Biology subjects

Greenberg, E. P.

Publications and source records attributed to Greenberg, E. P..

5 recordsLinked to original sources

bioRxiv2026

COPAL: An ensemble of protein-ligand co-folding models enriches preferred ligand predictions for the LuxR-family of quorum sensing receptors

Acyl-homoserine lactone (AHL) quorum sensing enables many species of proteobacteria to coordinate collective behaviors. In such systems, a synthase produces an AHL signal, which is sensed by a LuxR-family receptor. Despite extensive genomic annotation of LuxR homologs, preferred AHLs for most receptors remain unknown, limiting functional understanding of quorum sensing across diverse bacteria. Here, we present the COPAL (combining ordered predictions of audited ligands) pipeline, which integrates multiple protein-ligand co-folding models to identify preferred AHLs for a specific LuxR. Benchmarking on a leakage-controlled subset of 96 experimentally characterized LuxR-AHL pairs shows that COPAL places the preferred AHL within the top-6 candidates (out of 58) for 68% of receptors, outperforming every individual co-folding model. Further, inter-model agreement correlates with ranking accuracy, offering an indication of confidence. We show that COPAL resolves the specificity shift induced by three-point mutations in LasR and correctly nominates C8-HSL as the preferred ligand for the previously uncharacterized Mesorhizobium sp. NJ3 receptor, which we verified experimentally. Finally, we release the Ranked AHL-LuxR Prediction Hub (RALPH), comprising precomputed rankings for about 10,000 unique LuxR homologs. More broadly, COPAL shows that unweighted rank aggregation of complementary co-folding models offers a general strategy for predicting receptor-ligand specificity in data-scarce biological systems.

biochemistry↗

bioRxiv2025

Inactivation of MexT in Pseudomonas aeruginosa destabilizes cooperation and favors the emergence of a unique quorum sensing variant

Pseudomonas aeruginosa, an opportunistic gram-negative pathogen, uses a cell-cell signaling system called quorum sensing to coordinate group behaviors. Quorum sensing in P. aeruginosa is a model to study cooperative behaviors in populations. Several studies of cooperation have been conducted using strain PAO1. Wildtype PAO1 harbors a mutation in mexS, which encodes a negative regulator of the transcription factor MexT, which in turn activates many genes, including the efflux pump MexEF-OprN. We hypothesized that the PAO1 mexS mutation might affect cooperative behaviors. When P. aeruginosa is passaged daily on casein as a sole carbon source, quorum sensing is required to induce synthesis of the extracellular proteases needed to acquire carbon and energy. During growth on casein, individuals with inactivating mutations in the quorum sensing regulator LasR are reproducibly enriched in the population. These LasR mutants are cheaters that benefit from cooperatively-produced proteases and have a fitness advantage over cooperators. We passaged wildtype PAO1, PAO1 with a gene-corrected version of mexS, or PAO1 with a null mutation of mexT on casein as the sole carbon and energy source. We found that correcting the mexS mutation resulted in unstable cooperation: bacterial cultures failed to propagate after about 15 days, whereas the wildtype propagated for the duration of our 30-day experiment. The MexS-corrected and MexT-deficient populations also reproducibly exhibited emergence of a particular quorum sensing variant, LasR-V226I. This variant activated a subset of quorum-sensing regulated genes, suggesting an evolutionary pathway to alter P. aeruginosa quorum sensing regulons. ImportanceQuorum sensing governs cooperative activities and has been used as a model for studying cooperative behaviors in bacterial populations. Pseudomonas aeruginosa has two interlinked acyl-homoserine lactone quorum sensing circuits, LasR-I and RhlR-I; the relationship between these circuits is influenced by a regulator called MexT. Inactivation of MexT results in enhanced activity of the quorum sensing transcription factor, RhlR, and we found that it also destabilized cooperative behaviors in this bacterium. MexT-inactive strains also reproducibly support the emergence of a specific LasR variant, V226I, of P. aeruginosa, offering insight into evolutionary pressures that select for mutations in quorum sensing transcription factors and, by extension, a method for bacteria to alter the cohort of genes that are quorum-controlled.

