Regulation of carbon metabolism in Pichia pastoris by Mxr1p and identification of novel regulators

Abstract

Pichia pastoris (a.k.a. Komagataella phaffii), a widely used yeast for recombinant protein production, is cultured under a variety of conditions ranging from shake flasks to large bioreactors employing minimal, chemically defined, and complex media containing an appropriate source of carbon such as glucose, glycerol, methanol, ethanol or acetate. P. pastoris strains GS115 (his4), a histidine auxotroph, and X33, a prototroph, are used extensively for recombinant protein production employing expression vectors containing HIS4 and ZeoR, respectively as selection markers. The latter confers resistance to the antibiotic zeocin. High growth rates are attained when metabolic intermediates in the form of yeast extract and peptone are provided in the medium. The zinc-finger transcription factor Mxr1p regulates the transcription of genes of methanol, acetate, ethanol, and amino acid metabolism in P. pastoris by binding to Mxr1p response elements (MXREs) in their promoters. While the DNA binding properties of Mxr1p are well known, the transactivation domains of Mxr1p involved in the activation of target genes of different metabolic pathways are not well characterized. In this study, we have identified a nine amino acid transactivation domain located between amino acids 365 and 373, which is essential for the transactivation of ALD6-1 encoding an aldehyde dehydrogenase during ethanol metabolism. The basic amino acid residues between 75 and 85 amino acids are essential for nuclear localization of Mxr1p in a medium containing ethanol. While the N-terminal 400 amino acids of Mxr1p are sufficient for the activation of target genes essential for ethanol metabolism, the region between 401 and 1155 amino acids is also required for the regulation of genes essential for methanol metabolism. Several novel genes whose expression is differentially regulated by Mxr1p during methanol metabolism have been identified by DNA microarray. This study demonstrates that Mxr1p is a key regulator of ethanol metabolism and provides new insights i...