Morphology engineering ofAspergillus oryzaeforl‐malate production

Synthetic biology meets Aspergillus: engineering strategies for next-generation organic acid production

Organic acids constitute a vital category of chemical raw materials. They have extensive applications in industries such as polymers, food, and pharmaceuticals. Currently, industrial production predominantly relies on microbial fermentation. Aspergillus, due to its unique metabolic capabilities, has become an important microbial resource for organic acid production. In recent years, there has been a growing emphasis on genetic engineering of Aspergillus to increase its yield of organic acids. This review provides a comprehensive overview of the current advancement and future directions in the application of genetic engineering techniques to enhance organic production in Aspergillus, specifically highlighting achievement in reconstructing metabolic pathways for desired products, eliminating by-products, modifying regulatory pathways, and engineering mycelial morphology. Furthermore, this review also focuses on the strategies and genetic tools applied in Aspergillus, with particular emphasis on the potential applications and challenges of CRISPR-based biosensors in organic acid fermentation. By providing insights into these developments, we aim to offer theoretical guidance and innovative approaches for enhancing the efficiency of Aspergillus strains in industrial organic acid production.

Morphological responses of filamentous fungi to stressful environmental conditions

The filamentous growth mode of fungi, with its modular design, facilitates fungal adaptation to stresses they encounter in diverse terrestrial and anthropogenic environments. Surface growth conditions elicit diverse morphological responses in filamentous fungi, particularly demonstrating the remarkable adaptability of mycelial systems to metal- and mineral-rich environments. These responses are coupled with fungal biogeochemical activity and can ameliorate hostile conditions. A tessellated agar tile system, mimicking natural environmental heterogeneity, revealed negative chemotropism to toxic metals, distinct extreme growth strategies, such as phalanx and guerrilla movements and transitions between them, and the formation of aggregated re-allocation structures (strands, cords, synnemata). Other systems showed intrahyphal growth, intense biomineralization, and extracellular hair-like structures. Studies on submerged mycelial growth, using the thermophilic fungus Thielavia terrestris as an example, provided mechanistic insights into the morphogenesis of two extreme forms of fungal submerged culture-pelleted and dispersed growth. It was found that the development of fungal pellets was related to fungal adaptation to unfavorable stressful conditions. The two key elements affecting morphogenesis leading to the formation of either pelleted or dispersed growth were found to be (1) a lag phase (or conidia swelling stage) as a specific period of fungal morphogenesis when a certain growth form is programmed in response to morphogenic stressors, and (2) cAMP as a secondary messenger of cell signaling, defining the implementation of the particular growth strategy. These findings can contribute to knowledge of fungal-based biotechnologies, providing a means for controllable industrial processes at both morphological and physiological levels.

Morphological Engineering of Filamentous Fungi: Research Progress and Perspectives

Filamentous fungi are important cell factories for the production of high-value enzymes and chemicals for the food, chemical, and pharmaceutical industries. Under submerged fermentation, filamentous fungi exhibit diverse fungal morphologies that are influenced by environmental factors, which in turn affect the rheological properties and mass transfer of the fermentation system, and ultimately the synthesis of products. In this review, we first summarize the mechanisms of mycelial morphogenesis and then provide an overview of current developments in methods and strategies for morphological regulation, including physicochemical and metabolic engineering approaches. We also anticipate that rapid developments in synthetic biology and genetic manipulation tools will accelerate morphological engineering in the future.

Synthetic Biology Tools for Engineering Aspergillus oryzae

For more than a thousand years, Aspergillus oryzae has been used in traditional culinary industries, including for food fermentation, brewing, and flavoring. In recent years, A. oryzae has been extensively used in deciphering the pathways of natural product synthesis and value-added compound bioproduction. Moreover, it is increasingly being used in modern biotechnology industries, such as for the production of enzymes and recombinant proteins. The investigation of A. oryzae has been significantly accelerated through the successive application of a diverse array of synthetic biology techniques and methodologies. In this review, the advancements in biological tools for the synthesis of A. oryzae, including DNA assembly technologies, gene expression regulatory elements, and genome editing systems, are discussed. Additionally, the challenges associated with the heterologous expression of A. oryzae are addressed.

