Engineering heterologous molybdenum-cofactor-biosynthesis and nitrate-assimilation pathways enables nitrate utilization by Saccharomyces cerevisiae

Development of a nitrate-responsive whole-cell biosensor based on engineered probiotic Saccharomyces boulardii

This study aimed to construct a probiotic Saccharomyces boulardii-based biosensor that can sense and respond to nitrate, a biomarker of gut inflammation. To this end, a portion of the nitrate assimilation pathway in Ogataea polymorpha required for the designed nitrate-responsive genetic circuit was introduced into S. boulardii, which lacks the corresponding pathway. Specifically, the genes involved in nitrate transport (YNT1) and nitrate-responsive transcriptional activation (YNA1 and YNA2) were introduced into S. boulardii using the CRISPR/Cas9-based genome editing system to construct the SKSC499 strain. Next, we investigated whether YNT1, YNI1, and YNR1 promoters, which are activated by nitrate-bound YNA1/YNA2 transcription factor in O. polymorpha, induced expression of the reporter gene (G418 resistance marker) in the SKSC499 strain in a nitrate concentration-dependent manner. Among the candidate promoters, the YNR1 promoter effectively induced growth of the SKSC499 strain only when nitrate was present in the medium containing the G418 antibiotic.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-025-01850-x.

Tungsten containing aldehyde oxidoreductase (AOR)-family enzymes; past, present and future production strategies

The transition metals tungsten and molybdenum are the heaviest metals found in biological systems and are embedded in the cofactor of several metalloenzymes. As a result of their redox activity, they provide great catalytic power in these enzymes and facilitate chemical reactions that would not occur using only the functionalities of natural amino acids. For their functionality these enzymes depend on a metal cofactor, which consists of at least one metal binding pterin (MPT) and a tungsten or molybdenum ion, but the complete make-up of the cofactor differs per enzyme group. One of these enzyme groups comprises the AOR-family enzymes. These enzymes have the ability to oxidize a range of aldehyde substrates into their corresponding carboxylic acid products. Next to this, they are also the only known catalysts able to perform the thermodynamically challenging reduction reaction of carboxylic acids to aldehydes. These enzymes are currently obtained by purification from the hyperthermophilic archaeon Pyrococcus furiosus. This process, however, does not yield a large amount of enzyme, since it is naturally expressed at moderate levels. For that reason, other production methods need to be considered if the enzyme is to be used on a large scale. These alternatives include the use of a recombinant expression system. The recombinant expression of W-dependent enzymes in different host organisms, such as Escherichia coli, has already been attempted for different enzymes, but with varying success. This shows that more research on the production, and especially incorporation of the metal cofactor, is necessary to achieve a successful production and use of recombinant AOR-family enzymes.

Engineering Saccharomyces cerevisiae for fast vitamin-independent aerobic growth

Chemically defined media for cultivation of Saccharomyces cerevisiae strains are commonly supplemented with a mixture of multiple Class-B vitamins, whose omission leads to strongly reduced growth rates. Fast growth without vitamin supplementation is interesting for industrial applications, as it reduces costs and complexity of medium preparation and may decrease susceptibility to contamination by auxotrophic microbes. In this study, suboptimal growth rates of S. cerevisiae CEN.PK113-7D in the absence of pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and/or biotin were corrected by single or combined overexpression of ScFMS1, ScABZ1/ScABZ2, ScSNZ1/ScSNO1, ScINO1 and Cyberlindnera fabianii BIO1, respectively. Several strategies were explored to improve growth of S. cerevisiae CEN.PK113-7D in thiamine-free medium. Overexpression of ScTHI4 and/or ScTHI5 enabled thiamine-independent growth at 83% of the maximum specific growth rate of the reference strain in vitamin-supplemented medium. Combined overexpression of seven native S. cerevisiae genes and CfBIO1 enabled a maximum specific growth rate of 0.33 ± 0.01 h-1 in vitamin-free synthetic medium. This growth rate was only 17 % lower than that of a congenic reference strain in vitamin-supplemented medium. Physiological parameters of the engineered vitamin-independent strain in aerobic glucose-limited chemostat cultures (dilution rate 0.10 h-1) grown on vitamin-free synthetic medium were similar to those of similar cultures of the parental strain grown on vitamin-supplemented medium. Transcriptome analysis revealed only few differences in gene expression between these cultures, which primarily involved genes with roles in Class-B vitamin metabolism. These results pave the way for development of fast-growing vitamin-independent industrial strains of S. cerevisiae.

