Metabolic Engineering of Trichoderma reesei for l-Malic Acid Production

Flavor characteristics and metabolomics of sweet rice wine fermented with different non-Saccharomyces yeasts

Non-Saccharomyces yeasts (Clavispora lusitaniae, Hanseniaspora uvarum, Kodamaea ohmeri, Meyerozyma caribbica, and Rhodotorula mucilaginosa) showed potential use in taste and flavor enhancement of fermented products, including sweet rice wine. Herein, various parameters, including physicochemical indices, antioxidant activities, amino acids, volatile organic compounds (VOCs), and metabolites, were examined to investigate the effects of five non-Saccharomyces yeasts on the organoleptic and nutritional properties for sweet rice wine. The results indicated that inoculating non-Saccharomyces yeasts exerted substantial effects on the physicochemical indices and antioxidant activities of sweet rice wine. H. uvarum might provide the most favorable in terms of pleasant VOCs leading to a higher sensory acceptance, compared to other non-Saccharomyces yeasts. Additionally, H. uvarum also exhibited the strongest antioxidant capacities, with significant superiority to C. lusitaniae, M. caribbica, and R. mucilaginosa. The content of bitterness and astringency amino acids, including leucine, valine, phenylalanine, and tyrosine, in sweet rice wine decreased, which might be related to their transformation in tricarboxylic acid (TCA) cycle. Twelve significant contributors to the flavor of sweet rice wine inoculated with non-Saccharomyces yeasts and 11 pivotal metabolic pathways were identified via VOCs and metabolomics analyses, respectively. Of these, ethyl decanoate was the key compound contributing most to the unique flavor, and TCA cycle and pyruvate were the critical metabolic pathways involved in the flavor development of sweet rice wine. These findings offer suitable strategies and ideas for diversifying the sweet rice wine industry.

Advancements in metabolic engineering: unlocking the potential of key organic acids for sustainable industrial applications

This review explores the advancements, application potential, and challenges of microbial metabolic engineering strategies for sustainable organic acid production. By integrating gene editing, pathway reconstruction, and dynamic regulation, microbial platforms have achieved enhanced biosynthesis of key organic acids such as pyruvate, lactic acid, and succinic acid. Strategies including by-product pathway knockout, key enzyme overexpression, and improved CO2 fixation have contributed to higher production efficiency. Additionally, utilizing non-food biomass sources, such as lignocellulose, algal feedstocks, and industrial waste, has reduced reliance on conventional carbon sources, supporting sustainability goals. However, challenges remain in substrate inhibition, purification complexity, and metabolic flux imbalances. Addressing these requires omics-driven metabolic optimization, stress-resistant strain development, and biorefinery integration. Future research should focus on system-level design to enhance cost-effectiveness and sustainability, advancing industrial bio-manufacturing of organic acids.

Metabolic Engineering of Filamentous Fungus Trichoderma reesei for Itaconic Acid Production

Itaconic acid (IA) is a multifunctional platform chemical with numerous biological functions. Here, Trichoderma reesei was engineered as a remarkable cell factory to produce IA. Heterologous overexpression of the mitochondrial tricarboxylate transport protein and cis-aconitate decarboxylase from Aspergillus terreus in T. reesei initiated IA production with a titer of 20 g/L. By increasing the copy number of mttA and cadA and the overexpression of the plasma membrane transporter proteins (MFSA), the titer of IA reached 56.7 g/L. The precursor synthesis pathway of IA was overexpressed by the overexpression of aconitase and citrate synthase, and the IA competition pathway was blocked by the deletion of the P450 monooxygenase gene cyp3 to further enhance IA production. The final strain resulted in a final IA titer of 93.5 g/L through fed-batch fermentation in a 1 L bioreactor. Our study demonstrates that T. reesei can serve as a relevant platform in industry for IA production.