Stepwise genetic modification for efficient expression of heterologous proteins in Aspergillus nidulans

Filamentous fungi are widely used in food fermentation and therapeutic protein production due to their prominent protein secretion and post-translational modification system. Aspergillus nidulans is an important model strain of filamentous fungi, but not a fully developed cell factory for heterologous protein expression. One of the limitations is its relatively low capacity of protein secretion. To alleviate this limitation, in this study, the protein secretory pathway and mycelium morphology were stepwise modified. With eGFP as a reporter protein, protein secretion was significantly enhanced through reducing the degradation of heterologous proteins by endoplasmic reticulum-associated protein degradation (ERAD) and vacuoles in the secretory pathway. Elimination of mycelial aggregation resulted in a 1.5-fold and 1.3-fold increase in secretory expression of eGFP in typical constitutive and inducible expression systems, respectively. Combined with these modifications, high secretory expression of human interleukin-6 (HuIL-6) was achieved. Consequently, a higher yield of secretory HuIL-6 was realized by further disruption of extracellular proteases. Overall, a superior chassis cell of A. nidulans suitable for efficient secretory expression of heterologous proteins was successfully obtained, providing a promising platform for biosynthesis using filamentous fungi as hosts. KEY POINTS: • Elimination of mycelial aggregation and decreasing the degradation of heterologous protein are effective strategies for improving the heterologous protein expression. • The work provides a high-performance chassis host △agsB-derA for heterologous protein secretory expression. • Human interleukin-6 (HuIL-6) was expressed efficiently in the high-performance chassis host △agsB-derA.

Engineering growth phenotypes of Aspergillus oryzae for L-malate production

Improving the growth status of Aspergillus oryzae is an efficient way to enhance L-malate production. However, the growth mechanism of filamentous fungi is relatively complex, which limits A. oryzae as a cell factory to produce L-malate industrially. This study determined the relationship between growth status and L-malate production. The optimal ranges of colony diameter, percentage of vegetative mycelia, and pellet number of A. oryzae were determined to be 26-30 mm, 35-40%, and 220-240/mL, respectively. To achieve this optimum range, adaptive evolution was used to obtain the evolved strain Z07 with 132.54 g/L L-malate and a productivity of 1.1 g/L/h. Finally, a combination of transcriptome analysis and morphological characterization was used to identify the relevant pathway genes that affect the growth mechanism of A. oryzae. The strategies used in this study and the growth mechanism provide a good basis for efficient L-malate production by filamentous fungi.

Recent advances in producing food additive L-malate: Chassis, substrate, pathway, fermentation regulation and application

In addition to being an important intermediate in the TCA cycle, L-malate is also widely used in the chemical and beverage industries. Due to the resulting high demand, numerous studies investigated chemical methods to synthesize L-malate from petrochemical resources, but such approaches are hampered by complex downstream processing and environmental pollution. Accordingly, there is an urgent need to develop microbial methods for environmentally-friendly and economical L-malate biosynthesis. The rapid progress and understanding of DNA manipulation, cell physiology, and cell metabolism can improve industrial L-malate biosynthesis by applying intelligent biochemical strategies and advanced synthetic biology tools. In this paper, we mainly focused on biotechnological approaches for enhancing L-malate synthesis, encompassing the microbial chassis, substrate utilization, synthesis pathway, fermentation regulation, and industrial application. This review emphasizes the application of novel metabolic engineering strategies and synthetic biology tools combined with a deep understanding of microbial physiology to improve industrial L-malate biosynthesis in the future.

