Read about our scientific results here!
Summary of Overall Approach: The following summary of experimental results highlights the experiments performed to develop and test a functional manganese sensor. Our approach involved two gene block constructs derived from manganese homeostatic signaling systems native to E. coli. The first included the pmntP promoter that responds to MntR after it has bound to Mn(II) and a riboswitch that forms a hairpin and blocks translation of mRNA unless in the presence of Mn(II). We chose to clone the sensor geneblock (pmntP-rs-sfGFP) into the pSB3K3 plasmid backbone which contains a KAN resistance gene and the required elements for expression in MG1655 E. coli.
In addition, we constructed a plasmid for the IPTG inducible expression of 6xHIS-tagged MntR. This approach provides control over the levels of the manganese-responsive transcription factor MntR and a 6xHIS tag to facilitate monitoring of its expression level. This geneblock was inserted into a separate plasmid backbone containing the pTrc promoter with a lac operator that allows us to treat with IPTG and control the amount of MntR in the cells. This plasmid contains an AMP resistance gene.
A 1796-nucleotide geneblock was ordered from Addgene which incorporates 5’ and 3’ homology to the pSB3K3 vector to facilitate HiFi cloning (Fig. 1). The geneblock contains the full E. coli mntP promoter (BBa_K4217000). The full promoter has been shown to be more effective than an alternate truncated form which was previously used by the Calgary 2020 iGEM team (BBa_K902073). The manganese-responsive riboswitch (BBa_K902074), sfGFP (BBa_I746916), T1 and T7 terminator (BBa_K902073) were placed downstream of the mntP promoter.
Fig. 1. Description of the pSB3K3-pmntP-rs-sfGFP sensor plasmid.
pSB3K3-RFP plasmid DNA was purified from an overnight 250ml culture of pSB3K3-RFP in LB media with 50µg/ml Kanamycin using the Omega E.Z.N.A. Plasmid DNA Maxi Kit (catalog #D6922-02) according to manufacturer’s instructions. A final concentration of 87.1ng/µL (1.82 A260/280, 1.79 A260/230) was obtained and subsequently used for restriction digest as shown in the following table:
The resulting digest was run on a 0.8% gel, and the backbone was gel purified using the Monarch DNA Gel Extraction Kit (#T1020S).
The pSB3K3 backbone and pmntP-rs-sfGFP geneblock were assembled and transformed into NEB5α using the NEB HiFi Assembly Cloning Kit (catalog # E5520S) according to manufacturer’s instructions.
Approximately 400ng of plasmid DNA was digested with EcoRI, SpeI-HF or both in order to confirm insertion of the sensor geneblock into pSB3K3. The digest was set up as follows and incubated for 4hr at 37°C in a thermocycler. Subsequently, 25 µL of each reaction was run on a 0.8% agarose gel and imaged on a Fuji LAS 4000.
Fig. 2. Restriction digest confirmation of the pSB3K3-pmntP-rs-sfGFP plasmid. 5µL of Purple 1Kb Plus DNA ladder (#N0550S) and 25µL of each sample was run on a 0.8% agarose gel and imaged on a Fuji LAS 4000.
Conclusions:
Chemically competent MG1655 cells prepared by the 2020 WSU iGEM team and chemically competent MG1655 ΔmntR prepared by the 2022 team were thawed on ice and transformed with pSB3K3-pmntP-rs-sfGFP as follows:
Result: Transformants of pSB3K3-pmntP-rs-sfGFP were obtained and used to prepare glycerol stocks for future use. The pUC19 plates had lots of colonies, and the no DNA control showed no growth.
The initial test of the pSB3K3-pmntP-rs-sfGFP sensor was a confirmation that sfGFP protein was produced in response to MnCl2 treatment. A 1.5M stock solution of Manganese (II) chloride tetrahydrate was diluted roughly into a 10-fold dilution series for use in the assay.
Overnight cultures were set up of:
Cultures were back-diluted 1:100 in LB+Kan and grown to an OD600 of 0.5. The pSB3K3-pmntP-rs-sfGFP sensor cultures were then aliquoted into 1.2 ml cultures for treatment with MnCl2 as indicated in the table below:
1 mM IPTG was added to the positive control to induce eGFP expression. The cultures were then grown at 37°C, 250rpm. At 3hr, 100µL aliquots were read on a black-shielded 96-well plate (A600 and Fluor485/515). At 3hr, 0.1 OD600 equivalent of each sample was collected in 1.5 mL centrifuge tubes and processed for immunoblot to detect GFP levels.
