Metabolic engineering of Saccharomyces cerevisiae for the biotechnological production of succinic acid

Establishment of Saccharomyces cerevisiae as a cell factory for efficient de novo production of monogalactosyldiacylglycerol

Monogalactosyldiacylglycerol (MGDG), a predominant photosynthetic membrane lipid derived from plants and microalgae, has important applications in feed additives, medicine, and other fields. The low content and various structural stereoselectivity differences of MGDG in plants limited the biological extraction or chemical synthesis of MGDG, resulting in a supply shortage of monogalactosyldiacylglycerol with a growing demand. Herein, we established Saccharomyces cerevisiae as a cell factory for efficient de novo production of monogalactosyldiacylglycerol for the first time. Heterologous production of monogalactosyldiacylglycerol was achieved by overexpression of codon-optimized monogalactosyldiacylglycerol synthase gene MGD1, the key Kennedy pathway genes (i.e. GAT1, ICT1, and PAH1), and multi-copy integration of the MGD1 expression cassette. The final engineered strain (MG-8) was capable of producing monogalactosyldiacylglycerol with titers as high as 16.58 nmol/mg DCW in a shake flask and 103.2 nmol/mg DCW in a 5 L fed-batch fermenter, respectively. This is the first report of heterologous biosynthesis of monogalactosyldiacylglycerol in microorganisms, which will provide a favorable reference for study on heterologous production of monogalactosyldiacylglycerol in yeasts.

Recent advances in bio-based production of top platform chemical, succinic acid: an alternative to conventional chemistry

Succinic acid (SA) is one of the top platform chemicals with huge applications in diverse sectors. The presence of two carboxylic acid groups on the terminal carbon atoms makes SA a highly functional molecule that can be derivatized into a wide range of products. The biological route for SA production is a cleaner, greener, and promising technological option with huge potential to sequester the potent greenhouse gas, carbon dioxide. The recycling of renewable carbon of biomass (an indirect form of CO2), along with fixing CO2 in the form of SA, offers a carbon-negative SA manufacturing route to reduce atmospheric CO2 load. These attractive attributes compel a paradigm shift from fossil-based to microbial SA manufacturing, as evidenced by several commercial-scale bio-SA production in the last decade. The current review article scrutinizes the existing knowledge and covers SA production by the most efficient SA producers, including several bacteria and yeast strains. The review starts with the biochemistry of the major pathways accumulating SA as an end product. It discusses the SA production from a variety of pure and crude renewable sources by native as well as engineered strains with details of pathway/metabolic, evolutionary, and process engineering approaches for enhancing TYP (titer, yield, and productivity) metrics. The review is then extended to recent progress on separation technologies to recover SA from fermentation broth. Thereafter, SA derivatization opportunities via chemo-catalysis are discussed for various high-value products, which are only a few steps away. The last two sections are devoted to the current scenario of industrial production of bio-SA and associated challenges, along with the author's perspective.

An Eclectic Review on Dicarboxylic Acid Production Through Yeast Cell Factories and Its Industrial Prominence

Dicarboxylic acid (DCA) is a multifaceted chemical intermediate, recoursed to produce many industrially important products such as adhesives, plasticizers, lubricants, polymers, etc. To bypass the shortcomings of the chemical methods of synthesis of DCA and to reduce fossil fuel footprints, bio-based synthesis is gaining attention. In pursuit of an eco-friendly sustainable alternative method of DCA production, microbial cell factories, and renewable organic resources are gaining popularity. Among the plethora of microbial communities, yeast is being favored industrially compared to bacterial fermentation due to its hyperosmotic and low pH tolerance and flexibility for gene manipulations. By application of rapidly evolving genetic manipulation techniques, the bio-based DCA production could be made more precise and economical. To bridge the gap between supply and demand of DCA, many strategies are employed to improve the fermentation. This review briefly outlines the advancements in DCA production using yeast cell factories with the exemplification of strain improvement strategies.

Codon-optimization in gene therapy: promises, prospects and challenges

Codon optimization has evolved to enhance protein expression efficiency by exploiting the genetic code's redundancy, allowing for multiple codon options for a single amino acid. Initially observed in E. coli, optimal codon usage correlates with high gene expression, which has propelled applications expanding from basic research to biopharmaceuticals and vaccine development. The method is especially valuable for adjusting immune responses in gene therapies and has the potenial to create tissue-specific therapies. However, challenges persist, such as the risk of unintended effects on protein function and the complexity of evaluating optimization effectiveness. Despite these issues, codon optimization is crucial in advancing gene therapeutics. This study provides a comprehensive review of the current metrics for codon-optimization, and its practical usage in research and clinical applications, in the context of gene therapy.

Towards a hybrid model-driven platform based on flux balance analysis and a machine learning pipeline for biosystem design

Metabolic modeling and machine learning (ML) are crucial components of the evolving next-generation tools in systems and synthetic biology, aiming to unravel the intricate relationship between genotype, phenotype, and the environment. Nonetheless, the comprehensive exploration of integrating these two frameworks, and fully harnessing the potential of fluxomic data, remains an unexplored territory. In this study, we present, rigorously evaluate, and compare ML-based techniques for data integration. The hybrid model revealed that the overexpression of six target genes and the knockout of seven target genes contribute to enhanced ethanol production. Specifically, we investigated the influence of succinate dehydrogenase (SDH) on ethanol biosynthesis in Saccharomyces cerevisiae through shake flask experiments. The findings indicate a noticeable increase in ethanol yield, ranging from 6 % to 10 %, in SDH subunit gene knockout strains compared to the wild-type strain. Moreover, in pursuit of a high-yielding strain for ethanol production, dual-gene deletion experiments were conducted targeting glycerol-3-phosphate dehydrogenase (GPD) and SDH. The results unequivocally demonstrate significant enhancements in ethanol production for the engineered strains Δsdh4Δgpd1, Δsdh5Δgpd1, Δsdh6Δgpd1, Δsdh4Δgpd2, Δsdh5Δgpd2, and Δsdh6Δgpd2, with improvements of 21.6 %, 27.9 %, and 22.7 %, respectively. Overall, the results highlighted that integrating mechanistic flux features substantially improves the prediction of gene knockout strains not accounted for in metabolic reconstructions. In addition, the finding in this study delivers valuable tools for comprehending and manipulating intricate phenotypes, thereby enhancing prediction accuracy and facilitating deeper insights into mechanistic aspects within the field of synthetic biology.