Recent Advances in Chitin Biosynthesis Associated with the Morphology and Secondary Metabolite Synthesis of Filamentous Fungi in Submerged Fermentation

Metabolites produced by filamentous fungi are used extensively in the food and drug industries. With the development of the morphological engineering of filamentous fungi, numerous biotechnologies have been applied to alter the morphology of fungal mycelia and enhance the yields and productivity of target metabolites during submerged fermentation. Disruption of chitin biosynthesis can modify the cell growth and mycelial morphology of filamentous fungi and regulate the biosynthesis of metabolites during submerged fermentation. In this review, we present a comprehensive coverage of the categories and structures of the enzyme chitin synthase, chitin biosynthetic pathways, and the association between chitin biosynthesis and cell growth and metabolism in filamentous fungi. Through this review, we hope to increase awareness of the metabolic engineering of filamentous fungal morphology, provide insights into the molecular mechanisms of morphological control via chitin biosynthesis, and describe strategies for the application of morphological engineering to enhance the production of target metabolites in filamentous fungi during submerged fermentation.

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.

Effect of Microparticles on Fungal Fermentation for Fermentation-Based Product Productions

Ranging from simple food ingredients to complex pharmaceuticals, value-added products via microbial fermentation have many advantages over their chemically synthesized alternatives. Some of such advantages are environment-friendly production pathways, more specificity in the case of enzymes as compared to the chemical catalysts and reduction of harmful chemicals, such as heavy metals or strong acids and bases. Fungal fermentation systems include yeast and filamentous fungal cells based on cell morphology and culture conditions. However, filamentous fungal fermentation has gained attention in the past few decades because of the diversity of microbial products and robust production of some of the most value-added commodities. This type of fungal fermentation is usually carried out by solid-state fermentation. However, solid-state fermentation poses problems during the scale-up for industrial production. Therefore, submerged fermentation for value-added products is usually preferred for scaling-up purposes. The main problem with submerged fungal fermentation is the formation of complex mycelial clumps or pellets. The formation of such pellets increases the viscosity of the media and hinders the efficient transfer of oxygen and nutrient resources in the liquid phase. The cells at the center of the clump or pellet start to die because of a shortage of resources and, thus, productivity decreases substantially. To overcome this problem, various morphological engineering techniques are being researched. One approach is the use of microparticles. Microparticles are inert particles with various size ranges that are used in fermentation. These microparticles are shown to have positive effects, such as high enzyme productivity or smaller pellets with fungal fermentation. Therefore, this review provides a background about the types of microparticles and summarizes some of the recent studies with special emphasis on the fungal morphology changes and microparticle types along with the applications of microparticles in filamentous fungal fermentations.

Recent advances in microbial production of L-malic acid

Over the last few decades, increasing concerns regarding fossil fuel depletion and excessive CO2 emissions have led to extensive fundamental studies and industrial trials regarding microbial chemical production. As an additive or precursor, L-malic acid has been shown to exhibit distinctive properties in the food, pharmaceutical, and daily chemical industries. L-malic acid is currently mainly fabricated through a fumarate hydratase-based biocatalytic conversion route, wherein petroleum-derived fumaric acid serves as a substrate. In this review, for the first time, we comprehensively describe the methods of malic acid strain transformation, raw material utilization, malic acid separation, etc., especially recent progress and remaining challenges for industrial applications. First, we summarize the various pathways involved in L-malic acid biosynthesis using different microorganisms. We also discuss several strain engineering strategies for improving the titer, yield, and productivity of L-malic acid. We illustrate the currently available alternatives for reducing production costs and the existing strategies for optimizing the fermentation process. Finally, we summarize the present challenges and future perspectives regarding the development of microbial L-malic acid production. KEY POINTS: • A range of wild-type, mutant, laboratory-evolved, and metabolically engineered strains which could produce L-malic acid were comprehensively described. • Alternative raw materials for reducing production costs and the existing strategies for optimizing the fermentation were sufficiently summarized. • The present challenges and future perspectives regarding the development of microbial L-malic acid production were elaboratively discussed.

