Combining metabolic engineering and evolutionary adaptation in Klebsiella oxytoca KMS004 to significantly improve optically pure D-(-)-lactic acid yield and specific productivity in low nutrient medium

Advances and new horizons in metabolic engineering of heterotrophic bacteria and cyanobacteria for enhanced lactic acid production

Bacteria species such as E.Coli, Lactobacilli, and pediococci play an important role as starter strains in fermentation food or polysaccharides into lactic acid. These bacteria were metabolically engineered using multiple proven genome editing methods to enhance relevant phenotypes. The efficacy of these procedures varies depending on the editing tool used and researchers' ability to pick suitable recombinants, which significantly increased genome engineering throughput. Cyanobacteria produce oxygenic photosynthesis and play an important role in carbon dioxide fixing. The fixed carbon dioxide is then retained as polysaccharides in cells and metabolised into various low carbon molecules such as lactate, succinate, and ethanol. Lactate is used as a building ingredient in various bioplastics, food additives, and medicines. This review covers the recent advances in lactic acid production through metabolic and genetic engineering in bacteria and cyanobacteria.

Simultaneous saccharification and fermentation for D-lactic acid production using a metabolically engineered Escherichia coli adapted to high temperature

BACKGROUND

Escherichia coli JU15 is a metabolically engineered strain capable to metabolize C5 and C6 sugars with a high yield of D-lactic acid production at its optimal growth temperature (37 °C). The simultaneous saccharification and fermentation process allow to use lignocellulosic biomass as a cost-effective and high-yield strategy. However, this process requires microorganisms capable of growth at a temperature close to 50 °C, at which the activity of cellulolytic enzymes works efficiently.

RESULTS

The thermotolerant strain GT48 was generated by adaptive laboratory evolution in batch and chemostat cultures under temperature increments until 48 °C. The strain GT48 was able to grow and ferment glucose to D-lactate at 47 °C. It was found that a pH of 6.3 conciliated with GT48 growth and cellulase activity of a commercial cocktail. Hence, this pH was used for the SSF of a diluted acid-pretreated corn stover (DAPCS) at a solid load of 15% (w/w), 15 FPU/g-DAPCS, and 47 °C. Under such conditions, the strain GT48 exhibited remarkable performance, producing D-lactate at a level of 1.41, 1.42, and 1.48-fold higher in titer, productivity, and yield, respectively, compared to parental strain at 45 °C.

CONCLUSIONS

In general, our results show for the first time that a thermal-adapted strain of E. coli is capable of being used in the simultaneous saccharification and fermentation process without pre-saccharification stage at high temperatures.

Microbial Protein and Metabolite Profiles of Klebsiella oxytoca M5A1 in a Bubble Column Bioreactor

The production of microbial proteins (MPs) has emerged as a critical focus in biotechnology, driven by the need for sustainable and scalable alternatives to traditional protein sources. This study investigates the efficacy of two experimental setups in producing MPs using the nitrogen-fixing bacterium Klebsiella oxytoca M5A1. K. oxytoca M5A1, known for its facultative anaerobic growth and capability to fix atmospheric nitrogen, offers a promising avenue for environmentally friendly protein production. This research compares the performance of a simple bubble column (BC) bioreactor, which promotes efficient mixing and cross-membrane gas transfer, with static fermentation, a traditional method lacking agitation and aeration. The study involved the parallel cultivation of K. oxytoca M5A1 in both systems, with key parameters such as microbial growth, glucose utilization, protein concentration, and metabolite profiles monitored over a 48 h period. The results indicate that the BC bioreactor consistently outperformed static fermentation regarding the growth rate, protein yield, and glucose utilization efficiency. The BC exhibited a significant increase in protein production, reaching 299.90 µg/mL at 48 h, compared to 219.44 µg/mL in static fermentation. The organic acid profile reveals both synthesis and utilization regimes of varying patterns. These findings highlight the advantages of the BC bioreactor for MP production, particularly its ability to maintain aerobic conditions that support higher growth and yield.

Production of α-ketoisovalerate with whey powder by systemic metabolic engineering of Klebsiella oxytoca

BACKGROUND

Whey, which has high biochemical oxygen demand and chemical oxygen demand, is mass-produced as a major by-product of the dairying industry. Microbial fermentation using whey as the carbon source may convert this potential pollutant into value-added products. This study investigated the potential of using whey powder to produce α-ketoisovalerate, an important platform chemical.

