LitR directly upregulates autoinducer synthesis and luminescence in Aliivibrio logei

Bacterial strains and plasmids

All experiments were conducted with the E. coli MG1655 F^-, rph⁻¹ strain (Guyer et al., 1981), which were obtained from VKPM collection (Russia). Plasmids used in this study are listed in Table 1 and illustrated in Fig. S1. Primers and a detailed description of plasmids constructed in this study are presented in a Supplemental File (see Plasmid constructions). Genes and promoters of Aliivibrio bacteria were from A. fischeri MGU-6, A. logei KCh1 (Khrulnova et al., 2010) and A. salmonicida NCIMB 2262^T (provided by Jesus L. Romalde (Egidius, Wiik & Andersen, 1986)).

Culture media and growth conditions

Bacteria were grown in Luria-Bertani (LB) broth. The liquid LB medium was composed of 1% tryptone, 0.5% yeast extract and 0.5% NaCl, for the preparation of solid medium, agar was added to a final concentration of 1.5% m/v. The medium was supplemented with appropriate antibiotics: 100 μg/ml ampicillin, 10 μg/ml tetracycline, or their composition. Overnight cultures were grown at 37 °C with continuous agitation and then were used to inoculate liquid LB. The resulting cultures were grown at 22–25 °C with continuous agitation (200 rpm). The optical density (OD) of cell suspensions was measured with a KFK-3 photometer (Zagorsk Optical-Mechanical Plant, Russia). An induction of the litR gene expression (plasmid p15Tc-litR) was made at the early exponential growth phase (OD about 0.1) by addition of IPTG (isopropyl β-D-1-thiogalactopyranoside) to a final concentration of one mM.

DNA isolation, restriction, ligation and transformation

Plasmid DNA was isolated by alkaline lysis. Cell transformation with hybrid plasmids followed standard protocols. Endonuclease restriction, DNA fragment ligation, agarose gel electrophoresis and isolation of DNA fragments from agarose gel were performed according to Green & Sambrook (2012). Restriction and ligation reactions were carried out using enzymes from Promega (USA): EcoRI, BamHI and KpnI restriction enzymes and T4 DNA ligase were used for constructing new plasmids (see Supplemental File for details).

Chemical substances

Isopropyl β-D-1-thiogalactopyranoside (IPTG) was from Anatrace (USA).

Measurement of bioluminescence

Bioluminescence intensities were measured in volume of 200 μl in plastic microtubes placed in front of a photomultiplier photocathode at room temperature using Biotox-7MB (BioPhisTech, Russia) or in 96-well plates using SynergyHT (Biotek Instruments, Winooski, VT, USA). Luminescence values were expressed in relative light units (RLU).

Determination of LitR-dependent promoter regulation

The effect of LitR on the expression of genes from lux regulons of the Aliivibrio genus bacteria was investigated for three species: A. fischeri, A. logei and A. salmonicida. For this purpose we used the heterological system of E. coli cells transformed with different biosensor plasmids from a set (Table 1, Fig. S1) that carry luxCDABE genes of P. luminescens transcriptionally fused with promoters of interest. To introduce the litR gene from A. logei into this system, the p15Tc-litR plasmid was constructed. It comprises a p15 origin, the litR A. logei gene under a lac promoter, and a lacI gene, which lowers the base transcription from P_lac and allows regulating litR with IPTG.

Luminescence induction factor calculation

The culture of E. coli cells carrying the A. logei litR gene under the IPTG-inducible promoter on the p15Tc-litR plasmid and the P. luminescens luxCDABE genes under control of the promoter of interest on a biosensor plasmid was grown to OD~0.1 in liquid LB medium, then divided into two equal parts: “control” and “induced”. The “induced” portion was supplemented with one mM IPTG. Further, the cultures were grown under equal conditions with periodic measurements of optical density and luminescence. The induction factor is the induced/control ratio of cell cultures’ luminescence. All figures show representative kinetic curves of biological independent triplicates.

Statistics

Error bars at the graphs are the SD of three independent experiment replications.

Computer analysis

Amino acid sequences alignment was performed using the Vector NTI software (Thermo Fisher Scientific, Waltham, MA, USA). The intrinsic disorder of proteins was predicted by their aa sequences with “Predictor of Naturally Disordered Regions” (pondr.com), one can find description of VL-XT, VSL2, VL3 and Charge-Hydropathy algorithms in Obradovic et al. (2003).

Effect of LitR A. logei on promoters of regulatory genes luxR, luxR1 and luxR2

Firstly, the effect of LitR on the expression of luxR A. fischeri, luxR1 A. logei and luxR2 A. logei was investigated. Figure 2 shows the coefficient of increase in luminescence of biosensors after the activation of the litR gene expression.

The data presented in Fig. 2 shows that LitR from A. logei is capable of a significant activation of the luxR A. fischeri gene transcription. This result is consistent with previous work (Fidopiastis et al., 2002) and means that the LitR homologues from A. fischeri and A. logei are interchangeable and have a common function. The amino acid sequence of LitR is highly conservative among the Aliivibrio species. In particular, LitR proteins from psychrophilic bacteria have almost the same sequences, comparing of them with mesophilic LitR A. fischeri gives that DNA-binding regions three compared proteins are identical and whole “helix-turn-helix” domain differs only by several aa substitutions (Fig. S2). Interesting that psychrophilic LitR variants are more ordered than mesophilic one according to analysis with VL-XT, VSL2, VL3 and Charge-Hydropathy instruments at pondr.com (Fig. S3). The increase in LitR content in the cell activates the expression of luxR1 A. logei, although to a lesser extent than that of A. fischeri luxR, and does not affect the expression of the luxR2 A. logei gene. The obtained result was in conflict with the data of Norwegian colleagues on a decrease in the production of an autoinducer in A. salmonicida litR mutant cells (Hansen et al., 2015); therefore, it was decided to test the effect of litR on the transcription of the “rightward” promoters of lux regulon.

