P. pastoris strains were inoculated into 50 mL falcon tubes containing 5 mL of YPG (1% yeast extract, 2% peptone and 1% v/v glycerol) supplemented with 100 μg mL−1 zeocin (InvivoGen, CA, United States). The cells were grown overnight at 30°C and 200 rpm in an incubator shaker Multitron Standard (Infors HT, Bottmingen, Switzerland) with a 2.5 cm orbit. 50 μL of overnight-grown cultures were used to inoculate each well of a 24 deep-well plate containing 2 mL of Buffered Minimal Glycerol (BMG) medium, containing 100 mM potassium phosphate buffer pH 6, 1.34% yeast nitrogen base (YNB), 1% v/v glycerol, and 0.4 mg L−1 biotin. The cultures were incubated at 28°C and 220 rpm in the same incubator shaker using a platform with a slope of 20° to improve the aeration. The cultures were grown for 48 h to ensure the full consumption of the substrate. Thereafter, culture samples were centrifuged at 12,000 g for 5 min and filtered through a 0.20 µm pore size syringe filter (SLLGX13NK, Merck Millipore, CA, United States). The 3-HP was quantified using HPLC.
The parental clones PpHP2 and PpHP6 were screened in triplicates. Six to eight clones were screened in triplicates for the strains generated by single-homology integration (PpHP7, PpHP8, and PpHP9). One single clone was screened in triplicates for the strains generated using CRISPR-Cas9.