Cofactor Engineering for Enhanced Production of Diols by Klebsiella pneumoniae From Co-Substrate

De novo biosynthesis of α‐aminoadipate via multi‐strategy metabolic engineering in Escherichia coli

As a non‐protein amino acid, α‐aminoadipate is used in the fields of medicine, chemical engineering, food science, and others. For example, α‐aminoadipate is an important precursor for the production of β‐lactam antibiotics. Currently, the synthesis of α‐aminoadipate depends on chemical catalysis that has the disadvantages of high cost, low yield, and serious pollution. In this study, we construct a biosynthesis pathway of α‐aminoadipate in Escherichia coli using lysine as a precursor. In addition, we regulate the cell metabolism to improve the titer of α‐aminoadipate via multi‐strategy metabolic engineering. First, a novel synthetic pathway was constructed to realize de novo synthesis of α‐aminoadipate with titers of 82 mg/L. Second, the key enzymes involved in enhancing precursor synthesis were overexpressed and the CO₂ fixation process was introduced, and these led to 80% and 34% increases in the α‐aminoadipate concentration, reaching 147 and 110 mg/L, respectively. Third, cofactor regulation was used to maintain the coupling balance of material and energy, with the intracellular α‐aminoadipate concentration reaching 140 mg/L. Fourth, the weakening of the synthesis of acetic acid was used to strengthen the synthesis of α‐aminoadipate, and this resulted in the enhancement of the α‐aminoadipate concentration by 2.2 times, reaching 263 mg/L. Finally, combination optimization was used to promote the production of α‐aminoadipate. The titers of α‐aminoadipate reached 368 mg/L (strain EcN11#) and 415 mg/L (strain EcN11##), which was 3.5 and 4 times higher than that of the parent strain. With these efforts, 1.54 g/L of α‐aminoadipate was produced under fed‐batch conditions by strain EcN11#. This study is the first to present the effective biosynthesis of α‐aminoadipate in E. coli using multi‐strategy metabolic engineering.

Recent advances in the microbial production of C4 alcohols by metabolically engineered microorganisms

BACKGROUND

The heavy global dependence on petroleum-based industries has led to serious environmental problems, including climate change and global warming. As a result, there have been calls for a paradigm shift towards the use of biorefineries, which employ natural and engineered microorganisms that can utilize various carbon sources from renewable resources as host strains for the carbon-neutral production of target products.

PURPOSE AND SCOPE

C4 alcohols are versatile chemicals that can be used directly as biofuels and bulk chemicals and in the production of value-added materials such as plastics, cosmetics, and pharmaceuticals. C4 alcohols can be effectively produced by microorganisms using DCEO biotechnology (tools to design, construct, evaluate, and optimize) and metabolic engineering strategies.

SUMMARY OF NEW SYNTHESIS AND CONCLUSIONS

In this review, we summarize the production strategies and various synthetic tools available for the production of C4 alcohols and discuss the potential development of microbial cell factories, including the optimization of fermentation processes, that offer cost competitiveness and potential industrial commercialization.

Regulation of Pyruvate Formate Lyase-Deficient Klebsiella pneumoniae for Efficient 1,3-Propanediol Bioproduction

Anaerobic growth defect of pyruvate formate lyase (PFL)-deficient Klebsiella pneumoniae limits its industrial application, and the reason for this growth defect was analyzed in this study. The obtained evidences, combined with normal intracellular redox status and no further inhibition by adhE deletion, strongly suggested that growth defect in PFL-deficient K. pneumoniae was probably caused by lack of carbon flux from pyruvate to acetyl-CoA (AcCoA). Correspondingly, the anaerobic growth of PFL-deficient K. pneumoniae was promoted by deletion of pdhR, a negative transcriptional regulator gene for AcCoA generation. Through the regulation of pdhR deletion, the PFL-deficient K. pneumoniae exhibited highly efficient 1,3-propanediol production. Besides, in a 2-L fed-batch fermentation process, the cell growth of PFL-deficient K. pneumoniae strain almost recovered, when compared with that of the normal strain, and the 1,3-propanediol yield increased by 14%, while the byproducts acetate and 2,3-butanediol contents decreased by 29% and 24%, respectively.

Improved xylose tolerance and 2,3-butanediol production of Klebsiella pneumoniae by directed evolution of rpoD and the mechanisms revealed by transcriptomics

BACKGROUND

The biological production of 2,3-butanediol from xylose-rich raw materials from Klebsiella pneumoniae is a low-cost process. RpoD, an encoding gene of the sigma factor, is the key element in global transcription machinery engineering and has been successfully used to improve the fermentation with Escherichia coli. However, whether it can regulate the tolerance in K. pneumoniae remains unclear.

