Structure-Guided Biochemical Analysis of Quorum Signal Synthase Specificities

Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence-Function Landscape

Programmable intercellular signaling using components of naturally occurring quorum sensing can allow for coordinated functions to be engineered in microbial consortia. LuxR-type transcriptional regulators are widely used for this purpose and are activated by homoserine lactone (HSL) signals. However, they often suffer from imperfect molecular discrimination of structurally similar HSLs, causing misregulation within engineered consortia containing multiple HSL signals. Here, we studied one such example, the regulator LasR from Pseudomonas aeruginosa. We elucidated its sequence-function relationship for ligand specificity using targeted protein engineering and multiplexed high-throughput biosensor screening. A pooled combinatorial saturation mutagenesis library (9,486 LasR DNA sequences) was created by mutating six residues in LasR's β5 sheet with single, double, or triple amino acid substitutions. Sort-seq assays were performed in parallel using cognate and noncognate HSLs to quantify each corresponding sensor's response to each HSL signal, which identified hundreds of highly specific variants. Sensor variants identified were individually assayed and exhibited up to 60.6-fold (p = 0.0013) improved relative activation by the cognate signal compared to the wildtype. Interestingly, we uncovered prevalent mutational epistasis and previously unidentified residues contributing to signal specificity. The resulting sensors with negligible signal crosstalk could be broadly applied to engineer bacteria consortia.

A Mesorhizobium japonicum quorum sensing circuit that involves three linked genes and an unusual acyl-homoserine lactone signal

Members of the genus Mesorhizobium, which are core components of the rhizosphere and specific symbionts of legume plants, possess genes for acyl-homoserine lactone (AHL) quorum sensing (QS). Here we show Mesorhizobium japonicum MAFF 303099 (formerly M. loti) synthesizes and responds to N-[(2E, 4E)-2,4-dodecadienoyl] homoserine lactone (2E, 4E-C12:2-HSL). We show that the 2E, 4E-C12:2-HSL QS circuit involves one of four luxR-luxI-type genes found in the sequenced genome of MAFF 303099. We refer to this circuit, which appears to be conserved among Mesorhizobium species, as R1-I1. We show that two other Mesorhizobium strains also produce 2E, 4E-C12:2-HSL. The 2E, 4E-C12:2-HSL is unique among known AHLs in its arrangement of two trans double bonds. The R1 response to 2E, 4E-C12:2-HSL is extremely selective in comparison with other LuxR homologs, and the trans double bonds appear critical for R1 signal recognition. Most well-studied LuxI-like proteins use S-adenosylmethionine and an acyl-acyl carrier protein as substrates for synthesis of AHLs. Others that form a subgroup of LuxI-type proteins use acyl-coenzyme A substrates rather than acyl-acyl carrier proteins. I1 clusters with the acyl-coenzyme A-type AHL synthases. We show that a gene linked to the I1 AHL synthase is involved in the production of the QS signal. The discovery of the unique I1 product enforces the view that further study of acyl-coenzyme A-dependent LuxI homologs will expand our knowledge of AHL diversity. The involvement of an additional enzyme in AHL generation leads us to consider this system a three-component QS circuit. IMPORTANCE We report a Mesorhizobium japonicum quorum sensing (QS) system involving a novel acyl-homoserine lactone (AHL) signal. This system is known to be involved in root nodule symbiosis with host plants. The chemistry of the newly described QS signal indicated that there may be a dedicated cellular enzyme involved in its synthesis in addition to the types known for production of other AHLs. Indeed, we report that an additional gene is required for synthesis of the unique signal, and we propose that this is a three-component QS circuit as opposed to the canonical two-component AHL QS circuits. The signaling system is exquisitely selective. The selectivity may be important when this species resides in the complex microbial communities around host plants and may make this system useful in various synthetic biology applications of QS circuits.

Identification of AHL Synthase in Desulfovibrio vulgaris Hildenborough Using an In-Silico Methodology

Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL, but no AHL synthase have been annotated in SRB so far. In this computational study, we used a combination of data mining, multiple sequence alignment (MSA), homology modeling and docking to decode a putative AHL synthase in the model SRB, Desulfovibrio vulgaris Hildenborough (DvH). Through data mining, we shortlisted 111 AHL synthase genes. Conserved domain analysis of 111 AHL synthase genes generated a consensus sequence. Subsequent MSA of the consensus sequence with DvH genome indicated that DVU_2486 (previously uncharacterized protein from acetyltransferase family) is the gene encoding for AHL synthase. Homology modeling revealed the existence of seven α-helices and six β sheets in the DvH AHL synthase. The amalgamated study of hydrophobicity, binding energy, and tunnels and cavities revealed that Leu99, Trp104, Arg139, Trp97, and Tyr36 are the crucial amino acids that govern the catalytic center of this putative synthase. Identifying AHL synthase in DvH would provide more comprehensive knowledge on QS mechanism and help design strategies to control biofilm formation.