Self-assembly systems to troubleshoot metabolic engineering challenges

Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.

Application of adaptive laboratory evolution for Yarrowia lipolytica: A comprehensive review

Adaptive laboratory evolution is an innovative approach utilized by researchers to enhance the characteristics of microorganisms in the field of biology. With the advancement of this technology, it is now being extended to non-model strains. Yarrowia lipolytica, an oleaginous yeast with significant industrial potential, stands out among the non-conventional fungi. However, the activity of Yarrowia lipolytica is frequently affected by specific substances and environmental factors, necessitating the development of techniques to address these challenges. This manuscript provides an overview of adaptive laboratory evolution experiments conducted on Yarrowia lipolytica, and categorizes the contents into two aspects including improving lignocellulose utilization and enhancing the production in Yarrowia lipolytica. Additionally, we selected several representative examples to illustrate how adaptive laboratory evolution can be combined with other techniques to elucidate the potential mechanisms underlying strain evolution. Lastly, we anticipate a promising future for adaptive laboratory evolution technology and Yarrowia lipolytica in tandem.

Moonlighting Arabidopsis molybdate transporter 2 family and GSH-complex formation facilitate molybdenum homeostasis

Molybdenum (Mo) as essential micronutrient for plants, acts as active component of molybdenum cofactor (Moco). Core metabolic processes like nitrate assimilation or abscisic-acid biosynthesis rely on Moco-dependent enzymes. Although a family of molybdate transport proteins (MOT1) is known to date in Arabidopsis, molybdate homeostasis remained unclear. Here we report a second family of molybdate transporters (MOT2) playing key roles in molybdate distribution and usage. KO phenotype-analyses, cellular and organ-specific localization, and connection to Moco-biosynthesis enzymes via protein-protein interaction suggest involvement in cellular import of molybdate in leaves and reproductive organs. Furthermore, we detected a glutathione-molybdate complex, which reveals how vacuolar storage is maintained. A putative Golgi S-adenosyl-methionine transport function was reported recently for the MOT2-family. Here, we propose a moonlighting function, since clear evidence of molybdate transport was found in a yeast-system. Our characterization of the MOT2-family and the detection of a glutathione-molybdate complex unveil the plant-wide way of molybdate.

Engineering of molybdenum-cofactor-dependent nitrate assimilation in Yarrowia lipolytica

Engineering a new metabolic function in a microbial host can be limited by the availability of the relevant cofactor. For instance, in Yarrowia lipolytica, the expression of a functional nitrate reductase is precluded by the absence of molybdenum cofactor (Moco) biosynthesis. In this study, we demonstrated that the Ogataea parapolymorpha Moco biosynthesis pathway combined with the expression of a high affinity molybdate transporter could lead to the synthesis of Moco in Y. lipolytica. The functionality of Moco was demonstrated by expression of an active Moco-dependent nitrate assimilation pathway from the same yeast donor, O. parapolymorpha. In addition to 11 heterologous genes, fast growth on nitrate required adaptive laboratory evolution which, resulted in up to 100-fold increase in nitrate reductase activity and in up to 4-fold increase in growth rate, reaching 0.13h-1. Genome sequencing of evolved isolates revealed the presence of a limited number of non-synonymous mutations or small insertions/deletions in annotated coding sequences. This study that builds up on a previous work establishing Moco synthesis in S. cerevisiae demonstrated that the Moco pathway could be successfully transferred in very distant yeasts and, potentially, to any other genera, which would enable the expression of new enzyme families and expand the nutrient range used by industrial yeasts.

