Enhancing the expression of the unspecific peroxygenase in Komagataella phaffii through a combination strategy

The unspecific peroxygenase (UPO) from Cyclocybe aegerita (AaeUPO) can selectively oxidize C-H bonds using hydrogen peroxide as an oxygen donor without cofactors, which has drawn significant industrial attention. Many studies have made efforts to enhance the overall activity of AaeUPO expressed in Komagataella phaffii by employing strategies such as enzyme-directed evolution, utilizing appropriate promoters, and screening secretion peptides. Building upon these previous studies, the objective of this study was to further enhance the expression of a mutant of AaeUPO with improved activity (PaDa-I) by increasing the gene copy number, co-expressing chaperones, and optimizing culture conditions. Our results demonstrated that a strain carrying approximately three copies of expression cassettes and co-expressing the protein disulfide isomerase showed an approximately 10.7-fold increase in volumetric enzyme activity, using the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) as the substrate. After optimizing the culture conditions, the volumetric enzyme activity of this strain further increased by approximately 48.7%, reaching 117.3 U/mL. Additionally, the purified catalytic domain of PaDa-I displayed regioselective hydroxylation of R-2-phenoxypropionic acid. The results of this study may facilitate the industrial application of UPOs. KEY POINTS: • The secretion of the catalytic domain of PaDa-I can be significantly enhanced through increasing gene copy numbers and co-expressing of protein disulfide isomerase. • After optimizing the culture conditions, the volumetric enzyme activity can reach 117.3 U/mL, using the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) as the substrate. • The R-2-phenoxypropionic acid can undergo the specific hydroxylation reaction catalyzed by catalytic domain of PaDa-I, resulting in the formation of R-2-(4-hydroxyphenoxy)propionic acid.

Hydrophobic substrate binding pocket remodeling of echinocandin B deacylase based on multi-dimensional rational design

Actinoplanes utahensis deacylase (AAC)-catalyzed deacylation of echinocandin B (ECB) is a promising method for the synthesis of anidulafungin, the newest of the echinocandin antifungal agents. However, the low activity of AAC significantly limits its practical application. In this work, we have devised a multi-dimensional rational design strategy for AAC, conducting separate analyses on the substrate-binding pocket's volume, curvature, and length. Furthermore, we quantitatively analyzed substrate properties, particularly on hydrophilic and hydrophobic. Accordingly, we tailored the linoleic acid-binding pocket of AAC to accommodate the extended long lipid chain of ECB. By fine-tuning the key residues, the resulting AAC mutants can accommodate the ECB lipid chain with a lower curvature binding pocket. The D53A/I55F/G57M/F154L/Q661L mutant (MT) displayed 331 % higher catalytic efficiency than the wild-type (WT) enzyme. The MT product conversion was 94.6 %, reaching the highest reported level. Utilizing a multi-dimensional rational design for a customized mutation strategy of the substrate-binding pocket is an effective approach to enhance the catalytic efficiency of enzymes in handling complicated substrates.

Hyperthermophilic pretreatment significantly accelerates thermophilic composting humification through improving bacterial communities and promoting microbial cooperation

Thermophilic composting (TC) can effectively shorten maturity period with satisfactory sanitation. However, the higher energy consumption and lower composts quality limited its widespread application. In this study, hyperthermophilic pretreatment (HP) was introduced as a novel approach within TC, and its effects on humification process and bacterial community during food waste TC was investigated from multiple perspectives. Results showed that a 4-hour pretreatment at 90 °C increased the germination index and humic acid/fulvic acid by 25.52% and 83.08%. Microbial analysis demonstrated that HP stimulated the potential functional thermophilic microbes, and significantly up-regulated the genes related to amino acid biosynthesis. Further network and correlation analysis suggested that pH was the key factor affecting bacterial communities, and higher HP temperatures help to restore bacterial cooperation and showed higher humification degree. In summary, this study contributed to a better understanding of the mechanism towards the accelerated humification by HP.

Effects of fungal agents and biochar on odor emissions and microbial community dynamics during in-situ treatment of food waste

The effects of the co-addition of fungal agents and biochar on physicochemical properties, odor emissions, microbial community structure, and metabolic functions were investigated during the in-situ treatment of food waste. The combined addition of fungal agents and biochar decreased cumulative NH₃, H₂S, and VOCs emissions by 69.37%, 67.50%, and 52.02%, respectively. The predominant phyla throughout the process were Firmicutes, Actinobacteria, Cyanobacteria, and Proteobacteria. Combined treatment significantly impacted the conversion and release of nitrogen from the perspective of the variation of nitrogen content between different forms. FAPROTAX analysis revealed that the combined application of fungal agents and biochar could effectively inhibit nitrite ammonification and reduce the emission of odorous gases. This work aims to clarify the combined effect of fungal agents and biochar on odor emission and provide a theoretical basis for developing an environmentally friendly in-situ efficient biological deodorization (IEBD) technology.