Structural insights into acyl-ACP selective recognition by the Aeromonas hydrophila AHL synthase AhyI

Background

Aeromonas hydrophila is a gram-negative bacterium and the major causative agent of the fish disease motile aeromonad septicemia (MAS). It uses N-acyl-homoserine lactone (AHL) quorum sensing signals to coordinate biofilm formation, motility, and virulence gene expression. The AHL signaling pathway is therefore considered to be a therapeutic target against pathogenic A. hydrophila infection. In A. hydrophila, AHL autoinducers biosynthesis are specifically catalyzed by an ACP-dependent AHL synthase AhyI using the precursors SAM and acyl-ACP. Our previously reported AhyI was heterologously expressed in E. coli, which showed the production characteristics of medium-long chain AHLs. This contradicted the prevailing understanding that AhyI was only a short-chain C₄/C₆-HSL synthase.

Results

In this study, six linear acyl-ACP proteins with C-terminal his-tags were synthesized in Vibrio harveyi AasS using fatty acids and E. coli produced active holo-ACP proteins, and in vitro biosynthetic assays of six AHL molecules and kinetic studies of recombinant AhyI with a panel of four linear acyl-ACPs were performed. UPLC-MS/MS analyses indicated that AhyI can synthesize short-, medium- and long-chain AHLs from SAM and corresponding linear acyl-ACP substrates. Kinetic parameters measured using a DCPIP colorimetric assay, showed that there was a notable decrease in catalytic efficiency with acyl-chain lengths above C6, and hyperbolic or sigmoidal responses in rate curves were observed for varying acyl-donor substrates. Primary sequence alignment of the six representative AHL synthases offers insights into the structural basis for their specific acyl substrate preference. To further understand the acyl chain length preference of AhyI for linear acyl-ACP, we performed a structural comparison of three ACP-dependent LuxI homologs (TofI, BmaI1 and AhyI) and identified three key hydrophobic residues (I67, F125 and L157) which confer AhyI to selectively recognize native C₄/C₆-ACP substrates. These predictions were further supported by a computational Ala mutation assay.

Conclusions

In this study, we have redefined AhyI as a multiple short- to long-chain AHL synthase which uses C₄/C₆-ACP as native acyl substrates and longer acyl-ACPs (C8 ~ C14) as non-native ones. We also theorized that the key residues in AhyI would likely drive acyl-ACP selective recognition.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02244-9.

Role of nitrogen deficiency on growth and development near isogenic by E genes lines of soybean co-inoculated with nitrogen-fixing bacteria

Nitrogen deficiency is a limiting factor in increasing efficiency of crop production in terrestrial ecosystems, and the transformation of inert nitrogen to forms that can be assimilated by plants is mediated by soil microorganisms. Symbiotic nitrogen-fixing bacteria and roots depend on each other and have developed various mechanisms for symbiotic coexistence. The aim of this work was to investigate the role of nitrogen deficiency on growth and development near isogenic by E genes lines of soybean (Glycine max (L.) Merr.): short-day (SD) line with genotype Е1е2е3(Е4е5Е7), and photoperiodic insensitive (PPI) line with genotype е1е2е3(Е4е5Е7) grown from seeds inoculated with active strains of Bradyrhizobium japonicum against the background of local populations of diazotrophs of the genus Azotobacter spp. and establish how the soybean – Bradyrhizobium symbiosis will develop as the genes of both microsymbionts and macrosymbionts are responsible for the formation of the symbiotic complex. Plants were grown in a vegetation chamber, in sand culture. To assess the quantitative composition of microorganisms in the rhizosphere and rhizoplanes, 6 plants were selected from each soybean line, then separation of the zones of the rhizosphere and rhizoplanes was performed using the method of washing and the resulting suspension was used for inoculation on dense nutrient media (mannitol-yeast agar medium and Ashby medium). The results of study showed that seed inoculation and co-inoculation provides faster formation of the symbiotic soybean – Bradyrhizobium complex. Differences in nodulation rates between the short-day line with genotype Е1е2е3(Е4е5Е7), and a photoperiodic insensitive line with genotype е1е2е3(Е4е5Е7) were identified. Determination of the amount of B. japonicum on the medium of mannitol-yeast agar in the rhizosphere and rhizoplane showed that inoculation by B. japonicum strain 634b caused a significant increase in the amount B. japonicum in the rhizosphere and rhizoplane in both soybean lines, comparison with non-inoculated seeds. Then, co-inoculation by B. japonicum strain 634b + Azotobacter chroococcum significantly increased the amount of B. japonicum only in the rhizoplane and decreased their number in the rhizosphere. Determination of the amount of A. chroococcum on the Ashby elective medium in the rhizosphere and rhizoplane showed that the inoculation by B. japonicum strain 634b caused a significant decrease in the amount of A. chroococcum both in the rhizosphere and in the rhizoplane of the PPI line of soybean, and in the rhizosphere the SD line, in comparison with non-inoculated seeds. That can testify to the competitive interaction of these microorganisms. However, the co-inoculation by B. japonicum strain 634b + A. chroococcum in the SD line significantly increased the number of A. chroococcum in the rhizoplane and decreased their number in the rhizosphere, in the PPI line their number decreased in the rhizoplane and increased in the rhizosphere, in comparison with non-inoculated seeds. Probably, the E genes (their dominant or recessive state) of soybean isogenic lines affect the regulation of the content and distribution of sugars. It was established that the nitrogen deficiency stimulated development of the root system of plants and the synthesized sugars were distributed predominantly to the root system growth. We suppose that the seeds’ inoculation had extended sugar consumption to the symbiont, due to which it compensates the lack of nitrogen, but leads to a slower growth of the root system.