Promoter engineering enables precise metabolic regulation towards efficient β-elemene production in Ogataea polymorpha

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.

Rational metabolic engineering of Escherichia coli for the industrial-scale production of l-phenylalanine

Rational metabolic engineering has numerous applications in the optimization of microorganisms for the production of valuable compounds at the laboratory-scale. However, the existing strategies and tools are far from sufficient for engineering of industrial strains due to their specificity. The aim of this project was to implement novel strategies to enhance industrial l-phenylalanine (l-PHE) production and yield, including the regulation of key gene expressions, modifications of global transcription factors, creation of NADPH-independent pentose phosphate pathway and pyruvate-oxaloacetate-phosphoenolpyruvate cycle. The project also involved the identification and engineering of novel byproduct pathways and the development of a tyrosine-nonauxotrophic strain. Through comprehensive rational engineering, an industrial l-PHE producer, designated PHE17, achieved the highest production (103.15 g/L) and yield (0.229 g/g) of l-PHE reported thus far. This study also represents the first report on the iterative engineering of industrial l-PHE producers, thereby offering great significance for the engineering of other aromatic animo acids-producing strains.

Fluorescent protein-based anaerobic reporter for construction of promoter libraries in Clostridium autoethanogenum

Clostridium autoethanogenum, a key organism for syngas fermentation, has great industrial potential as an anaerobic microbe. However, tools for monitoring and characterizing gene expression, such as fluorescent protein-based anaerobic reporters (FPARs), and promoter libraries for regulating expression intensity, are lacking. In this study, we developed a fluorescent protein-based anaerobic reporter (FPAR) tailored for C. autoethanogenum. The FPAR enabled intuitive and precise assessment of promoter activity, facilitating the creation of libraries of constitutive promoters with varying expression strengths, as well as lactose-inducible promoter libraries. The strongest constitutive promoter exhibited approximately 7.5-fold greater activity than the weakest, while the strongest inducible promoter demonstrated a 10-fold increase compared to the weakest. This work not only establishes an efficient FPAR system for C. autoethanogenum, but also provides key genetic elements for advancing metabolic engineering and optimizing industrial processes involving this microbe.

Transcriptome-Based Mining of the Strong Promoters for Hyperproduction of Gibberellin GA3 in Fusarium fujikuroi

Gibberellin GA3 is a plant growth regulator with significant applications in agriculture, and Fusarium fujikuroi has gained attention as an excellent host for the industrial production of GA3. Although numerous gene-editing tools have been developed, the precise metabolic flux regulation in F. fujikuroi was significantly hindered because the endogenous promoters were rarely identified. In this study, a library containing 20 potential promoters was mined and constructed for the first time through transcriptome sequencing. Using β-glucuronidase as a reporter gene, promoter P10594 showed the highest relative activity and had a stable expression in different media, which was identified as a strong constitutive promoter. Subsequently, P10594 was used to regulate the metabolic flux for GA3 overproduction. The yield reached 0.89 g/L in the shake flask, 17.1% higher than the control strain. Finally, 2.38 g/L GA3 can be obtained in a 5 L bioreactor using the engineered strain FF-2. In general, the work enriched the promoter library in F. fujikuroi and provided help for reshaping the complex metabolic flow.

Introduction of human m6Am methyltransferase PCIF1 facilitates the biosynthesis of terpenoids in Saccharomyces cerevisiae

BACKGROUND

The application of synthetic biology techniques has been recognized as an efficient alternative for the biosynthesis of high-value natural products, and various metabolic engineering strategies have been employed to develop microbial cell factories. However, exploration of more efficient metabolic pathway optimization strategies is still required to further improve the producing potential of microbial cell factories to meet the industrial requirements.

RESULTS

In this study, we found that the introduction of human N6,2'-O-dimethyladenosine (m6Am) methyltransferase PCIF1 into Saccharomyces cerevisiae significantly promoted the biosynthesis of squalene, increased by 2.3-fold. Transcriptome analysis revealed that PCIF1 upregulated genes associated with glycolysis and acetyl-CoA biosynthesis pathways, and also activated the cell wall integrity mitogen-activated protein kinase (MAPK) pathway to improve the cell wall stress response. Importantly, PCIF1 expression notably enhanced squalene and sesquiterpenoid longifolene production in engineered yeast strains, with 2.3-fold and 1.4-fold higher increase, respectively.