RESULTS

Klebsiella oxytoca VKO-9, an efficient L-valine producing strain belonging to Risk Group 1 organism, was selected for the production of α-ketoisovalerate. The leucine dehydrogenase and branched-chain α-keto acid dehydrogenase, which catalyzed the reductive amination and oxidative decarboxylation of α-ketoisovalerate, respectively, were inactivated to enhance the accumulation of α-ketoisovalerate. The production of α-ketoisovalerate was also improved through overexpressing α-acetolactate synthase responsible for pyruvate polymerization and mutant acetohydroxyacid isomeroreductase related to α-acetolactate reduction. The obtained strain K. oxytoca KIV-7 produced 37.3 g/L of α-ketoisovalerate from lactose, the major utilizable carbohydrate in whey. In addition, K. oxytoca KIV-7 also produced α-ketoisovalerate from whey powder with a concentration of 40.7 g/L and a yield of 0.418 g/g.

CONCLUSION

The process introduced in this study enabled efficient α-ketoisovalerate production from low-cost substrate whey powder. Since the key genes for α-ketoisovalerate generation were integrated in genome of K. oxytoca KIV-7 and constitutively expressed, this strain is promising in stable α-ketoisovalerate fermentation and can be used as a chassis strain for α-ketoisovalerate derivatives production.

Techno-economical valorization of sugarcane bagasse for efficiently producing optically pure D-(-)-lactate approaching the theoretical maximum yield in low-cost salt medium by metabolically engineered Klebsiella oxytoca

Sugarcane bagasse (SCB) was utilized for efficiently producing optically pure D-(-)-lactate by Klebsiella oxytoca KIS004-91T strain. Cellulase (15 U/g NaOH-treated SCB) sufficiently liberated high sugars with saccharifications of 79.8 % cellulose and 52.5 % hemicellulose. For separated hydrolysis and fermentation, D-(-)-lactate was produced at 53.5 ± 2.1 g/L (0.98 ± 0.01 g/g sugar utilized or 0.71 ± 0.01 g/g total sugars) while D-(-)-lactate at 47.2 ± 1.8 g/L (0.78 ± 0.03 g/g sugar used or 0.69 ± 0.01 g/g total sugars) was obtained under simultaneous saccharification and fermentation (SSF). D-(-)-lactate at 99.9 ± 0.9 g/L (0.97 ± 0.01 g/g sugar utilized or 0.78 ± 0.01 g/g total sugars) was improved via fed-batch SSF. Based on mass balance, raw SCB of 7 kg is required to produce 1 kg D-(-)-lactate. Unlike others, D-(-)-lactate production was performed in low-cost salt medium without requirements of rich nutrients. Costs regarding medium, purification, and waste disposal may be reduced. This unlocks economic capability of SCB bioconversion or agricultural and agro-industrial wastes into high valuable D-(-)-lactate.

Designing a highly efficient type III polyketide whole-cell catalyst with minimized byproduct formation

BACKGROUND

Polyketide synthases (PKSs) are classified into three types based on their enzyme structures. Among them, type III PKSs, catalyzing the iterative condensation of malonyl-coenzyme A (CoA) with a CoA-linked starter molecule, are important synthases of valuable natural products. However, low efficiency and byproducts formation often limit their applications in recombinant overproduction.

RESULTS

Herein, a rapid growth selection system is designed based on the accumulation and derepression of toxic acyl-CoA starter molecule intermediate products, which could be potentially applicable to most type III polyketides biosynthesis. This approach is validated by engineering both chalcone synthases (CHS) and host cell genome, to improve naringenin productions in Escherichia coli. From directed evolution of key enzyme CHS, beneficial mutant with ~ threefold improvement in capability of naringenin biosynthesis was selected and characterized. From directed genome evolution, effect of thioesterases on CHS catalysis is first discovered, expanding our understanding of byproduct formation mechanism in type III PKSs. Taken together, a whole-cell catalyst producing 1082 mg L-1 naringenin in flask with E value (evaluating product specificity) improved from 50.1% to 96.7% is obtained.

CONCLUSIONS

The growth selection system has greatly contributed to both enhanced activity and discovery of byproduct formation mechanism in CHS. This research provides new insights in the catalytic mechanisms of CHS and sheds light on engineering highly efficient heterologous bio-factories to produce naringenin, and potentially more high-value type III polyketides, with minimized byproducts formation.

