Part:BBa_K2916047

Expression of NDK in E.coli

This part is used for expression of Nucleotide Diphosphate Kinase (NDK) needed for the OnePot PURE cell-free system.

Usage and Biology

NDK plays a big part in the energy-recycling system. It catalyzes the reactions of phosphorylation of a histidine residue that produces NTP, which then initiates a chain of reactions in the system. Analyzing those reactions we can conclude that NDK is involved in the synthesis of nucleoside triphosphates (NTP), such as guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP) that are all parts of our energy solution.

In our project we used NDK as a part of the protein solution needed for OnePot PURE cell-free system produced with the method of gravity flow affinity chromatography, as described in the protocol we designed.

Expression and purification of NDK

NDK is one of the proteins we used for the OnePot PURE cell-free system. We expressed it in M15 E.coli strain using a pQE30 vector. The expression system has a T5 lac operator, RBS and a lambda t0 Terminator, enabling us to regulate the expression with IPTG.

Methods

NDK was purified using our protocol . To test if the protein was actually expressed, we performed a SDS-PAGE that is presented below. On the left side we can see the results included in the initial OnePot PURE paper (Lavickova et al, 2019) while on the right (batch1_a,b and batch2_a,b) are the solutions we produced ourselves. (The procedure we followed and the conditions of the experiment can be found here).

Figure 1: SDS-PAGE of OnePot PURE protein solution.

Conclusion
NDK has a molecular weight of around 17kDa, and since there is a band shown at this level of molecular weight, we may assume that it is expressed. To verify the functionality of this protein we need to proceed with more experiments that would be mainly focused on the efficiency of the system.

OnePot PURE functionality test

To make sure that we have all the proteins in our OnePot PURE protein solution, and that they all function properly we need check if proteins can be expressed in our OnePot PURE cell-free system.

Methods

We expressed superfolding GFP following the protocol we designed in 10μl reactions, and measured the fluorescence on a plate reader at excitation wavelength of 535nm. We tested the expression using different concentrations of the sf GFP DNA template and also compared it with the fluorescence produced in PURExpress from NEB.

Figure 2: sf GFP expression using 10nM DNA template.

Figure 3: sf GFP expression using 5nM DNA template.

Figure 4: sf GFP expression using 2.5nM DNA template.

Figure 5: Comparison between OnePot PURE and PURExpress at saturation.

Conclusion
The expression was successful so we can confirm that NDK exists in our protein solution and is also functioning properly.

Used in OnePot PURE Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal BamHI site found at 140
  
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]