CONCLUSION

This study presents a PCIF1-based metabolic engineering strategy that could serve as an effective approach for the optimization of terpene biosynthesis in yeast cell factories.

Creation of a eukaryotic multiplexed site-specific inversion system and its application for metabolic engineering

The site-specific recombination system is a versatile tool in genome engineering, enabling controlled DNA inversion or deletion at specific sites to generate genetic diversity. The multiplexed inversion system, which preferentially facilitates inversion at reverse-oriented sites rather than deletion at same-oriented sites, has not been found in eukaryotes. Here, we establish a multiplexed site-specific inversion system, Rci51-5/multi-sfxa101, in yeast. Firstly, we develop a high-throughput screening system based on the on/off transcriptional control of multiple markers by DNA inversion. After two rounds of progressively stringent directed evolution, a mutant Rci51-5 shows an ability of multisite inversion and a ~ 1000-fold increase in total inversion efficiency against the wild-type Rci derived from Salmonella typhimurium. Subsequently, we demonstrate that the Rci51-5/multi-sfxa101 system exhibits significantly lower deletion rate than the Cre/multi-loxP system. Using the synthetic metabolic pathway of β-carotene as an example, we illustrate that the system can effectively facilitate promoter substitution in the metabolic pathway, resulting in a more than 7-fold increase in the yield of β-carotene. In summary, we develop a multiplexed site-specific inversion system in eukaryotes, providing an approach to metabolic engineering and a tool for eukaryotic genome manipulation.

Promoter engineering with programmable upstream activating sequences in Aspergillus Niger cell factory

BACKGROUND

Aspergillus niger is an important industrial filamentous fungus used to produce organic acids and enzymes. A wide dynamic range of promoters, particularly strong promoters, are required for fine-tuning the regulation of gene expression to balance metabolic flux and achieve the high yields of desired products. However, the limited understanding of promoter architectures and activities restricts the efficient transcription regulation of targets in strain engineering in A. niger.

RESULTS

In this study, we identified two functional upstream activation sequences (UAS) located upstream of the core promoters of highly expressed genes in A. niger. We constructed and characterized a synthetic promoter library by fusing the efficient UAS elements upstream of the strong constitute PgpdA promoter in A. niger. It demonstrated that the strength of synthetic promoters was fine-tuned with a wide range by tandem assembly of the UAS elements. Notably, the most potent promoter exhibited 5.4-fold higher activity than the strongest PgpdA promoter reported previously, significantly extending the range of strong promoters. Using citric acid production as a case study, we employed the synthetic promoter library to enhance citric acid efflux by regulating the cexA expression in A. niger. It showed a 1.6-2.3-fold increase in citric acid production compared to the parent strain, achieving a maximum titer of 145.3 g/L.

CONCLUSIONS

This study proved that the synthetic promoter library was a powerful toolkit for precise tuning of transcription in A. niger. It also underscores the potential of promoter engineering for gene regulation in strain improvement of fungal cell factories.

Ogataea polymorpha as a next-generation chassis for industrial biotechnology

Ogataea (Hansenula) polymorpha is a nonconventional yeast with some unique characteristics, including fast growth, thermostability, and broad substrate spectrum. Other than common applications for protein production, O. polymorpha is attracting interest for chemical and protein production from methanol; a promising feedstock for the next-generation biomanufacturing due to its abundant sources and excellent characteristics. Benefiting from the development of synthetic biology, it has been engineered to produce value-added chemicals by extensively rewiring cellular metabolism. This Review discusses recently developed synthetic biology tools of O. polymorpha. The advances of chemicals production and systems biology were reviewed comprehensively. Finally, we look ahead to the developments of biomanufacturing in O. polymorpha to make an overall understanding of this chassis for academia and industry.

