Identification and Characterization of the Mitochondrial Replication Origin for Stable and Episomal Expression in Yarrowia lipolytica

Advances and perspectives in genetic expression and operation for the oleaginous yeast Yarrowia lipolytica

The utilization of industrial biomanufacturing has emerged as a viable and sustainable alternative to fossil-based resources for producing functional chemicals. Moreover, advancements in synthetic biology have created new opportunities for the development of innovative cell factories. Notably, Yarrowia lipolytica, an oleaginous yeast that is generally regarded as safe, possesses several advantageous characteristics, including the ability to utilize inexpensive renewable carbon sources, well-established genetic backgrounds, and mature genetic manipulation methods. Consequently, there is increasing interest in manipulating the metabolism of this yeast to enhance its potential as a biomanufacturing platform. Here, we reviewed the latest developments in genetic expression strategies and manipulation tools related to Y. lipolytica, particularly focusing on gene expression, chromosomal operation, CRISPR-based tool, and dynamic biosensors. The purpose of this review is to serve as a valuable reference for those interested in the development of a Y. lipolytica microbial factory.

Comparative transcriptomics analysis-guided metabolic engineering of Yarrowia lipolytica for improved erythritol and fructooligosaccharides production

Currently, fructooligosaccharides (FOS) are converted from sucrose by purified enzymes or fungal cells, but these methods are costly and time-consuming. Here, the optimal fermentation conditions for strain E326 were determined through fermentation optimization: initial glucose 200 g/L, NaCl 25 g/L, inoculum volume 20 %, dissolved oxygen 20-30 %, pH 3, and glucose feeding concentration 100 g/L, which increased erythritol titer by 1.5 times. The co-expression of HGT1 and APC11 genes alleviated the erythritol synthesis stagnation, shorten the fermentation time by 16.7 %, and increased the erythritol productivity by 17.2 %. The episomal plasmids based on yeast mitochondrial replication origins (mtORIs) were constructed to surface display fructosyltransferase, effectively utilizing waste yeast cells generated during erythritol fermentation. Under the conditions of 60℃ and pH 6, the FOS yield reached 65 %, which to our best of knowledge is so-far the highest yield of FOS obtained. These findings will contribute to the industrial production of erythritol and FOS.

Research progress on biosynthesis of erythritol and multi-dimensional optimization of production strategies

Erythritol, as a new type of natural sweetener, has been widely used in food, medical, cosmetics, pharmaceutical and other fields due to its unique physical and chemical properties and physiological functions. In recent years, with the continuous development of strategies such as synthetic biology, metabolic engineering, omics-based systems biology and high-throughput screening technology, people's understanding of the erythritol biosynthesis pathway has gradually deepened, and microbial cell factories with independent modification capabilities have been successfully constructed. In this review, the cheap feedstocks for erythritol synthesis are introduced in detail, the environmental factors affecting the synthesis of erythritol and its regulatory mechanism are described, and the tools and strategies of metabolic engineering involved in erythritol synthesis are summarized. In addition, the study of erythritol derivatives is helpful in expanding its application field. Finally, the challenges that hinder the effective production of erythritol are discussed, which lay a foundation for the green, efficient and sustainable production of erythritol in the future and breaking through the bottleneck of production.

Exploiting synthetic biology platforms for enhanced biosynthesis of natural products in Yarrowia lipolytica

With the rapid development of synthetic biology, researchers can design, modify, or even synthesize microorganisms de novo, and microorganisms endowed with unnatural functions can be considered "artificial life" and facilitate the development of functional products. Based on this concept, researchers can solve critical problems related to the insufficient supply of natural products, such as low yields, long production cycles, and cumbersome procedures. Due to its superior performance and unique physiological and biochemical characteristics, Yarrowia lipolytica is a favorable chassis cell used for green biomanufacturing by numerous researchers. This paper mainly reviews the development of synthetic biology techniques for Y. lipolytica and summarizes the recent research progress on the synthesis of natural products in Y. lipolytica. This review will promote the continued innovative development of Y. lipolytica by providing theoretical guidance for research on the biosynthesis of natural products.