Mitochondrial membrane transporters as attractive targets for the fermentative production of succinic acid from glycerol in Saccharomyces cerevisiae

Previously, we reported an engineered Saccharomyces cerevisiae CEN.PK113-1A derivative able to produce succinic acid (SA) from glycerol with net CO2 fixation. Apart from an engineered glycerol utilization pathway that generates NADH, the strain was equipped with the NADH-dependent reductive branch of the TCA cycle (rTCA) and a heterologous SA exporter. However, the results indicated that a significant amount of carbon still entered the CO2-releasing oxidative TCA cycle. The current study aimed to tune down the flux through the oxidative TCA cycle by targeting the mitochondrial uptake of pyruvate and cytosolic intermediates of the rTCA pathway, as well as the succinate dehydrogenase complex. Thus, we tested the effects of deletions of MPC1, MPC3, OAC1, DIC1, SFC1, and SDH1 on SA production. The highest improvement was achieved by the combined deletion of MPC3 and SDH1. The respective strain produced up to 45.5 g/L of SA, reached a maximum SA yield of 0.66 gSA/gglycerol, and accumulated the lowest amounts of byproducts when cultivated in shake-flasks. Based on the obtained data, we consider a further reduction of mitochondrial import of pyruvate and rTCA intermediates highly attractive. Moreover, the approaches presented in the current study might also be valuable for improving SA production when sugars (instead of glycerol) are the source of carbon.

Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica

Succinic acid (SA) is an important C4-dicarboxylic acid. Microbial production of SA at low pH results in low purification costs and hence good overall process economics. However, redox imbalances limited SA biosynthesis from glucose via the reductive tricarboxylic acid (TCA) cycle in yeast. Here, we engineer the strictly aerobic yeast Yarrowia lipolytica for efficient SA production without pH control. Introduction of the reductive TCA cycle into the cytosol of a succinate dehydrogenase-disrupted yeast strain causes arrested cell growth. Although adaptive laboratory evolution restores cell growth, limited NADH supply restricts SA production. Reconfiguration of the reductive SA biosynthesis pathway in the mitochondria through coupling the oxidative and reductive TCA cycle for NADH regeneration results in improved SA production. In pilot-scale fermentation, the engineered strain produces 111.9 g/L SA with a yield of 0.79 g/g glucose within 62 h. This study paves the way for industrial production of biobased SA.

Genome engineering of Kluyveromyces marxianus for high D-( -)-lactic acid production under low pH conditions

Saccharomyces cerevisiae is the workhorse of fermentation industry. Upon engineering for D-lactate production by a series of gene deletions, this yeast had deficiencies in cell growth and D-lactate production at high substrate concentrations. Complex nutrients or high cell density were thus required to support growth and D-lactate production with a potential to increase medium and process cost of industrial-scale D-lactate production. As an alternative microbial biocatalyst, a Crabtree-negative and thermotolerant yeast Kluyveromyces marxianus was engineered in this study to produce high titer and yield of D-lactate at a lower pH without growth defects. Only pyruvate decarboxylase 1 (PDC1) gene was replaced by a codon-optimized bacterial D-lactate dehydrogenase (ldhA). Ethanol, glycerol, or acetic acid was not produced by the resulting strain, KMΔpdc1::ldhA. Aeration rate at 1.5 vvm and culture pH 5.0 at 30 °C provided the highest D-lactate titer of 42.97 ± 0.48 g/L from glucose. Yield and productivity of D-lactate, and glucose-consumption rate were 0.85 ± 0.01 g/g, 0.90 ± 0.01 g/(L·h), and 1.06 ± 0.00 g/(L·h), respectively. Surprisingly, D-lactate titer, productivity, and glucose-consumption rate of 52.29 ± 0.68 g/L, 1.38 ± 0.05 g/(L·h), and 1.22 ± 0.00 g/(L·h), respectively, were higher at 42 °C compared to 30 °C. Sugarcane molasses, a low-value carbon, led to the highest D-lactate titer and yield of 66.26 ± 0.81 g/L and 0.91 ± 0.01 g/g, respectively, in a medium without additional nutrients. This study is a pioneer work of engineering K. marxianus to produce D-lactate at the yield approaching theoretical maximum using simple batch process. Our results support the potential of an engineered K. marxianus for D-lactate production on an industrial scale. KEY POINTS: • K. marxianus was engineered by deleting PDC1 and expressing codon-optimized D-ldhA. • The strain allowed high D-lactate titer and yield under pH ranging from 3.5 to 5.0. • The strain produced 66 g/L D-lactate at 30 °C from molasses without any additional nutrients.