Community scale in-situ rapid biological reduction and resource recovery of food waste

In this study, a community-scale in-situ rapid biological reduction (IRBR) system was applied to achieve the rapid disposal and resource recovery of food waste (FW). A total of 5263 kg FW was processed in the 35 days of stably operation, during which 84.37% total mass reduction and 43.30% volatile solid removal were achieved, and the odor had been effectively controlled. Microbial sequencing results showed that aerobic and facultative thermophilic bacteria were major bacterial community, and vigorous metabolism of both carbohydrate and amino acid were maintained during the IRBR process. The final products have the potential to be recycled as organic fertilizers or bio-solid fuel to realize resource recovery. The results of economic analysis showed that the IRBR system had lower FW disposal costs due to the high automation. These results suggested that the IRBR system was an environmentally friendly, economical and practical method for the FW rapid treatment.

A light-controlled biocatalytic system for precise regulation of enzymatic decarboxylation

A light-controlled biocatalytic one-pot system is developed, which enables precise regulation of gene expression and photocatalysis by illumination and yields high conversion and stereoselectivity.

Fed-in-situ biological reduction treatment of food waste via high-temperature-resistant oil degrading microbial consortium

This study aims to construct a high-temperature-resistant microbial consortium to effectively degrade oily food waste by Fed-in-situ biological reduction treatment (FBRT). Oil degrading bacteria were screened under thermophilic conditions of mineral salt medium with increased oil content. The oil degradation and emulsification ability of each stain was evaluated and their synergetic improvement was further confirmed. Consortium of Bacillus tequilensis, Bacillus licheniformis, Bacillus sonorensis and Ureibacillus thermosphaericus was selected and applicated as bacterial agents in FBRT under 55 °C. Changes in pH, moisture, bacterial community and key components of food waste were monitored for 5 days during processing. Facilitated by the bacterial consortium, FBRT gave superior total mass reduction (86.61 ± 0.58% vs. 67.25 ± 1.63%) and non-volatile solids reduction (65.91 ± 1.53% vs. 28.53 ± 2.29%) compared with negative control, the feasibility and efficiency of present FBRT providing a promising in-situ disposal strategy for rapid reduction of oily food waste.

Overproduction of D-pantothenic acid via fermentation conditions optimization and isoleucine feeding from recombinant Escherichia coli W3110

D-pantothenic acid (D-PA), as a crucial vitamin, is widely used in food, animal feed, cosmetics, and pharmaceutical industries. In our previous work, recombinant Escherichia coli W3110 for production of D-PA was constructed through metabolic pathway modification. In this study, to enhance D-PA production, statistical optimization techniques including Plackett-Burman (PB) design and Box-Behnken design (BBD) first were adopted to optimize the culture condition. The results showed that the glucose, β-alanine and (NH₄)₂SO₄ have the most significant effects on D-PA biosynthesis. The response surface model based on BBD predicted that the optimal concentration is glucose 56.0 g/L, β-alanine 2.25 g/L and (NH4)₂SO₄ 11.8 g/L, the D-PA titer increases from 3.2 g/L to 6.73 g/L shake flask fermentation. For the fed-batch fermentation in 5 L fermenter, the isoleucine feeding strategy greatly increased the titer and productivity of D-PA. As a result, titer (31.6 g/L) and productivity (13.2 g/L·d) of D-PA were achieved, they increased by 4.66 times and 2.65 times, respectively, compared with batch culture. At the same time, the accumulation of acetate reduced from 29.79 g/L to 8.55 g/L in the fed-batch fermentation. These results demonstrated that the optimization of medium composition and the cell growth rate are important to increase the concentration of D-PA for microbial fermentation. This work laid the foundation for further research on the application of D-PA microbial synthesis.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02773-0.

Effects of lipids and surfactants on the fermentation production of echinocandin B by Aspergillus nidulans

AIMS

Echinocandin B (ECB) is a kind of lipopeptide antifungal antibiotic, as well as the key precursor of antifungal drug Anidulafungin. Its efficient bioproduction plays an important role in promoting the industrial production of Anidulafungin.

