Orthogonal cloning of clpXP

Steps:

1. Get plasmids from Samantha. These are in E. coli that she has plated 14 July.
2. Clone clpX, clpP, YFP, YFP+ssRAtag (8peptide-LAA) into yeast. Use PCR on plasmids containing these genes. Clone these genes into different yeast plasmid shuttle vectors. Transform plasmids into yeast.
3. Test for expression of clpX and clpP by Western blot.
4. Test for functional protein degradation by clpXP. Determine if clpX is degrading proteins independent of clpP.
5. Check if yeast is surviving the addition of clpXP. This may have come up after step 1.
6. Measure rate of protein degradation via fluorescent signal of YFP.
7. Troubleshoot in unlikely event that it doesn't work perfectly the first time.

Techniques to use

• PCR
• Restriction enzyme use
• Cloning into plasmids
• Transforming yeasts
• Culturing yeasts
• Western blot
• Fluorescence measurements

Considerations

• Use Gal control of clpX, since it needs strongest control. Must have strong off, Drew thinks this has worked for Samantha. Glucose would provide suppression in this system.
• Use Western rather than just fluorescence at start to make sure proteins are being expressed. Won't know if they are folding/working but would know if they're being expressed (and how much?). Antibodies exist in Sauer lab to all these proteins and to SSRA tag so you can follow any of these proteins.

[advanced techniques and troubleshooting options]

• Can't do polysystronic cloning in yeast, unless maybe using IRES (internal ribosomal entry site).
• ura-3 tag: can use dropout media, or introduce 5' FOA which creates a toxic byproduct, so positive and negative selection possible
• sterility factor