genes in prokaryotic genomes.
abstract: luxR genes encode transcriptional regulators that control acyl homoserine lactone-based quorum sensing (AHL QS) in Gram negative bacteria. On the bacterial chromosome, luxR genes are usually found next or near to a luxI gene encoding the AHL signal synthase. Recently, a number of luxR genes were described that have no luxI genes in their vicinity on the chromosome. These so-called solo luxR genes may either respond to internal AHL signals produced by a non-adjacent luxI in the chromosome, or can respond to exogenous signals. Here we present a survey of solo luxR genes found in complete and draft bacterial genomes in the NCBI databases using HMMs. We found that 2698 of the 3550 luxR genes found are solos, which is an unexpectedly high number even if some of the hits may be false positives. We also found that solo LuxR sequences form distinct clusters that are different from the clusters of LuxR sequences that are part of the known luxR-luxI topological arrangements. We also found a number of cases that we termed twin luxR topologies, in which two adjacent luxR genes were in tandem or divergent orientation. Many of the luxR solo clusters were devoid of the sequence motifs characteristic of AHL binding LuxR proteins so there is room to speculate that the solos may be involved in sensing hitherto unknown signals. It was noted that only some of the LuxR clades are rich in conserved cysteine residues. Molecular modeling suggests that some of the cysteines may be involved in disulfide formation, which makes us speculate that some LuxR proteins, including some of the solos may be involved in redox regulation.
authors: Protein Structure and Bioinformatics, International Center for Genetic Engineering and Biotechnology Trieste, Italy.
authors: Sanjarbek
authors: S
authors: Hudaiberdiev
authors: Protein Structure and Bioinformatics, International Center for Genetic Engineering and Biotechnology Trieste, Italy.
authors: Kumari S
authors: KS
authors: Choudhary
authors: Faculty of Information Technology and Bionics, Pázmány Peter Catholic University Budapest, Hungary.
authors: Roberto
authors: R
authors: Vera Alvarez
authors: Faculty of Information Technology and Bionics, Pázmány Peter Catholic University Budapest, Hungary.
authors: Zsolt
authors: Z
authors: Gelencsér
authors: Faculty of Information Technology and Bionics, Pázmány Peter Catholic University Budapest, Hungary.
authors: Balázs
authors: B
authors: Ligeti
authors: Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, U.O.S di Trieste, Area Science Park Basovizza, Trieste, Italy.
authors: Doriano
authors: D
authors: Lamba
authors: Protein Structure and Bioinformatics, International Center for Genetic Engineering and Biotechnology Trieste, Italy ; Faculty of Information Technology and Bionics, Pázmány Peter Catholic University Budapest, Hungary.
authors: Sándor
authors: S
authors: Pongor
mesh_terms: D020816:Amino Acid Motifs; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D016680:Genome, Bacterial; D008958:Models, Molecular; D012097:Repressor Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015534:Trans-Activators / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C085427:LuxI protein, Bacteria; D012097:Repressor Proteins; D015534:Trans-Activators; D014157:Transcription Factors; C064778:LuxR autoinducer binding proteins
keywords: LuxR; N-acyl homoserine lactone; orphan; quorum sensing; solo