Engineering Corynebacterium glutamicum for efficient production of succinic acid from corn stover pretreated by concentrated-alkali under steam-assistant conditions

Corynebacterium glutamicum was developed for efficient production of succinic acid from corn stover (CS) pretreated by concentrated-alkali under steam-assistant (CASA) conditions. First, C. glutamicum was engineered by 1) blocking the by-products pathways (deletion of ldh, pta-ackA, and cat), 2) enhancing the carbon flux to succinate (overexpression of pyc and ppc), and 3) releasing the end-product inhibition (overexpression of Ncgl0275). The recombinant strain produced 117.8 g/L succinate in fed-batch fermentation. Second, to fully utilize xylose in lignocellulosic hydrolysate, two xylose utilization pathways-the isomerase pathway and the Weimberg pathway-were introduced into the recombinant strain. Third, CS was pretreated by CASA with a higher sugars yield and a lower black liquid. Finally, 64.16 g/L of succinic acid was obtained from 150 g/L CASA-pretreated CS by engineered C. glutamicum. These results showed a succinate high-producing C. glutamicum strain using glucose and xylose simultaneously as well as an effective and environmentally acceptable pretreatment strategy.

Advances in the optimization of central carbon metabolism in metabolic engineering

Central carbon metabolism (CCM), including glycolysis, tricarboxylic acid cycle and the pentose phosphate pathway, is the most fundamental metabolic process in the activities of living organisms that maintains normal cellular growth. CCM has been widely used in microbial metabolic engineering in recent years due to its unique regulatory role in cellular metabolism. Using yeast and Escherichia coli as the representative organisms, we summarized the metabolic engineering strategies on the optimization of CCM in eukaryotic and prokaryotic microbial chassis, such as the introduction of heterologous CCM metabolic pathways and the optimization of key enzymes or regulatory factors, to lay the groundwork for the future use of CCM optimization in metabolic engineering. Furthermore, the bottlenecks in the application of CCM optimization in metabolic engineering and future application prospects are summarized.

Evaluating proteome allocation of Saccharomyces cerevisiae phenotypes with resource balance analysis

Saccharomyces cerevisiae is an important model organism and a workhorse in bioproduction. Here, we reconstructed a compact and tractable genome-scale resource balance analysis (RBA) model (i.e., named scRBA) to analyze metabolic fluxes and proteome allocation in a computationally efficient manner. Resource capacity models such as scRBA provide the quantitative means to identify bottlenecks in biosynthetic pathways due to enzyme, compartment size, and/or ribosome availability limitations. ATP maintenance rate and in vivo apparent turnover numbers (k_app) were regressed from metabolic flux and protein concentration data to capture observed physiological growth yield and proteome efficiency and allocation, respectively. Estimated parameter values were found to vary with oxygen and nutrient availability. Overall, this work (i) provides condition-specific model parameters to recapitulate phenotypes corresponding to different extracellular environments, (ii) alludes to the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency in glycolysis and electron transport chain, and (iii) reveals that the Crabtree effect is underpinned by specific limitations in mitochondrial proteome capacity and secondarily ribosome availability rather than overall proteome capacity.

Constructing recombinant Saccharomyces cerevisiae strains for malic-to-fumaric acid conversion

Saccharomyces cerevisiae with its robustness and good acid tolerance, is an attractive candidate for use in various industries, including waste-based biorefineries where a high-value organic acid is produced, such as fumaric acid could be beneficial. However, this yeast is not a natural producer of dicarboxylic acids, and genetic engineering of S. cerevisiae strains is required to achieve this outcome. Disruption of the natural FUM1 gene and the recombinant expression of fumarase and malate transporter genes improved the malic acid-to-fumaric acid conversion by engineered S. cerevisiae strains. The efficacy of the strains was significantly influenced by the source of the fumarase gene (yeast versus bacterial), the presence of the XYNSEC signal secretion signal and the available oxygen in synthetic media cultivations. The ΔFUM1Ckr_fum + mae1 and ΔFUM1(ss)Ckr_fum + mae1 strains converted extracellular malic acid into 0.98 and 1.11 g/L fumaric acid under aerobic conditions.

Recent advances in microbial production of diamines, aminocarboxylic acids, and diacids as potential platform chemicals and bio-based polyamides monomers

Recently, bio-based manufacturing processes of value-added platform chemicals and polymers in biorefineries using renewable resources have extensively been developed for sustainable and carbon dioxide (CO₂) neutral-based industry. Among them, bio-based diamines, aminocarboxylic acids, and diacids have been used as monomers for the synthesis of polyamides having different carbon numbers and ubiquitous and versatile industrial polymers and also as precursors for further chemical and biological processes to afford valuable chemicals. Until now, these platform bio-chemicals have successfully been produced by biorefinery processes employing enzymes and/or microbial host strains as main catalysts. In this review, we discuss recent advances in bio-based production of diamines, aminocarboxylic acids, and diacids, which has been developed and improved by systems metabolic engineering strategies of microbial consortia and optimization of microbial conversion processes including whole cell bioconversion and direct fermentative production.

Metabolic engineering of Schizosaccharomyces pombe for itaconic acid production

The economical production of value-added chemicals from renewable biomass is a promising aspect of producing a sustainable economy. Itaconic acid (IA) is a high value-added compound that is expected to be an alternative to petroleum-based chemicals. In this study, we developed a metabolic engineering strategy for the large-scale production of IA from glucose using the fission yeast Schizosaccharomyces pombe. Heterologous expression of the cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus, which encodes cis-aconitate decarboxylase in the cytosol, led to the production of 0.132 g/L of IA. We demonstrated that mitochondrial localization of CAD enhanced the production of IA. To prevent the leakage of carbon flux from the TCA cycle, we generated a strain in which the endogenous malate exporter, citrate lyase, and citrate transporter genes were disrupted. A titer of 1.110 g/L of IA was obtained from a culture of this strain started with 50 g/L of glucose. By culturing the multiple mutant strain at increased cell density, we succeeded in enhancing the IA production to 1.555 g/L. The metabolic engineering strategies presented in this study have the potential to improve the titer of the biosynthesis of derivatives of intermediates of the TCA cycle.

