Potassium as a Macro-nutrient

Potassium is an essential plant macronutrient as it has numerous important roles in plants including osmoregulation, CO₂ regulation, starch and protein synthesis. The deficiency of K⁺ ion will result in abnormalities in plant growth and metabolism. Our aim is to engineer a potassium sensor that can detect a range of K⁺ concentration in the soil to ensure the suitable soil condition for the plant. We utilized kdpFp, a promoter activated at under low [K⁺] condition. We put it upstream of a GFP reporter so as to characterize the promoter activity.

Figure 1. Engineered E. coli as a biosensor of K⁺.

Endogenous K⁺ sensing system in E. coli

The potassium ion uptake in E. coli is regulated by several systems under different conditions. The potassium ion transporters, Trk and Kup are constitutively expressed (Epstein & Kim, 1971) while KdpFABC, another transporter is activated under low [K+] condition (Laimins et al., 1981).

Figure 2. Endogenous K⁺ uptake systems.

The kdpFABC operon is controlled by the KdpDE two-component system (TCS) which consists of KdpD, a membrane-bound sensor kinase, and KdpE, a cytoplasmic response regulator (Polarek, 1992; Walderhaug, 1992). KdpD is stimulated by both intracellular and extracellular potassium ion concentration (Jung, 2000; Jung, 2001; Roe, 2000; Yan, 2011a; Laermann, 2013). KdpD phosphorylates KdpE upon low potassium concentration (Voelkner, 1993; Puppe, 1996; Jung, 1997a; Jung, 2000). Under an increase in potassium ion concentration, KdpD phosphatase activity will be enhanced, causing a decrease in phospho-KdpE and kdpFABC expression. Phosphorylated KdpE turns on the expression of kdpFABC (Zhang, 2014a; Laermann, 2013).

The kdpFp adopted is upstream of the kdpFABC operon with -28 position of transcription start site relative to start the first gene, kdpF. The -10 and -35 box elements have been mapped are TACCCT and TTGCGA respectively (Sugiura et al., 1992). The transcription factor, phosphorylated KdpE, binds to the P_kdpF at binding site located from -71 to -55 site with reference to the transcription start site to initiate the transcription of downstream gene (Sugiura et al., 1992; Narayanan et al., 2012).

Design of K⁺ sensing Device

To make a potassium-sensing device, we obtained the promoter, P_kdpF, and combined it with a GFP reporter, BBa_E0240, in BioBrick RFC10 standard so that the promoter activity in different potassium level can be detected and characterized.

Figure 3. K⁺ sensing construct with reporter.

EcoRI Illegal Site

To make our promoters compatible with RFC10 standard and so that readily accessible to the iGEM community, we removed the EcoRI illegal site within. We mutated the thymine at -15 position with reference to the transcription start site (TSS) to guanine, cytosine and adenine to give rise to 3 promoter mutants.The four promoters are expected to be different in activity because of the difference in binding energy between the promoter and RNA polymerase due to the base-pair changes (Brewster, 2012). Therefore, we characterized all of the promoters to compare their strengths by means of their respective fluorescence levels and RPU measurements so as to obtain a more comprehensive knowledge in the activity and working range of the four promoters. For convenience, we denote them as A mutant, G mutant and C mutant respectively in the following context.

Interference from other Endogenous Systems

Another concern is the masking of P_kdpF activity by other native constitutive potassium transport systems in E. coli. Other than the inducible KdpFABC system, E. coli has Trk and Kup systems which are constitutively expressed, low-affinity potassium transport systems (Epstein & Kim, 1971). A study has found that the expression level of KdpFABC is generally higher in a strain without Trk and Kup system (Laermann et al., 2013). As the result, the activity of P_kdpF may be masked by Trk and Kup system and cannot be truly reflected. We decided to measure the activity of P_kdpF in E. coli TK2240 (kdp+ Δtrk Δkup) strain, which is a strain defective in Trk and Kup system. Such that we are able to characterize P_kdpF promoter in a more accurate manner.

Measurement and Characterization

In order to assemble a device that can be widely used by iGEM community, we characterized the kdpFp promoter by relative promoter unit (RPU) measurement. Additionally, relative fluorescence unit (RFU) measurement has also been done to compare the activities between wild type promoters and 3 variants.

Relative promoter unit measurement

Figure 4. Relative promoter unit (RPU) of kdpFp[-15,T>G] at different concentration of K⁺. Cells were pre-cultured in K115 medium overnight at 37°C. The cells were washed 3 times in 0.85% saline and then sub-cultured in medium with specific [K⁺]. Cells were fixed when OD₆₀₀=0.4. The measurement was carried out using fluorescence-activated cell sorting. Error bar are represented as SEM.

At lowest [K⁺], the strength of the G mutant promoter was found to be about 0.5 RPU. RPU of the promoter decreased when concentration increased. At 0.025 mM [K⁺], RPU values was found to be 0.13. There was about 3.8 fold change in RPU from 0 mM to 0.4 mM [K⁺]. As expected, kdpFp is turned off at high [K⁺] due to inhibition of kinase activity of kdpD by K⁺.

