Regulation of Peroxisome Homeostasis by Post-Translational Modification in the Methylotrophic Yeast Komagataella phaffii

Insights into the transcriptomic mechanism and characterization of endoglucanases from Aspergillus terreus in cellulose degradation

Filamentous fungi are the main industrial source of cellulases which are important in the process of converting cellulose to fermentable sugars. In this study, transcriptome analysis was conducted on Aspergillus terreus NEAU-7 cultivated using corn stover and glucose as carbon sources. Four putative endoglucanases (EG5A, EG7A, EG12A, and EG12C) from A. terreus NEAU-7 were efficiently expressed in Pichia pastoris. Among them, EG7A exhibited the highest enzyme activity (75.17 U/mg) with an optimal temperature of 40 °C and pH 5.0. EG5A and EG12A displayed specific activities of 19.92 U/mg and 14.62 U/mg, respectively, at 50 °C. EG12C showed acidophilic characteristics with an optimal pH of 3.0 and a specific activity of 12.21 U/mg at 40 °C. With CMC-Na as the substrate, the Km value of EG5A, EG7A, EG12A or, EG12C was, 11.08 ± 0.87 mg/mL, 6.82 ± 0.74 mg/mL, 7.26 ± 0.64 mg/mL, and 9.88 ± 0.86 mg/mL, with Vmax values of 1258.23 ± 51.62 μmol∙min-1∙mg-1, 842.65 ± 41.53 μmol∙min-1∙mg-1, 499.38 ± 20.42 μmol∙min-1∙mg-1, and 681.41 ± 30.08 μmol∙min-1∙mg-1, respectively. The co-treatment of EG7A with the commercial cellulase increased the yield of reducing sugar by 155.77 % (filter paper) and 130.49 % (corn stover). Molecular docking assay showed the interaction energy of EG7A with cellotetraose at -10.50 kcal/mol, surpassing EG12A (-10.43 kcal/mol), EG12C (-10.28 kcal/mol), and EG5A (-9.00 kcal/mol). Root Mean Square Deviation (RMSD) and Solvent Accessible Surface Area (SASA) values revealed that the presence of cellotetraose stabilized the molecular dynamics simulation of the cellotetraose-protein complex over a 100 ns time scale. This study provides valuable insights for developing recombinant enzymes and biomass degradation technologies.

CRISPR/Cas9-based toolkit for rapid marker recycling and combinatorial libraries in Komagataella phaffii

Komagataella phaffii, a nonconventional yeast, is increasingly attractive to researchers owing to its posttranslational modification ability, strict methanol regulatory mechanism, and lack of Crabtree effect. Although CRISPR-based gene editing systems have been established in K. phaffii, there are still some inadequacies compared to the model organism Saccharomyces cerevisiae. In this study, a redesigned gRNA plasmid carrying red and green fluorescent proteins facilitated plasmid construction and marker recycling, respectively, making marker recycling more convenient and reliable. Subsequently, based on the knockdown of Ku70 and DNA ligase IV, we experimented with integrating multiple DNA fragments at a single locus. A 26.5-kb-long DNA fragment divided into 11 expression cassettes for lycopene synthesis could be successfully integrated into a single locus at one time with a success rate of 57%. A 27-kb-long DNA fragment could also be precisely knocked out with a 50% positive rate in K. phaffii by introducing two DSBs simultaneously. Finally, to explore the feasibility of rapidly balancing the expression intensity of multiple genes in a metabolic pathway, a yeast combinatorial library was successfully constructed in K. phaffii using lycopene as an indicator, and an optimal combination of the metabolic pathway was identified by screening, with a yield titer of up to 182.73 mg/L in shake flask fermentation. KEY POINTS: • Rapid marker recycling based on the visualization of a green fluorescent protein • One-step multifragment integration and large fragment knockout in the genome • A random assembly of multiple DNA elements to create yeast libraries in K. phaffii.

Fundamental and Applicative Aspects of the Unfolded Protein Response in Yeasts

Upon the dysfunction or functional shortage of the endoplasmic reticulum (ER), namely, ER stress, eukaryotic cells commonly provoke a protective gene expression program called the unfolded protein response (UPR). The molecular mechanism of UPR has been uncovered through frontier genetic studies using Saccharomyces cerevisiae as a model organism. Ire1 is an ER-located transmembrane protein that directly senses ER stress and is activated as an RNase. During ER stress, Ire1 promotes the splicing of HAC1 mRNA, which is then translated into a transcription factor that induces the expression of various genes, including those encoding ER-located molecular chaperones and protein modification enzymes. While this mainstream intracellular UPR signaling pathway was elucidated in the 1990s, new intriguing insights have been gained up to now. For instance, various additional factors allow UPR evocation strictly in response to ER stress. The UPR machineries in other yeasts and fungi, including pathogenic species, are another important research topic. Moreover, industrially beneficial yeast strains carrying an enforced and enlarged ER have been produced through the artificial and constitutive induction of the UPR. In this article, we review canonical and up-to-date insights concerning the yeast UPR, mainly from the viewpoint of the functions and regulation of Ire1 and HAC1.

Role of Dissimilative Pathway of Komagataella phaffii (Pichia pastoris): Formaldehyde Toxicity and Energy Metabolism

Komagataella phaffii (aka Pichia pastoris) is a yeast able to grow in methanol as the sole carbon and energy source. This substrate is converted into formaldehyde, a toxic intermediary that can either be assimilated to biomass or dissimilated to CO₂ through the enzymes formaldehyde dehydrogenase (FLD) and formate dehydrogenase, also producing energy in the form of NADH. The dissimilative pathway has been described as an energy producing and a detoxifying route, but conclusive evidence has not been provided for this. In order to elucidate this theory, we generated mutants lacking the FLD activity (Δfld1) and used flux analysis to evaluate the metabolic impact of this disrupted pathway. Unexpectedly, we found that the specific growth rate of the Δfld1 strain was only slightly lower (92%) than the control. In contrast, the sensitivity to formaldehyde pulses (up to 8mM) was significantly higher in the Δfld1 mutant strain and was associated with a higher maintenance energy. In addition, the intracellular flux estimation revealed a high metabolic flexibility of K. phaffii in response to the disrupted pathway. Our results suggest that the role of the dissimilative pathway is mainly to protect the cells from the harmful effect of formaldehyde, as they were able to compensate for the energy provided from this pathway when disrupted.