Screening and modification of (+)-germacrene A synthase for the production of the anti-tumor drug (-)-β-elemene in engineered Saccharomyces cerevisiae

(-)-β-Elemene is a primary bioactive compound derived from Curcuma wenyujin and has been widely utilized as an anti-tumor agent for various types of cancer. Due to the inefficiency of plant extraction methods for β-elemene, significant efforts have been directed toward the heterogeneous biosynthesis of β-elemene using microbial cell factories. However, there has been less emphasis on the stereochemical configuration of germacrene A and its rearranged product, β-elemene. In this study, we constructed a yeast cell factory to produce (-)-β-elemene by optimizing the mevalonate pathway and screening for germacrene A synthases (GASs) from both plant and microbial sources. Notably, we discovered that the rearranged products of GASs exhibited different conformations, and only (+)-germacrene A produced by plant-derived GASs could rearrange to form (-)-β-elemene. Building on this discovery, we further investigated the catalytic mechanisms of GASs and developed an efficient catalytic gene module for generating (+)-germacrene A. Ultimately, the engineered yeast produced 1152 mg/L of (-)-β-elemene, marking the highest titer reported in yeast to date. Overall, this work highlights the differences in the stereoconformations of catalytic products between plant- and microbial-derived germacrene A synthases and establishes a foundation for the green and efficient production of β-elemene with a specific stereochemical configuration.

The Construction of an Extreme Radiation-Resistant Perchlorate-Reducing Bacterium Using Deinococcus deserti Promoters

Perchlorate is one of the major inorganic pollutants in the natural environment and the living environment, which is toxic to organisms and difficult to degrade due to its special structure. As previously reported, the Phoenix Mars lander detected approximately 0.6% perchlorate in the Martian soil, indicating challenges for Earth-based life to survive there. Currently, biological approaches using dissimilatory perchlorate-reducing bacteria (DPRB) are the most promising methods for perchlorate degradation. However, the majority of DPRB exhibit limited radiation resistance, rendering them unsuitable for survival on Mars. In this study, we obtained the transcriptome data of Deinococcus deserti, and predicted and identified multiple constitutive expression promoters of D. deserti with varying activities. The top-five most active promoters were separately fused to specific genes involved in the degradation of perchlorate from DPRB Dechloromonas agitata CKB, and transformed into Deinococcus radiodurans R1, forming a novel dissimilatory perchlorate-reducing bacterium, R1-CKB. It exhibited both efficient perchlorate degradation capability and strong radiation resistance, potentially offering a valuable tool for the further enhancement of the Martian atmosphere in the future.

Dynamically Regulating Homologous Recombination Enables Precise Genome Editing in Ogataea polymorpha

Methylotrophic yeast Ogataea polymorpha has become a promising cell factory due to its efficient utilization of methanol to produce high value-added chemicals. However, the low homologous recombination (HR) efficiency in O. polymorpha greatly hinders extensive metabolic engineering for industrial applications. Overexpression of HR-related genes successfully improved HR efficiency, which however brought cellular stress and reduced chemical production due to constitutive expression of the HR-related gene. Here, we engineered an HR repair pathway using the dynamically regulated gene ScRAD51 under the control of the l-rhamnose-induced promoter PLRA3 based on the previously constructed CRISPR-Cas9 system in O. polymorpha. Under the optimal inducible conditions, the appropriate expression level of ScRAD51 achieved up to 60% of HR rates without any detectable influence on cell growth in methanol, which was 10-fold higher than that of the wild-type strain. While adopting as the chassis strain for bioproductions, the dynamically regulated recombination system had 50% higher titers of fatty alcohols than that static regulation system. Therefore, this study provided a feasible platform in O. polymorpha for convenient genetic manipulation without perturbing cellular fitness.

Engineering yeast for high-level production of β-farnesene from sole methanol

Methanol, a rich one-carbon feedstock, can be massively produced from CO2 by the liquid sunshine route, which is helpful to realize carbon neutrality. β-Farnesene is widely used in the production of polymers, surfactants, lubricants, and also serves as a suitable substitute for jet fuel. Constructing an efficient cell factory is a feasible approach for β-farnesene production through methanol biotransformation. Here, we extensively engineered the methylotrophic yeast Ogataea polymorpha for the efficient bio-production of β-farnesene using methanol as the sole carbon source. Our study demonstrated that sufficient supply of precursor acetyl-CoA and cofactor NADPH in an excellent yeast chassis had a 1.3-fold higher β-farnesene production than that of wild-type background strain. Further optimization of the mevalonate pathway and enhancement of acetyl-CoA supply led to a 7-fold increase in β-farnesene accumulation, achieving the highest reported sesquiterpenoids production (14.7 g/L with a yield of 46 mg/g methanol) from one-carbon feedstock under fed-batch fermentation in bioreactor. This study demonstrates the great potential of engineering O. polymorpha for high-level terpenoid production from methanol.