Technological advancements in valorization of second generation (2G) feedstocks for bio-based succinic acid production

Succinic acid (SA) is used as a commodity chemical and as a precursor in chemical industry to produce other derivatives such as 1,4-butaneidol, tetrahydrofuran, fumaric acid, and bio-polyesters. The production of bio-based SA from renewable feedstocks has always been in the limelight owing to the advantages of renewability, abundance and reducing climate change by CO₂ capture. Considering this, the current review focuses on various 2G feedstocks such as lignocellulosic biomass, crude glycerol, and food waste for cost-effective SA production. It also highlights the importance of producing SA via separate enzymatic hydrolysis and fermentation, simultaneous saccharification and fermentation, and consolidated bioprocessing. Furthermore, recent advances in genetic engineering, and downstream SA processing are thoroughly discussed. It also elaborates on the techno-economic analysis and life cycle assessment (LCA) studies carried out to understand the economics and environmental effects of bio-based SA synthesis.

Inducible expression of large gRNA arrays for multiplexed CRISPRai applications

CRISPR gene activation and inhibition (CRISPRai) has become a powerful synthetic tool for influencing the expression of native genes for foundational studies, cellular reprograming, and metabolic engineering. Here we develop a method for near leak-free, inducible expression of a polycistronic array containing up to 24 gRNAs from two orthogonal CRISPR/Cas systems to increase CRISPRai multiplexing capacity and target gene flexibility. To achieve strong inducibility, we create a technology to silence gRNA expression within the array in the absence of the inducer, since we found that long gRNA arrays for CRISPRai can express themselves even without promoter. Using this method, we create a highly tuned and easy-to-use CRISPRai toolkit in the industrially relevant yeast, Saccharomyces cerevisiae, establishing the first system to combine simultaneous activation and repression, large multiplexing capacity, and inducibility. We demonstrate this toolkit by targeting 11 genes in central metabolism in a single transformation, achieving a 45-fold increase in succinic acid, which could be precisely controlled in an inducible manner. Our method offers a highly effective way to regulate genes and rewire metabolism in yeast, with principles of gRNA array construction and inducibility that should extend to other chassis organisms.

Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae

Background

The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO₂). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO₂-fixation yield compared to sugars. Recently, we described an engineered Saccharomyces cerevisiae strain which allowed SA production in synthetic glycerol medium with a maximum yield of 0.23 Cmol Cmol⁻¹. The results of that previous study suggested that the glyoxylate cycle considerably contributed to SA accumulation in the respective strain. The current study aimed at improving the flux into the rTCA pathway accompanied by a higher CO₂-fixation and SA yield.

Results

By changing the design of the expression cassettes for the rTCA pathway, overexpressing PYC2, and adding CaCO₃ to the batch fermentations, an SA yield on glycerol of 0.63 Cmol Cmol⁻¹ was achieved (i.e. 47.1% of the theoretical maximum). The modifications in this 2nd-generation SA producer improved the maximum biomass-specific glycerol consumption rate by a factor of nearly four compared to the isogenic baseline strain solely equipped with the dihydroxyacetone (DHA) pathway for glycerol catabolism. The data also suggest that the glyoxylate cycle did not contribute to the SA production in the new strain. Cultivation conditions which directly or indirectly increased the concentration of bicarbonate, led to an accumulation of malate in addition to the predominant product SA (ca. 0.1 Cmol Cmol⁻¹ at the time point when SA yield was highest). Off-gas analysis in controlled bioreactors with CO₂-enriched gas-phase indicated that CO₂ was fixed during the SA production phase.

Conclusions

The data strongly suggest that a major part of dicarboxylic acids in our 2nd-generation SA-producer was formed via the rTCA pathway enabling a net fixation of CO₂. The greatly increased capacity of the rTCA pathway obviously allowed successful competition with other pathways for the common precursor pyruvate. The overexpression of PYC2 and the increased availability of bicarbonate, the co-substrate for the PYC reaction, further strengthened this capacity. The achievements are encouraging to invest in future efforts establishing a process for SA production from (crude) glycerol and CO₂.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01817-1.

Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate

BACKGROUND

Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars-in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized. If they could be converted into value-added chemicals, overall economic profitability of the process would increase. SSLs are typically very inhibitory to microorganisms, which presents a challenge for a biotechnological process. The aim of the present work was to develop a robust yeast strain able to convert xylose in SSL to carboxylic acids.

RESULTS

The industrial strain Ethanol Red of the yeast Saccharomyces cerevisiae was engineered for efficient utilization of xylose in a Eucalyptus globulus lignosulfonate stream at low pH using CRISPR/Cas genome editing and adaptive laboratory evolution. The engineered strain grew in synthetic medium with xylose as sole carbon source with maximum specific growth rate (µ_max) of 0.28 1/h. Selected evolved strains utilized all carbon sources in the SSL at pH 3.5 and grew with µ_max between 0.05 and 0.1 1/h depending on a nitrogen source supplement. Putative genetic determinants of the increased tolerance to the SSL were revealed by whole genome sequencing of the evolved strains. In particular, four top-candidate genes (SNG1, FIT3, FZF1 and CBP3) were identified along with other gene candidates with predicted important roles, based on the type and distribution of the mutations across different strains and especially the best performing ones. The developed strains were further engineered for production of dicarboxylic acids (succinic and malic acid) via overexpression of the reductive branch of the tricarboxylic acid cycle (TCA). The production strain produced 0.2 mol and 0.12 mol of malic acid and succinic acid, respectively, per mol of xylose present in the SSL.

CONCLUSIONS

The combined metabolic engineering and adaptive evolution approach provided a robust SSL-tolerant industrial strain that converts fermentable carbon content of the SSL feedstock into malic and succinic acids at low pH.in production yields reaching 0.1 mol and 0.065 mol per mol of total consumed carbon sources.. Moreover, our work suggests potential genetic background of the tolerance to the SSL stream pointing out potential gene targets for improving the tolerance to inhibitory industrial feedstocks.

