Fine-Tuned Gene Expression Elements from Hybrid Promoter Libraries in Pichia pastoris

Engineering strategies for producing medium-long chain dicarboxylic acids in oleaginous yeasts

Medium-long chain dicarboxylic acids (DCAs, C ≥ 6) are essential chemical raw materials, with wide applications in the chemical, pharmaceutical, material and food industries. However, the traditional chemical synthesis methods cause environmental pollution and are not in line with goals of sustainable development. With the development of synthetic biology, high-value-added DCAs can be biosynthesized from hydrophobic substrates (HSs) using suitable microorganisms. This review first summarizes the biosynthetic pathway of DCAs in oleaginous yeasts and then emphasizes the related engineering strategies for increasing the product yield, including promoter, enzyme, pathway, cell, fermentation, and downstream engineering. In addition, the challenges and development trends in the biosynthesis of DCAs are discussed, in light of the current progress, challenges, and trends in this field. Finally, guidelines for future research are proposed. Overall, this review systematically summarizes recent engineering strategies for DCAs production in oleaginous yeasts and offers valuable insights for future DCAs biosynthesis.

High-level secretory expression of recombinant type III human-like collagen α1 in Pichia pastoris via multilevel systematic optimization

Collagen is the main component that makes up the internal structure of animals and is extensively used in several industrial fields including food, materials, chemicals, and pharmaceuticals. Despite the variety of preparation methods available, there is significant potential for enhancing the yield of recombinant collagen produced through engineered Pichia pastoris (P. pastoris). Increasing the copy number of the recombinant type III human collagen α1 (hlCOLIII) gene to improve the level of expression of the recombinant protein and co-expression of molecular chaperones to alleviate the resulting endoplasmic reticulum stress further promotes hlCOLIII secretion. By optimizing transcription driven by the AOX1 promoter and improving translation efficiency, a strain of P. pastoris expressing hlCOLIII efficiently was constructed, achieving a yield of 10.3 g/L in a 5 L fermenter. Further, hlCOLIII demonstrated notable antioxidant capacity and performed well in bioactivity analyses, including cell proliferation, migration, and adhesion. This study lays a solid foundation for the scalable industrial production of recombinant collagen and opens new avenues for its exploration in advanced biomedical materials.

Establishment and application of an RNAi system in Pichia pastoris

Introduction

Reducing endogenous gene expression is key in microbial metabolic engineering. Traditional methods for gene knockout or suppression can be slow and complex. RNA interference (RNAi) provides a faster way to regulate gene expression using plasmids with hairpin RNA. This study examines single- and double-gene suppression in P. pastoris, a common system for expressing heterologous proteins. We also use reporter strains displaying EGFP on the cell surface to identify factors affecting protein secretion.

Methods

We established an RNAi system in P. pastoris by introducing plasmids containing hairpin RNA targeting specific genes. Reporter strains expressing EGFP on the cell surface were used to monitor the impact of gene suppression on protein secretion. Genes such as YAP1, YPS1, PRB1, and PEP4 were targeted for RNAi. Additionally, RNAi was applied to inhibit fatty acid synthesis to improve the conversion of malonyl-CoA to 3-hydroxypropionate (3-HP).

Results

Suppressing YAP1 and YPS1 reduced EGFP display by 83% and 48.8%, respectively. In contrast, suppressing PRB1 and PEP4 increased EGFP display by 33.8% and 26.5%, respectively. These findings show that regulating endogenous genes can significantly impact protein secretion in P. pastoris. Furthermore, RNAi inhibition of fatty acid synthesis improved 3-HP production.

Discussion

This study demonstrates the successful establishment of an RNAi system in P. pastoris, enabling efficient gene suppression for metabolic engineering. RNAi offers a faster and more efficient method for regulating gene expression, improving heterologous protein secretion and 3-HP production. This system is a valuable tool for optimizing P. pastoris as a microbial cell factory, with strong potential for industrial applications.

A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity

Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements.

25SrRNA Methyltransferase CgBMT5 From Candida glycerinogenes Improves Tolerance and Fermentation Performance of Saccharomyces cerevisiae and Yarrowia lipolytica From Undetoxified Cellulose Hydrolysate

The hydrolysis of cellulose generates inhibitors like acetate, suppressing fermentation performance. Here, 25SrRNA methyltransferase CgBMT5 from stress-tolerant yeast Candida glycerinogenes was used as an anti-stress gene element in Saccharomyces cerevisiae and Yarrowia lipolytica. Expression of CgBMT5 in S. cerevisiae increased cell tolerance to acetate, high osmolarity, and heat stress and rescued the delay in cell growth under acetate stress. Ethanol productivity was improved from 0.52 g·(L/h) to 0.69 g·(L/h). CgBMT5 improved GFP expression. The transcription factor ARG81 binds to the promoter of CgBMT5. CgBMT5 upregulated HOG1, GPD1, HAA1, and PMA1 and reduced ROS level, thereby improving cell resistance to acetate. CgBMT5 also improved resistance of Y. lipolytica Po1g to multiple-stress. The lipid titer was improved by 37% in the typical medium. Y. lipolytica-CgBMT5 produced 94 mg/L lipid in the undetoxified cellulose hydrolysate.

Engineering artificial cross-species promoters with different transcriptional strengths

As a fundamental tool in synthetic biology, promoters are pivotal in regulating gene expression, enabling precise genetic control and spurring innovation across diverse biotechnological applications. However, most advances in engineered genetic systems rely on host-specific regulation of the genetic portion. With the burgeoning diversity of synthetic biology chassis cells, there emerges a pressing necessity to broaden the universal promoter toolkit spectrum, ensuring adaptability across various microbial chassis cells for enhanced applicability and customization in the evolving landscape of synthetic biology. In this study, we analyzed and validated the primary structures of natural endogenous promoters from Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Pichia pastoris, and through strategic integration and rational modification of promoter motifs, we developed a series of cross-species promoters (Psh) with transcriptional activity in five strains (prokaryotic and eukaryotic). This series of cross species promoters can significantly expand the synthetic biology promoter toolkit while providing a foundation and inspiration for standardized development of universal components The combinatorial use of key elements from prokaryotic and eukaryotic promoters presented in this study represents a novel strategy that may offer new insights and methods for future advancements in promoter engineering.