microbiology↗

bioRxiv2024

The Relationship of pqs Gene Expression to Acylhomoserine Lactone Signaling in Pseudomonas aeruginosa

The opportunistic pathogen Pseudomonas aeruginosa has complex quorum sensing (QS) circuitry, which involves two acylhomoserine lactone (AHL) systems, the LasI AHL synthase and LasR AHL-dependent transcriptional activator system and the RhlI AHL synthase-RhlR AHL-responsive transcriptional activator. There is also a quinoline signaling system (the Pseudomonas quinolone signal, PQS, system). Although there is a core set of genes regulated by the AHL circuits, there is substantial strain-to-strain variation in the non-core QS regulated genes. Reductive evolution of the QS regulon, and variation in specific genes activated by QS, occurs in laboratory evolution experiments with the model strain PAO1. We used a transcriptomics approach to test the hypothesis that reductive evolution in the PAO1 QS regulon can in large part be explained by a simple null mutation in pqsR, the gene encoding the transcriptional activator of the pqs operon. We found that PqsR had very little influence on the AHL QS regulon. This was a surprising finding because the last gene in the PqsR-dependent pqs operon, pqsE, codes for a protein, which physically interacts with RhlR and this interaction is required for RhlR-dependent activation of some genes. We used comparative transcriptomics to examine the influence of a pqsE mutation on the QS regulon and identified only three transcripts, which were strictly dependent on PqsE. By using reporter constructs we showed that the PqsE influence on other genes was dependent on experimental conditions and we have gained some insight about those conditions. This work adds to our understanding of the plasticity of the P. aeruginosa QS regulon and to the role PqsE plays in RhlR-dependent gene activation.

microbiology↗

bioRxiv2021

Evolution of the quorum sensing regulon in cooperating populations of Pseudomonas aeruginosa

The bacterium Pseudomonas aeruginosa is an opportunistic pathogen and it thrives in many different saprophytic habitats. In this bacterium acyl-homoserine lactone quorum sensing (QS) can activate expression of over 100 genes, many of which code for extracellular products. P. aeruginosa has become a model for studies of cell-cell communication and coordination of cooperative activities. We hypothesized that long-term growth of bacteria under conditions where only limited QS-controlled functions were required would result in a reduction in the size of the QS-controlled regulon. To test this hypothesis, we grew P. aeruginosa for about 1000 generations in a condition in which expression of QS-activated genes is required for growth. We compared the QS regulons of populations after about 35 generations to those after about 1000 generations in two independent lineages by using quorum quenching and RNA-seq technology. In one evolved lineage the number of QS-activated genes identified was reduced by about 70% and in the other by about 45%. Our results lend important insights about the variations in the number of QS-activated genes reported for different bacterial strains and, more broadly, about the environmental histories of P. aeruginosa.

microbiology↗

bioRxiv2021

A covariation analysis reveals elements of selectivity in quorum sensing systems

Many bacteria communicate with kin and coordinate group behaviors through a form of cell-cell signaling called acyl-homoserine lactone (AHL) quorum sensing (QS). In these systems, a signal synthase produces an AHL to which its paired receptor selectively responds. Selectivity is fundamental to cell signaling. Despite its importance, it has been challenging to determine how this selectivity is achieved and how AHL QS systems evolve and diversify. We hypothesized that we could use covariation within the protein sequences of AHL synthases and receptors to identify selectivity residues. We began by identifying about 6,000 unique synthase-receptor pairs. We then used the protein sequences of these pairs to identify covariation patterns and mapped the patterns onto the LasI/R system from Pseudomonas aeruginosa PAO1. The covarying residues in both proteins cluster around the ligand binding sites. We demonstrate that these residues are involved in system selectivity toward the cognate signal and go on to engineer the Las system to both produce and respond to an alternate AHL signal. We have thus demonstrated a new application for covariation methods and have deepened our understanding of how communication systems evolve and diversify.

microbiology↗