Engineering Yarrowia lipolytica to Produce l-Malic Acid from Glycerol

The declining availability of cheap fossil-based resources has sparked growing interest in the sustainable biosynthesis of organic acids. l-Malic acid, a crucial four-carbon dicarboxylic acid, finds extensive applications in the food, chemical, and pharmaceutical industries. Synthetic biology and metabolic engineering have enabled the efficient microbial production of l-malic acid, albeit not in Yarrowia lipolytica, an important industrial microorganism. The present study aimed to explore the potential of this fungal species for the production of l-malic acid. First, endogenous biosynthetic genes and heterologous transporter genes were overexpressed in Y. lipolytica to identify bottlenecks in the l-malic acid biosynthesis pathway grown on glycerol. Second, overexpression of isocitrate lyase, malate synthase, and malate dehydrogenase in the glyoxylate cycle pathway and introduction of a malate transporter from Schizosaccharomyces pombe significantly boosted l-malic acid production, which reached 27.0 g/L. A subsequent increase to 37.0 g/L was attained through shake flask medium optimization. Third, adaptive laboratory evolution allowed the engineered strain Po1g-CEE2+Sp to tolerate a lower pH and to accumulate a higher amount of l-malic acid (56.0 g/L). Finally, when scaling up to a 5 L bioreactor, a titer of 112.5 g/L was attained. In conclusion, this study demonstrates for the first time the successful production of l-malic acid in Y. lipolytica by combining metabolic engineering and laboratory evolution, paving the way for large-scale sustainable biosynthesis of this and other organic acids.

Bioupcycling Methane and CO2 for Succinate Production by an Engineered Type I Methanotrophic Bacterium

Methane, a byproduct of agricultural activities, has shown potential as a nonedible substrate for biomanufacturing. The production of succinate by a methanotrophic bacterium utilizing methane presents an innovative route for the sustainable synthesis of chemicals. In this study, Methylotuvimicrobium buryatense 5GB1S was genetically modified through the reconstruction of an artificial serine cycle to enable the bioconversion of both methane and CO2 into succinate. The 13C labeling analysis confirmed the CO2 fixing in M. buryatense 5GB1S, leading to a 46% improvement in carbon conversion efficiency and a 107% increase in succinate production compared to the wild-type strain. The transcriptome data on carbon metabolisms was assessed to guide future optimizations for strengthening the overall carbon flux from methane to succinate. Finally, the maximum succinate titer of 299.36 mg/L was achieved under oxygen-limited conditions in 3 L bioreactors, which resulted in the volumetric productivity of 199.60 mg/L/day, representing a 23-fold enhancement compared to the wild-type strain. This study offers a new strategy for upcycling greenhouse gases into succinate in a sustainable manner through methanotrophic-based biomanufacturing.

Enhancing l-Malic Acid Production in Aspergillus niger via Natural Activation of sthA Gene Expression

The efficient production of l-malic acid using Aspergillus niger requires overcoming challenges in synthesis efficiency and excessive byproduct buildup. This study addresses these hurdles, improving the activity of NADH-dependent malate dehydrogenase (Mdh) in the early stages of the fermentation process. By employing a constitutive promoter to express the Escherichia coli sthA responsible for the transfer of reducing equivalents between NAD(H) and NADP(H) in A. niger, the l-malic acid production was significantly elevated. However, this resulted in conidiation defects of A. niger, limiting industrial viability. To mitigate this, we discovered and utilized the PmfsA promoter, enabling the specific expression of sthA during the fermentation stage. This conditional expression strain showed similar phenotypes to its parent strain while exhibiting exceptional performance in a 5 L fermenter. Notably, it achieved a 65.5% increase in productivity, reduced fermentation cycle by 1.5 days, and lowered succinic acid by 76.2%. This work marks a promising advancement in industrial l-malic acid synthesis via biological fermentation, showcasing the potential of synthetic biology in A. niger for broader applications.