Examining organic acid production potential and growth-coupled strategies in Issatchenkia orientalis using constraint-based modeling

Growth-coupling product formation can facilitate strain stability by aligning industrial objectives with biological fitness. Organic acids make up many building block chemicals that can be produced from sugars obtainable from renewable biomass. Issatchenkia orientalis is a yeast strain tolerant to acidic conditions and is thus a promising host for industrial production of organic acids. Here, we use constraint-based methods to assess the potential of computationally designing growth-coupled production strains for I. orientalis that produce 22 different organic acids under aerobic or microaerobic conditions. We explore native and engineered pathways using glucose or xylose as the carbon substrates as proxy constituents of hydrolyzed biomass. We identified growth-coupled production strategies for 37 of the substrate-product pairs, with 15 pairs achieving production for any growth rate. We systematically assess the strain design solutions and categorize the underlying principles involved.

Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.

Potential Valorization of Organic Waste Streams to Valuable Organic Acids through Microbial Conversion: A South African Case Study

The notion of a “biobased economy” in the context of a developing country such as South Africa (SA) necessitates the development of technologies that utilize sustainable feedstocks, have simple and robust operations, are feasible at small scale and produce a variety of valuable bioproducts, thus fitting the biorefinery concept. This case study focuses on the microbial production of higher-value products from selected organic waste streams abundant in the South African agricultural sector using microbes adapted to utilize different parts of biomass waste streams. A ruminant-based carboxylate platform based on mixed or undefined anaerobic co-cultures of rumen microorganisms can convert the carbohydrate polymers in the lignocellulosic part of organic waste streams to carboxylic acids that can be upgraded to biofuels or green chemicals. Furthermore, yeast and fungi can convert the simpler carbohydrates (such as the sugars and malic acid in grape and apple pomace) to ethanol and high-value carboxylic acids, such as lactic, fumaric, succinic and citric acid. This review will discuss the combinational use of the ruminal carboxylate platform and native or recombinant yeasts to valorize biomass waste streams through the production of higher-value organic acids with various applications.

Influence of Synthetic Flavorings on the Migration Activity of Tribolium confusum and Sitophilus granarius

Flavorings and volatile biologically active substances, used by humans for various purposes, may potentially have fumigating, repellent, or attractive effects on various species of anthropod storage pests. Tribolium confusum Jacquelin du Val, 1863 (Tenebrionidae) and Sitophilus granarius (Linnaeus, 1758) (Curculionidae) are the two most abundant pests of grain and grain products; the damage they cause to stored products of horticulture is 5–20% of the total yield of grain crops. In the experiment, we video-recorded migratory activity of beetles and evaluated it according to standard time periods (10, 20, 30, 60, and 120 seconds after the start of the experiment). No reliable influence of the 15 tested flavoring substances (benzyl alcohol, benzoic acid, toluene, hydroquinone, phenethyl alcohol, pinene, methylparaben, kojic acid, formic acid, isoamyl alcohol, tartaric acid, glycine, succinic acid, stearic acid, and ethylenediaminetetraacetic acid) on moving activity of Tribolium confusum was found. Exposure to benzyl alcohol brought a reliable decrease in locomotor activity of Sitophilus granarius (it exerted an attractant effect on imagoes as compared with the variant of the experiment without aromatic substances): 6.09 times more imagoes of S. granarius remained at a minimal distance from the aroma source than in the control, 6.07 more while exposed to hydroquinone, 5.50 to phenethyl alcohol, 4.50 to glycine, 3.44 to EDTA, 3.30 to toluene, 3.18 to methylparaben, 2.84 to succinic acid, 2.65 to benzoic acid, and 2.15 more when exposed to formic acid compared with the control variant of the experiment. Other surveyed flavoring substances (benzyl alcohol, pinene, kojic acid, isoamyl alcohol, tartaric acid, and stearic acid) had no significant effect on migratory activity of imagoes of S. granarius. The results allow us to recommend benzyl alcohol, hydroquinone, phenethyl alcohol, and glycine as potential luring substances or components of multicomponent flavoring mixtures during the assessment of the number of S. granarius in grain storage and processing facilities.

Impact of nitrogen deficiency on succinic acid production by engineered strains of Yarrowia lipolytica

Yarrowia lipolytica strains PGC01003 and PGC202 engineered for succinic acid production were studied and compared to the wild type strain W29. For the first time, these two strains were characterized in a chemically defined medium. Strain growth and organic acid production were investigated in fed-batch mode with glycerol as carbon and energy source. This study evaluated the impact of nitrogen deficiency strategy to redirect carbon flux toward succinic acid synthesis. Strain PGC01003 produced 19 g L^-1 succinic acid with an overall yield of 0.23 g g^-1 and an overall productivity of 0.23 g L^-1 h^-1, while strain PGC202 produced 33 g L^-1 succinic acid with an overall yield of 0.12 g g^-1 and a productivity of 0.57 g L^-1 h^-1. Nitrogen limitation effectively stopped biomass growth and increased succinic acid yield of PGC01003 and PGC202 by 18 % and 62 %, respectively. However, the specific succinic acid production rate was reduced by 77 % and 66 %, respectively.

