Enhanced Pyruvate Production in Candida glabrata by Engineering ATP Futile Cycle System

Catabolism of 2-keto-3-deoxy-galactonate and the production of its enantiomers

2-Keto-3-deoxy-galactonate (KDGal) serves as a pivotal metabolic intermediate within both the fungal D-galacturonate pathway, which is integral to pectin catabolism, and the bacterial DeLey-Doudoroff pathway for D-galactose catabolism. The presence of KDGal enantiomers, L-KDGal and D-KDGal, varies across these pathways. Fungal pathways generate L-KDGal through the reduction and dehydration of D-galacturonate, whereas bacterial pathways produce D-KDGal through the oxidation and dehydration of D-galactose. Two distinct catabolic routes further metabolize KDGal: a nonphosphorolytic pathway that employs aldolase and a phosphorolytic pathway involving kinase and aldolase. Recent findings have revealed that L-KDGal, identified in the bacterial catabolism of 3,6-anhydro-L-galactose, a major component of red seaweeds, is also catabolized by Escherichia coli, which is traditionally known to be catabolized by specific fungal species, such as Trichoderma reesei. Furthermore, the potential industrial applications of KDGal and its derivatives, such as pyruvate and D- and L-glyceraldehyde, are underscored by their significant biological functions. This review comprehensively outlines the catabolism of L-KDGal and D-KDGal across different biological systems, highlights stereospecific methods for discriminating between enantiomers, and explores industrial application prospects for producing KDGal enantiomers. KEY POINTS: • KDGal is a metabolic intermediate in fungal and bacterial pathways • Stereospecific enzymes can be used to identify the enantiomeric nature of KDGal • KDGal can be used to induce pectin catabolism or produce functional materials.

Recent advances and prospects of Bacillus amyloliquefaciens as microbial cell factories: from rational design to industrial applications

Bacillus amyloliquefaciens is one of the most characterized Gram-positive bacteria. This species has unique characteristics that are beneficial for industrial applications, including its utilization of: cheap carbon as a substrate, a transparent genetic background, and large-scale robustness in fermentation. Indeed, the productivity characteristics of B. amyloliquefaciens have been thoroughly analyzed and further optimized through systems biology and synthetic biology techniques. Following the analysis of multiple engineering design strategies, B. amyloliquefaciens is now considered an efficient cell factory capable of producing large quantities of multiple products from various raw materials. In this review, we discuss the significant potential advantages offered by B. amyloliquefaciens as a platform for metabolic engineering and industrial applications. In addition, we systematically summarize the recent laboratory research and industrial application of B. amyloliquefaciens, including: relevant advances in systems and synthetic biology, various strategies adopted to improve the cellular performances of synthetic chemicals, as well as the latest progress in the synthesis of certain important products by B. amyloliquefaciens. Finally, we propose the current challenges and essential strategies to usher in an era of broader B. amyloliquefaciens use as microbial cell factories.

Metabolic engineering of fast-growing Vibrio natriegens for efficient pyruvate production

BACKGROUND

Pyruvate is a widely used value-added chemical which also serves as a hub of various metabolic pathways. The fastest-growing bacterium Vibrio natriegens is a promising chassis for synthetic biology applications with high substrate uptake rates. The aim of this study was to investigate if the high substrate uptake rates of V. natriegens enable pyruvate production at high productivities.

RESULTS

Two prophage gene clusters and several essential genes for the biosynthesis of byproducts were first deleted. In order to promote pyruvate accumulation, the key gene aceE encoding pyruvate dehydrogenase complex E1 component was down-regulated to reduce the carbon flux into the tricarboxylic acid cycle. Afterwards, the expression of ppc gene encoding phosphoenolpyruvate carboxylase was fine-tuned to balance the cell growth and pyruvate synthesis. The resulting strain PYR32 was able to produce 54.22 g/L pyruvate from glucose within 16 h, with a yield of 1.17 mol/mol and an average productivity of 3.39 g/L/h. In addition, this strain was also able to efficiently convert sucrose or gluconate into pyruvate at high titers.

