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Genome-wide map of Flagx3-DnaA bound to DNA in exponentially growing Sinorhizobium meliloti cultures

ABSTRACT: The genome of Sinorhizobium meliloti, a model for studying plant-bacteria symbiosis, contains the genes coding for eight LuxR-like proteins. Two of these, SinR and ExpR, are essential for quorum sensing (QS). Roles and regulation surrounding the others are mostly unknown. Here, we reveal the DNA recognition sequence and regulon of the LuxR-like protein SMc00877. Unlike ExpR, which uses the long chain acyl homoserine lactones (AHLs) as inducers, SMc00877 functioned independently of AHLs and was even functional in Escherichia coli. A target of SMc00877 is sinR, the major regulator of AHL production in S. meliloti. Disruption of SMc00877 decreased AHL production. A weaker production of AHLs resulted in smaller microcolonies, starting from single cells, and delayed AHL dependent regulation. SMc00877 was expressed only in growing cells in the presence of replete nutrients. Therefore, we renamed it NurR (nutrient sensitive LuxR-like regulator). We traced this nutrient-sensitive expression to transcription control by the DNA replication initiation factor, DnaA, which is essential for growth. These results indicate that NurR has a role in modulating the threshold of QS activation according to growth. We propose growth behavior as an additional prerequisite to population density for the activation of QS in S. meliloti.

ORGANISM(S): Sinorhizobium meliloti

PROVIDER: GSE131423 | GEO | 2019/05/18

REPOSITORIES: GEO

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Effect of the LuxI/R gene on AHL-signaling Molecules and QS Regulatory Mechanism in Hafnia alvei H4

Project description:Hafnia alvei H4 is a bacteria subject to regulation by N-acyl-l-homoserine lactone (AHL)-mediated quorum sensing system and is closely related to the corruption of instant sea cucumber. Studying the effect of Hafnia alvei H4 quorum sensing regulatory genes on AHLs is necessary for the quality and preservation of instant sea cucumber. In this study, the draft genome of H. alvei H4, which comprises a single chromosome of 4,687,151 bp, was sequenced and analyzed and the types of AHLs were analyzed employing thin-layer chromatography (TLC) and LC-MS/MS. Then the wild-type strain of H. alvei H4 and the luxI/R double mutant (ΔluxIR) were compared by transcriptome sequencing (RNA-seq). The results indicate that the incomplete genome sequence revealed the presence of one quorum-sensing (QS) gene set, designated as lasI/expR. Three major AHLs, N-hexanoyl-L-homoserine lactone (C6-HSL), N-butyryl-L-homoserine lactone (C4-HSL), and N-(3-oxo-octanoyl)-L-homoserine lactone (3-oxo-C8-HSL) were found, with C6-HSL being the most abundant. C6-HSL was not detected in the culture of the luxI mutant (ΔluxI) and higher levels of C4-HSL was found in the culture of the luxR mutant (ΔluxR), which suggested that the luxR gene may have a positive effect on C4-HSL production. It was also found that AHL and QS genes are closely related in the absence of luxIR double deletion. The results of this study can further elucidate at the genetic level that luxI and luxR genes are involved in the regulation of AHL.

2019-10-10 | GSE137815 | GEO

Lyngbyoic Acid, a "Tagged" Fatty Acid from a Marine Cyanobacterium, Disrupts Quorum Sensing in Pseudomonas aeruginosa

Project description:Quorum sensing (QS) is a mechanism of bacterial gene regulation in response to increases in population density. Production of small molecule QS signals, their accumulation within a diffusion-limited environment and their binding to the LuxR-type receptor trigger QS-controlled gene regulatory cascades. QS pathways mediated by acylhomoserine lactones (AHLs) in Gram-negative bacteria are the best studied. In Pseudomonas aeruginosa, for example, binding of AHLs to their cognate receptors (LasR, RhlR) controls production of virulence factors, pigments, antibiotics and other behaviors important for its interactions with eukaryotic hosts and other bacteria. We isolated a new small cyclopropane-containing fatty acid, lyngbyoic acid (1), as a major metabolite of the marine cyanobacterium, Lyngbya sp., collected off Fort Pierce, Florida. The structure of 1 was determined by NMR, MS and optical rotation. We screened 1 against four reporters based on AHL receptors from Vibrio fischeri (LuxR), Aeromonas hydrophila (AhyR), Agrobacterium tumefaciens (TraR) and P. aeruginosa (LasR) and found that 1 most strongly affected LasR. We show, by using a defined set of reporters, that compound 1 acts both through the AHL-binding site of LasR and independent of it. We also show that 1 reduces pyocyanin and LasB, both on the protein and transcript level, in wild-type P. aeruginosa, and that 1 directly inhibits LasB enzymatic activity. Conversely, dodecanoic acid (11) increased pyocanin and LasB, demonstrating that 1 is a “tagged” fatty acid potentially resistant to β-oxidation. 1 mL Cultures of P. aeruginosa PAO1 were grown for 6h at 37 °C with shaking either in the presence of lyngbyoic acid (1 mM) or EtOH alone (10 μL) as a control. RNA samples were obtained from one treated and one control culture, and were reverse transcribed, labeled and fragmented according to Affymetrix's protocol. The two samples were hybridized in duplicate.

