AHL-driven quorum-sensing circuits: their frequency and function among the Proteobacteria

Abstract

It is now apparent that bacteria utilize regulatory systems called quorum sensing (QS) to sense their population density. Such systems are dependant on the production of signaling molecules that activate specific genes when the signal reaches a critical threshold concentration. Such QS-regulated genes produce phenotypes that require coordinate behavior to convey competitive advantage to the population (such as biofilm formation and pathogenesis). The best-characterized QS system is that driven by acylated homoserine lactone (AHL) molecules. Quorum sensing-regulated phenotypes are diverse; however, their evolutionary selection is based on the competitive advantage conveyed by coordinating gene expression with the establishment of a quorum. Population density and coordinated gene expression are coupled for either (1) the multicellular characteristic of behaviors such as cell differentiation (for example swarming, biofilm formation), or (2) the fitness benefit of many individual cells simultaneously expressing the same phenotype (for example virulence factors, luminescence). QS enables a population to differentiate under favorable conditions where the population is dense enough to support the division and coordination of labor into subpopulations. In undifferentiated populations, QS coordinates gene expression so that it is simultaneous for cells within the population. In both scenarios, having QS regulation provides a competitive advantage for a population to both produce and respond to QS molecules. A selective pressure also exists for non-QS bacteria to sense and respond to QS molecules produced within the community. Examples of QS bacteria and bacteria able to detect and respond to exogenous signals are found in the literature; however, the frequency of QS and QS cheaters in the environment is poorly documented. With the growing number of bacterial genomes sequenced, especially genomes of nonclinically isolated bacteria, it may not be surprising that the number of genomes containing homologs of AHL-QS circuitry is ever growing. In this article, we use all current bacterial genomes to examine the frequency of AHL-QS among these bacteria, and the surprising number of bacteria with the genetic potential for eavesdropping on AHL signals from other bacteria. The AHL-QS system is characterized by two core proteins, the LuxI-type protein (the AHL synthase), and the LuxR-type protein (the response regulator). Almost all AHL-producing bacteria rely on only these two protein families for active QS circuits; however, exceptions exist such as the LuxM AHL synthase in Vibrio harveyi and the putative HdtS AHL synthase identified in Pseudomonas fluorescens F113, both of which replace the LuxI-type AHL synthase. Using the 512 completed bacterial genomes as a data set (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi on 26 July 2007), LuxI and LuxR homologs were found only within proteobacterial genomes. Complete QS circuits (that is, containing at least one LuxI and LuxR homolog) were identified from 68 (13%) of the bacterial genomes, or 26% of the 265 proteobacterial genomes (Table 1). When compared to metagenomic data, these statistics seem high. The predicted proteome of the marine metagenome (Rusch et al., 2007) recovered 20 LuxI and 31 LuxR homologs, and a 130-genome equivalent metagenomic library of Alaskan sediments recovered a single clone capable of inducing an AHL reporter and containing a luxI homolog (Williamson et al., 2005). However, all of these figures are biased, for instance whole-organism genomics rely on culturing, there is a sampling bias of filtered seawater used to construct the marine metagenome (mainly free-living bacteria are represented in the metagenome), there are limitations in expressing environmental DNA from metagenomic libraries and AHL reporters are unable to detect the structural diversity of AHLs. Whatever be the limitations of our methodologies, the number of bacteria in which we identify QS is ever increasing, with genome sequencing a major source of this discovery. Bacterial genomes with AHL-driven quorum-sensing networks Abbreviation: AHL, acylated homoserine lactone. Homologs of LuxI and LuxR were identified using the following definitions: a LuxI homolog is 190–230 amino acids long and defined by a BLASTP e-value greater than 10−6 to a characterized LuxI-type AHL synthase. A LuxR homolog is 200–240 amino acids long, has a BLASTP e-value greater than 10−6 to a characterized LuxR-type, AHL response regulator and shows homology to an AHL-binding domain within 30 amino acids of its N terminus and homology to the GerE-type DNA-binding domain at the C terminus. Some two-component response regulators have DNA-binding domains homologous to the GerE-type; however, they were excluded as their ligand-binding domain lacked homology to an AHL-binding domain. Among the bacterial genomes in which QS is identified, several are surprising. The role of QS among several such environmental bacteri