CONCLUSION

A novel strain of V. natriegens was engineered which was capable to provide higher productivity in pyruvate synthesis. This study lays the foundation for the biosynthesis of pyruvate and its derivatives in fast-growing V. natriegens.

A Modular Cloning Toolkit Including CRISPRi for the Engineering of the Human Fungal Pathogen and Biotechnology Host Candida glabrata

The yeast Candida glabrata is an emerging, often drug-resistant opportunistic human pathogen that can cause severe systemic infections in immunocompromised individuals. At the same time, it is a valuable biotechnology host that naturally accumulates high levels of pyruvate─a valuable chemical precursor. Tools for the facile engineering of this yeast could greatly accelerate studies on its pathogenicity and its optimization for biotechnology. While a few tools for plasmid-based expression and genome engineering have been developed, there is no well-characterized cloning toolkit that would allow the modular assembly of pathways or genetic circuits. Here, by characterizing the Saccharomyces cerevisiae-based yeast molecular cloning toolkit (YTK) in C. glabrata and by adding missing components, we build a well-characterized CgTK (C. glabrata toolkit). We used the CgTK to build a CRISPR interference system for C. glabrata that can be used to generate selectable phenotypes via single-gRNA targeting such as is required for genome-wide library screens.

Engineering Streptomyces albulus to enhance ε-poly-L-lysine production by introducing a polyphosphate kinase-mediated ATP regeneration system

BACKGROUND

ε-Poly-L-lysine (ε-PL) is a natural and safe food preservative that is mainly produced by filamentous and aerobic bacteria Streptomyces albulus. During ε-PL biosynthesis, a large amount of ATP is used for the polymerization of L-lysine. A shortage of intracellular ATP is one of the major factors limiting the increase in ε-PL production. In previous studies, researchers have mainly tried to increase the oxygen supply to enhance intracellular ATP levels to improve ε-PL production, which can be achieved through the use of two-stage dissolved oxygen control, oxygen carriers, heterologous expression of hemoglobin, and supplementation with auxiliary energy substrates. However, the enhancement of the intracellular ATP supply by constructing an ATP regeneration system has not yet been considered.

RESULTS

In this study, a polyphosphate kinase (PPK)-mediated ATP regeneration system was developed and introduced into S. albulus to successfully improve ε-PL production. First, polyP:AMP phosphotransferase (PAP) from Acinetobacter johnsonii was selected for catalyzing the conversion of AMP into ADP through an in vivo test. Moreover, three PPKs from different microbes were compared by in vitro and in vivo studies with respect to catalytic activity and polyphosphate (polyP) preference, and PPK2B^cg from Corynebacterium glutamicum was used for catalyzing the conversion of ADP into ATP. As a result, a recombinant strain PL05 carrying coexpressed pap and ppk2B^cg for catalyzing the conversion of AMP into ATP was constructed. ε-PL production of 2.34 g/L was achieved in shake-flask fermentation, which was an increase of 21.24% compared with S. albulus WG608; intracellular ATP was also increased by 71.56%. In addition, we attempted to develop a dynamic ATP regulation route, but the result was not as expected. Finally, the conditions of polyP₆ addition were optimized in batch and fed-batch fermentations, and the maximum ε-PL production of strain PL05 in a 5-L fermenter was 59.25 g/L by fed-batch fermentation, which is the highest ε-PL production reported in genetically engineered strains.

CONCLUSIONS

In this study, we proposed and developed a PPK-mediated ATP regeneration system in S. albulus for the first time and significantly enhanced ε-PL production. The study provides an efficient approach to improve the production of not only ε-PL but also other ATP-driven metabolites.

