Transport of alkaline phosphatase (ALP) to the vacuole via autophagy and subsequent activation of its enzymatic activity by proteolysis has been used to measure rates of bulk autophagy (Noda et al., 1995 BBRC) as well as mitophagy (Mendl et al., 2011 J Cell Sci; Müller et al., 2015 Cell Rep) in baker's yeast. If you want to measure pexophagy in this organism you could design a strain that synthesizes ALP with a peroxisomal targeting signal (e.g., ALP-SKL) and then conduct assays to see under which conditions peroxisomes are degraded via autophagy. However, ALP-SKL is imported into peroxisomes already folded. Therefore it is theoretically possible that you would not be able to distinguish between degradation of ALP-SKL present in the cytoplasm (bulk autophagy) and ALP-SKL present in peroxisomes (pexophagy). Have you tried to construct such an assay? Do you think it could work?

Thanks!

Best regards,

Christian