Isolation and evaluation of strong endogenous promoters for the heterologous expression of proteins in Pichia pastoris

Multi-gene metabolic engineering of Pichia pastoris to synthesize ectoine

As a promising osmolyte, ectoine has been widely applied in cosmetics, food, and pharmaceutical industries in recent years, therefore its biomanufacturer has attracted increasing interest. Ectoine-producing isolates were previously screened from halophilic microorganisms. After ectoine synthetase was identified, genetic engineering of Escherichia coli, Corynebacterium glutamicum, and Hansenula polymorpha were employed to produce ectoine. However, Pichia pastoris, another successful host capable of high-density cell culture, had not yet been exploited as an ectoine-synthesizing host. In this study, therefore, P. pastoris was employed for the first time to produce ectoine through multi-gene metabolic engineering. Firstly, Chromohalobacter salexigens HZS/E, a halophilic isolate producing 46.96 mg/mL ectoine, was identified, while ectABC encoding ectoine synthetase was cloned. Later, ectABC was introduced into P. pastoris GS115 under the control of two different promoters. The results showed that PGAP-based HZS02 accumulated 8.03 g/L, 12.62 % higher than 7.13 g/L produced by PAOX-based HZS01. Finally, to enhance the supply of the precursor l-aspartate-β-semialdehyde, three genes (aspC, aK, and asD) were individually and collectively overexpressed. The highest ectoine yield was achieved at 10.88 g/L by GS115/pGAPZ A-ectABC-aspC-aK-asD. This study demonstrated that P. pastoris was a highly effective host for ectoine biosynthesis.

Codon-tRNA Coadaptation Bias for Identifying Strong Native Promoters in Komagataella phaffii

Promoters are crucial elements for engineering microbial production strains used in bioprocesses. For the increasingly popular chassis Komagataella phaffii (formerly Pichia pastoris), a limited number of well-characterized promoters constrain the data-driven engineering of production strains. Here, we present an in silico approach for condition-independent de novo identification of strong native promoters. The method relies on tRNA-codon coadaptation of coding sequences in the K. phaffii genome and is based on two complementary scores: the number of effective codons and the tRNA adaptation index. Genes with high codon bias are expected to be translated efficiently and, thus, also be under control of strong promoters. Using this approach, we identified promising strong promoter candidates and experimentally assessed their activity using fluorescent reporter assays characterizing 50 promoters spanning a 76-fold difference in expression levels in a glucose medium. Overall, we report several promoters that should be added to the molecular toolbox for engineering of K. phaffii and present an approach for identifying promoters in microbial genomes.

Advances in Metabolic Engineering of Pichia pastoris Strains as Powerful Cell Factories

Pichia pastoris is the most widely used microorganism for the production of secreted industrial proteins and therapeutic proteins. Recently, this yeast has been repurposed as a cell factory for the production of chemicals and natural products. In this review, the general physiological properties of P. pastoris are summarized and the readily available genetic tools and elements are described, including strains, expression vectors, promoters, gene editing technology mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, and adaptive laboratory evolution. Moreover, the recent achievements in P. pastoris-based biosynthesis of proteins, natural products, and other compounds are highlighted. The existing issues and possible solutions are also discussed for the construction of efficient P. pastoris cell factories.