Fig.3: Immunoblot analysis of soluble lysate fraction from MnCl2-treated MG1655 ΔmntR cells expressing the pSB3K3-pmntP-rs-sfGRP sensor. 5µL of Low MW protein ladder (Thermo Fisher #26616) was run in the first lane followed by 0.01 OD600 equivalents from each of the test samples ranging from 0mM (“-C”) to 100 mM MnCl2-treated. The 10% SDS-PAGE gel was run at 135V and then transferred to a 0.45µm PVDF membrane with 0.35A for 60min and immunoblotted for GFP. Briefly, the blot was blocked 1hr in 5% milk, washed 3 times 15 minutes in TTBS, probed with mouse anti-GFP at 1:1000 in 5% milk overnight at 4°C, washed 3 times 15 minutes in TTBS, probed with goat anti-mouse at 1:5000 in 5% milk for 1 hour at room temperature, and washed 3 times 15 minutes in TTBS. The blot was developed with Western Lightning Plus ECL bioluminescence substrate (2-5min) and imaged on a Fuji LAS 4000.
Conclusions:
A600 and Fluor485/515 readings were collected using a BioTek Synergy H1 plate reader for the samples prepared in step 1 above (“Determine if sfGFP is induced in response to MnCl2”). (Fluorescence was not visible on a standard light box, but was detectable on the plate reader.) Data was analyzed as shown in Fig.4 below, and the fold-change in fluorescence obtained in MG1655 WT and MG1655 ΔmntR E. coli was plotted against the MnCl2 treatment concentration Fig.5.
Fig. 4: Example calculation of fold-change relative to untreated control. Raw measurements were obtained on the BioTek Synergy H1 plate reader. The average LB media reading was subtracted to obtain blanked A600 and Fluor485/515 values. Next, OD600 corrected values were calculated as the ratio of Fluor485/515 to A600. Finally, the fold-change from untreated control was calculated and plotted against the manganese treatment concentration (as shown in Fig.5).
Fig. 5: MnCl2 dose curve of MG1655 WT and MG1655 ΔmntR cells expressing the pSB3K3-pmntP-rs-mntR sensor. Overnight cultures were diluted 1:100 in LB-Kan and grown at 37oC 250RPM to an OD600 of 0.5. Cultures were aliquoted into 1.2ml volumes for treatment with the indicated concentrations of MnCl2. After 3hr of treatment, A600 and Fluor485/515 readings were collected and the fold-change relative to untreated control were calculated. (No biological replicates used in this initial screen.)
Conclusions:
The manganese treatment assay was repeated with a narrowed range of MnCl2 based on the results in Fig.5. pSB3K3 vector negative controls were also included as a confirmation of sensor specificity (Fig.6).
Fig. 6: Narrowed range MnCl2 dose curve of MG1655 WT and MG1655 ΔmntR cells expressing the pSB3K3-pmntP-rs-mntR sensor or control pSB3K3 vector plasmids.Overnight cultures were diluted 1:100 in LB-Kan and grown at 37°C 250RPM to an OD600 of 0.5. Cultures were aliquoted into 1.9 mL volumes for treatment with the indicated concentrations of MnCl2. After 3hr of treatment, A600 and Fluor485/515 readings were collected and the fold-change relative to untreated control were calculated. (No biological replicates used in this initial screen.)
Conclusions:
To determine the time-course of sfGFP expression in response to MnCl2, the sensor assay was repeated with biological and technical triplicates with 1mM and 2.5 mM MnCl2 treatment. A600 and Fluor485/515 readings were taken at 2hr, 4hr, 6hr, 8hr and after overnight incubation (Fig.7).
Fig. 7. Time-course of MnCl2-induced sfGFP expression in MG1655 WT pBS3K3-pmntP-rs-sfGFP cultures. Overnight cultures were diluted 1:20 in LB-Kan and grown at 37°C 250RPM to an OD600 of 0.5. Cultures were aliquoted into 3 mL volumes for treatment with 1 mM or 2.5 mM MnCl2. At the indicated timepoints, A600 and Fluor485/515 readings were collected and the fold-change relative to untreated (0 mM) control were calculated. 95% confidence intervals are shown.
Conclusions:
LB has 0.25μM Mn2+ that may contribute to observed background fluorescence observed in the no manganese control cultures (Anjem et al 2009). To determine if the use of minimal media could improve sensor performance, MG1655 WT cultures carrying the pSB3K3-pmntP-rs-sfGFP sensor were grown in minimal media lacking manganese and the sensor response to 0.1 mM, 1 mM and 3 mM MnCl2 was determined (Fig.8).
Fig. 8. Comparison of pBS3K3-pmntP-rs-sfGFP sensor performance in LB and M9 minimal medium. Overnight cultures were grown in LB or M9 medium, diluted 1:100 and grown at 37oC 250RPM to an OD600 of 0.5. Cultures were aliquoted into 2 mL volumes for treatment with 0.1 mM, 1 mM or 3 mM MnCl2. At 2hr of treatment, A600 and Fluor485/515 readings were collected and the fold-change relative to untreated (0mM) control were calculated. 95% confidence intervals are indicated by error bars. All samples run in technical duplicate.
