Difference between revisions of "Part:BBa K1216001"

Revision as of 13:41, 30 October 2013

Alkaline Phosphatase (phoA) from Citrobacter

3D representation of the alkaline phosphatase from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1ANJ RCSB]

A form of this protein with added TEV and poly-HIS tags can be found here.

Usage and Biology

Alkaline phosphatases are used as reporter enzymes in different assays such as Western Blotting and in situ hybridization^[1]. Testing human blood for Alkaline Phosphatase levels is a routine test that can reveal different conditions^[2].

Alkaline phosphatases cleave phosphate groups from organic compounds by hydrolysis while retaining stereochemistry^[3]. A good explanation of the mechanism can be found [http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter_10%3A_Phosphoryl_transfer_reactions/Section_10.3%3A_Hydrolysis_of__phosphates here].
Alkaline phosphatases, respectively their serum levels, are also related to several diseases e.g. metabolic myopathies and Paget Disease. ^[4]

Sequence and Features

Characterization

The final construct was sequenced.

Colorimetric response

Figure 2. Liquid culture from the triple knockout E.Coli strain overexpressing PhoA or PhoA-His respectively after reacting with pNPP. The negative control contains liquid culture without pNPP added.

Figure 3. Liquid culture from the triple knockout E.Coli strain overexpressing PhoA after reacting with BCIP. The negative control contains liquid culture without BCIP added.

[http://2013.igem.org/Team:ETH_Zurich ETH Zurich 2013] used PhoA in their project as reporter enzyme. To test the functionality of the enzyme, liquid culture of the ΔaesΔgusAΔnagZ Escherichia coli strain overexpressing PhoA was incubated with 4-Nitrophenol phosphate (pNPP). Another suitable chromogenic substrate for detection of PhoA is 5-Bromo-4-Chloro-3-indolyl phosphate (BCIP).

Figure 1. Enzymatic reaction of PhoA with pNPP or BCIP.

Figure 5. Cell lysate from the ΔaesΔgusAΔnagZ E scherichia coli strain overexpressing PhoA after reacting with 4-MU-phosphate.

Cell lysate for the assay described below was tested for active enzyme in the same way, but with the fluorescent substrate 4-MU-phosphate. The picture was taken with a common single lens reflex camera mounted on a dark hood at λ_Ex 365 nm.

Figure 4. Enzymatic reaction of PhoA with 4-MU-phosphate.

Kinetics

To characterize the enzyme they conducted fluorometric assays to obtain K_m values. To this end bacterial cells were grown until in exponential growth phase. Upon reaching this, gene expression was induced by AHL (see [http://http://2013.igem.org/Team:ETH_Zurich/Infoproc ETHZ system 2013]). After another 4-5 h of growth, cells were harvested and lysed, the cell free extract (CFX) used for the fluorometric assay. The properly diluted CFX was measured on a 96 well plate in triplicates per substrate concentration. A plate reader took measurements at λ_Ex 365 nm and λ_Em 445 nm. The obtained data was evaluated and finally fitted to Michaelis-Menten-Kinetics with SigmaPlot™. See the resulting graph below.

Figure 5. Michaelis-Menten-Kinetics of PhoA cell lysate from E.Coli overexpressing PhoA: plots velocity versus substrate concentration (2.5 μL, 5 μL, 10 μL, 30 μL, 60 μL, 120 μL, 240 μL) in 20 mM Tris buffer of pH 8. A kinetic value for K_m obtained by fitting the raw data to standard the Michaelis Menten equation; K_m = 105.9 ± 5.3 μM. All assays were carried out in triplicates, results are presented as means.

The experimental procedure was as following:

1. Prepare buffers
   • Lysis buffer: 10 mg/ml Lysozyme, 20 mM Tris buffer, pH 8
   • Reaction buffer: 20 mM Tris buffer, pH 8
   • NOTE: For other enzymes than the ones we tested (Aes,GusA,NagZ,PhoA) you might need different buffers
2. Cell culture
   • Inoculate bacteria in 20 mL of LB with antibiotics
   • Let grow at 37°C shaking(200 rpm) to an OD₆₀₀ of 0.6
   • Induce enzyme expression (100nM AHL in our case)
   • Let grow at 37°C shaking(200 rpm) for 4-5h
     
3. Cell lysis
   • Transfer to 50 mL Falcon™ tube
   • Spin down at 4°C for 5 min with 4 rcf
   • Resuspend in lysis buffer, 1 μL/mg pellet
   • Transfer to eppendorf tubes
   • Incubate at room temperature for 10 min at 220 rpm
   • Spin down at 4°C for 10 min with max. speed
   • Transfer the supernatant to new tubes, discard pellets
   • Cell free extract can be stored at -20°C or continue processing
4. Dilution
   • The following values were provided by Johannes Haerle
     • Aes: Dilute CFX 1:100 in reaction buffer
     • GusA: Dilute CFX 1:100 in reaction buffer
     • NagZ: Use pure
     • PhoA: Dilute CFX 1:10 in reaction buffer
5. Hydrolysis reaction
   • Perform this measurement in a 96 well plate or similar
   • Perform 3 replicates for each substrate concentration
   • Present 41.6 μL reaction buffer in each well
   • Add 8 μL diluted CFX (the further dilution ocurring here is intended)
   • Add 30.4 μL of corresponding substrate
   • Detection of fluorescence in suitable plate reader (λ_Ex 365 nm, λ_Em 445 nm)

Crosstalk

To ensure specificity of the enzyme-substrate pairs used in [http://2013.igem.org/Team:ETH_Zurich Colisweeper] (ETH Zurich 2013), a crosstalk test was done to make sure that all overexpressed enzymes specifically cleave their assigned substrate.

Figure 7. Liquid cultures of the ΔaesΔgusAΔnagZ Escherichia coli strain overexpressing Aes, GusA, NagZ or none in a 96-well plate, with substrates indicated on the left added horizontally.

This crosstalk test was done in a 96-well plate, each well containing 200 μl from liquid cultures of our ΔaesΔgusAΔnagZ Escherichia coli strain overexpressing either Aes, GusA, NagZ or none, each distributed among the column-wells of the plate. Horizontally, the chromogenic substrates were pipetted to the liquid cultures in the same order as their corresponding hydrolase. If specificity of the chosen enzyme-substrates pairs were given, we would expect an output as shown in the figure below (Figure 6). As Figure 7 shows, the overexpressed hydrolases cleave only the substrates they were expected to.

Figure 6. Expected outcome. Added substrates should be specifically cleaved by their hydrolases.

References

1. Molecular Cell Biology, Fifth Edition, W.H. Freeman & Co., 2004.
2. [http://www.nlm.nih.gov/medlineplus/ency/article/003470.htm Medline Plus]
3. [http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter_10%3A_Phosphoryl_transfer_reactions/Section_10.3%3A_Hydrolysis_of__phosphates Section 10.3: Hydrolysis of phosphates]
4. Adams & Victor's Principles Of Neurology, 7th edition, McGraw-Hill Professional, 2000.