2011-01-24 | E-GEOD-22999 | biostudies-arrayexpress

Lyngbyoic Acid, a "Tagged" Fatty Acid from a Marine Cyanobacterium, Disrupts Quorum Sensing in Pseudomonas aeruginosa

2011-01-24 | GSE22999 | GEO

Quorum Quenching of Nitrobacter winogradskyi Suggests that Quorum Sensing Regulates Fluxes of Nitrogen Oxide(s) during Nitrification.

Project description:Quorum sensing (QS) is a widespread process in bacteria used to coordinate gene expression with cell density, diffusion dynamics, and spatial distribution through the production of diffusible chemical signals. To date, most studies on QS have focused on model bacteria that are amenable to genetic manipulation and capable of high growth rates, but many environmentally important bacteria have been overlooked. For example, representatives of proteobacteria that participate in nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, produce QS signals called acyl-homoserine lactones (AHLs). Nitrification emits nitrogen oxide gases (NO, NO2, and N2O), which are potentially hazardous compounds that contribute to global warming. Despite considerable interest in nitrification, the purpose of QS in the physiology/ecology of nitrifying bacteria is poorly understood. Through a quorum quenching approach, we investigated the role of QS in a well-studied AHL-producing nitrite oxidizer, Nitrobacter winogradskyi.We added a recombinant AiiA lactonase to N. winogradskyi cultures to degrade AHLs to prevent their accumulation and to induce a QS-negative phenotype and then used mRNA sequencing (mRNA-Seq) to identify putative QS-controlled genes. Our transcriptome analysis showed that expression of nirK and nirK cluster genes (ncgABC) increased up to 19.9-fold under QS-proficient conditions (minus active lactonase). These data led to us to query if QS influenced nitrogen oxide gas fluxes in N. winogradskyi. Production and consumption of NOx increased and production of N2O decreased under QS-proficient conditions. Quorum quenching transcriptome approaches have broad potential to identify QS-controlled genes and phenotypes in organisms that are not genetically tractable.

2016-10-05 | GSE84969 | GEO

Response of Lactobacillus plantarum WCSF1 to the Gram-negative pathogen-associated quorum sensing molecule N-3-oxododecanoyl homoserine lactone.

Project description:The bacterial quorum sensing (QS) phenomenon has been well studied since its discovery and has traditionally been considered to include signaling pathways recognized exclusively within either Gram-positive (Gm+) or Gram-negative (Gm-) bacteria. The Gm+ bacteria are known to utilize quorum sensing pathways mediated by various small autoinducing peptides (AIP), while the Gm- bacteria use small molecules known collectively as acyl-homoserine lactones (AHL). Distinct structural differences between the types of signaling molecules have historically implied a lack of cross-talk among Gm+ and Gm- QS systems. Recent investigations, however, have demonstrated the ability for AIPs and AHLs to be produced by noncanonical organisms, implying QS systems may be more universally recognized than previously hypothesized. With that in mind, our interests were piqued by the organisms Lactobacillus plantarum, a Gm+ commensal probiotic known to participate in AIP-mediated QS, and Pseudomonas aeruginosa, a characterized Gm- pathogen whose virulence is controlled by AHL-mediated QS. Both health-related organisms are known to inhabit the human gut in various instances, both are characterized to elicit distinct effects on host immunity, and some studies hint at the putative ability of L. plantarum to degrade AHLs produced by P. aeruginosa. We therefore wanted to determine if L. plantarum cultures would respond to the addition of N-(3-oxododecanoyl)-L-homoserine lactone (3OC12) from P. aeruginosa by analyzing changes on both the transcriptome and proteome over time. Based on the observed upregulation of various two-component systems, response regulators, and native quorum sensing related genes, the resulting data provide evidence of an AHL recognition and response by L. plantarum.

2018-12-19 | GSE124050 | GEO

Lactonase Specificity is Key to Quorum Quenching in Pseudomonas aeruginosa

Project description:The human opportunistic pathogen Pseudomonas aeruginosa orchestrates the expression of many genes in a cell density-dependent manner by using a molecular communication system referred to as quorum sensing (QS). This bacterium uses an intricate network of regulators and QS molecules known as autoinducers. Among these autoinducers are two acyl-homoserine lactones (AHL) involved in QS circuits which modulate virulence factors production, biofilm formation, and antimicrobial sensitivity. Disrupting QS, a strategy referred to as quorum quenching (QQ), is a promising approach to modulate virulence while not directly challenging bacterial survival. For P. aeruginosa, QQ can be achieved using exogenous AHL-degrading lactonases. However, the importance of enzyme specificity on quenching efficacy has never been investigated. Here, we used two lactonases both targeting the signal molecules N-(3-oxododecanoyl)-L-Homoserine lactone (3-oxo-C12 HSL) and butyryl-homoserine lactone (C4 HSL) albeit with different efficacy on C4 HSL. Interestingly, both lactonases similarly decreased the concentrations of AHL and comparably impacted the expression of AHL-based circuits. Conversely, strong variations were observed in Pseudomonas Quinolone Signal (PQS) regulation. Both lactonases were then found to decrease virulence factors production and biofilm formation in vitro, albeit with different efficiencies. Unexpectedly, only the lactonase with substrate preference for 3-oxo-C12 HSL was able to inhibit P. aeruginosa pathogenicity in vivo in an amoeba infection model. Similarly, large variations between lactonases were observed in proteins involved in antibiotic resistance, biofilm formation, virulence and diverse cellular mechanisms. This global analysis provides the first evidence that QQ enzyme specificity is crucial to modulate QS-associated behavior in P. aeruginosa PA14.

