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

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 KIS004-91 T 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.

Systematic reengineering of Klebsiella oxytoca KC004-TF160 for enhancing metabolic carbon flux towards succinate production pathway

Klebsiella oxytoca KP001-TF60 (ΔadhEΔpta-ackAΔldhAΔbudABΔpflBΔtdcDΔpmd) was re-engineered to direct more carbon flux towards succinate production with less acetate. Glucose uptake, cell growth, and carbon distribution were restricted by alterations in relative expressions and nucleotide sequences of genes associated with PEP and pyruvate metabolisms. Transcripts of pck, ppc, and frd genes were up-regulated for enhancing NADH reoxidation during succinate production while increased pyk and tdcE transcripts were observed due to maintenance of acetyl-CoA through the oxidative branch of TCA cycle. Based on whole-genome sequencing, several genes in sugars-specific PTS (ptsG, bglF, chbR, fruA, mtlR, and treY), ABC transporters (alsK, and rbsK), Major Facilitator Superfamily (uhpB and setB), and catabolite repression (cyaA and csrB) were found to be mutated. The strain produced succinate yield up to 0.89 g/g (∼80 % theoretical maximum) with acetate < 1 g/L, and may be one of the succinate producers applied in an industrial-production scale with simplified purification processes.

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.

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.

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.