New Insights into the Modification of the Non-Core Metabolic Pathway of Steroids in Mycolicibacterium and the Application of Fermentation Biotechnology in C-19 Steroid Production

Androsta-4-ene-3,17-dione (AD), androsta-1,4-diene-3,17-dione (ADD), and 9α-hydroxy-4-androstene-3,17-dione (9-OHAD), which belong to C-19 steroids, are critical steroid-based drug intermediates. The biotransformation of phytosterols into C-19 steroids by Mycolicibacterium cell factories is the core step in the synthesis of steroid-based drugs. The production performance of engineered mycolicibacterial strains has been effectively enhanced by sterol core metabolic modification. In recent years, research on the non-core metabolic pathway of steroids (NCMS) in mycolicibacterial strains has made significant progress. This review discusses the molecular mechanisms and metabolic modifications of NCMS for accelerating sterol uptake, regulating coenzyme I balance, promoting propionyl-CoA metabolism, reducing reactive oxygen species, and regulating energy metabolism. In addition, the recent applications of biotechnology in steroid intermediate production are summarized and compared, and the future development trend of NCMS research is discussed. This review provides powerful theoretical support for metabolic regulation in the biotransformation of phytosterols.

Microbial cell factories based on filamentous bacteria, yeasts, and fungi

BACKGROUND

Advanced DNA synthesis, biosensor assembly, and genetic circuit development in synthetic biology and metabolic engineering have reinforced the application of filamentous bacteria, yeasts, and fungi as promising chassis cells for chemical production, but their industrial application remains a major challenge that needs to be solved.

RESULTS

As important chassis strains, filamentous microorganisms can synthesize important enzymes, chemicals, and niche pharmaceutical products through microbial fermentation. With the aid of metabolic engineering and synthetic biology, filamentous bacteria, yeasts, and fungi can be developed into efficient microbial cell factories through genome engineering, pathway engineering, tolerance engineering, and microbial engineering. Mutant screening and metabolic engineering can be used in filamentous bacteria, filamentous yeasts (Candida glabrata, Candida utilis), and filamentous fungi (Aspergillus sp., Rhizopus sp.) to greatly increase their capacity for chemical production. This review highlights the potential of using biotechnology to further develop filamentous bacteria, yeasts, and fungi as alternative chassis strains.

CONCLUSIONS

In this review, we recapitulate the recent progress in the application of filamentous bacteria, yeasts, and fungi as microbial cell factories. Furthermore, emphasis on metabolic engineering strategies involved in cellular tolerance, metabolic engineering, and screening are discussed. Finally, we offer an outlook on advanced techniques for the engineering of filamentous bacteria, yeasts, and fungi.

Metabolic engineering of Corynebacterium glutamicum for efficient production of optically pure (2R,3R)-2,3-butanediol

Background

2,3-butanediol is an important platform compound which has a wide range of applications, involving in medicine, chemical industry, food and other fields. Especially the optically pure (2R,3R)-2,3-butanediol can be employed as an antifreeze agent and as the precursor for producing chiral compounds. However, some (2R,3R)-2,3-butanediol overproducing strains are pathogenic such as Enterobacter cloacae and Klebsiella oxytoca.

Results

In this study, a (3R)-acetoin overproducing C. glutamicum strain, CGS9, was engineered to produce optically pure (2R,3R)-2,3-butanediol efficiently. Firstly, the gene bdhA from B. subtilis 168 was integrated into strain CGS9 and its expression level was further enhanced by using a strong promoter P_sod and ribosome binding site (RBS) with high translation initiation rate, and the (2R,3R)-2,3-butanediol titer of the resulting strain was increased by 33.9%. Then the transhydrogenase gene udhA from E. coli was expressed to provide more NADH for 2,3-butanediol synthesis, which reduced the accumulation of the main byproduct acetoin by 57.2%. Next, a mutant atpG was integrated into strain CGK3, which increased the glucose consumption rate by 10.5% and the 2,3-butanediol productivity by 10.9% in shake-flask fermentation. Through fermentation engineering, the most promising strain CGK4 produced a titer of 144.9 g/L (2R,3R)-2,3-butanediol with a yield of 0.429 g/g glucose and a productivity of 1.10 g/L/h in fed-batch fermentation. The optical purity of the resulting (2R,3R)-2,3-butanediol surpassed 98%.

Conclusions

To the best of our knowledge, this is the highest titer of optically pure (2R,3R)-2,3-butanediol achieved by GRAS strains, and the result has demonstrated that C. glutamicum is a competitive candidate for (2R,3R)-2,3-butanediol production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01875-5.