Transportome-wide engineering of Saccharomyces cerevisiae

Synthetic biology enables the production of small molecules by recombinant microbes for pharma, food, and materials applications. The secretion of products reduces the cost of separation and purification, but it is challenging to engineer due to the limited understanding of the transporter proteins' functions. Here we describe a method for genome-wide transporter disruption that, in combination with a metabolite biosensor, enables the identification of transporters impacting the production of a given target metabolite in yeast Saccharomyces cerevisiae. We applied the method to study the transport of xenobiotic compounds, cis,cis-muconic acid (CCM), protocatechuic acid (PCA), and betaxanthins. We found 22 transporters that influenced the production of CCM or PCA. The transporter of the 12-spanner drug:H(+) antiporter (DHA1) family Tpo2p was further confirmed to import CCM and PCA in Xenopus expression assays. We also identified three transporter proteins (Qdr1p, Qdr2p, and Apl1p) involved in betaxanthins transport. In summary, the described method enables high-throughput transporter identification for small molecules in cell factories.

Metabolic engineering of Saccharomyces cerevisiae for the production of top value chemicals from biorefinery carbohydrates

The implementation of biorefineries for a cost-effective and sustainable production of energy and chemicals from renewable carbon sources plays a fundamental role in the transition to a circular economy. The US Department of Energy identified a group of key target compounds that can be produced from biorefinery carbohydrates. In 2010, this list was revised and included organic acids (lactic, succinic, levulinic and 3-hydroxypropionic acids), sugar alcohols (xylitol and sorbitol), furans and derivatives (hydroxymethylfurfural, furfural and furandicarboxylic acid), biohydrocarbons (isoprene), and glycerol and its derivatives. The use of substrates like lignocellulosic biomass that impose harsh culture conditions drives the quest for the selection of suitable robust microorganisms. The yeast Saccharomyces cerevisiae, widely utilized in industrial processes, has been extensively engineered to produce high-value chemicals. For its robustness, ease of handling, genetic toolbox and fitness in an industrial context, S. cerevisiae is an ideal platform for the founding of sustainable bioprocesses. Taking these into account, this review focuses on metabolic engineering strategies that have been applied to S. cerevisiae for converting renewable resources into the previously identified chemical targets. The heterogeneity of each chemical and its manufacturing process leads to inevitable differences between the development stages of each process. Currently, 8 of 11 of these top value chemicals have been already reported to be produced by recombinant S. cerevisiae. While some of them are still in an early proof-of-concept stage, others, like xylitol or lactic acid, are already being produced from lignocellulosic biomass. Furthermore, the constant advances in genome-editing tools, e.g. CRISPR/Cas9, coupled with the application of innovative process concepts such as consolidated bioprocessing, will contribute for the establishment of S. cerevisiae-based biorefineries.

Promising advancement in fermentative succinic acid production by yeast hosts

As a platform chemical with various applications, succinic acid (SA) is currently produced by petrochemical processing from oil-derived substrates such as maleic acid. In order to replace the environmental unsustainable hydrocarbon economy with a renewable environmentally sound carbohydrate economy, bio-based SA production process has been developed during the past two decades. In this review, recent advances in the valorization of solid organic wastes including mixed food waste, agricultural waste and textile waste for efficient, green and sustainable SA production have been reviewed. Firstly, the application, market and key global players of bio-SA are summarized. Then achievements in SA production by several promising yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica are detailed, followed by calculation and comparison of SA production costs between oil-based substrates and raw materials. Lastly, challenges in engineered microorganisms and fermentation processes are presented together with perspectives on the development of robust yeast SA producers via genome-scale metabolic optimization and application of low-cost raw materials as fermentation substrates. This review provides valuable insights for identifying useful directions for future bio-SA production improvement.

High level production of itaconic acid at low pH by Ustilago maydis with fed-batch fermentation

The metabolically engineered plant pathogen Ustilago maydis MB215 Δcyp3 P_etefria1 has been cultivated to produce more than 80 g/L itaconate in 16 L scale pH and temperature controlled fermentation, in fed-batch mode with two successive feedings. The effect of pH as well as successive rounds of feeding has been quantified via elemental balances. Volumetric itaconic acid productivity gradually decreased with successive glucose feedings with increasing itaconic titers, with nearly constant product yield. Extracellular pH was decreased from 6 down to 3.5 and the fermentation was characterized in specific uptake, production, and growth rates. Notable is that the biomass composition changes significantly from growth phase to itaconic acid production phase, carbon content increases from 42% to around 62%. Despite the gradual decrease in itaconic acid levels with decreasing pH (nearly 50% decrease in itaconic acid at pH 3.5, compared to pH 6), significant itaconate production is still observed at pH 4 (around 63 g/L). Biomass yield remained nearly constant until pH 4. Taken together, these results strongly illustrate the potential of engineered Ustilago maydis in itaconate production at commercial levels.

Production of biodiesel and succinic acid from the biomass of the microalga Micractinium sp. IC-44

In this study, a combined approach to produce fatty acid methyl esters (FAMEs) and succinic acid from the biomass of the microalga Micractinium sp. IC-44 using ionic liquids (ILs) was presented. After 22 days of cultivation, the biomass productivity was 0.034 ± 0.001 g L^-1day^-1, and the lipid content was 11.5 ± 0.5%. Direct biomass transesterification using H₂SO₄ in the presence of IL [BMIM][HSO₄] resulted in a FAME yield of 42.0 ± 4.3%, which exceeded the yields obtained after transesterification of extracted lipids (20.5 ± 3.5% using ILs and 27.1 ± 2.4% using methanol/chloroform) and direct biomass transesterification without using ILs (31.6 ± 1.7%). The residual biomass obtained after direct transesterification using ILs was subjected to acid hydrolysis (sugar yield was 81.1 ± 2.4%). The purified hydrolysate was fermented using Actinobacillus succinogenes 130Z to obtain a succinic acid yield of 0.67 g g^-1 of fermentable sugars. Therefore, this study demonstrated the successful conversion of the Micractinium sp. IC-44 biomass into biodiesel and succinic acid.