Adaptive Evolution for the Efficient Production of High-Quality d-Lactic Acid Using Engineered Klebsiella pneumoniae

d-Lactic acid serves as a pivotal platform chemical in the production of poly d-lactic acid (PDLA) and other value-added products. This compound can be synthesized by certain bacteria, including Klebsiella pneumoniae. However, industrial-scale lactic acid production in Klebsiella pneumoniae faces challenges due to growth inhibition caused by lactic acid stress, which acts as a bottleneck in commercial microbial fermentation processes. To address this, we employed a combination of evolutionary and genetic engineering approaches to create an improved Klebsiella pneumoniae strain with enhanced lactic acid tolerance and production. In flask fermentation experiments, the engineered strain achieved an impressive accumulation of 19.56 g/L d-lactic acid, representing the highest production yield observed in Klebsiella pneumoniae to date. Consequently, this strain holds significant promise for applications in industrial bioprocessing. Notably, our genome sequencing and experimental analyses revealed a novel correlation between UTP-glucose-1-phosphate uridylyltransferase GalU and lactic acid resistance in Klebsiella pneumoniae. Further research is warranted to explore the potential of targeting GalU for enhancing d-lactic acid production.

Efficient L-valine production using systematically metabolic engineered Klebsiella oxytoca

L-Valine, a branched-chain amino acid with diversified applications, is biosynthesized with α-acetolactate as the key precursor. In this study, the metabolic flux in Klebsiella oxytoca PDL-K5, a Risk Group 1 organism producing 2,3-butanediol as the major fermentation product, was rearranged to L-valine production by introducing exogenous L-valine biosynthesis pathway and blocking endogenous 2,3-butanediol generation at the metabolic branch point α-acetolactate. After further enhancing L-valine efflux, strengthening pyruvate polymerization and selecting of key enzymes for L-valine synthesis, a plasmid-free K. oxytoca strain VKO-9 was obtained. Fed-batch fermentation with K. oxytoca VKO-9 in a 7.5 L fermenter generated 122 g/L L-valine with a yield of 0.587 g/g in 56 h. In addition, repeated fed-batch fermentation was conducted to prevent precipitation of L-valine due to oversaturation. The average concentration, yield, and productivity of produced L-valine in three cycles of repeated fed-batch fermentation were 81.3 g/L, 0.599 g/g, and 3.39 g/L/h, respectively.

An efficient production of bio-succinate in a novel metabolically engineered Klebsiella oxytoca by rational metabolic engineering and evolutionary adaptation

Klebsiella oxytoca KC004 (ΔadhEΔpta-ackAΔldhAΔbudABΔpflB) was engineered to enhance succinate production. The strain exhibited poor growth without succinate production due to its deficiencies in ATP production and NADH reoxidation. To overcome obstacles, evolutionary adaptation with over 6,000 generations of growth-based selection was conducted. Under anaerobic conditions, enhanced productions of ATP for growth and succinate for NADH reoxidation by the evolved KC004-TF160 strain were coupled to an increased transcript of PEP carboxykinase (pck) while those of genes in the oxidative branch of TCA cycle (gltA, acnAB, and icd), and pyruvate and acetate metabolisms (pykA, acs, poxB and tdcD) were alleviated. The expression of pyruvate dehydrogenase repressor (pdhR) decreased whereas threonine decarboxylase (tdcE) increased. KC004-TF160 produced succinate at 84 g/L (0.84 g/g, 79 % theoretical maximum). KC004-TF160 produced succinate at 0.87 g/g non-pretreated sugarcane molasses without addition of nutrients and buffers. KC004-TF160 may be a microbial platform for commercial production of bio-succinate.

High titer (>200 g/L) lactic acid production from undetoxified pretreated corn stover

Lignocellulosic biomass is a reliable feedstock for lactic acid fermentation, low product titers hamper the scale production of cellulosic lactic acid. In this study, a Densifying Lignocellulosic biomass with Chemicals (sulfuric acid) pretreatment based cellulosic lactic acid biorefinery system was developed and demonstrated from multi-dimensions of producing bacteria, fermentation modes, corn stover solid loadings, fermentation vessels, and product purification. Results suggested that several lactic acid bacteria exhibited high fermentation activity in high solid loading corn stover hydrolysates. Remarkably, simultaneous saccharification co-fermentation performed in 100-mL flasks enabled 210.1 g/L lactic acid from 40% solid loading corn stover hydrolysate. When simultaneous saccharification co-fermentation was performed in 3-L bioreactors, 157.4 g/L lactic acid was obtained from 35% solid loading corn stover hydrolysate. These obtained lactic acid titers are the highest reports until now when lignocellulosic biomasses are used as substrates, making it efficient for scale production of cellulosic lactic acid.