2020-05-27 | PXD017421 | Pride

Alterations in the extracellular proteome of human pathogen Pseudomonas aeruginosa in response to natural and modified N-acyl-L-homoserine lactones

Project description:The common opportunistic human pathogen Pseudomonas aeruginosa employs quorum sensing QS to regulate a large set of genes involved in virulence and host-pathogen interactions. The Las circuit positioned on the top of the QS hierarchy in P. aeruginosa, makes use of N-acyl-L-homoserine lactones (AHL) as signal molecules, like N-3-oxo-dodecanoyl-L-homoserine lactone (3O-C12-HSL). Here, a quantitative proteomic approach was used to study the effect of natural 3O-C12-HSL and four AHL analogues on the expression and excretion of QS-regulated extracellular proteins. Treatment with AHL compounds resulted in significant difference in appearance of the 3O-C12-HSL-responsive reference proteins related to QS communication and virulence, i.e., a distinct activity as QS modulators. In summary, 3O-C12-HSL has a profound effect on extracellular proteome involved in the pathogenicity of P. aeruginosa, and the four AHL analogues have achieved a distinct inhibitory effect on the extracellular proteome.

2023-10-06 | PXD045881 | Pride

A novel TetR-like transcriptional regulator in Stenotrophomonas maltophilia is involved in fatty acid metabolism, including quorum sensing signal turnover

Project description:Stenotrophomonas maltophilia is an emerging opportunistic multidrug-resistant pathogen frequently co-isolated with other relevant nosocomial pathogens in respiratory tract infections. S. maltophilia uses the endogenous DSF quorum sensing (QS) system to regulate virulence processes but can also respond to exogenous AHL signals produced by neighboring bacteria. A whole-transcriptome sequencing analysis was performed for S. maltophilia strain K279a in the exponential and stationary phases and in exponential cultures after a treatment with exogenous DSF or AHLs. Among the common top upregulated genes, the putative TetR-like regulator Smlt2053 was selected for functional characterization. This regulator was found to sense long-chain fatty acids, including the QS signal DSF, and activate a β-oxidation catabolic pathway.

2023-05-16 | GSE206554 | GEO

Transcriptomic and proteomic profiling of Rhodospirillum rubrum M68 cultivated in MELiSSA related culture conditions

Project description:In the context of the Micro-Ecological Life Support System Alternative (MELiSSA) project, the quorum sensing system (QS) of R. rubrum S1H has been shown to rely on acyl homoserine lactones (AHLs) as communication signals. In addition, previous studies in our lab have suggested that pigment content and photosynthetic membrane production could be under the control of QS. In the present study, the transcriptomic and proteomic profiles of a QS-deficient mutant (R. rubrum strain M68) that does not produce AHLs as the WT strain (R. rubrum S1H) were compared when cultivated in light anaerobic conditions using acetate as carbon source. Transcriptomic and proteomic approaches revealed that 330 genes and 217 proteins were differentially expressed in M68 compared to S1H, indicating that several operons were QS-regulated i.e. flagellar assembly, chemotaxis, photosynthesis, electron transport, stress proteins. These results showed the importance of a functional QS system in R. rubrum.

2019-02-01 | GSE76666 | GEO

Transcriptional profiling by RNA-seq of A. baumannii AB5075 wild-type, abaI::Tn26 and ∆abaM::Tn26 QS mutants.

Project description:Acinetobacter baumannii possesses a single divergent luxR/luxI-type quorum sensing (QS) locus named abaR/abaI. This locus also contains a third gene located between abaR and abaI which we term abaM that codes for an uncharacterized member of the RsaM protein family known to regulate N-acylhomoserine lactone (AHL) dependent QS and the expression of diverse genes in other β- and γ-proteobacteria. However, abaM has never been charatcerized in Acinetobacter baumannii, and the studies about the regulon of abaI are limited. In this study we revealed that AbaM differentially regulates at least 76 genes including the csu pilus operon and the acinetin 505 lipopeptide biosynthetic operon, that are involved in surface adherence, biofilm formation and virulence. A comparison of the wild type, abaM::Tn26 and abaI::Tn26 transcriptomes, indicates that AbaM regulates ~21% of the QS regulon including the csu operon. Moreover, the QS genes (abaI/abaR) were among the most upregulated in the abaM::Tn26 mutant. Overall, our data suggests that abaM is a key regulator of Acinetobacter baumannii QS and gene expression.

2020-09-30 | GSE151925 | GEO

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