Optimization of l-malic acid production from acetate with Aspergillus oryzae DSM 1863 using a pH-coupled feeding strategy

Background

Malic acid, a dicarboxylic acid mainly used in the food industry, is currently produced from fossil resources. The utilization of low-cost substrates derived from biomass could render microbial processes economic. Such feedstocks, like lignocellulosic hydrolysates or condensates of fast pyrolysis, can contain high concentrations of acetic acid. Acetate is a suitable substrate for l-malic acid production with the filamentous fungus Aspergillus oryzae DSM 1863, but concentrations obtained so far are low. An advantage of this carbon source is that it can be used for pH control and simultaneous substrate supply in the form of acetic acid. In this study, we therefore aimed to enhance l-malate production from acetate with A. oryzae by applying a pH-coupled feeding strategy.

Results

In 2.5-L bioreactor fermentations, several feeding strategies were evaluated. Using a pH-coupled feed consisting of 10 M acetic acid, the malic acid concentration was increased about 5.3-fold compared to the batch process without pH control, resulting in a maximum titer of 29.53 ± 1.82 g/L after 264 h. However, it was not possible to keep both the pH and the substrate concentration constant during this fermentation. By using 10 M acetic acid set to a pH of 4.5, or with the repeated addition of NaOH, the substrate concentration could be maintained within a constant range, but these strategies did not prove beneficial as lower maximum titers and yields were obtained. Since cessation of malic acid production was observed in later fermentation stages despite carbon availability, a possible product inhibition was evaluated in shake flask cultivations. In these experiments, malate and succinate, which is a major by-product during malic acid production, were added at concentrations of up to 50 g/L, and it was found that A. oryzae is capable of organic acid production even at high product concentrations.

Conclusions

This study demonstrates that a suitable feeding strategy is necessary for efficient malic acid production from acetate. It illustrates the potential of acetate as carbon source for microbial production of the organic acid and provides useful insights which can serve as basis for further optimization.

Effect of process mode, nitrogen source and temperature on L-malic acid production with Aspergillus oryzae DSM 1863 using acetate as carbon source

Malic acid, mainly used as acidulant and taste enhancer in the food industry, is currently produced from fossil resources. In this study, microbial L-malate production with the filamentous fungus A. oryzae using the carbon source acetate was evaluated. Acetate is for example contained in biomass-derived substrates such as lignocellulosic hydrolysates and condensates of fast pyrolysis, thus avoiding competition with food production. Since research on malic acid synthesis from acetate is limited and reported productivities and yields are low, this work aimed to improve the process. First, different cultivation temperatures were tested. This parameter was found to affect the ratio between malic and succinic acid, which is the major by-product of organic acid production with A. oryzae. At 32°C, the malate share was highest (53.7 ± 1.6%), while it was lowest at 38°C (43.3 ± 1.1%) whereas succinate represented the main product (51.5 ± 1.0%). Besides the temperature, the type of nitrogen source was also found to affect malate synthesis as well as biomass production. In the pre-culture, the biomass concentration was increased by a factor of 3.4–3.9, and germination started earlier with the complex nitrogen sources yeast extract, casein hydrolysate and peptone compared to the defined nitrogen source (NH₄)₂SO₄. Especially with yeast extract, malate synthesis in the main culture was accelerated and the titer obtained after 48 h was about 2.6 times higher than that quantified with (NH₄)₂SO₄. To reduce substrate inhibition in acetate medium, fed-batch and repeated-batch processes were evaluated using (NH₄)₂SO₄ or yeast extract as nitrogen source. In the fed-batch process, the period of malate production was extended, and the maximum product concentration was increased to 11.49 ± 1.84 g/L with (NH₄)₂SO₄ and 12.08 ± 1.25 g/L with yeast extract. In the repeated-batch process, the total acid production was highest within the first 240 h of fermentation, but optimization is required to maintain high production rates in later cycles. The lessons learned in this study will help in the development of further process strategies to maximize malate production using acetate as alternative substrate to the commonly used glucose.

