Biotransformation of indole to indigo by the whole cells of phenol hydroxylase engineered strain in biphasic systems

Auto-inducible synthetic pathway in E. coli enhanced sustainable indigo production from glucose

Indigo is widely used in textile industries for denim garments dyeing and is mainly produced by chemical synthesis which, however, raises environmental sustainability issues. Bio-indigo may be produced by fermentation of metabolically engineering bacteria, but current methods are economically incompetent due to low titer and the need for an inducer. To address these problems, we first characterized several synthetic promoters in E. coli and demonstrated the feasibility of inducer-free indigo production from tryptophan using the inducer-free promoter. We next coupled the tryptophan-to-indigo and glucose-to-tryptophan pathways to generate a de novo glucose-to-indigo pathway. By rational design and combinatorial screening, we identified the optimal promoter-gene combinations, which underscored the importance of promoter choice and expression levels of pathway genes. We thus created a new E. coli strain that exploited an indole pathway to enhance the indigo titer to 123 mg/L. We further assessed a panel of heterologous tryptophan synthase homologs and identified a plant indole lyase (TaIGL), which along with modified pathway design, improved the indigo titer to 235 mg/L while reducing the tryptophan byproduct accumulation. The optimal E. coli strain expressed 8 genes essential for rewiring carbon flux from glucose to indole and then to indigo: mFMO, ppsA, tktA, trpD, trpC, TaIGL and feedback-resistant aroG and trpE. Fed-batch fermentation in a 3-L bioreactor with glucose feeding further increased the indigo titer (≈965 mg/L) and total quantity (≈2183 mg) at 72 h. This new synthetic glucose-to-indigo pathway enables high-titer indigo production without the need of inducer and holds promise for bio-indigo production.

Efficient biosynthesis of Vibegron intermediate using a novel carbonyl reductase based on molecular modification of hydrogen bonding network regulation

Vibegron is a novel, potent, highly selective β3-adrenergic receptor agonist for the treatment of overactive bladder with higher therapeutic capacity and lower side effects. Methyl(2S,3R)-2-((tert-butoxycarbonyl)amino)-3-hydroxy-3-phenylpropanoate ((2S,3R)-aminohydroxy ester) is a key chiral intermediate for the synthesis of Vibegron. A novel carbonyl reductase from Exiguobacterium sp. s126 (EaSDR6) was isolated using data mining technology from GenBank database with preferable catalytic activity. Hydrogen bond network regulation was performed using site-directed saturation mutagenesis and combination mutagenesis. The mutant EaSDR6A138L/S193A was obtained with the activity improvement by 4.58 folds compared with the wild type EaSDR6. The Km of EaSDR6A138L/S193A was decreased from 1.57 mM to 0.67 mM, kcat was increased by 2.17 folds, and the overall catalytic efficiency kcat/Km was increased by 5.07 folds. The organic-aqueous biphasic bioreaction system for the asymmetric synthesis of (2S,3R)-aminohydroxy ester was constructed for the first time. Under the substrate concentration of 150 g/L, the yield of (2S,3R)-aminohydroxy ester was > 99.99%, the e.e. was > 99.99%, and the spatiotemporal yield was 1.55 g/(L·h·g DCW) after 12 h reaction. While the substrate concentration was increased to 200 g/L and the reaction lasted for 36 h, the yield of (2S,3R)-aminohydroxy ester was > 99.99%, the e.e. was > 99.99% and the spatiotemporal yield was 1.05 g/(L·h·g DCW). The substrate concentration and spatiotemporal yield were higher than ever reported.

Characterization of a novel monooxygenase originating from a deep-sea sediment metagenomic library

Oxygenases are important biocatalysts to produce many industrially important biomolecules. Here, a novel oxygenase, named MoxA, was identified through screening of a deep-sea sediment metagenomic library. Sequence analysis showed MoxA contains 424 amino acid residues with a predicated molecular mass of 46.9 kDa. Multiple sequence alignment and phylogenetic analysis indicated the sequence might be a new member of monooxygenase subfamily. A recombinant MoxA was obtained through the functional expression of moxA gene in Escherichia coli. Characterization of the purified MoxA indicated that it is an alkaline oxygenase showing maximal activity at pH 8.0. The optimal temperature of MoxA was 37 ℃, and it retained more than 70% of its initial activity after 1 h at 20-50 ℃ exhibiting good thermostability. Furthermore, effect of metal ions and organic solvents on enzymatic activity was investigated, and the results showed that the activity of MoxA was enhanced by Cu2+, Zn2+, Co2+ and Mg2+ at 1 mM, and by Co2+, Ca2+ and Mg2+ at 5 mM. Moreover, the recombinant strain harboring MoxA was used as a whole-cell biocatalyst for the efficient biosynthesis of indigo showing promising conversion efficiency. The biochemical properties of MoxA indicated that it would provide great contribution for the indigo bioproduction. KEY POINTS: • A novel monooxygenase from a metagenomic library was characterized. • The activity of MoxA was enhanced by metal ions at 1 mM and 5 mM. • MoxA has an optimal temperature of 37 ℃ and exhibited high conversion capacity.