YaliCMulti and YaliHMulti: Stable, efficient multi-copy integration tools for engineering Yarrowia lipolytica

Yarrowia lipolytica is widely used in biotechnology to produce recombinant proteins, food ingredients and diverse natural products. However, unstable expression of plasmids, difficult and time-consuming integration of single and low-copy-number plasmids hampers the construction of efficient production pathways and application to industrial production. Here, by exploiting sequence diversity in the long terminal repeats (LTRs) of retrotransposons and ribosomal DNA (rDNA) sequences, a set of vectors and methods that can recycle multiple and high-copy-number plasmids was developed that can achieve stable integration of long-pathway genes in Y. lipolytica. By combining these sequences, amino acids and antibiotic tags with the Cre-LoxP system, a series of multi-copy site integration recyclable vectors were constructed and assessed using the green fluorescent protein (HrGFP) reporter system. Furthermore, by combining the consensus sequence with the vector backbone of a rapidly degrading selective marker and a weak promoter, multiple integrated high-copy-number vectors were obtained and high levels of stable HrGFP expression were achieved. To validate the universality of the tools, simple integration of essential biosynthesis modules was explored, and 7.3 g/L of L-ergothioneine and 8.3 g/L of (2S)-naringenin were achieved in a 5 L fermenter, the highest titres reported to date for Y. lipolytica. These novel multi-copy genome integration strategies provide convenient and effective tools for further metabolic engineering of Y. lipolytica.

Construction of a novel plasmid for an industrial yeast Candida glycerinogenes by dual-autonomously replicating sequence strategy

Due to the lack of available episomal plasmid, the improvement of many industrial strains, especially exogenous gene expression, is severely restricted. The failure of autonomous replication or low copy number of episomal plasmids is the main reason for the failure of many episomal plasmids construction. In this paper, Candida glycerinogenes, an industrial strain lacking episomal plasmids, was employed as the topic. A series of GFP-based plasmids containing autonomously replicating sequence (ARS) from different strain sources were constructed and analyzed for performance, and it was found that only the panARS from Kluyveromyces lactis compared with other nine low capacity ARSs proved to have the best performance and could be used to construct episomal plasmid. Further, the dual-ARS strategy was used to optimize the episomal plasmid, and the results indicated that only the dual-ARS plasmid +PPARS2 with double different ARSs, not the dual-ARS plasmid +panARS with double same ARSs, showed an improvement in all properties, with an increase in transformation efficiency of about 36% and a synchronous trend of fluorescence intensity and copy number, both by about 40%. In addition, constructed episomal plasmids were used to express the exogenous gene CrGES, and the fact that geraniol was found proved the versatility of the plasmids. The successful construction of episomal plasmids will also substantially facilitate genetic engineering research and industrial use of C. glycerinogenes in the future, as well as providing a feasible approach to create episomal plasmids for industrial strains.

Valorization of Polyethylene Terephthalate to Muconic Acid by Engineering Pseudomonas Putida

Plastic waste is rapidly accumulating in the environment and becoming a huge global challenge. Many studies have highlighted the role of microbial metabolic engineering for the valorization of polyethylene terephthalate (PET) waste. In this study, we proposed a new conceptual scheme for upcycling of PET. We constructed a multifunctional Pseudomonas putida KT2440 to simultaneously secrete PET hydrolase LCC, a leaf-branch compost cutinase, and synthesize muconic acid (MA) using the PET hydrolysate. The final product MA and extracellular LCC can be separated from the supernatant of the culture by ultrafiltration, and the latter was used for the next round of PET hydrolysis. A total of 0.50 g MA was produced from 1 g PET in each cycle of the whole biological processes, reaching 68% of the theoretical conversion. This new conceptual scheme for the valorization of PET waste should have advantages over existing PET upcycling schemes and provides new ideas for the utilization of other macromolecular resources that are difficult to decompose, such as lignin.