Effect of LitR A. logei on promoters of structural genes luxICDABEG

Results of investigation of LitR A. logei effect on expression of autoinducer synthase (luxI), luciferase and reductase (luxCDABE) genes are given in Fig. 3. Promoters of different Aliivibrio species were tested with LitR A. logei in the heterological system of E. coli cells.

In response to the addition of one mM IPTG at OD~0.1 there was an increase in luminescence of the E. coli MG1655 cells carrying combinations of the plasmid p15Tc-litR (litR under P_lac) with different biosensor plasmids containing P. luminescens luxCDABE genes under control of P_luxI and P_luxCDABEG promoters of A. logei (Fig. 3A) and A. salmonicida (Fig. 3B). The following plasmids with the investigated promoters were used: pSV16 with P_luxI A. logei lux-reporter, pIVA with A. logei P_luxCDABEG lux-reporter, pAS2 with A. salmonicida P_luxI lux-reporter, and pAS1 with A. salmonicida P_luxCDABEG lux-reporter (Table 1, Fig. S1).

As can be seen from the graphs, LitR activates the transcription from the promoters of the luxI and luxCDABEG genes of both psychrophilic luminescent bacteria species A. logei and A. salmonicida. It should be noted that in both cases the activation of the luxI gene promoter in response to an increased expression of the litR gene was somewhat stronger than the activation of the luxCDABEG gene promoter. It can be seen that the amplitude of activation of A. salmonicida promoters is almost twice lower than that of A. logei promoters. This can be explained by the influence of other regulatory elements. These promoters are still the subject of research, but it is already known that their regulation is influenced by many factors, such as Lon, GroEL/ES, H-NS, CRP. We assume that the observed twofold difference may be due to differences in the sequences of promoters and surrounding regions, although the lux-box elements for these species are identical.

The data from Fig. 3C indicates that the induction of litR A. logei in the heterological system of E. coli leads to a notable (more than one order of magnitude) activation of expression from the A. fischeri P_luxICDABEG promoter. This effect has not been previously described and may indicate that litR is able to induce LuxI/R QS system through stimulation of both luxI and luxR gene expressions in A. fischeri cells. Moreover, the effect on luxI expression was higher in magnitude. The data obtained contradicts the results published by (Fidopiastis et al., 2002), which investigated the effect of litR on the expression of lacZ of the gene inserted into luxC ORF. Perhaps it could be connected with the differences in the sensitivity of the reporter genes used. However, LitR proteins from mesophilic and psychrophilic bacteria have some differences and it needs more detailed investigation.

LuxR-independent activation of promoters by LitR depends on the lux-box sequence

To make sure that the observed activation of “rightward” promoters determined by LitR occurs independently of the presence of regulatory genes from the luxI/R QS system in the cell, measurements of LitR-dependent activation of A. logei luxI gene transcription were carried out in the presence of the luxR2 regulatory gene and without it. Plasmids pSV16 and pR2 were used (Table 1, Fig. S1), in which the luxCDABE P. luminescens genes are under control of the A. logei P_luxI promoter with and without the luxR2 gene, respectively. The litR gene was introduced as before on a separate plasmid p15Tc-litR. Measurement results are shown in Fig. 4A, the increase in luminescence was calculated as the ratio of luminescence of IPTG-induced cells to the luminescence of the same cells without IPTG. As a negative control, cells carrying the p15Tc-lac vector without the litR gene were used.

We assumed that LitR could bind DNA in the promoter upstream region, the same site LuxR binds to (lux-box). To assess the effect of the lux-box sequence on the transcription activation of A. logei P_luxCDABEG by the LitR protein, we compared the LitR-dependent activation of two variants of the A. logei P_luxCDABEG promoter, which differ only in the lux-box sequences (Fig. 4B). The native P_luxCDABEG promoter was truncated exactly upstream of the lux-box and introduced into pDEW201 upstream of P. luminescens luxCDABE gene cassette (line lb1 on Fig. 4B, the pD-lb1 plasmid was used); to obtain another promoter variant, the lux-box was changed to match P_luxI (lb2 lines on Fig. 4B, the pD-lb2 plasmid was used). The difference between the obtained chimeric promoters is limited to only five bp (Fig. S4), in both cases, the cells don’t contain any of the luxR, luxR1 or luxR2 genes. All genetic elements, with the exception of lux-boxes, were identical in the compared cultures. The litR gene, as in previous experiments, was introduced into the cell on the p15Tc-litR plasmid, where it was under control of P_lac.

As can be seen from the data presented in Fig. 4A, LitR activates P_luxI and P_luxCDABEG A. logei promoters regardless of the presence of LuxR2 in the cells: luminescence induction in response to litR expression stimulation is almost equal for cells with luxR2 gene and without it (p15Tc-litR in combination with pSV16 and pR2, correspondently). The observed induction of P_luxI and P_luxCDABEG A. logei and consequently luminescence of cells is completely determined by the litR gene: in its absence (vector p15Tc-lac in combination with pSV16, pR2, pDlb1, or pD-lb2 biosensor plasmids), the luminescence of cells does not change in response to the addition of IPTG. The data in Fig. 4B shows that the change in the lux-box sequence affects the activation of the promoter by LitR. This indicates that the LitR binding site in the promoter region of A. logei luxCDABEG genes coincides or at least intersects with the LuxR binding site.