Development of a strategy induction AOX1 promoter methylotrophic yeast Komagataella phaffii

Currently, there is a significant increase in interest in the industrial production of enzyme preparations (and other recombinant proteins) using various microorganisms, including methylotrophic yeasts such as Komagataella phaffii. At the same time, the most significant productivity of the target proteins is achieved by methanol induction of heterologous genes cloned under the control of the AOX1 promoter. Thus, the efficiency of biosynthesis is largely determined by the metabolism of methanol. In this connection, the aim of the work is to develop an optimal strategy for methanol induction of the AOX1 promoter of Komagataella phaffii. The object of the study is the culture of the recombinant phospholipase A2 producing strain Komagataella phaffii. The studies were carried out in a laboratory fermenter Infors Minifors (Switzerland) on a liquid nutrient medium BSM (Basal Salt Medium) We used the generally accepted methods of studying the characteristics of metabolic activity, including the calculation of specific characteristics and productivity of the strain. The result of the study is the determination of the specific rate of consumption of methanol used as a carbon source, which was 19.2±1.8 mg/g*h. Also, the specific growth rate of Komagataella phaffii was determined and amounted to 0.24 h-1.Based on the data obtained during the research, a strategy for the induction of the AOX1 promoter in the cultivation of the methylotrophic yeast Komagataella phaffii was developed by maintaining the methanol concentration in the range of 0.6 to 2% based on the concentration of dissolved oxygen in the medium. The developed strategy of induction of the AOX1 promoter made it possible to obtain at least 1.87 g / l of recombinant protein (phospholipase A2) during cultivation of Komagataella phaffii for 96 h, which is 3.7 times higher than the known results.

Full-length Genome of the Ogataea polymorpha strain HU-11 reveals large duplicated segments in subtelomeric regions

Background: Currently, methylotrophic yeasts (e.g., Pichia pastoris, Hansenula polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains—CBS4732, NCYC495, and DL-1. However, these three strains are of independent origin and unclear relationship. As a high-yield engineered O. polymorpha strain, HU-11 can be regarded as identical to CBS4732, because the only difference between them is a 5-bp insertion. Results: In the present study, we have assembled the full-length genome of O. polymorpha HU-11 using high-depth PacBio and Illumina data. Long terminal repeat (LTR) retrotransposons, rDNA, 5' and 3' telomeric, subtelomeric, low complexity and other repeat regions were curated to improve the genome quality. We took advantage of the full-length HU-11 genome sequence for the genome annotation and comparison. Particularly, we determined the exact location of the rDNA genes and LTR retrotransposons in seven chromosomes and detected large duplicated segments in the subtelomeric regions. Three novel findings are: (1) O. polymorpha NCYC495 is so phylogenetically close to CBS4732/HU-11 that the syntenic regions covers nearly 100% of their genomes with a nucleotide identity of 99.5%, while NCYC495 is significantly distinct from DL-1; (2) large segment duplication in subtelomeric regions is the main reason for genome expansion in yeasts; and (3) the duplicated segments in subtelomeric regions may be integrated at telomeric tandem repeats (TRs) through a molecular mechanism, which can be used to develop a simple and highly efficient genome editing system to integrate or cleave large segments into yeast genomes. Conclusions: Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha HU-11 and CBS4732. The full-length genome of the O. polymorpha strain HU-11 should be included into the NCBI RefSeq database for future studies of O. polymorpha CBS4732, NCYC495, and their derivative strains.

Full-length Genome of the Ogataea polymorpha strain HU-11 reveals large duplicated segments in subtelomeic regions

Background: Currently, methylotrophic yeasts (e.g., Pichia pastoris, Hansenula polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains—CBS4732, NCYC495, and DL-1. However, these three strains are of independent origin and unclear relationship. As a high-yield engineered O. polymorpha strain, HU-11 can be regarded as identical to CBS4732, because the only difference between them is a 5-bp insertion. Results: In the present study, we have assembled the full-length genome of O. polymorpha HU-11 using high-depth PacBio and Illumina data. Long terminal repeat (LTR) retrotransposons, rDNA, 5' and 3' telomeric, subtelomeric, low complexity and other repeat regions were curated to improve the genome quality. We took advantage of the full-length HU-11 genome sequence for the genome annotation and comparison. Particularly, we determined the exact location of the rDNA genes and LTR retrotransposons in seven chromosomes and detected large duplicated segments in the subtelomeic regions. Three novel findings are: (1) the O. polymorpha NCYC495 is so phylogenetically similar to HU11 that a nearly 100% of their genomes is covered by their syntenic regions, while NCYC495 is significantly distinct from DL-1; (2) large segment duplication in subtelomeic regions is the main reason for genome expansion in yeasts; and (3) the duplicated segments in subtelomeric regions may be integrated at telomeric tandem repeats (TRs) through a molecular mechanism, which can be used to develop a simple and highly efficient genome editing system to integrate or cleave large segments at telomeric TRs. Conclusions: Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha CBS4732 and HU11. The full-length genome of the O. polymorpha strain HU-11 should be included into the NCBI RefSeq database for future studies of O. polymorpha CBS4732 and its derivatives LR9, RB11 and HU-11.