Identification of genome integration sites for developing a CRISPR-based gene expression toolkit in Yarrowia lipolytica

With the rapid development of synthetic biology, the oleaginous yeast Yarrowia lipolytica has become an attractive microorganism for chemical production. To better optimize and reroute metabolic pathways, we have expanded the CRISPR‐based gene expression toolkit of Y. lipolytica. By sorting the integration sites associated with high expression, new neutral integration sites associated with high expression and high integration efficiency were identified. Diverse genetic components, including promoters and terminators, were also characterized to expand the expression range. We found that in addition to promoters, the newly characterized terminators exhibited large variations in gene expression. These genetic components and integration sites were then used to regulate genes involved in the lycopene biosynthesis pathway, and different levels of lycopene production were achieved. The CRISPR‐based gene expression toolkit developed in this study will facilitate the genetic engineering of Y. lipolytica.

Sophorolipids bioproduction in the yeast Starmerella bombicola: Current trends and perspectives

Sophorolipids are highly active green surfactants (glycolipid biosurfactants) getting tremendous appreciation worldwide due to their low toxicity, biodegradability, broad spectrum of applications, and significant biotechnological potential. Sophorolipids are mainly produced by an oleaginous budding yeast Starmerella bombicola using low-cost substrates. Therefore, the recent state-of-art literature information about S. bombicola yeast is hereby provided, especially the underlying production pathways, biosynthetic gene cluster, and regulatory enzymes. Moreover, the S. bombicola offers flexibility for regulating the structural diversity of sophorolipids, either genetically or by varying fermentative conditions. The emergence of advanced technologies like 'Omics and CRISPR/Cas have certainly boosted rational engineering research for designing high-performing platform strains. Therefore, currently available genetic engineering tools in S. bombicola were reviewed, thereby opening up exciting new possibilities for improving the overall bioproduction titers, structural variability, and stability of sophorolipids. Finally, some technical perspectives to address the current challenges were discussed.

Highly efficient rDNA ‐mediated multicopy integration based on the dynamic balance of rDNA in Saccharomyces cerevisiae

Engineered Saccharomyces cerevisiae strains are good cell factories, and developing additional genetic manipulation tools will accelerate construction of metabolically engineered strains. Highly repetitive rDNA sequence is one of two main sites typically used for multicopy integration of genes. Here, we developed a simple and high‐efficiency strategy for rDNA‐mediated multicopy gene integration based on the dynamic balance of rDNA in S. cerevisiae. rDNA copy number was decreased by pre‐treatment with hydroxyurea (HU). Then, heterologous genes were integrated into the rDNA sequence. The copy number of the integrated heterologous genes increased along with restoration of the copy number of rDNA. Our results demonstrated that HU pre‐treatment doubled the number of integrated gene copies; moreover, compared with removing HU stress during transformation, removing HU stress after selection of transformants had a higher probability of resulting in transformants with high‐copy integrated genes. Finally, we integrated 18.0 copies of the xylose isomerase gene into the S. cerevisiae genome in a single step. This novel rDNA‐mediated multicopy genome integration strategy provides a convenient and efficient tool for further metabolic engineering of S. cerevisiae.

Morphological and Metabolic Engineering of Yarrowia lipolytica to Increase β-Carotene Production

The oleaginous yeast Yarrowia lipolytica represents an environmentally friendly platform cell factory for β-carotene production. However, Y. lipolytica is a dimorphic species that can undergo a yeast-to-mycelium transition when exposed to stress. The mycelial form is unfavorable for industrial fermentation. In this study, β-carotene-producing Y. lipolytica strains were constructed via the integration of multiple copies of 13 genes related to the β-carotene biosynthesis pathway. The β-carotene content increased by 11.7-fold compared with the start strain T1. As the β-carotene content increased, the oval-shaped yeast form was gradually replaced by hyphae, implying that the accumulation of β-carotene in Y. lipolytica induces a morphological transition. To relieve this metabolic stress, the strains were morphologically engineered by deleting CLA4 and MHY1 genes to convert the mycelium back to the yeast form, which further increased the β-carotene production by 139%. In fed-batch fermentation, the engineered strain produced 7.6 g/L and 159 mg/g DCW β-carotene, which is the highest titer and content reported to date. The morphological engineering strategy developed here may be useful for enhancing chemical synthesis in dimorphic yeasts.