Based on the observation that the pSB3K3-pmntP-rs-sfGFP sensor doesn’t work in ΔmntR mutant E. coli and is thus dependent on mntR, it was hypothesized that an inducible mntR plasmid would allow us to optimize sensor performance. A 535 nucleotide geneblock was ordered from Addgene which incorporates 5’ and 3’ homology to the pTrc vector to facilitate HiFi cloning (Fig.9). The geneblock contains the N-terminal 6xHIS tag and the coding sequence for mntR (source). The full promoter has been shown to be more effective than an alternate truncated form which was previously used by the Calgary 2020 iGEM team (BBa_K902073). The manganese-responsive riboswitch (BBa_K902074), sfGFP (BBa_I746916), T1 and T7 terminators (BBa_B0015) were placed downstream of the mntP promoter.
Fig. 9. Description of the pTrc-6xHIS-mntR plasmid.
The pTrc-VvTs-trGPPS plasmid produced by the 2021 Wright State iGEM team was used as the source of the plasmid backbone used to make the pTrc-6xHIS-mntR plasmid. Plasmid DNA was purified from an overnight 250 mL culture of pTrc-VvTs-trGPPS in LB media with 100µg/ml Ampicillin using the Omega E.Z.N.A. Plasmid DNA Maxi Kit (catalog #D6922-02) according to manufacturer’s instructions. A final concentration of 351ng/µL (1.85 A260/280, 2.2 A260/230) was obtained and subsequently used for restriction digest as shown in the following table:
The resulting digest was run on a 0.8% gel and the backbone was gel purified using the Monarch DNA Gel Extraction Kit (#T1020S).
The pTrc backbone prepared above and the 6xHIS-mntR geneblock were assembled and transformed into NEB5α using the NEB HiFi Assembly Cloning Kit (catalog # E5520S) according to manufacturer’s instructions.
Approximately 500ng of plasmid DNA was digested with NcoI-HF and HindIII-HF or both in order to confirm insertion of 6xHIS-mntR into the pTrc backbone. The digest was set up as follows and incubated for 4hr at 37°C in a thermocycler. Subsequently, 25 µL of each reaction was run on a 0.8% agarose gel and imaged on a Fuji LAS 4000.
Fig. 10. Restriction digest confirmation of the pTrc-6xHIS-mntR plasmid. 5 µL of Purple 1Kb Plus DNA ladder (#N0550S) and 25 µL of each sample was run on a 0.8% agarose gel and imaged on a Fuji LAS 4000.
Conclusions:
Chemically competent MG1655 cells prepared by the 2020 WSU iGEM team and chemically competent MG1655 ΔmntR prepared by the 2022 team were thawed on ice and transformed with pTrc-6xHIS-mntR as follows:
Result: Transformants of pTrc-6xHIS-mntR were obtained and used to prepare glycerol stocks for future use. The pUC19 plates had lots of colonies, and the no DNA control showed no growth.
To confirm that IPTG induces the expression of mntR from the pTrc-6xHIS-mntR plasmid, several different concentrations of IPTG were tested and the induction of mntR was monitored by Coomsasie and immunoblot. Our data showed that 6xHIS mntR protein was expressed in response to 0.1 mM, 1 mM and 10 mM IPTG by 2hr and continuing through an overnight incubation (see Contribution).
To determine the effect of mntR expression on the performance of the pSB3K3-pmntP-rs-sfGFP sensor, two colonies of double transformants (i.e. carrying both pTrc-mntR and pSB3K3-pmntP-rs-sfGFP) were subjected to the MnCl2 treatment assay (Fig.11). Coomassie and immunoblot of samples from the first colony were performed as confirmation that MntR was induced in these samples (Fig.12).
Fig. 11: Time-course of pSB3K3-pmntP-rs-sfGFP induction in uninduced and IPTG-induced cultures co-expressing the pTrc-6xHIS-mntR plasmid. Overnight cultures of MG1655 WT E. coli expressing the dual plasmid system (i.e. both the pSB3K3-pmntP-rs-sfGFP sensor and pTrc-6xHIS-mntR) were diluted 1:20 in LB-Kan+Amp and grown at 37°C 250RPM to an OD600 of 0.5. Cultures were divided into 25 mL batches and treated with either vehicle or 1mM IPTG for 2hrs at 34°C. Cultures were then aliquoted into 3 mL volumes for treatment with vehicle or 2.5 mM MnCl2. After 2hr and 4hr of treatment, A600 and Fluor485/515 readings were collected and the fold-changes relative to untreated control were calculated.