Comprehensively dissecting the hub regulation of PkaC on high-productivity and pellet macromorphology in citric acid producing Aspergillus niger

Aspergillus niger, an important industrial workhorse for citric acid production, is characterized by polar hyphal growth with complex pelleted, clumped or dispersed macromorphologies in submerged culture. Although organic acid titres are dramatically impacted by these growth types, studies that assess productivity and macromorphological changes are limited. Herein, we functionally analysed the role of the protein kinase A (PKA)/cyclic adenosine monophosphate (cAMP) signalling cascade during fermentation by disrupting and conditionally expressing the pkaC gene. pkaC played multiple roles during hyphal, colony and conidiophore growth. By overexpressing pkaC, we could concomitantly modify hyphal growth at the pellet surface and improve citric acid titres up to 1.87‐fold. By quantitatively analysing hundreds of pellets during pilot fermentation experiments, we provide the first comprehensive correlation between A. niger pellet surface morphology and citric acid production. Finally, by intracellular metabolomics analysis and weighted gene coexpression network analysis (WGCNA) following titration of pkaC expression, we unveil the metabolomic and transcriptomic basis underpin hyperproductivity and pellet growth. Taken together, this study confirms pkaC as hub regulator linking submerged macromorphology and citric acid production and provides high‐priority genetic leads for future strain engineering programmes.

Enhanced l-Malic Acid Production by Aspergillus oryzae DSM 1863 Using Repeated-Batch Cultivation

l-Malic acid is a C4-dicarboxylic acid and a potential key building block for a bio-based economy. At present, malic acid is synthesized petrochemically and its major market is the food and beverages industry. In future, malic acid might also serve as a building block for biopolymers or even replace the commodity chemical maleic anhydride. For a sustainable production of l-malic acid from renewable resources, the microbial synthesis by the mold Aspergillus oryzae is one possible route. As CO₂ fixation is involved in the biosynthesis, high yields are possible, and at the same time greenhouse gases can be reduced. In order to enhance the production potential of the wild-type strain Aspergillus oryzae DSM 1863, process characteristics were studied in shake flasks, comparing batch, fed-batch, and repeated-batch cultivations. In the batch process, a prolonged cultivation time led to malic acid consumption. Keeping carbon source concentration on a high level by pulsed feeding could prolong cell viability and cultivation time, however, did not result in significant higher product levels. In contrast, continuous malic acid production could be achieved over six exchange cycles and a total fermentation time of 19 days in repeated-batch cultivations. Up to 178 g/L l-malic acid was produced. The maximum productivity (0.90 ± 0.05 g/L/h) achieved in the repeated-batch cultivation had more than doubled than that achieved in the batch process and also the average productivity (0.42 ± 0.03 g/L/h for five exchange cycles and 16 days) was increased considerably. Further repeated-batch experiments confirmed a positive effect of regular calcium carbonate additions on pH stability and malic acid synthesis. Besides calcium carbonate, nitrogen supplementation proved to be essential for the prolonged malic acid production in repeated-batch. As prolonged malic acid production was only observed in cultivations with product removal, product inhibition seems to be the major limiting factor for malic acid production by the wild-type strain. This study provides a systematic comparison of different process strategies under consideration of major influencing factors and thereby delivers important insights into natural l-malic acid production.

Transcriptomic Analysis of Morphology Regulatory Mechanisms of Microparticles to Paraisaria dubia in Submerged Fermentation

Liquid submerged fermentation is an effective strategy to achieve large-scale production of active ingredients by macrofungi, and controlling mycelium morphology is a key factor restricting the development of this technology. Mining for superior morphological regulatory factors and elucidation of their regulatory mechanisms are vital for the further development of macrofungal fermentation technology. In this study, microparticles were used to control the morphology of Paraisaria dubia (P. dubia) in submerged fermentation, and the underlying regulatory mechanisms were revealed by transcriptomic. The relative frequency of S-type pellet diameter increased significantly from 7.14 to 88.31%, and biomass increased 1.54 times when 15 g/L talc was added. Transcriptome analysis showed that the morphological regulation of filamentous fungi was a complex biological process, which involved signal transduction, mycelium polar growth, cell wall synthesis and cell division, etc. It also showed a positive impact on the basic and secondary metabolism of P. dubia. We provided a theoretical basis for controlling the mycelium morphology of P. dubia in submerged fermentation, which will promote the development of macrofungal fermentation technology.