Interaction of Isocitrate Lyase with Proteins Involved in the Energetic Metabolism in Paracoccidioides lutzii

Background: Systemic mycosis is a cause of death of immunocompromised subjects. The treatment directed to evade fungal pathogens shows severe limitations, such as time of drug exposure and side effects. The paracoccidioidomycosis (PCM) treatment depends on the severity of the infection and may last from months to years. Methods: To analyze the main interactions of Paracoccidioides lutzii isocitrate lyase (ICL) regarding the energetic metabolism through affinity chromatography, we performed blue native PAGE and co-immunoprecipitation to identify ICL interactions. We also performed in silico analysis by homology, docking, hot-spot prediction and contact preference analysis to identify the conformation of ICL complexes. Results: ICL interacted with 18 proteins in mycelium, 19 in mycelium-to-yeast transition, and 70 in yeast cells. Thirty complexes were predicted through docking and contact preference analysis. ICL has seven main regions of interaction with protein partners. Conclusions: ICL seems to interfere with energetic metabolism of P. lutzii, regulating aerobic and anaerobic metabolism as it interacts with proteins from glycolysis, gluconeogenesis, TCA and methylcitrate cycles, mainly through seven hot-spot residues.

Metabolic pathway engineering: Perspectives and applications

BACKGROUND

Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering.

CONCLUSION

In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.

Engineering Saccharomyces cerevisiae for Succinic Acid Production From Glycerol and Carbon Dioxide

Previously, our lab replaced the endogenous FAD-dependent pathway for glycerol catabolism in S. cerevisiae by the synthetic NAD-dependent dihydroxyacetone (DHA) pathway. The respective modifications allow the full exploitation of glycerol’s higher reducing power (compared to sugars) for the production of the platform chemical succinic acid (SA) via a reductive, carbon dioxide fixing and redox-neutral pathway in a production host robust for organic acid production. Expression cassettes for three enzymes converting oxaloacetate to SA in the cytosol (“SA module”) were integrated into the genome of UBR2_CBS-DHA, an optimized CEN.PK derivative. Together with the additional expression of the heterologous dicarboxylic acid transporter DCT-02 from Aspergillus niger, a maximum SA titer of 10.7 g/L and a yield of 0.22 ± 0.01 g/g glycerol was achieved in shake flask (batch) cultures. Characterization of the constructed strain under controlled conditions in a bioreactor supplying additional carbon dioxide revealed that the carbon balance was closed to 96%. Interestingly, the results of the current study indicate that the artificial “SA module” and endogenous pathways contribute to the SA production in a highly synergistic manner.

Recent progress on bio-based production of dicarboxylic acids in yeast

Dicarboxylic acids are widely used in fine chemical and food industries as well as the monomer for polymerisation of high molecular material. Given the problems of environmental contamination and sustainable development faced by traditional production of dicarboxylic acids based on petrol, new approaches such as bio-based production of dicarboxylic acids drew more attentions. The yeast, Saccharomyces cerevisiae, was regarded as an ideal organism for bio-based production of dicarboxylic acids with high tolerance to acidic and hyperosmotic environments, robust growth using a broad range of substrates, great convenience for genetic manipulation, stable inheritance via sub-cultivation, and food compatibility. In this review, the production of major dicarboxylates via S. cerevisiae was concluded and the challenges and opportunities facing were discussed.Key Points• Summary of current production of major dicarboxylic acids by Saccharomyces cerevisiae.• Discussion of influence factors on four-carbon dicarboxylic acids production by Saccharomyces cerevisiae.• Outlook of potential production of five- and six-carbon dicarboxylic acids by Saccharomyces cerevisiae.

Advances in microbial production of medium-chain dicarboxylic acids for nylon materials

Medium-chain dicarboxylic acids (MDCAs) are widely used in the production of nylon materials, and among which, succinic, glutaric, adipic, pimelic, suberic, azelaic and sebacic acids are particularly important for that purpose.

Involvement of the external mitochondrial NADH dehydrogenase Nde1 in glycerol metabolism by wild-type and engineered Saccharomyces cerevisiae strains

Glycerol is an attractive substrate for microbial fermentations due to its higher degree of reduction compared to glucose. The replacement of the native FAD-dependent glycerol catabolic pathway in Saccharomyces cerevisiae by an artificial NADH-delivering dihydroxyacetone (DHA) pathway is supposed to facilitate the capturing of electrons in fermentation products. This requires that the electrons from the cytosolic NADH are not exclusively transferred to oxygen. However, the external NADH dehydrogenases (Nde1/2) and the L-glycerol 3-phosphate shuttle (composed of Gpd1/2 and Gut2), both coupled to the respiratory chain, are known to contribute to cytosolic NAD+ regeneration during growth on non-fermentable carbon sources. In order to evaluate the role of these mechanisms during growth on glycerol, we deleted GPD1/2, GUT2 as well as NDE1/2, separately and in combinations in both the glycerol-utilizing wild-type strain CBS 6412-13A and the corresponding engineered strain CBS DHA in which glycerol is catabolized by the DHA pathway. Particularly, the nde1Δ mutants showed a significant reduction in growth rate and the nde1∆ nde2∆ double deletion mutants did not grow at all in synthetic glycerol medium. The current work also demonstrates a positive impact of deleting NDE1 on the production of the fermentation product 1,2-propanediol in an accordingly engineered S. cerevisiae strain.

