Construction Overview

Characterizing the parts:

In order to characterize the parts we have created a new BioBrick compatible with our chassis. As E.coli DH5α does not have a lac repressor system we have assembled together basic parts J32100, B0033, C0012, B0010, B0012 and R0010 to create the composite regulator Lac Repressor System (LacRS)

Our first functionalization test coupling LacRS upstream the Green Fluorescent Protein (GFP) Biobrick (E0040) showed expression of GFP under UV light when the system is previously induced by IPTG.

We have successfully cloned and tested the functionality of LacRS in pSB1A3 (BBa_K1526009) into E.coli DH5α

Creating Inducible monofunctional constructs:

Each gene from our project was assembled downstream our LacRS Biobrick in order to allow a better characterization of the parts.

• We have successfully cloned LacRS+Gsh1* in pSB1C3 (BBa_K1526005) into E.coli DH5α

• We have successfully cloned LacRS+SpPCS in pSB1C3 (BBa_K1526006) into E.coli DH5α

• We have successfully cloned LacRS+MntH (BBa_K1526007) in pSB1C3 into E.coli DH5α

• We have successfully cloned LacRS+CysP in pSB1C3 (BBa_K1526008) into E.coli DH5α

Characterising CysP:

In order to characterise the sulfate secondary transporter from Bacillus subtilis we have adquired E. coli BW25113 strain mutants from the Keio collection for complementation assays.

We have used CysW (GenoBase code: JW2416) and CysA (GenoBase code: JW2415) mutants from the Keio collection as they represent deletions of different subunits (respectively, permease and ATPase) of the main sulfate transporter in E. coli (ABC transporter).

We have transformed both the mutants and the wild type with our LacRS+CysP plasmid and put them to grow on M9 media (1mM of Sulfate and 0.4%w/v of glucose) .

We still did not have time to make the optical density measurements on a 96-well plate on the FlouStar Omega plate reader kindly loaned to our team by BMG.

Improving the characterization of pYodA

pYodA (also called ZinTp) is a cadmium sensitive promoter endogenous to E. coli, where it regulates the bacterial response to stress stimulus after exposure to metal ions. As our final construct relies strongly on the sensing of Cadmium we wanted to improve the characterisation of BioBrick BBa_K896008 submitted in 2012 by the NYMU Taiwan team.

We assembled the Green Fluorescence Protein GFP (BBa_E0240) under PYoda in order to assess the strength of promoter in response to different concentrations of Cadmium chloride (CdCl2) and its specificity to this metal.

First test: E. coli DH5A viability assay

To characterise PYoda we adjusted the OD600 of an E.coli DH5alpha overnight transformed with pSB3K3 carrying BioBrick to 0.1 in LB broth.

The same procedure was done to an overnight culture of E. coli DH5 alpha (WT) and to a DH5 alpha transformed with pSB3K3 carrying GFP under the control of the constitutive promoter BBa_I20260 (ConstGFP). These would be our negative and positive control in fluorescence expression respectively.

Then, different concentrations of CdCl2 was added to the cultures with adjusted OD600 and 200uL were transferred onto a 96 well plate (Diagram 1.) and incubated overnight at 37ºC in a plate reader.

We measured the absorbance overnight of the different mutants using LB broth as blank -after assessing that Cadmium chloride did not affect absorbance-. The concentration of Cadmium reflects a negative effect around 0.9 mM concentration in all mutants, being pYoda the best growing mutant. However, the wild type presents depleted growth compared to the mutants in absence of CdCl2.

Second test: Inducing pYodA with different cadmium concentrations and assessing its strength by using GFP expression as a proxy

(The test has not presented inducibility of the promoter by cadmium what could suggest our chassis (Dh5Alpha) may not have the necessary apparatus for the induction of PyodA as it is known that the induction of the promoter by the heavy metal is not direct. It is mediated by many different genes related to facing stressful conditions in E. coli as Soxs and Fur (Puškárová, A., et al., 2002).

(Puškárová, A., et al. "Regulation of yodA encoding a novel cadmium-induced protein in Escherichia coli." Microbiology 148.12 (2002): 3801-3811.)

Measuring fluorescence.

Fluorescence of the 96 well plate arranged as shown in Diagram 1. was measured in a plate reader (brand) overnight. GAIN was set to 1000 (check Caua).

Fig 2.

The conclusions extracted from the measurements indicate that PYoda is not inducing the expression of GFP regardless of the concentration of Cadmium since the Fluorescence units remain at a basal level (that of the wild type). The test suggest that our chassis (DH5 alpha) may not have the necessary apparatus for the induction of PyodA as it it known t

Conclusions.

Due to the time restrictions at the time of the wiki freeze have been unable to optimise the characterisation of PYoda. However, our aim is to repeat the experiments shown above using transformed E. coli bw25113 strain instead of DH5alpha due to the . Moreover,

Third Test: Try inducing PyodA with other metals to test its efficiency as a cadmium biosensor.

This test is being done by Imperial College team as part of a collaboration.