Beyond alcohol oxidase: the methylotrophic yeast Komagataella phaffii utilizes methanol also with its native alcohol dehydrogenase Adh2

ABSTRACT Methylotrophic yeasts are considered to use alcohol oxidases to assimilate methanol, different to bacteria which employ alcohol dehydrogenases with better energy conservation. The yeast Komagataella phaffii carries two genes coding for alcohol oxidase, AOX1 and AOX2. The deletion of the AOX1 leads to the MutS phenotype and the deletion of AOX1 and AOX2 to the Mut– phenotype. The Mut– phenotype is commonly regarded as unable to utilize methanol. In contrast to the literature, we found that the Mut– strain can consume methanol. This ability was based on the promiscuous activity of alcohol dehydrogenase Adh2, an enzyme ubiquitously found in yeast and normally responsible for ethanol consumption and production. Using 13C labeled methanol as substrate we could show that to the largest part methanol is dissimilated to CO2 and a small part is incorporated into metabolites, the biomass, and the secreted recombinant protein. Overexpression of the ADH2 gene in K. phaffii Mut– increased both the specific methanol uptake rate and recombinant protein production, even though the strain was still unable to grow. These findings imply that thermodynamic and kinetic constraints of the dehydrogenase reaction facilitated the evolution towards alcohol oxidase-based methanol metabolism in yeast.

Microbe Profile: Komagataella phaffii: a methanol devouring biotech yeast formerly known as Pichia pastoris

Methylotrophic yeasts of the genus Komagataella are abundantly found in tree exudates. Their ability to utilize methanol as carbon and energy source relies on an assimilation pathway localized in largely expanded peroxisomes, and a cytosolic methanol dissimilation pathway. Other substrates like glucose or glycerol are readily utilized as well. Komagataella yeasts usually grow as haploid cells and are secondary homothallic as they can switch mating type. Upon mating diploid cells sporulate readily, forming asci with four haploid spores. Their ability to secrete high amounts of heterologous proteins made them interesting for biotechnology, which expands today also to other products of primary and secondary metabolism.

Diversity and occurrence of methylotrophic yeasts used in genetic engineering

Methylotrophic yeasts have been used as the platform for expression of heterologous proteins since the 1980’s. They are highly productive and allow producing eukaryotic proteins with an acceptable glycosylation level. The first Pichia pastoris-based system for expression of recombinant protein was developed on the basis of the treeexudate-derived strain obtained in the US southwest. Being distributed free of charge for scientific purposes, this system has become popular around the world. As methylotrophic yeasts were classified in accordance with biomolecular markers, strains used for production of recombinant protein were reclassified as Komagataella phaffii. Although patent legislation suggests free access to these yeasts, they have been distributed on a contract basis. Whereas their status for commercial use is undetermined, the search for alternative stains for expression of recombinant protein continues. Strains of other species of methylotrophic yeasts have been adapted, among which the genus Ogataearepresentatives prevail. Despite the phylogenetic gap between the genus Ogataeaand the genus Komagataellarepresentatives, it turned out possible to use classic vectors and promoters for expression of recombinant protein in all cases. There exist expression systems based on other strains of the genus Komagataellaas well as the genus Candida. The potential of these microorganisms for genetic engineering is far from exhausted. Both improvement of existing expression systems and development of new ones on the basis of strains obtained from nature are advantageous. Historically, strains obtained on the southwest of the USA were used as expression systems up to 2009. Currently, expression systems based on strains obtained in Thailand are gaining popularity. Since this group of microorganisms is widely represented around the world both in nature and in urban environments, it may reasonably be expected that new expression systems for recombinant proteins based on strains obtained in other regions of the globe will appear.