Characterization of the transactivation and nuclear localization functions of Pichia pastoris zinc finger transcription factor Mxr1p

Overexpression of the transcriptional activators Mxr1 and Mit1 enhances lactic acid production on methanol in Komagataellaphaffii

A bio-based production of chemical building blocks from renewable, sustainable and non-food substrates is one key element to fight climate crisis. Lactic acid, one such chemical building block is currently produced from first generation feedstocks such as glucose and sucrose, both requiring land and water resources. In this study we aimed for lactic acid production from methanol by utilizing Komagataella phaffii as a production platform. Methanol, a single carbon source has potential as a sustainable substrate as technology allows (electro)chemical hydrogenation of CO2 for methanol production. Here we show that expression of the Lactiplantibacillus plantarum derived lactate dehydrogenase leads to L-lactic acid production in Komagataella phaffii, however, production resulted in low titers and cells subsequently consumed lactic acid again. Gene expression analysis of the methanol-utilizing genes AOX1, FDH1 and DAS2 showed that the presence of lactic acid downregulates transcription of the aforementioned genes, thereby repressing the methanol-utilizing pathway. For activation of the methanol-utilizing pathway in the presence of lactic acid, we constructed strains deficient in transcriptional repressors Nrg1, Mig1-1, and Mig1-2 as well as strains with overrepresentation of transcriptional activators Mxr1 and Mit1. While loss of transcriptional repressors had no significant impact on lactic acid production, overexpression of both transcriptional activators, MXR1 and MIT1, increased lactic acid titers from 4 g L-1 to 17 g L-1 in bioreactor cultivations.

Efficient Secretory Expression and Purification on Three Insoluble Amidohydrolases for Ochratoxin A Hydrolysis by Pichia pastoris

As a highly toxic mycotoxin, ochratoxin A (OTA) is widely contaminating agricultural products and has various toxicological effects. Bioenzymes for OTA degradation have shown promising potential for detoxification. Other than the efficient amidohydrolase ADH3 previously, two novel amidohydrolases ADH1 and AMD3 were obtained in this study. During Escherichia coli expression, the expressed protein solubility was very low and will limit future industrial application. Here, high copy number integrations were screened, and the amidohydrolases were efficiently secretory expressed by Pichia pastoris GS115. The protein yields from 1.0 L of fermentation supernatant were 53.5 mg for ADH1, 89.15 mg for ADH3, and 79.5 mg for AMD3. The catalytic efficiency (Kcat/Km) of secretory proteins was 124.95 s-1 mM-1 for ADH3, 123.21 s-1 mM-1 for ADH1, and 371.99 s-1 mM-1 for AMD3. In comparison to E. coli expression, the active protein yields substantially increased 15.78-51.53 times. Meanwhile, two novel amidohydrolases (ADH1 and AMD3) showed much higher activity than ADH3 that produced by secretory expression.

Evaluation of reference genes for transcript analyses in Komagataella phaffii (Pichia pastoris)

Background

The yeast Komagataella phaffii (Pichia pastoris) is routinely used for heterologous protein expression and is suggested as a model organism for yeast. Despite its importance and application potential, no reference gene for transcript analysis via RT-qPCR assays has been evaluated to date. In this study, we searched publicly available RNASeq data for stably expressed genes to find potential reference genes for relative transcript analysis by RT-qPCR in K. phaffii. To evaluate the applicability of these genes, we used a diverse set of samples from three different strains and a broad range of cultivation conditions. The transcript levels of 9 genes were measured and compared using commonly applied bioinformatic tools.

Results

We could demonstrate that the often-used reference gene ACT1 is not very stably expressed and could identify two genes with outstandingly low transcript level fluctuations. Consequently, we suggest the two genes, RSC1, and TAF10 to be simultaneously used as reference genes in transcript analyses by RT-qPCR in K. phaffii in future RT-qPCR assays.

Conclusion

The usage of ACT1 as a reference gene in RT-qPCR analysis might lead to distorted results due to the instability of its transcript levels. In this study, we evaluated the transcript levels of several genes and found RSC1 and TAF10 to be extremely stable. Using these genes holds the promise for reliable RT-qPCR results.

Phosphoregulation of the transcription factor Mxr1 plays a crucial role in the concentration-regulated methanol induction in Komagataella phaffii

Methylotrophic yeasts can utilize methanol as the sole carbon and energy source, and the expression of their methanol-induced genes is regulated based on the environmental methanol concentration. Our understanding of the function of transcription factors and Wsc family of proteins in methanol-induced gene expression and methanol sensing is expanding, but the methanol signal transduction mechanism remains undetermined. Our study has revealed that the transcription factor KpMxr1 is involved in the concentration-regulated methanol induction (CRMI) in Komagataella phaffii (Pichia pastoris) and that the phosphorylation state of KpMxr1 changes based on methanol concentration. We identified the functional regions of KpMxr1 and determined its multiple phosphorylation sites. Non-phosphorylatable substitution mutations of these newly identified phosphorylated threonine and serine residues resulted in significant defects in CRMI. We revealed that KpMxr1 receives the methanol signal from Wsc family proteins via KpPkc1 independent of the mitogen-activated protein kinase (MAPK) cascade and speculate that the activity of KpPkc1 influences KpMxr1 phosphorylation state. We propose that the CRMI pathway from Wsc to KpMxr1 diverges from KpPkc1 and that phosphoregulation of KpMxr1 plays a crucial role in CRMI.

Coordinate regulation of methanol utilization pathway genes of Komagataella phaffii by transcription factors and chromatin modifiers

The methylotrophic yeast Komagataella phaffii (a.k.a. Pichia pastoris) harbors a methanol utilization (MUT) pathway, enabling it to utilize methanol as the sole source of carbon. The nexus between transcription factors such as Mxr1p and Trm1p and chromatin-modifying enzymes in the regulation of genes of MUT pathway has not been well studied in K. phaffii. Using transcriptomics, we demonstrate that Gcn5, a histone acetyltransferase, and Gal83, one of the beta subunits of nuclear-localized SNF1 (sucrose non-fermenting 1) kinase complex are essential for the transcriptional regulation by the zinc finger transcription factors Mxr1p and Trm1p. We conclude that interactions among Gcn5, Snf1, Mxr1p, and Trm1p play a critical role in the transcriptional regulation of genes of MUT pathway of K. phaffii.