METHODS AND RESULTS

In this study, methyl oleate and Tween 80 were firstly used to enhance the ECB fermentation by Aspergillus nidulans, the results showed that the ECB titre was significantly enhanced with the addition of methyl oleate and Tween 80. Among the lipids, methyl oleate was found to play a pivotal role in increasing the ECB titre to 2123 mg l^-1 , which was more than five times higher than that of the control. The addition of Tween 80 in the medium resulted in ECB titre increased to 2584 mg l^-1 . The scanning electron microscope (SEM) and N-phenyl-1-naphthylamine (NPN) assay indicated that Tween 80 could influence the cell membrane permeability of A. nidulans, and enhance the intracellular and extracellular substance exchange, therefore lead to the increasing of ECB titre.

CONCLUSIONS

Methyl oleate and Tween 80 are optimal carbon sources and surfactants for efficient ECB biosynthesis respectively.

SIGNIFICANCE AND IMPACT OF THE STUDY

Surfactant was used in ECB fermentation for the first time, which provided feasible ideas for optimizing the fermentation process of other fungi.

Identification of a novel promoter for driving antibiotic-resistant genes to reduce the metabolic burden during protein expression and effectively select multiple integrations in Pichia Pastoris

Routine approaches for the efficient expression of heterogenous proteins in Pichia pastoris include using the strong methanol-regulated alcohol oxidase (AOX1) promoter and multiple inserts of expression cassettes. To screen the transformants harboring multiple integrations, antibiotic-resistant genes such as the Streptoalloteichus hindustanus bleomycin gene are constructed into expression vectors, given that higher numbers of insertions of antibiotic-resistant genes on the expression vector confer resistance to higher concentrations of the antibiotic for transformants. The antibiotic-resistant genes are normally driven by the strong constitutive translational elongation factor 1a promoter (P_TEF1). However, antibiotic-resistant proteins are necessary only for the selection process. Their production during the heterogenous protein expression process may increase the burden in cells, especially for the high-copy strains which harbor multiple copies of the expression cassette of antibiotic-resistant genes. Besides, a high concentration of the expensive antibiotic is required for the selection of multiple inserts because of the effective expression of the antibiotic-resistant gene by the TEF1 promoter. To address these limitations, we replaced the TEF1 promoter with a weaker promoter (P_Dog2p300) derived from the potential promoter region of 2-deoxyglucose-6-phosphate phosphatase gene for driving the antibiotic-resistant gene expression. Importantly, the P_Dog2p300 has even lower activity under carbon sources (glycerol and methanol) used for the AOX1 promoter-based production of recombinant proteins compared with glucose that is usually used for the selection process. This strategy has proven to be successful in screening of transformants harboring more than 3 copies of the gene of interest by using plates containing 100 μg/ml of Zeocin. Meanwhile, levels of Zeocin resistance protein were undetectable by immunoblotting in these multiple-copy strains during expression of heterogenous proteins.Key points• P_Dog2p300 was identified as a novel glucose-regulated promoter.• The expression of antibiotic-resistant gene driven by P_Dog2p300 was suppressed during the recombinant protein expression, resulting in reducing the metabolic burden.• The transformants harboring multiple integrations were cost-effectively selected by using the P_Dog2p300 for driving antibiotic-resistant genes.

Efficient bio-degradation of food waste through improving the microbial community compositions by newly isolated Bacillus strains

This study aims to screen high-degradability strains and develop a novel microbial agent for efficient food waste degradation. The effects of the novel microbial agent on organic matter degradation, enzyme activity, and bacterial succession during the in-situ reduction of food waste were evaluated and compared with other two microbial agents previously developed. Results showed that the novel agent containing four Bacillus strains received maximum organic degradation rates, volatile solid removal (46.91%) and total mass reduction (76.16%). Pyrosequencing analysis revealed that there was a significant difference in the microbial community structure of the matrix among the three biodegradation systems, and the novel agent greatly improved the stability of in-situ reduction process that Bacillus was the dominant genus (>98%) since day 4. These results indicated that the inoculant containing only Bacillus was more stable and cost-effective in FW in-situ reduction.

Effects of methyl oleate and microparticle-enhanced cultivation on echinocandin B fermentation titer

Echinocandin B (ECB) is a key precursor of antifungal agent Anidulafungin, which has demonstrated clinical efficacy in patients with invasive candidiasis. In this study, the effects of microparticle-enhanced cultivation and methyl oleate on echinocandin B fermentation titer were investigated. The results showed that the titer was significantly influenced by the morphological type of mycelium, and mycelium pellet was beneficial to improve the titer of this secondary metabolism. First, different carbon sources were chosen for the fermentation, and methyl oleate achieved the highest echinocandin B titer of 2133 ± 50 mg/L, which was two times higher than that of the mannitol. The study further investigated the metabolic process of the fermentation, and the results showed that L-threonine concentration inside the cell could reach 275 mg/L at 168 h with methyl oleate, about 2.5 times higher than that of the mannitol. Therefore, L-threonine may be a key precursor of echinocandin B. In the end, a new method of adding microparticles for improving the mycelial morphology was used, and the addition of talcum powder (20 g/L, diameter of 45 µm) could make the maximum titer of echinocandin B reach 3148 ± 100 mg/L.