Fig. 12. Immunoblot (top) and Coomassie (bottom) of cell lysates from MG1655 ΔmntR E. coli expressing the pTrc-6xHIS-mntR plasmid. Overnight cultures of MG1655 ΔmntR E. coli transformed with the pTrc-6xHIS-mntR plasmid were grown in LB medium with 50 µg/ml Kanamycin, diluted 1:20 and grown to an OD600 of 0.5. The cultures were split and treated with 1mM IPTG or vehicle for 2hrs at 34°C 250RPM followed by 2 additional hours with vehicle or 2.5mM MgCl2 (as indicated). 5 µL of Low MW protein ladder (Thermo Fisher #26616) was run in the first lane. A positive control of pet29b-6xHIS-GFP was run as a positive control for IPTG induction. 0.1 OD600 equivalent of whole cell lysates were run in each lane. Proteins were separated on a 15% SDS-PAGE gel run at 135V and either stained with Coomassie stain or transferred to a 0.45 µm PVDF membrane with 0.35A for 60 min for immunoblot for the 6xHIS tag. Immunoblot was performed using mouse anti-HIS tag (Cell Signaling Technology) at 1:1000 in 5% milk overnight at 4°C and goat anti-mouse IgG at 1:5000 in 5% milk for 1 hour at room temperature. Blots were developed using Lightning Plus ECL bioluminescence substrate and imaged on a Fuji LAS 4000.
Conclusions:
To determine if the timing of IPTG induction affects sensor performance in MG1655 WT E. coli expressing both the pSB3K3-pmntP-rs-sfGFP and the pTrc-mntR plasmid, the effect of 2hr pre-treatment with 1 mM IPTG and concurrent treatment with 1 mM IPTG was determined (Fig.13).
Fig. 13: 1mM IPTG pre- and concurrent treatment of MG1655 WT E. coli expressing the dual plasmid system (i.e both pSB3K3-pmntP-rs-sfGFP and pTrc-mntR) Overnight cultures of MG1655 WT E. coli expressing both the pSB3K3-pmntP-rs-sfGFP sensor and pTrc-mntR were diluted 1:20 in LB-Kan+Amp and grown at 37°C 250RPM to an OD600 of 0.5. Cultures were divided into three batches and treated with vehicle, 1 mM IPTG at 0hr, or 1mM IPTG at 2hr. Cultures were then aliquoted into 3 mL volumes for treatment with vehicle or 2.5 mM MnCl2. After 4hr of treatment, A600 and Fluor485/515 readings were collected and the fold-changes relative to untreated control were calculated. 95% confidence intervals are indicated by error bars. All samples run in technical and biological triplicate.
Conclusions:
Based on our observation that co-expression of the uninduced pTrc-mntR plasmid improved the fold-change in sfGFP produced in response to MnCl2, we hypothesized that co-expression of the uninduced pTrc-6xHIS-mntR plasmid might improve the sensitivity of the pSB3K3-pmntP-rs-mntR sensor. To test this hypothesis, a 0.01 mM – 2.5 mM dose series of MnCl2 was used to treat MG1655 WT E. coli expressing the pSB3K3-pmntP-rs-sfGFP sensor alone to uninduced and IPTG induced cultures expression the sensor and the pTrc-mntR plasmid (Fig.14).
Fig. 14: 1 mM IPTG pre- and concurrent treatment of MG1655 WT E. coli expressing the the sensor alone or the dual plasmid system (i.e. both pSB3K3-pmntP-rs-sfGFP and pTrc-mntR). Overnight cultures of MG1655 WT E. coli expressing both the pSB3K3-pmntP-rs-sfGFP sensor and pTrc-mntR were diluted 1:20 in LB-Kan+Amp and grown at 37°C 250RPM to an OD600 of 0.5. Cultures were divided into three batches and treated with vehicle, 1 mM IPTG at 0hr, or 1mM IPTG at 2hr. Cultures were then aliquoted into 3 mL volumes for treatment with vehicle, 0.01 mM, 0.1 mM, 1 mM or 2.5 mM MnCl2. After 4hr of treatment, A600 and Fluor485/515 readings were collected and the fold-changes relative to untreated control were calculated. 95% confidence intervals are indicated by error bars. All samples run in technical duplicate and biological triplicate.
Conclusions:
Co-expression of uninduced pTRC-6xHIS mntR with the pSB3K3-pmntP-rs-sfGFP sensor in MG1655 WT E. coli was confirmed as an effective cell-based system for the detection of manganese in water samples down to 0.01 mM (0.5ppm) MnCl2. This level of detection allows the testing of water samples for manganese contamination near the level at which it is visible (0.05ppm) or deemed unsafe (0.3ppm). Further, the sensor is effective down to the 1mM (5µg/L, 5ppm) practical quantitation limit (PQL) of routine water tests for manganese.