RESULTS

In this study, the kpC mutant strain was constructed by altering the expression quantity and genotype of the rpoD gene, and this exhibited high xylose tolerance and 2,3-butanediol production. The xylose tolerance of kpC strain was increased from 75 to 125 g/L, and the yield of 2,3-butanediol increased by 228.5% compared with the parent strain kpG, reaching 38.6 g/L at 62 h. The RNA sequencing results showed an upregulated expression level of 500 genes and downregulated expression level of 174 genes in the kpC mutant strain. The pathway analysis further showed that the differentially expressed genes were mainly related to signal transduction, membrane transport, carbohydrate metabolism, and energy metabolism. The nine most-promising genes were selected based on transcriptome sequencing, and were evaluated for their effects on xylose tolerance. The overexpression of the tktA encoding transketolase, pntA encoding NAD(P) transhydrogenase subunit alpha, and nuoF encoding NADH dehydrogenase subunit F conferred increased xylose consumption and increased 2,3-butanediol production to K. pneumoniae.

CONCLUSIONS

These results suggest that the xylose tolerance and 2,3-butanediol production of K. pneumoniae can be greatly improved by the directed evolution of rpoD. By applying transcriptomic analysis, the upregulation of tktA, pntA, and nuoF that were coded are essential for the xylose consumption and 2,3-butanediol production. This study will provide reference for further research on improving the fermentation abilities by means of other organisms.

A Recombinant 12-His Tagged Pyrococcus furiosus Soluble [NiFe]-Hydrogenase I Overexpressed in Thermococcus kodakarensis KOD1 Facilitates Hydrogen-Powered in vitro NADH Regeneration

Soluble hydrogenase I (SHI) from the hyperthermophilic archaeon Pyrococcus furiosus is a heterotetrameric [NiFe] hydrogenase that catalyzes the reversible reduction of protons by NADPH into hydrogen gas (H₂ ). Here, the authors expressed the four αβγδ subunits of SHI encoded by one gene cluster in another hyperthermophilic archaeon, Thermococcus kodakarensis KOD1, which uses its hydrogenase maturation apparatus without the coexpression of native P. furiosus hydrogenase endopeptidases (maturation proteases). The SHI overexpression of T. kodakarensis resulted in more than 1200-fold enhancement in the hydrogenase activity of the cell lysate compared to that of the host strain with an empty vector. An active, purified 12-His tagged recombinant SHI (rSHI) is obtained by one-step affinity adsorption on nickel-charged resin. Size-exclusion chromatography show that purified rSHI is heterotetrameric and has a molecular mass of 150 kDa. The purified rSHI has a half-life of 70 h at 80 °C. This rSHI is used to design a novel in vitro synthetic enzymatic biosystem to convert pyruvate and H₂ gas into lactate in a theoretical yield, whereas rSHI is used for NADPH regeneration; an FMN-containing diaphorase (DI) is used to match NADP-preferred SHI and NAD-preferred lactate dehydrogenase (LDH). This study provides a cost-efficient method to obtain hyperthermostable hydrogenases, which can be used in in vitro synthetic enzymatic biosystems for cofactor regeneration and hydrogen production.

Inactivating NADH:quinone oxidoreductases affects the growth and metabolism of Klebsiella pneumoniae

NADH:quinone oxidoreductases (NQOs) act as the electron entry sites in bacterial respiration and oxidize intracellular NADH that is essential for the synthesis of numerous molecules. Klebsiella pneumoniae contains three NQOs (NDH-1, NDH-2, and NQR). The effects of inactivating these NQOs, separately and together, on cell metabolism were investigated under different culture conditions. Defective growth was evident in NDH-1-NDH-2 double and NDH-1-NDH-2-NQR triple deficient mutants, which was probably due to damage to the respiratory chain. The results also showed that K. pneumoniae can flexibly use NQOs to maintain normal growth in single NQO-deficient mutants. And more interestingly, under aerobic conditions, inactivating NDH-1 resulted in a high intracellular NADH:NAD⁺ ratio, which was proven to be beneficial for 2,3-butanediol production. Compared with the parent strain, 2,3-butanediol production by the NDH-1-deficient mutant was increased by 46% and 62% in glycerol- and glucose-based media, respectively. Thus, our findings provide a practical strategy for metabolic engineering of respiratory chains to promote the biosynthesis of 2,3-butanediol in K. pneumoniae.

Redox cofactor engineering in industrial microorganisms: strategies, recent applications and future directions

NAD and NADP, a pivotal class of cofactors, which function as essential electron donors or acceptors in all biological organisms, drive considerable catabolic and anabolic reactions. Furthermore, they play critical roles in maintaining intracellular redox homeostasis. However, many metabolic engineering efforts in industrial microorganisms towards modification or introduction of metabolic pathways, especially those involving consumption, generation or transformation of NAD/NADP, often induce fluctuations in redox state, which dramatically impede cellular metabolism, resulting in decreased growth performance and biosynthetic capacity. Here, we comprehensively review the cofactor engineering strategies for solving the problematic redox imbalance in metabolism modification, as well as their features, suitabilities and recent applications. Some representative examples of in vitro biocatalysis are also described. In addition, we briefly discuss how tools and methods from the field of synthetic biology can be applied for cofactor engineering. Finally, future directions and challenges for development of cofactor redox engineering are presented.