A Multiphase Multiobjective Dynamic Genome-Scale Model Shows Different Redox Balancing among Yeast Species of the Saccharomyces Genus in Fermentation

Yeasts constitute over 1,500 species with great potential for biotechnology. Still, the yeast Saccharomyces cerevisiae dominates industrial applications, and many alternative physiological capabilities of lesser-known yeasts are not being fully exploited. While comparative genomics receives substantial attention, little is known about yeasts’ metabolic specificity in batch cultures. Here, we propose a multiphase multiobjective dynamic genome-scale model of yeast batch cultures that describes the uptake of carbon and nitrogen sources and the production of primary and secondary metabolites. The model integrates a specific metabolic reconstruction, based on the consensus Yeast8, and a kinetic model describing the time-varying culture environment. In addition, we proposed a multiphase multiobjective flux balance analysis to compute the dynamics of intracellular fluxes. We then compared the metabolism of S. cerevisiae and Saccharomyces uvarum strains in a rich medium fermentation. The model successfully explained the experimental data and brought novel insights into how cryotolerant strains achieve redox balance. The proposed model (along with the corresponding code) provides a comprehensive picture of the main steps occurring inside the cell during batch cultures and offers a systematic approach to prospect or metabolically engineering novel yeast cell factories.

IMPORTANCE Nonconventional yeast species hold the promise to provide novel metabolic routes to produce industrially relevant compounds and tolerate specific stressors, such as cold temperatures. This work validated the first multiphase multiobjective genome-scale dynamic model to describe carbon and nitrogen metabolism throughout batch fermentation. To test and illustrate its performance, we considered the comparative metabolism of three yeast strains of the Saccharomyces genus in rich medium fermentation. The study revealed that cryotolerant Saccharomyces species might use the γ-aminobutyric acid (GABA) shunt and the production of reducing equivalents as alternative routes to achieve redox balance, a novel biological insight worth being explored further. The proposed model (along with the provided code) can be applied to a wide range of batch processes started with different yeast species and media, offering a systematic and rational approach to prospect nonconventional yeast species metabolism and engineering novel cell factories.

Engineering oxygen-independent biotin biosynthesis in Saccharomyces cerevisiae

An oxygen requirement for de novo biotin synthesis in Saccharomyces cerevisiae precludes the application of biotin-prototrophic strains in anoxic processes that use biotin-free media. To overcome this issue, this study explores introduction of the oxygen-independent Escherichia coli biotin-biosynthesis pathway in S. cerevisiae. Implementation of this pathway required expression of seven E. coli genes involved in fatty-acid synthesis and three E. coli genes essential for the formation of a pimelate thioester, key precursor of biotin synthesis. A yeast strain expressing these genes readily grew in biotin-free medium, irrespective of the presence of oxygen. However, the engineered strain exhibited specific growth rates 25% lower in biotin-free media than in biotin-supplemented media. Following adaptive laboratory evolution in anoxic cultures, evolved cell lines that no longer showed this growth difference in controlled bioreactors, were characterized by genome sequencing and proteome analyses. The evolved isolates exhibited a whole-genome duplication accompanied with an alteration in the relative gene dosages of biosynthetic pathway genes. These alterations resulted in a reduced abundance of the enzymes catalyzing the first three steps of the E. coli biotin pathway. The evolved pathway configuration was reverse engineered in the diploid industrial S. cerevisiae strain Ethanol Red. The resulting strain grew at nearly the same rate in biotin-supplemented and biotin-free media non-controlled batches performed in an anaerobic chamber. This study established an unique genetic engineering strategy to enable biotin-independent anoxic growth of S. cerevisiae and demonstrated its portability in industrial strain backgrounds.