Mutagenesis of echinocandin B overproducing Aspergillus nidulans capable of using starch as main carbon source

Echinocandin B, a kind of antimycotic with cyclic lipo-hexapeptides, was produced by fermentation with Aspergillus nidulans using fructose as main carbon source. The objective of this study was to screen a high-yield mutant capable of using cheap starch as main carbon source by atmospheric and room temperature plasma (ARTP) treatment in order to decrease the production cost of echinocandin B. A stable mutant A. nidulans ZJB19033, which can use starch as optimal carbon source instead of expensive fructose, was selected from two thousands isolates after several cycles of ARTP mutagenesis. To further increase the production of echinocandin B, the optimization of fermentation medium was performed by response surface methodology (RSM), employing Plackett-Burman design (PBD) followed by Box-Behnken design (BBD). The optimized fermentation medium provided the optimal yield of echinocandin B, 2425.9 ± 43.8 mg/L, 1.3-fold compared to unoptimized medium. The results indicated that the mutant could achieve high echinocandin B production using cheap starch as main carbon source, and the cost of carbon sources in fermentation medium reduced dramatically by about 45%.

Integrated strategy of temperature shift and mannitol feeding for enhanced production of echinocandin B by Aspergillus nidulans CCTCC M2012300

The production of echinocandin B (ECB) by Aspergillus nidulans CCTCC M2012300 was improved by integrating the temperature-shift and fed-batch control strategies. The kinetic characteristics of batch cultures were analyzed at different culture temperatures, and then a two-stage temperature control strategy was established. In the first 6 days, the temperature was maintained at 30 °C to obtain the maximal cell growth rate; subsequently, 25 °C was used to gain a high ECB formation rate. On the basis of temperature control, the ECB productivity was increased to 143.3 mg/(L day), which was a 1.3-fold improvement compared with the optimal constant-temperature cultivations. The influences of fed-batch cultures were further investigated. A maximal ECB productivity of 170.8 mg/(L day) was obtained through a three-stage mannitol pulse-feeding strategy, which was another 1.2-fold improvement than that of the batch fermentation. This is the first report of the use of a two-stage temperature control fed-batch strategy in ECB fermentation. This strategy was simple and economical to operate and may provide new guidance for the industrial-scale production of ECB.

Highly enantioselective oxidation of α-hydroxyacids bearing a substituent with an aryl group: co-production of optically active α-hydroxyacids and α-ketoacids

A novel and simple methodology for co-obtaining of enantiomerically pure α-hydroxyacids and α-ketoacids was developed by enantioselective oxidation of α-hydroxyacids bearing a substituent with an aryl group using α-hydroxyacid dehydrogenase (α-HADH). A high-throughput method was firstly established for screening of enantioselective α-HADHs. Sinorhizobium sp. ZJB1 101 with high activity and excellent enantioselectivity of α-HADH for oxidation of α-hydroxyacids bearing a substituent with an aryl group was isolated and identified. This strain has potential for co-production of (R)-α-hydroxyacids and α-ketoacids in near theoretical yields, while no consecutive oxidation of α-ketoacids was observed. The green conversion system appears promising for potential applications in industry.

Enhanced biotransformation of 1,3-dichloro-2-propanol to epichlorohydrin via resin-based in situ product removal process

Biotransformation of 1,3-dichloro-2-propanol (DCP) to epichlorohydrin (ECH) by the whole cells of recombinant Escherichia coli expressing halohydrin dehalogenase was limited by product inhibition. To solve this problem and improve the ECH yield, a biotransformation strategy using resin-based in situ product removal (ISPR) was investigated. Seven macroporous resins were examined to adsorb ECH: resin HZD-9 was the best. When 10 % (w/v) HZD-9 was added to batch biotransformation, 53.3 mM ECH was obtained with a molar yield of 88.3 %. The supplement of the HZD-9 increased the ECH volumetric productivity from 0.5 to 2.8 mmol/l min compared to without addition of resin. In fed-batch biotransformation, this approach increased ECH from 31 to 87 mM. These results provide a promising basis for the biosynthesis of ECH.