Engineering of a chromogenic enzyme screening system based on an auxiliary indole-3-carboxylic acid monooxygenase

Here, we present a proof‐of‐principle for a new high‐throughput functional screening of metagenomic libraries for the selection of enzymes with different activities, predetermined by the substrate being used. By this approach, a total of 21 enzyme‐coding genes were selected, including members of xanthine dehydrogenase, aldehyde dehydrogenase (ALDH), and amidohydrolase families. The screening system is based on a pro‐chromogenic substrate, which is transformed by the target enzyme to indole‐3‐carboxylic acid. The later compound is converted to indoxyl by a newly identified indole‐3‐carboxylate monooxygenase (Icm). Due to the spontaneous oxidation of indoxyl to indigo, the target enzyme‐producing colonies turn blue. Two types of pro‐chromogenic substrates have been tested. Indole‐3‐carboxaldehydes and the amides of indole‐3‐carboxylic acid have been applied as substrates for screening of the ALDHs and amidohydrolases, respectively. Both plate assays described here are rapid, convenient, easy to perform, and adaptable for the screening of a large number of samples both in Escherichia coli and Rhodococcus sp. In addition, the fine‐tuning of the pro‐chromogenic substrate allows screening enzymes with the desired substrate specificity.

Cloning of Toluene 4-Monooxygenase Genes and Application of Two-Phase System to the Production of the Anticancer Agent, Indirubin

Indirubin is a strong inhibitor of several eukaryotic cell signaling pathways and shows promise as a treatment for myelocytic leukemia and Alzheimer's disease. The tmoABCDEF operon, encoding the components of a novel toluene 4-monooxygenase from the paint factory soil isolate, Pseudomonas sp. M4, was cloned and expressed in Escherichia coli. E. coli::pKSR12 expressing the tmo genes was used to develop a two-phase [dioctyl phthalate (DOP)/aqueous medium] culture system that was optimized to obtain maximal yields of indirubin from the starting substrate, indole. DOP was used as the organic phase to solubilize and sequester the toxic indole substrate, making possible the use of high indole concentrations that would otherwise interfere with growth in aqueous media. A 50 % (v/v) DOP two-phase system using tryptophan medium containing 3 mM cysteine, 5 mM indole, and 1 mM isatin yielded 102.4 mg/L of indirubin with no conversion of indole to the less valuable alternate product, indigo.

Biosynthesis of 1,2-dihydroxydibenzofuran by magnetically immobilized cells of Escherichia coli expressing phenol hydroxylase in liquid-liquid biphasic systems

Escherichia coli cells expressing phenol hydroxylase (designated as PHIND) were used to biosynthesize 1,2-dihydroxydibenzofuran (1,2-dihydroxyDBF) from dibenzofuran (DBF). The pathway of DBF biotransformation by strain PHIND was proposed, in which DBF was initially monohydroxylated at C-1 and C-4 positions to produce 1- and 4-hydroxyDBF, then underwent successive hydroxylation to yield 1,2- and 3,4-dihydroxyDBF, of which 1,2-dihydroxyDBF was identified for the first time. Magnetically immobilized cells of strain PHIND in biphasic systems with dodecane as the solvent presented highest biosynthesis activity for 1,2-dihydroxyDBF, which was a 6.5-fold improvement compared to biosynthesis in aqueous system. The recycling experiments demonstrated that magnetically immobilized cells exhibited higher biosynthesis activity for 1,2-dihydroxyDBF than that by nonmagnetically immobilized cells during five cycles in biphasic systems. These works support the development of an efficient biosynthesis process using magnetically immobilized cells in biphasic systems and provide a promising technique for improving the productivity in 1,2-dihydroxyDBF biosynthesis.

Identification of new metabolites of bacterial transformation of indole by gas chromatography-mass spectrometry and high performance liquid chromatography

Arthrobacter sp. SPG transformed indole completely in the presence of an additional carbon source. High performance liquid chromatography and gas chromatography-mass spectrometry detected indole-3-acetic acid, indole-3-glyoxylic acid, and indole-3-aldehyde as biotransformation products. This is the first report of the formation of indole-3-acetic acid, indole-3-glyoxylic acid, and indole-3-aldehyde from indole by any bacterium.

Production of indirubin from tryptophan by recombinant Escherichia coli containing naphthalene dioxygenase genes from Comamonas sp. MQ

Indirubin, a red isomer of indigo, can be used for the treatment of various chronic diseases. However, the microbial production of indirubin did not receive much attention probably due to its low yield compared with indigo. In this study, the recombinant Escherichia coli containing the naphthalene dioxygenase (NDO) genes from Comamonas sp. MQ was used to produce indirubin from tryptophan. To enhance the production of indirubin, the induction conditions for NDO expression were optimized. The optimal induction conditions were carried out with 0.5 mM isopropyl-β-D-thiogalactopyranoside at 30 °C when cells were grown to OD600 ≈ 1.20. Subsequently, the effects of medium composition on indirubin production were investigated by response surface methodology, and 9.37 ± 1.01 mg/l indirubin was produced from 3.28 g/l tryptophan. Meanwhile, the indirubin production was further improved by adding 2-oxindole and isatin to the tryptophan medium after induction. About 57.98 ± 2.62 mg/l indirubin was obtained by the addition of 500 mg/l 2-oxindole after 1-h induction, which was approximately 6.2-fold to that without additional 2-oxindole. The present study provided a possible way to improve the production of indirubin and should lay the foundation for the application of microbial indirubin production.