Relative fluorescence measurement

Figure 5 & 6. Activity of kdpFp in E. coli DH10B in different K⁺ concentrations. Fluorescence/absorbance versus [K⁺] plot is shown on the left while the GFP synthesis rate versus [K⁺] plot is on the right. A, T(wild type), C, and G represent A mutant, wild type promoter, C mutant and G mutant respectively. Cells were pre-cultured, washed and sub-cultured as previously described in RPU measurement. Measurement took place when OD₆₀₀=0.4. 2 other measurements were taken every 15 mins afterwards for GFP synthesis rate. Error bar are represented as SEM.

Both C and G mutants similarly expressed higher fluorescence compared to the wild type and the A mutant. As the [K⁺] went up, the activity of kdpFp decreased. The expression level of both C and G mutant promoters were significantly higher than the wild type one, while A mutant was always the lowest.

The fluorescence intensity decreases over the concentration of potassium ion in K minimal medium. After several trials, we found the dynamic range of our promoters. It is between 0 to 0.1 mM of potassium ion in K minimal medium. Thus, we characterized our promoters at those range of concentrations (0 to 0.2 mM).

We observed that the fluorescence intensity expressed by C and G mutants are always at around similar values since the binding affinity might be the same with reference to the energy matrix (Brewster, 2012). Moreover, both of them are always higher than the one expressed by the wild type promoter. Meanwhile, the fluorescence intensity expressed by A mutant is lower than the the one expressed by the wild-type promoter. Also, the relationship of relative fluorescence intensity and K⁺ concentration of all the promoters are coherent with the previous RPU measurement of G mutant.

Figure 8. Comparison between the activities of P_kdpF [-15, T>G] in DH10B and TK2240 strain. Cells were pre-cultured in K115 medium overnight at 37°C. The cells were washed 3 times in 0.85% saline and then sub-cultured in medium with specific [K⁺]. Measurement took place when OD₆₀₀=0.4. Error bars are represented as SEM.

At the concentration of potassium ion lower than 0.0125 mM, the fluorescence intensity expressed by G mutant in DH10B was significantly greater than the one in TK2240 strain. The fluorescence intensity expressed by G mutant in DH10B strain decreased over the concentration, while the one in TK2240 remained the same. Starting from the concentration of potassium ion at 0.0125 mM onwards, the difference of GFP expressed by both strains was not significant. After passing the concentration of potassium ion at 0.05 mM, the expression level of P_kdpF in TK2240 strain exceeded the one in the DH10B strain.

We did another relative fluorescence measurement using TK2240 to observe a more accurate activity of P_kdpF. The TK2240 strain is defective in trk and kup gene. The only gene which could respond to potassium ion in TK2240 strain is only kdp gene. Therefore the expression of kdp gene would not be masked by the saturable low-affinity K⁺ transporter system. We were expecting that the activity of P_kdpF in TK2240 are higher than that in DH10B. The fact mentioned earlier corresponds to the graph at higher concentration of potassium ion, although the expression level in DH10B is higher than in TK2240 at low concentration of potassium ion.

We could observe the difference of the fluorescence intensity expressed by both strains at the concentration of potassium ion lower than 0.0125 mM. The fluorescence intensity expressed by G mutant in DH10B strain decreases over the concentration, while the one in TK2240 remains the same. Since TK2240 has a greater need of KdpFABC complex to help scavenge the external K⁺, so what might have caused this would be TK2240 spend too much energy at that stage to make KdpFABC complex and thus spare less energy on producing GFP.

At higher concentration of potassium ion, starting from 0.0125 mM onwards, the difference of fluorescence intensity expressed by both strains is not significant anymore. Both strains show decrease in fluorescence intensity over the increasing concentration of potassium ion in K minimal medium.

After passing the concentration of potassium ion at 0.05 mM, the fluorescence intensity expressed by TK2240 strain exceeds the one in the DH10B strain due to the constant need of potassium ion of the cells and in TK2240, there is only KdpFABC transporter system that can satisfy this need of E. coli. It is due to the fact that E. coli uses the two saturable transporters, Trk and Kup, under normal physiological conditions to uptake extracellular potassium ion. Only at a very low concentration of potassium ion, that these two systems can no longer satisfy the need of potassium ion of E. coli, the P_kdpF will be activated.

Considerations for replicating the experiments

a. OD₆₀₀= 0.4 referring to mid log phase of E. coli in K minimal medium
b. Dilution has always been done to make the OD₆₀₀ values of start culture around the same before subculturing in different concentration of K⁺.

Future Plan

In the interest of providing an efficient and accessible device that can identify the concentration of K+ ion into real field, we had a future plan on optimizing the device prepared using a paper-based cell-free transcription-translation (TX-TL) system for our construct.

References

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Jung, K., Veen, M., & Altendorf, K. (2000). K+ and ionic strength directly influence the autophosphorylation activity of the putative turgor sensor KdpD of Escherichia coli. Journal of Biological Chemistry, 275 (51), 40142-40147.

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