N- and C-terminal regions of the quorum-sensing activator TraR cooperate in interactions with the alpha and sigma-70 components of RNA polymerase

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community

Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.

Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression

We explore a model for 'quenching-like' repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model's predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10-11 bp insertions or deletions (INDELs) and sensitive to 5-6 bp INDELs. We test this prediction on 61 σ(54)-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers' sequences to the DNA's helical repeat.

Functions and regulation of quorum-sensing in Agrobacterium tumefaciens

In Agrobacterium tumefaciens, horizontal transfer and vegetative replication of oncogenic Ti plasmids involve a cell-to-cell communication process called quorum-sensing (QS). The determinants of the QS-system belong to the LuxR/LuxI class. The LuxI-like protein TraI synthesizes N-acyl-homoserine lactone molecules which act as diffusible QS-signals. Beyond a threshold concentration, these molecules bind and activate the LuxR-like transcriptional regulator TraR, thereby initiating the QS-regulatory pathway. For the last 20 years, A. tumefaciens has stood as a prominent model in the understanding of the LuxR/LuxI type of QS systems. A number of studies also unveiled features which are unique to A. tumefaciens QS, some of them being directly related to the phytopathogenic lifestyle of the bacteria. In this review, we will present the current knowledge of QS in A. tumefaciens at both the genetic and molecular levels. We will also describe how interactions with plant host modulate the QS pathway of A. tumefaciens, and discuss what could be the advantages for the agrobacteria to use such a tightly regulated QS-system to disseminate the Ti plasmids.

The quorum-sensing protein TraR of Agrobacterium tumefaciens is susceptible to intrinsic and TraM-mediated proteolytic instability

TraR of Agrobacterium tumefaciens is a LuxR-type transcription factor that regulates genes required for replication and conjugation of the tumour-inducing plasmid. TraR binds the pheromone 3-oxo-octanoylhomoserine lactone (OOHL) and requires this molecule for folding into a protease-resistant, soluble conformation. Even after binding to OOHL, TraR is degraded at readily detectable rates. Here we show that the N-terminal domain of TraR, which binds OOHL, is more resistant to degradation than the full length protein, suggesting that sites on the C-terminal DNA binding domain [TraR(170-234)] enhance protein turnover. A fusion between GFP and TraR(170-234) was poorly fluorescent, and truncations of this fusion protein allowed us to identify residues in this domain that contribute to protein degradation. TraR activity was previously shown to be inhibited by the antiactivator TraM. These proteins form 2:2 complexes that fail to bind DNA sequences. Here we show that TraM sharply decreased the accumulation of TraR in whole cells, indicating that TraM facilitates proteolysis of TraR. The TraM component of these complexes is spared from proteolysis, and could therefore act catalytically.

Building enhancers from the ground up: a synthetic biology approach

A challenge of the synthetic biology approach is to use our understanding of a system to recreate a biological function with specific properties. We have applied this framework to bacterial enhancers, combining a driver, transcription factor binding sites, and a poised polymerase to create synthetic modular enhancers. Our findings suggest that enhancer-based transcriptional control depends critically and quantitatively on DNA looping, leading to complex regulatory effects when the enhancer cassettes contain additional transcription factor binding sites for TetR, a bacterial transcription factor. We show through a systematic interplay of experiment and thermodynamic modeling that the level of gene expression can be modulated to convert a variable inducer concentration input into discrete or step-like output expression levels. Finally, using a different DNA-binding protein (TraR), we show that the regulatory output is not a particular feature of the specific DNA-binding protein used for the enhancer but a general property of synthetic bacterial enhancers.

Horizontal gene exchange in environmental microbiota

Horizontal gene transfer (HGT) plays an important role in the evolution of life on the Earth. This view is supported by numerous occasions of HGT that are recorded in the genomes of all three domains of living organisms. HGT-mediated rapid evolution is especially noticeable among the Bacteria, which demonstrate formidable adaptability in the face of recent environmental changes imposed by human activities, such as the use of antibiotics, industrial contamination, and intensive agriculture. At the heart of the HGT-driven bacterial evolution and adaptation are highly sophisticated natural genetic engineering tools in the form of a variety of mobile genetic elements (MGEs). The main aim of this review is to give a brief account of the occurrence and diversity of MGEs in natural ecosystems and of the environmental factors that may affect MGE-mediated HGT.

LuxR-type quorum-sensing regulators that are detached from common scents

The ability of LuxR-type proteins to regulate transcription is controlled by bacterial pheromones, N-acylhomoserine lactones (AHLs). Most LuxR-family proteins require their cognate AHLs for activity, and at least some of them require AHLs for folding and protease resistance. However, a few members of this family are able to fold, dimerize, bind DNA, and regulate transcription in the absence of AHLs; moreover, these proteins are antagonized by their cognate AHLs. Complexes between some of these proteins and their DNA binding sites are disrupted by AHLs in vitro. All such proteins are fairly closely related within the larger LuxR family, indicating that they share a relatively recent common ancestor. The 3' ends of the genes encoding these receptors invariably overlap with the 3' ends of the cognate AHL synthase genes, suggesting additional antagonism at the level of mRNA synthesis, stability or translation.

Functional roles for the GerE-family carboxyl-terminal domains of nitrate response regulators NarL and NarP of Escherichia coli K-12

NarL and NarP are paralogous response regulators that control anaerobic gene expression in response to the favoured electron acceptors nitrate and nitrite. Their DNA-binding carboxyl termini are in the widespread GerE–LuxR–FixJ subfamily of tetrahelical helix–turn–helix domains. Previous biochemical and crystallographic studies with NarL suggest that dimerization and DNA binding by the carboxyl-terminal domain (CTD) is inhibited by the unphosphorylated amino-terminal receiver domain. We report here that NarL-CTD and NarP-CTD, liberated from their receiver domains, activated transcription in vivo from the class II napF and yeaR operon control regions, but failed to activate from the class I narG and fdnG operon control regions. Alanine substitutions were made to examine requirements for residues in the NarL DNA recognition helix. Substitutions for Val-189 and Arg-192 blocked DNA binding as assayed both in vivo and in vitro, whereas substitution for Arg-188 had a strong effect only in vivo. Similar results were obtained with the corresponding residues in NarP. Finally, Ala substitutions identified residues within the NarL CTD as important for transcription activation. Overall, results are congruent with those obtained for other GerE-family members, including GerE, TraR, LuxR and FixJ.