Production of pyruvic acid with Candida glabrata using self-fermenting spent yeast cell dry powder as a seed nitrogen source

Pyruvic acid is an important organic acid and a key industrial raw material. It is widely used in the chemical, agricultural, and food fields. Candida glabrata is the preferred strain for pyruvic acid production. The waste yeast cell for pyruvic acid fermentation with C. glabrata are rich in protein, amino acid, nucleic acid, and vitamins, as potential and cost-effective nitrogen source raw material. In this study, the potential of C. glabrata to produce pyruvic acid using spent yeast cell dry powder was evaluated. When 30 g/L of spray-dried spent yeast cell powder was used as the seed nitrogen source, a high titer of pyruvic acid was obtained. The pyruvic acid production reached 63.4 g/L with a yield of 0.59 g/g in a 5 L bioreactor. After scale-up to a 50 L bioreactor using the fermented spent yeast cell dry powder as a seed nitrogen source, 65.1 g/L of pyruvic acid was harvested, with a yield of 0.61 g/g. This study proposes a promisingapproach for increasing the pyruvic acid titer and reducing the costs.

Efficient biosynthesis of exopolysaccharide in Candida glabrata by a fed-batch culture

Polysaccharides are important natural biomacromolecules. In particular, microbial exopolysaccharides have received much attention. They are produced by a variety of microorganisms, and they are widely used in the food, pharmaceutical, and chemical industries. The Candida glabrata mutant 4-C10, which has the capacity to produce exopolysaccharide, was previously obtained by random mutagenesis. In this study we aimed to further enhance exopolysaccharide production by systemic fermentation optimization. By single factor optimization and orthogonal design optimization in shaking flasks, an optimal fermentation medium composition was obtained. By optimizing agitation speed, aeration rate, and fed-batch fermentation mode, 118.6 g L⁻¹ of exopolysaccharide was obtained by a constant rate feeding fermentation mode, with a glucose yield of 0.62 g g⁻¹ and a productivity of 1.24 g L⁻¹ h⁻¹. Scaling up the established fermentation mode to a 15-L fermenter led to an exopolysaccharide yield of 113.8 g L⁻¹, with a glucose yield of 0.60 g g⁻¹ and a productivity of 1.29 g L⁻¹ h⁻¹.

Synergistic Improvement of 5-Aminolevulinic Acid Production with Synthetic Scaffolds and System Pathway Engineering

Engineered synthetic scaffolds to organize metabolic pathway enzymes and system pathway engineering to fine-tune metabolic fluxes play essential roles in microbial production. Here, we first obtained the most favorable combination of key enzymes for 5-aminolevulinic acid (5-ALA) synthesis through the C5 pathway by screening enzymes from different sources and optimizing their combination in different pathways. Second, we successfully constructed a multienzyme complex assembly system with PduA*, which spatially recruits the above three key enzymes for 5-ALA synthesis in a designable manner. By further optimizing the ratio of these key enzymes in synthetic scaffolds, the efficiency of 5-ALA synthesis through the C5 pathway was significantly improved. Then, the competitive metabolism pathway was fine-tuned by rationally designing different antisense RNAs, further significantly increasing 5-ALA titers. Furthermore, for efficient 5-ALA synthesis, obstacles of NADH and NADPH imbalances and feedback inhibition of the synthesis pathway were also overcome through engineering the NADPH regeneration pathway and transport pathway, respectively. Finally, combining these strategies with further fermentation optimization, we achieved a final 5-ALA titer of 11.4 g/L. These results highlight the importance of synthetic scaffolds and system pathway engineering to improve the microbial cell factory production performance.

Cell-Free Biosynthesis System: Methodology and Perspective of in Vitro Efficient Platform for Pyruvate Biosynthesis and Transformation

The modification of intracellular metabolic pathways by metabolic engineering has generated many engineered strains with relatively high yields of various target products in the past few decades. However, the unpredictable accumulation of toxic products, the cell membrane barrier, and competition between the carbon flux of cell growth and product synthesis have severely retarded progress toward the industrial-scale production of many essential chemicals. On the basis of an in-depth understanding of intracellular metabolic pathways, scientists intend to explore more sustainable methods and construct a cell-free biosynthesis system in vitro. In this review, the synthesis and application of pyruvate as a platform compound is used as an example to introduce cell-free biosynthesis systems. We systematically summarize a proposed methodology workflow of cell-free biosynthesis systems, including pathway design, enzyme mining, enzyme modification, multienzyme assembly, and pathway optimization. Some new methods, such as machine learning, are also mentioned in this review.