Effect of biosurfactant sophorolipids on Rhizomucor miehei lipase fermentation by Aspergillus oryzae

In this study, the effect of biosurfactant sophorolipids (SLs) on Rhizomucor miehei lipase (RML) fermentation by Aspergillus oryzae was investigated. With the exogenous addition of 0.3% (w/v) SLs in the initial medium, the RML activity reached 430.0 U/mL, an increase of 25.0% compared to the control group. Subsequently, the physiological metabolic responses of A. oryzae to the addition of SLs were further explored. The results showed that though SLs had almost no effect on the RML secretion, it would affect the morphology of the cells. During the late phase of the fermentation, the proportion of middle pellets, which was generally considered as an energetic and stable state for enzyme production was increased with the addition of SLs. Simultaneously, the viscosity of fermentation broth was reduced, which facilitated the increase of oxygen transfer, thereby improving the RML production. Finally, it could be found that the addition of SLs significantly increased the contents of precursor amino acids, especially for those rank first and second of the RML composition, and it could promote the synthesis of RML.

Effects of Impeller Geometry on the 11α-Hydroxylation of Canrenone in Rushton Turbine-Stirred Tanks

The 11α-hydroxylation of canrenone can be catalyzed by Aspergillus ochraceus in bioreactors, where the geometry of the impeller greatly influences the biotransformation. In this study, the effects of the blade number and impeller diameter of a Rushton turbine on the 11α-hydroxylation of canrenone were considered. The results of fermentation experiments using a 50 mm four-blade impeller showed that 3.40% and 11.43% increases in the conversion ratio were achieved by increasing the blade number and impeller diameter, respectively. However, with an impeller diameter of 60 mm, the conversion ratio with a six-blade impeller was 14.42% lower than that with a four-blade impeller. Data from cold model experiments with a large-diameter six-blade impeller indicated that the serious leakage of inclusions and a 22.08% enzyme activity retention led to a low conversion ratio. Numerical simulations suggested that there was good gas distribution and high fluid flow velocity when the fluid was stirred by large-diameter impellers, resulting in a high dissolved oxygen content and good bulk circulation, which positively affected hyphal growth and metabolism. However, a large-diameter six-blade impeller created overly high shear compared to a large-diameter four-blade impeller, thereby decreasing the conversion ratio. The average shear rates of the former and latter cases were 43.25 s^-1 and 35.31 s^-1, respectively. We therefore concluded that appropriate shear should be applied in the 11α-hydroxylation of canrenone. Overall, this study provides basic data for the scaled-up production of 11α-hydroxycanrenone.

Enhancing L-malate production of Aspergillus oryzae by nitrogen regulation strategy

Regulating morphology engineering and fermentation of Aspergillus oryzae makes it possible to increase the titer of L-malate. However, the existing L-malate-producing strain has limited L-malate production capacity and the fermentation process is insufficiently mature, which cannot meet the needs of industrial L-malate production. To further increase the L-malate production capacity of A. oryzae, we screened out a mutant strain (FMME-S-38) that produced 79.8 g/L L-malate in 250-mL shake flasks, using a newly developed screening system based on colony morphology on the plate. We further compared the extracellular nitrogen (N1) and intracellular nitrogen (N2) contents of the control and mutant strain (FMME-S-38) to determine the relationship between the curve of nitrogen content (N1 and N2) and the L-malate titer. This correlation was then used to optimize the conditions for developing a novel nitrogen supply strategy (initial tryptone concentration of 6.5 g/L and feeding with 3 g/L tryptone at 24 h). Fermentation in a 7.5-L fermentor under the optimized conditions further increased the titer and productivity of L-malate to 143.3 g/L and 1.19 g/L/h, respectively, corresponding to 164.9 g/L and 1.14 g/L/h in a 30-L fermentor. This nitrogen regulation-based strategy cannot only enhance industrial-scale L-malate production but also has generalizability and the potential to increase the production of similar metabolites.Key Points• Construction of a new screening system based on colony morphology on the plate.• A novel nitrogen regulation strategy used to regulate the production of L-malate.• A nitrogen supply strategy used to maximize the production of L-malate.

