In Vitro SUMOylation Assay to Study SUMO E3 Ligase Activity

The overall goal of this experiment is to verify a protein of interest that can be SUMOylated or is a SUMO E3 lygase. This method can help answer key questions in the SUMOylation field, such as SUMO E3 lygase identification. The main advantage of this technique is that it could be utilized for investigation of SUMO E3 lygase specificity toward different SUMO iso forms.

Demonstrating the procedure will be Wan-Shan Young, a PhD student from my laboratory. To purify the tag K-bZIP, first incubate 10 milliliters of cellular lysate with 50 microliters of antibody-tagged magnetic beads in a 14-milliliter polypropylene tube. Then rotate the tube at 50 revolutions per minute at four degrees Celsius for three hours in a suspension mixer.

Once the protein is captured centrifuge the sample at 800 times g for 30 seconds at four degrees Celsius to pellet the beads. Discard all but one milliliter of supernatant to re-suspend the beads. And transfer the dissolved beads into a 1.5-milliliter tube.

To wash the captured proteins, place the tube with the beads on a magnetic stand. Wait for about three seconds for the beads to adhere to the side walls of the tube and then remove the supernatant. To wash the beads, add one milliliter of lysis buffer into the 1.5-milliliter tube.

Then invert the tube ten times. Next, the place the 1.5-milliliter tube on the magnetic stand and remove the supernatant once the beads adhere to the walls. To wash the beads again, add one milliliter of phosphate buffered saline to the 1.5 milliliter tube, and invert it ten times.

Then transfer the tube to the magnetic stand, and remove the supernatant once the beads have attached to the side walls. To elute the K-bZIP tagged proteins from the antibody-tagged magnetic beads, add 100 microliters at 150 micrograms per milliliter of octapeptide diluted in phosphate buffered saline in the 1.5-milliliter tube. Then rotate the tube on a suspension mixer at 50 revolutions per minute for ten minutes at room temperature.

Transfer the tube to the magnetic stand. And then collect the K-bZIP containing supernatant. Next, to analyze the purified K-bZIP tag, subject one to five microliters of the purified protein to SDS page, followed by Coomassie blue staining.

Load 0.5, 1 and 2 micrograms of bovine serum albumin as standards on the gel for quantifying the K-bZIP concentration. While processing the image on Image J.Next, dilute the purified K-bZIP in phosphate buffered saline. To attain a final concentration of 100 nanograms per microliter.

And store at minus 80 degrees Celsius in small aliquots. Add three microliters of 100 nanograms per microliter of purified tagged K-bZIP in the in vitro SUMOylation master mix reaction. Then mix the contents of the master mix gently and incubate at 30 degrees Celsius for three hours.

Next, add 20 microliters of 2X SDS page with loading buffer to stop the reaction. Then heat the samples at 95 degrees Celsius for five minutes to denature the protein. Next, load 20 microliters of the sample on a 10%SDS page gel.

And run the gel at 80 volts for about 120 minutes till the dye reaches the bottom of the gel. Once the electro paresis is over, disconnect the gel apparatus. And transfer the gel in semi-dry transfer buffer for five minutes.

Then soak the PVDF membrane in another container filled with methanol for one minute. Remove the PVDF membrane from the methanol and soak in semi-dry transfer buffer. Then gently agitate the membrane for five minutes.

Remove the safety cover of the semi-dry electrophoretic apparatus. Pre-wet a filter paper. And prepare a gel sandwich on the bottom of the platinum anode.

After securing the cathode plate in the safety cover, run the blot at 15 volts constant current for 90 minutes. Then turn the power supply off and take the PVDF membrane out after disconnecting the semi-dry apparatus. Now block the PVDF membrane with blocking buffer for one hour at room temperature on an orbital shaker at 30 revolutions per minute.

Next, hybridize the PVDF membrane with anti-p53 antibody and blocking buffer for 12 to 16 hours at four degrees Celsius on a suspension mixer at 30 revolutions per minute. Then take the PVDF membrane out and transfer in a container filled with Tris-buffered saline tween 20. Next, soak the PVDF membrane in Tris-buffered saline tween 20 for 30 minutes on the orbital shaker at 45 revolutions per minute.

Then hybridize the PVDF membrane with anti-rabbit antibody conjugated with horseradish peroxidase diluted in blocking buffer for one hour at room temperature on the suspension mixer at 30 revolutions per minute. Next, wash the PVDF membrane with Tris-buffered saline tween 20 thrice. After washing, soak the PVDF membrane in Tris-buffered saline tween 20 for 30 minutes on the suspension mixer at 45 revolutions per minute.

Then replace the Tris-buffered saline tween 20 with phosphate-buffered saline. To preserve the PVDF membrane at four degrees Celsius for up to 12 hours. Next, mix the enhanced chemiluminescent substrate reagents one and two in a one-to-one ratio.

Then remove the PVDF membrane from the phosphate-buffered saline and blot briefly with the punch pockets to absorb the excess moisture. Immediately add 400 microliters of the Chemiluminescent reagent to the membrane surface and wait for three to five minutes. Briefly blot to drain the excess Chemiluminescent reagent, preventing the membrane from drying completely.

Use Luminescent's imaging system to expose the blot. Here immuno blot analysis was done to show the concentration of Ubc9 enzyme required to SUMOylate the p53 targets. This shows that 1/2 and 1/5 the concentration of Ubc9 enzyme can sufficiently SUMOylate p53 enzyme in an in vitro SUMOylation assay using SUMO 1 and SUMO 2 peptides.

To analyze the SUMOylated p53 the membrane was probed with anti-p53 antibody. Similar immuno blot analysis was done to show that half of E1 and 1/10 concentration of Ubc9 enzymes are required to SUMOylate the p53 target in an in vitro SUMOylation assay using SUMO 1, SUMO 2 and SUMO 3 peptides. Here the membrane was stained with Coomassie to show the purified K-bZIP protein.

Baculovirus expression system was used to express the purified K-bZIP which was analyzed on SDS page with bovine serum albumin as standard for comparison. Additional immuno blot analysis was also done which showed that on increasing the concentration of K-bZIP it catalyzes the SUMOylation of p53 in the presence of half the amount of E1, and 1/10 the amount of Ubc9 enzymes, respectively. Once mastered, this technique can be done in four hours if it is performed properly.

While attempting this procedure it is important to remember to keep all the reagent for the in vitro SUMOylation assay on ice, and to do the series dilution rather than in one giant dilution. Find this procedure other methods like over expression SUMOlygase can be performed in order to verify the SUMOylation in vitro. After its development, this technique paved the way for researchers in the field of SUMOylation to explore more SUMOlygase and validate their power of specificity.

After watching this video, you should have a good understanding of how to identify a SUMO e3 lygase using in vitro simulation assay.