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.

Synthetic microbes and biocatalyst designs in Thailand

Furthering the development of the field of synthetic biology in Thailand is included in the Thai government's Bio-Circular-Green (BCG) economic policy. The BCG model has increased collaborations between government, academia and private sectors with the specific aim of increasing the value of bioindustries via sustainable approaches. This article provides a critical review of current academic research related to synthetic biology conducted in Thailand during the last decade including genetic manipulation, metabolic engineering, cofactor enhancement to produce valuable chemicals, and analysis of synthetic cells using systems biology. Work was grouped according to a Design-Build-Test-Learn cycle. Technical areas directly supporting development of synthetic biology for BCG in the future such as enzyme catalysis, enzyme engineering and systems biology related to culture conditions are also discussed. Key activities towards development of synthetic biology in Thailand are also discussed.

[NiFe] Hydrogenase Accessory Proteins HypB-HypC Accelerate Proton Conversion to Enhance the Acid Resistance and d-Lactic Acid Production of Escherichia coli

Escherichia coli is a major industrial producer of d-lactic acid due to its well-known advantages, such as short cycle times and low demand. However, acid sensitivity limits production capacity and increases costs. Enhancing the resistance of E. coli to acid stress is essential for improving the cell performance and production value. Here, we propose a feasible strategy to increase the acid tolerance of cells by strengthening intracellular proton conversion. The transcriptome test of the acid-tolerant adaptive evolution strain identified the hydrogenase accessory proteins HypB and HypC as a class of acid-tolerant factors that can assist the hydrogenase in catalyzing the reduction of protons to produce hydrogen. Strengthening the expression of HypB and HypC can increase the cell survival rate by 336.3 times during the lethal stress of d-lactate. In addition, HypB and HypC will assist d-lactate-producing strains to show higher sustainable productivity in an acidic fermentation environment, and d-lactate titer will increase by 113.6%. In order to further improve the expression system of the hydrogenase accessory protein, the introduction of a strong acid stress-driven promoter tdcAp can reduce the demand for neutralizer delivery in the fermentation process by about 26.7% while maintaining the maximum intensity of d-lactic acid production. Therefore, this research developed a method to improve the acid resistance of E. coli cells and reduce the cost of organic acid production by transforming protons.

Engineering Escherichia coli for a high yield of 1,3-propanediol near the theoretical maximum through chromosomal integration and gene deletion

Glycerol dehydratase (gdrAB-dhaB123) operon from Klebsiella pneumoniae and NADPH-dependent 1,3-propanediol oxidoreductase (yqhD) from Escherichia coli were stably integrated on the chromosomal DNA of E. coli under the control of the native-host ldhA and pflB constitutive promoters, respectively. The developed E. coli NSK015 (∆ldhA::gdrAB-dhaB123 ∆ackA::FRT ∆pflB::yqhD ∆frdABCD::cat-sacB) produced 1,3-propanediol (1,3-PDO) at the level of 36.8 g/L with a yield of 0.99 mol/mol of glycerol consumed when glucose was used as a co-substrate with glycerol. Co-substrate of glycerol and cassava starch was also utilized for 1,3-PDO production with the concentration and yield of 31.9 g/L and 0.84 mol/mol of glycerol respectively. This represents a work for efficient 1,3-PDO production in which the overexpression of heterologous genes on the E. coli host genome devoid of plasmid expression systems. Plasmids, antibiotics, IPTG, and rich nutrients were omitted during 1,3-PDO production. This may allow a further application of E. coli NSK015 for the efficient 1,3-PDO production in an economically industrial scale. KEY POINTS:  • gdrAB-dhaB123 and yqhD were overexpressed in E. coli devoid of a plasmid system • E. coli NSK015 produced a high yield of 1,3-PDO at 99% theoretical maximum • Cassava starch was alternatively used as substrate for economical 1,3-PDO production.