Engineering Oleaginous Yeast as the Host for Fermentative Succinic Acid Production From Glucose

Oleaginous yeast Yarrowia lipolytica is a prospective host for production of succinic acid. The interruption of tricarboxylic acid cycle through succinate dehydrogenase gene (SDH) deletion was reported to result in strains incapable of glucose utilization and this ability had to be restored by chemical mutation or long adaptive laboratory evolution. In this study, a succinate producing strain of Y. lipolytica was engineered by truncating the promoter of SDH1 gene, which resulted in 77% reduction in SDH activity but did not impair the ability of the strain to grow on glucose. The flux toward succinic acid was further improved by overexpressing the genes in the glyoxylate pathway and the oxidative TCA branch, and expressing phosphoenolpyruvate carboxykinase from Actinobacillus succinogenes. A short adaptation on glucose reduced the lag phase of the strain and increased its tolerance to high glucose concentrations. The resulting strain produced 7.8 ± 0.0 g/L succinic acid with a yield of 0.105 g/g glucose in shake flasks without pH control, while mannitol (11.8 ± 0.8 g/L) was the main by-product. Further investigations showed that mannitol accumulation was caused by low pH stress and buffering the fermentation medium eliminated mannitol formation. In a fed-batch bioreactor in mineral medium at pH 5, at which point according to K_a values of succinic acid, the major fraction of product was in acidic form rather than dissociated form, the strain produced 35.3 ± 1.5 g/L succinic acid with 0.26 ± 0.00 g/g glucose yield.

Efficient Biosynthesis of High-Value Succinic Acid and 5-Hydroxyleucine Using a Multienzyme Cascade and Whole-Cell Catalysis

Succinic acid (SA) is applied in the food, chemical, and pharmaceutical industries. 5-Hydroxyleucine (5-HLeu) is a promising precursor for the biosynthesis of antituberculosis drugs. Here, we designed a promising synthetic route for the simultaneous production of SA and 5-HLeu by combining l-leucine dioxygenase (NpLDO), l-glutamate oxidase (LGOX), and catalase (CAT). Two bioconversion systems: "a multienzyme cascade catalysis in vitro" (MECCS) and "whole-cell catalysis system" (WCCS) were constructed. A high-activity NpLDO mutant was screened by error-prone polymerase chain reaction (PCR) and showed 6.1-fold improvement of catalytic activity. After optimization of reaction conditions, MECSS yielded 3.15 g/L SA and 3.92 g/L 5-HLeu, while the production of SA and 5-HLeu by the most effective WCSS reached 15.12 and 18.83 g/L, respectively. This is the first attempt to use ferrous iron/α-ketoglutarate-dependent dioxygenases for the simultaneous production of SA and hydroxy-amino-acid. This research provides a tool for industrial production of food of high-value products from low-cost raw materials.

Efficient production of gamma-aminobutyric acid by engineered Saccharomyces cerevisiae with glutamate decarboxylases from Streptomyces

Gamma-aminobutyric acid (GABA) is an industrially valuable natural product. This study was aimed to establish an efficient food-grade production process of GABA by engineering Saccharomyces cerevisiae that is generally recognized as safe (GRAS). GABA can be produced by catalytic decarboxylation of l-glutamate (l-Glu) by glutamate decarboxylase (GAD, EC4.1.1.15). Two GADs, SsGAD from Streptomyces sp. MJ654-NF4 and ScGAD from Streptomyces chromofuscus ATCC 49982, were heterologously expressed in S. cerevisiae BJ5464. The engineered yeast strains were used as whole-cell biocatalysts for GABA production. S. cerevisiae BJ5464/SsGAD exhibited significantly higher efficient catalytic activity than that of S. cerevisiae BJ5464/ScGAD. The optimal bioconversion system consisted of a cell density of OD₆₀₀ 30, 0.1 M l-Glu, and 0.28 mM pyridoxal phosphate in 0.2 M Na₂ HPO₄ -citric acid buffer with pH 5.4, and the reactions were performed at 50 °C for 12 H. S. cerevisiae BJ5464/SsGAD cells can be reused, and the accumulated GABA titer reached 62.6 g/L after 10 batches with an overall molar conversion rate of 60.8 mol%. This work thus provides an effective production process of GABA using engineered yeast for food and pharmaceutical applications.

Evaluation of pyruvate decarboxylase-negative Saccharomyces cerevisiae strains for the production of succinic acid

Dicarboxylic acids are important bio‐based building blocks, and Saccharomyces cerevisiae is postulated to be an advantageous host for their fermentative production. Here, we engineered a pyruvate decarboxylase‐negative S. cerevisiae strain for succinic acid production to exploit its promising properties, that is, lack of ethanol production and accumulation of the precursor pyruvate. The metabolic engineering steps included genomic integration of a biosynthesis pathway based on the reductive branch of the tricarboxylic acid cycle and a dicarboxylic acid transporter. Further modifications were the combined deletion of GPD1 and FUM1 and multi‐copy integration of the native PYC2 gene, encoding a pyruvate carboxylase required to drain pyruvate into the synthesis pathway. The effect of increased redox cofactor supply was tested by modulating oxygen limitation and supplementing formate. The physiologic analysis of the differently engineered strains focused on elucidating metabolic bottlenecks. The data not only highlight the importance of a balanced activity of pathway enzymes and selective export systems but also shows the importance to find an optimal trade‐off between redox cofactor supply and energy availability in the form of ATP.

Biotechnological Production of Organic Acids from Renewable Resources

Biotechnological processes are promising alternatives to petrochemical routes for overcoming the challenges of resource depletion in the future in a sustainable way. The strategies of white biotechnology allow the utilization of inexpensive and renewable resources for the production of a broad range of bio-based compounds. Renewable resources, such as agricultural residues or residues from food production, are produced in large amounts have been shown to be promising carbon and/or nitrogen sources. This chapter focuses on the biotechnological production of lactic acid, acrylic acid, succinic acid, muconic acid, and lactobionic acid from renewable residues, these products being used as monomers for bio-based material and/or as food supplements. These five acids have high economic values and the potential to overcome the "valley of death" between laboratory/pilot scale and commercial/industrial scale. This chapter also provides an overview of the production strategies, including microbial strain development, used to convert renewable resources into value-added products.