Unveiling malic acid biorefinery: Comprehensive insights into feedstocks, microbial strains, and metabolic pathways

The over-reliance on fossil fuels and resultant environmental issues necessitate sustainable alternatives. Microbial fermentation of biomass for malic acid production offers a viable, eco-friendly solution, enhancing resource efficiency and minimizing ecological damage. This review covers three core aspects of malic acid biorefining: feedstocks, microbial strains, and metabolic pathways. It emphasizes the significance of utilizing biomass sugars, including the co-fermentation of different sugar types to improve feedstock efficiency. The review discusses microbial strains for malic acid fermentation, addressing challenges related to by-products from biomass breakdown and strategies for overcoming them. It delves into the crucial pathways and enzymes for malic acid production, outlining methods to optimize its metabolism, focusing on enzyme regulation, energy balance, and yield enhancement. These insights contribute to advancing the field of consolidated bioprocessing in malic acid biorefining.

Engineering the metabolism and morphology of the filamentous fungus Trichoderma reesei for efficient L-malic acid production

L-malic acid (MA) is a vital platform chemical with huge market demand because of its broad industrial applications. A cell factory for MA production was engineered by strengthening the intrinsic pathway without inserting foreign genes into Trichoderma reesei. The native MA transporter gene in the T. reesei genome was characterized (trmae1), and its overexpression significantly improved MA production, which increased from 2 to 56.24 g/L. Native pyruvate carboxylase, malate dehydrogenase, malic enzyme, and glucose transporter were overexpressed further to improve the titer and yield of MA production. Fungal morphology was adapted to produce MA in the fermenter by deleting gul1. A titer of 235.8 g/L MA was produced from the final engineered strain in a 5-L fermenter with a yield of 1.48 mol of MA per mol of glucose and productivity of 1.23 g/L/h. This study provides novel insights for understanding and remodeling the MA synthesis pathway.

Fungal carboxylate transporters: recent manipulations and applications

Carboxylic acids containing acidic groups with additional keto/hydroxyl-groups or unsaturated bond have displayed great applicability in the food, agricultural, cosmetic, textile, and pharmaceutical industries. The traditional approach for carboxylate production through chemical synthesis is based on petroleum derivatives, resulting in concerns for the environmental complication and energy crisis, and increasing attention has been attracted to the eco-friendly and renewable bio-based synthesis for carboxylate production. The efficient and specific export of target carboxylic acids through the microbial membrane is essential for high productivity, yield, and titer of bio-based carboxylates. Therefore, understanding the characteristics, regulations, and efflux mechanisms of carboxylate transporters will efficiently increase industrial biotechnological production of carboxylic acids. Several transporters from fungi have been reported and used for improved synthesis of target products. The transport activity and substrate specificity are two key issues that need further improvement in the application of carboxylate transporters. This review presents developments in the structural and functional diversity of carboxylate transporters, focusing on the modification and regulation of carboxylate transporters to alter the transport activity and substrate specificity, providing new strategy for transporter engineering in constructing microbial cell factory for carboxylate production. KEY POINTS: • Structures of multiple carboxylate transporters have been predicted. • Carboxylate transporters can efficiently improve production. • Modification engineering of carboxylate transporters will be more popular in the future.

Simultaneous Production of Cellulase and β-Carotene in the Filamentous Fungus Trichoderma reesei

β-Carotene is an indispensable additive in beverage, cosmetic, feed, and pharmaceutical production. The fermentation industry annually generates abundant waste mycelia from Trichoderma reesei (T. reesei), a pivotal industrial strain for cellulase and heterologous protein production. In this study, we constructed a T. reesei cell factory for β-carotene production for the first time. Four key enzymes, CarRP, CarB, GGS1/CrtE, and HMG1, were overexpressed in T. reesei. The concentrations of medium components, including tryptone and glucose, were optimized. The modified strain accumulated β-carotene at a titer of 218.8 mg/L in flask culture. We achieved cellulase production (FPase, 22.33 IU/mL) with the concomitant production of β-carotene (286.63 mg/L) from T. reesei in a jar. Overall, this study offers a novel and unique approach to address the costly waste mycelium management process using T. reesei industrial strains that simultaneously produce proteins and carotenoids.