Engineering microorganisms for the biosynthesis of dicarboxylic acids

Dicarboxylic acids (DCAs) are important commodity chemicals which have been widely applied in polymer, food and pharmaceutical industries. Biosynthesis of DCAs from renewable carbon sources represents a promising alternative to chemical synthesis. Over the years, the recombinant strains have been constructed to produce an increasing number of DCAs. In this review, recent advances on the microbial synthesis of various DCAs have been summarized and categorized into three groups: the tricarboxylic acid cycle-derived, lysine metabolism-related, and aromatic compounds degradation-derived DCAs. We focused mainly on the metabolic engineering and synthetic biology strategies for improving the production efficiency, including metabolic flux analysis, fine-tuning of gene expression, cofactor balancing, metabolic compartmentalization, dynamic regulation and co-culture to regulate the production at multiple levels. The current challenges and perspectives have also been discussed.

Engineering microbial cell morphology and membrane homeostasis toward industrial applications

Microbial cell factory performance is significantly affected by the cell morphology and membrane homeostasis. It is important to ensure that cell factories are able to regulate cell morphology and maintain membrane homeostasis. Cell morphology can be controlled by regulating the formation of elongasomes and divisomes, which change the shapes of cells from rods to fibers, large spheres, or mini-cells. Membrane homeostasis can also be controlled by regulating the homeostasis of membrane lipids and proteins, thereby improving the robustness of microbes in toxic environments. In the present review, we discuss promising developments in cell morphology and membrane homeostasis engineering that have improved microbial cell factory performance.

Light-powered Escherichia coli cell division for chemical production

Cell division can perturb the metabolic performance of industrial microbes. The C period of cell division starts from the initiation to the termination of DNA replication, whereas the D period is the bacterial division process. Here, we first shorten the C and D periods of E. coli by controlling the expression of the ribonucleotide reductase NrdAB and division proteins FtsZA through blue light and near-infrared light activation, respectively. It increases the specific surface area to 3.7 μm⁻¹ and acetoin titer to 67.2 g·L⁻¹. Next, we prolong the C and D periods of E. coli by regulating the expression of the ribonucleotide reductase NrdA and division protein inhibitor SulA through blue light activation-repression and near-infrared (NIR) light activation, respectively. It improves the cell volume to 52.6 μm³ and poly(lactate-co-3-hydroxybutyrate) titer to 14.31 g·L⁻¹. Thus, the optogenetic-based cell division regulation strategy can improve the efficiency of microbial cell factories.

Manipulation of genes controlling microbial shapes can affect bio-production. Here, the authors employ an optogenetic method to realize dynamic morphological engineering of E. coli replication and division and show the increased production of acetoin and poly(lactate-co-3-hydroxybutyrate).

Cell surface display of proteins on filamentous fungi

Protein display approaches have been useful to endow the cell surface of yeasts with new catalytic activities so that they can act as enhanced whole-cell biocatalysts. Despite their biotechnological potential, protein display technologies remain poorly developed for filamentous fungi. The lignocellulolytic character of some of them coupled to the cell surface biosynthesis of valuable molecules by a single or a cascade of several displayed enzymes is an appealing prospect. Cell surface protein display consists in the co-translational fusion of a functional protein (passenger) to an anchor one, usually a cell-wall-resident protein. The abundance, spacing, and local environment of the displayed enzymes-determined by the relationship of the anchor protein with the structure and dynamics of the engineered cell wall-are factors that influence the performance of display-based biocatalysts. The development of protein display strategies in filamentous fungi could be based on the field advances in yeasts; however, the unique composition, structure, and biology of filamentous fungi cell walls require the customization of the approach to those microorganisms. In this prospective review, the cellular bases, the design principles, and the available tools to foster the development of cell surface protein display technologies in filamentous fungi are discussed.