Autophagic pathway is responsible for selective degradation of cytosolic enzymes formaldehyde and formate dehydrogenases in the methylotrophic yeast Komagataella phaffii.

In the methylotrophic yeast Komagataella phaffii (formerly Pichia pastoris), several methanol-induced enzymes are rapidly degraded upon a shift to glucose. We studied how deletion of autophagy-related genes affects turnover of two cytosolic enzymes, formaldehyde dehydrogenase (Fld1) and formate dehydrogenase (Fdh1), following the shift from methanol to glucose as a carbon source. GFP-tagged Fld1 and Fdh1 were expressed in wild-type and atg1Δ, atg6Δ, and atg15Δ strains, lacking, respectively, Atg1 (a serine/threonine kinase required for autophagosome formation), Atg6 (a subunit of phosphatidylinositol 3-kinase complexes I and II), and Atg15 (a phospholipase B required for lysis of autophagic bodies). Enzyme activities, Western blots, and fluorescence microscopy were used to monitor degradation. In wild-type cells Fld1 and Fdh1 levels and activities declined rapidly after the shift, whereas all atg1Δ, atg6Δ and atg15Δ mutants retained substantially higher Fld1/Fdh1 activity, similar to the peroxisomal enzyme alcohol oxidase, and cytosolic GFP signal. These data show that Atg1, Atg6 and Atg15 are required for efficient vacuolar degradation of cytosolic enzymes of methanol metabolism Fld1 and Fdh1. We conclude that these cytosolic enzymes are cleared via selective autophagy upon cell shift from methanol to glucose, underscoring the essential role of the autophagy-lysosome pathway in proteome remodeling of K. phaffii.