Physiological limitations and opportunities in microbial metabolic engineering

Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.

Comparative analysis of the chemical and biochemical synthesis of keto acids

Keto acids are essential organic acids that are widely applied in pharmaceuticals, cosmetics, food, beverages, and feed additives as well as chemical synthesis. Currently, most keto acids on the market are prepared via chemical synthesis. The biochemical synthesis of keto acids has been discovered with the development of metabolic engineering and applied toward the production of specific keto acids from renewable carbohydrates using different metabolic engineering strategies in microbes. In this review, we provide a systematic summary of the types and applications of keto acids, and then summarize and compare the chemical and biochemical synthesis routes used for the production of typical keto acids, including pyruvic acid, oxaloacetic acid, α-oxobutanoic acid, acetoacetic acid, ketoglutaric acid, levulinic acid, 5-aminolevulinic acid, α-ketoisovaleric acid, α-keto-γ-methylthiobutyric acid, α-ketoisocaproic acid, 2-keto-L-gulonic acid, 2-keto-D-gluconic acid, 5-keto-D-gluconic acid, and phenylpyruvic acid. We also describe the current challenges for the industrial-scale production of keto acids and further strategies used to accelerate the green production of keto acids via biochemical routes.

Fluorescence-activated droplet sorting for enhanced pyruvic acid accumulation by Candida glabrata

One of the goals of metabolic engineering is to engineer strains that can optimally produce target metabolites. However, the current workflow for rational engineering of the metabolic pathway is sometimes time-consuming and labor-intensive. Here, we have established a cost-effective approach for screening for variants secreting metabolites. Different surface display systems were adopted and verified, which anchored pHluorin to the Candida glabrata cell surface to associate pyruvic acid detection with the read out of this reporter. A generalizable simulation approach based on computational fluid dynamics and regularity of generated droplet dimension was presented, which was found to be an efficient design tool to explore microfluidic characteristics or optimization. Finally, a microfluidic platform based on simulation coupled with surface display system was constructed. A mutant exhibiting a 73.6% increase in pyruvic acid production was identified. This ultrahigh-throughput screening pattern offers a practical guide for identifying microbial strains with many traits of interest.

Regulation of intracellular ATP supply and its application in industrial biotechnology

Efficient cell factories are the core of industrial biotechnology. In recent years, synthetic biology develops rapidly, and more and more modified microbial cell factories are employed in industrial biotechnology. ATP plays vital roles in biosynthesis, metabolism regulation, and cellular maintenance. Regulating cellular ATP supply can effectively modify cellular metabolism. This paper presents a review of recent studies on the regulation of the intracellular ATP supply and its application in industrial biotechnology. Detailed strategies for regulating the ATP supply and the resulting impact on bioproduction are introduced. It is observed that regulating the cellular ATP supply can provide great possibilities for making microbial cells into efficient factories. Future perspectives for further understanding the function of ATP are also discussed.

Efficient repeated batch production of androstenedione using untreated cane molasses by Mycobacterium neoaurum driven by ATP futile cycle

The biotransformation of phytosterol to androstenedione (AD) by mycobacteria is a unique process accompanied by energy-producing. However, high intracellular ATP content can severely inhibit the efficient production of AD. In this study, a novel citrate-based ATP futile cycle (AFC) and pyruvate-based AFC were constructed for the first time. Application of AFCs reduced intracellular ATP and propionyl-CoA levels and increased NAD⁺/NADH ratios and cell viability. The forced consumption of ATP promotes the transcription of critical genes in propionyl-CoA metabolism. The synergistic effect of enhanced propionyl-CoA metabolism and AFC increased AD conversion yield from 60.6% to 97.3%. The AD productivity was further improved by repeated batch fermentation using untreated cane molasses. The maximum productivity was 181% higher than that of the original strain. Therefore, the strategy of combining AFC and repeated batch fermentation is a valuable tool for the efficient and low-cost production of AD and other steroidal pharmaceutical precursors.

