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We are dedicated to your success. Get back on track. View our expert recommendations for commonly encountered problem scenarios.
View the relevant questions below:
Here are some things to consider:
Here are possible causes and solutions:
| Cause | Solution |
The pH of Solution I or Solution III may have drifted. The pH of both | Check the pH of Solutions I and III. If the pH is low, increase it by adding NaOH. If the pH is high, decrease it by adding HCl. Store solutions at 4°C in order to minimize drift in pH. |
Transformation reaction not mixed | Be sure to mix the transformation reaction every 15 minutes throughout the 1 hour incubation at 30°C. Vortexing works best. |
Incubation time is too short or temperature is too low | Pichia pastoris transformations may be incubated for longer periods of time (up to 3 hours) and at higher temperature (35–37°C). This may, in some instances, result in higher transformation efficiencies. |
Cell density is too low (OD600 <0.6) | Resuspend cells from Preparation of Competent Cells, Step 6, page 1 of the manual, ina smaller volume (i.e.,500 μL). |
Generally, large colonies represent transformants containing pPIC6/pPIC6α integrants, while small colonies represent transformants containing pPIC6/pPIC6α non-integrants. These non-integrants have transduced the pPIC6/pPIC6α plasmid, and therefore, exhibit a low level of blasticidin resistance in the initial selection process. Upon subsequent screening, these non-integrant transformants do not retain blasticidin resistance.
When choosing a blasticidin-resistant transformant for your expression studies, we recommend that you pick blasticidin-resistant colonies from the initial transformation plate and streak them on a second YPD plate containing the appropriate concentration of blasticidin. Select transformants that remain blasticidin-resistant for further studies.
When using the pPink-HC vector, the transformation efficiency of the host strain may appear low because colonies with only a few copies of the marker will not produce enough ADE2 gene product to grow and will be selected against on medium lacking adenine (i.e.,adenine dropout medium or minimal medium). Only colonies that have integrated multiple copies of the ADE2 marker will able to grow without adenine. Since the gene of interest is linked to the selection marker, the white colonies could also result in higher expression of the gene of interest.
This is likely due to low inoculum. We recommend having a starter culture to use, as it is more accurate than using a colony. You can use the doubling time to calculate the starting OD. In YPD, the doubling time is about 1.5 hours. In MGY, the doubling time is going to be about 3 hours.
Here are possible causes and solutions:
| Problem | Cause | Solution |
No multimers or low number of multimers after transformation into E. coli | CIAP defective
Not enough insert DNA to ligate Construct is unstable in E. coli
Multimers are too long to ligate efficiently | Use fresh CIAP. Add more BamH I-Bgl II expression cassette to your ligation. Decrease the number of cassettes in the vector. Try ligating each expression cassette |
Recombinant vector rearranges and deletions are detected | Construct is unstable | Decrease the number of cassettes in the vector. |
No antibiotic-resistant Pichia transformants | Integration efficiency is low | Transform using more DNA and/or |
Here are possible causes and solutions:
| Problem | Cause | Solution |
No multimers or low number of multimers after transformation into E. coli | CIAP defective
Not enough insert DNA to ligate Construct is unstable in E. coli
Multimers are too long to ligate efficiently | Use fresh CIAP. Digest more pAO815 containing one copy of the expression cassette. Use the in vivo method to isolate multimers. Try ligating each expression cassette separately. |
Recombinant vector rearranges and deletions are detected | Construct is unstable | Use the in vivo method to isolate multimers. |
Pichia His+ transformants | Vector was linearized with the wrong enzyme (restriction enzymes in the | Linearize your construct with Sal I or Stu I to insert the construct into |
Here are common troubleshooting scenarios with possible causes and solutions:
| Problem | Cause | Solution |
False positives | Not enough levels of Geneticin® resistance | Colonies can appear to be Geneticin® resistant, but are actually not. To prevent this, purify your putative Geneticin®-resistant colonies and confirm the level of Geneticin® resistance observed for each colony before proceeding further. |
Low number of Geneticin®-resistant colonies isolated | Not enough His+ transformants were screened | The frequency of spontaneous, multiple-integration events occurs only at a rate of 1–10%. You will need to screen thousands of His+ transformants to isolate an optimal amount of colonies. |
Few recombinants with gene of interest | Not enough His+ transformants were screened | You will need to screen thousands of His+ transformants to isolate an optimal amount of recombinants with the most copies of your gene, as successive multiple insertions are more rare. |
Low isolation of His+ transformants | Low transformation efficiency | Using electroporation instead of spheroplasting may increase the transformation efficiency, thereby allowing you to isolate more His+ transformants. |
Here are possible causes and solutions:
| Cause | Solution |
Transformation reaction not mixed | Be sure to mix the transformation reaction every 15 minutes throughout the 1 hour incubation at 30°C. Vortexing works best. |
Incubation time is too short or temperature is too low | Transformations may be incubated for longer periods of time (up to 3 hours) and at higher temperature (35–37°C). This may, in some instances, result in higher transformation efficiencies. |
Cell density is too low (OD600 <0.6) | Resuspend cells from Preparing Competent Cells, Step 8, page 2 of the manual, ina smaller volume (i.e.,500 μl). |
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