Active tyrosine phenol-lyase aggregates induced by terminally attached functional peptides in Escherichia coli

The formation of inclusion bodies (IBs) without enzyme activity in bacterial research is generally undesirable. Researchers have attempted to recovery the enzyme activities of IBs, which are commonly known as active IBs. Tyrosine phenol-lyase (TPL) is an important enzyme that can convert pyruvate and phenol into 3,4-dihydroxyphenyl-L-alanine (L-DOPA) and IBs of TPL can commonly occur. To induce the correct folding and recover the enzyme activity of the IBs, peptides, such as ELK16, DKL6, L6KD, ELP10, ELP20, L6K2, EAK16, 18A, and GFIL16, were fused to the carboxyl terminus of TPL. The results showed that aggregate particles of TPL-DKL6, TPL-ELP10, TPL-EAK16, TPL-18A, and TPL-GFIL16 improved the enzyme activity by 40.9%, 50.7%, 48.9%, 86.6%, and 97.9%, respectively. The peptides TPL-DKL6, TPL-EAK16, TPL-18A, and TPL-GFIL16 displayed significantly improved thermostability compared with TPL. L-DOPA titer of TPL-ELP10, TPL-EAK16, TPL-18A, and TPL-GFIL16, with cells reaching 37.8 g/L, 53.8 g/L, 37.5 g/L, and 29.1 g/L, had an improvement of 111%, 201%, 109%, and 63%, respectively. A higher activity and L-DOPA titer of the TPL-EAK16 could be valuable for its industrial application to biosynthesize L-DOPA.

Application of a Pyruvate-Producing Escherichia coli Strain LAFCPCPt-accBC-aceE: A Case Study for d-Lactate Production

Pyruvate, a potential precursor of various chemicals, is one of the fundamental chemicals produced by the fermentation process. We previously reported a pyruvate-producing Escherichia coli strain LAFCPCPt-accBC-aceE (PYR) that has the potential to be applied to the industrial production of pyruvate. In this study, the availability of the PYR strain for the production of pyruvate-derivative chemicals was evaluated using a d-lactate-producing strain (LAC) based on the PYR strain. The LAC strain expresses a d-lactate dehydrogenase-encoding gene from Lactobacillus bulgaricus under the control of a T7 expression system. The d-lactate productivity of the LAC strain was further improved by limiting aeration and changing the induction period for the expression of d-lactate dehydrogenase-encoding gene expression. Under combined conditions, the LAC strain produced d-lactate at 21.7 ± 1.4 g·L−1, which was compatible with the pyruvate production by the PYR strain (26.1 ± 0.9 g·L−1). These results suggest that we have succeeded in the effective conversion of pyruvate to d-lactate in the LAC strain, demonstrating the wide versatility of the parental PYR strain as basal strain for various chemicals production.

Enhancement of pyruvic acid production in Candida glabrata by engineering hypoxia-inducible factor 1

Dissolved oxygen (DO) supply plays essential roles in microbial organic acid production. Candida glabrata, as a dominant strain for producing pyruvic acid, principally converts glucose to pyruvic acid through glycolysis. However, this process relies excessively on high extracellular DO content. In this study, in combination with specific motif analysis of gene promoters, hypoxia-inducible factor 1 (HIF1) was engineered to improve the transcription level of some enzymes related to pyruvic acid synthesis under low DO level and directly led to increased pyruvic acid production and glycolysis efficiency. Moreover, the intracellular stability of HIF1 was further optimized from different aspects to maximize pyruvic acid accumulation. Finally, the pyruvic acid titer in a 5-L batch bioreactor with 10% DO level reached 53.1 g/L. As pyruvic acid is involved in the biosynthesis of various products, these findings suggest that HIF1-enabled regulation method has significant potential for increasing the synthesis of other chemicals in microorganisms.