Identification of a Strong Quorum Sensing- and Thermo-Regulated Promoter for the Biosynthesis of a New Metabolite Pesticide Phenazine-1-carboxamide in Pseudomonas strain PA1201

Fluxomic, Metabolomic, and Transcriptomic Analyses Reveal Metabolic Responses to Phenazine-1-carboxamide Synthesized in Pseudomonas chlororaphis

Phenazine-1-carboxamide (PCN) has been exploited as a successful biopesticide due to its broad-spectrum antifungal activity. We engineered a PCN-overproducing Pseudomonas chlororaphis strain through overexpressing shikimate pathway genes (aroB, aroQ, aroE, and phzC) and deleting negative regulatory genes (relA, fleQ, and pykF). The optimized strain produced 1.92 g/L PCN with a yield of 0.11 g/g glycerol, the highest titer ever reported by using minimal media. To gain deeper insights into the underlying regulatory network, the final strain and the parental strain were examined using three distinct omic data sets. 13C-metabolic flux analysis revealed a substantial flux reconfiguration in the optimized strain, including the activation of the EDEMP cycle, the PP pathway, the glyoxylate shunt, and the shikimate pathway. Metabolomic results indicated that central carbon was rerouted to the shikimate pathway. Transcriptomic data identified global gene expression changes. This study forms the basis for further engineering of strains to achieve outstanding performance.

Recent Advances in Phenazine Natural Products: Biosynthesis and Metabolic Engineering

Phenazine natural products are a class of nitrogen-containing heterocyclic compounds produced by microorganisms. The tricyclic ring molecules show various chemical structures and extensive pharmacological activities, such as antimicrobial, anticancer, antiparasitic, anti-inflammatory, and insecticidal activities, with low toxicity to the environment. Since phenazine-1-carboxylic acid has been developed as a registered biopesticide, the application of phenazine natural products will be promising in the field of agriculture pathogenic fungi control based on broad-spectrum antifungal activity, minimal toxicity to the environment, and improvement of crop production. Currently, there are still plenty of intriguing hidden biosynthetic pathways of phenazine natural products to be discovered, and the titer of naturally occurring phenazine natural products is insufficient for agricultural applications. In this review, we spotlight the progress regarding biosynthesis and metabolic engineering research of phenazine natural products in the past decade. The review provides useful insights concerning phenazine natural products production and more clues on new phenazine derivatives biosynthesis.

Metabolic Degradation and Bioactive Derivative Synthesis of Phenazine-1-Carboxylic Acid by Genetically Engineered Pseudomonas chlororaphis HT66

Phenazine-1-carboxylic acid (PCA) secreted by Pseudomonas chlororaphis has been commercialized and widely employed as an antifungal pesticide. However, it displays potential hazards to nontarget microorganisms and the environment. Although the PCA degradation characteristics have received extensive attention, the biodegradation efficiency is still insufficient to address the environmental risks. In this study, an engineered Pseudomonas capable of degrading PCA was constructed by introducing heterologous PCA 1,2-dioxygenase (PcaA1A2A3A4). By integrating the PCA degradation module in the chemical mutagenesis mutant P3, 7.94 g/L PCA can be degraded in 60 h, which exhibited the highest PCA degradation efficiency to date and was 35.4-fold higher than that of the PCA natural degraders. Additionally, PCA was converted to 1-methoxyphenazine through structure modification by introducing the functional enzymes PhzS_Pa and PhzM_La, which has good antifungal activity and environmental compatibility. This work demonstrates new possibilities for developing PCA-derived biopesticides and enables targeted control of the impact of PCA in diverse environments.

Isolation and evaluation of strong endogenous promoters for the heterologous expression of proteins in Pichia pastoris

BACKGROUND

The heterologous expression of biosynthetic pathway genes for pharmaceutical or fine chemical production usually requires to express more than one gene in the host cells. In eukaryotes, the pathway flux is typically balanced by controlling the transcript levels of the genes involved. It is difficult to balance the stoichiometric fine-tuning of the reaction steps of the pathway by acting on one or two promoters. Furthermore, the promoter used should not be identical to avoid loss of inserted genes by recombination or dilute its transcription factors.

RESULTS

Based on RNA-seq data, 18 candidate genes with the highest transcription levels at three carbon sources (glucose, glycerol and methanol) were selected and their promoter regions were isolated from GS115 genome. The performance of these promoters on the level of protein production was evaluated using LacZ and EGFP genes as the reporters, respectively. These isolated promoters all exhibited activity to express LacZ gene. Using LacZ as a reporter, of the 18 promoter candidates, 9 promoters showed higher expression levels for the reporter compare to pGAP, a strong promoter widely used for constitutive expression of heterologous proteins in Pichia pastoris. These promoters with high expression levels were further employed to evaluate secreted expression using EGFP as a reporter. 6 promoters exhibited stronger protein expression compare to pGAP. Interestingly, the protein expression driven by pFDH1 was slightly higher than that of commonly used pAOX1 at methanol, and methanol-induced expression of pFDH1 was not repressed by glycerol.

CONCLUSION

The various promoters identified in this study could be used for heterologous expression of biosynthetic pathway genes for pharmaceutical or fine chemical production. the methanol-induced pFDH1 that is not repressed by glycerol is an attractive alternative to pAOX1 and may provide a novel way to produce heterologous proteins in Pichia pastoris.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Early activated quorum sensing enhanced a nosZ-deficient strain of Pseudomonas aeruginosa for stably recovering nitrous oxide from incineration leachate in microbial electrolysis cell

In this study, a quorum sensing (QS) signal molecule, 3-oxo-C12-HSL, was supplied into ΔnosZ Pseudomonas microbial electrolysis cell system for strengthening the N₂O recovery from incineration leachate. The resistance for high nitrite loading was strongly improved with nitrite removal efficiency of 80.35% compared to 67.07% from the control on day 13 due to the increasing biomass through early activated QS. Higher N₂O proportion in biogas (85.85% on average) was achieved in the QS early activated reactor, which indicated the better potential for N₂O recovery. Bacterial community analysis showed the purity of ΔnosZ strain with the abundance of 100% in the anode chamber at the end of the operation. This was plausibly related to the increased synthesis of phenazine derivatives by the early activated QS system. These results show a more promising way for N₂O recovery by a single engineering bacteria from the high nitrogen contained actual wastewater.

Enhanced Phenazine-1-Carboxamide Production in Pseudomonas chlororaphis H5△fleQ△relA through Fermentation Optimization

Phenazine-1-carboxamide (PCN) is effective to control many plant pathogens, and improving PCN production would be of great significance in promoting its development as a biopesticide. This study was conducted to improve the PCN production of Pseudomonas chlororaphis H5△fleQ△relA through fermentation optimization in both shake flask and bioreactor. The PCN production of H5△fleQ△relA was improved from 2.75 ± 0.23 g/L to 5.51 ± 0.17 g/L by medium optimization in shake flask using Plackett-Burman design, the path of steepest ascent experiment and central composite design. Then, PCN production reached 8.58 ± 0.25 g/L through optimizing pH in 1 L bioreactor. After pH optimization, the transcriptional levels of ccoO_2 and ccoQ_2 genes related to microbial aerobic respiration were significantly upregulated, and the relative abundance of 3-oxo-C14-HSL was significantly enhanced 15-fold, and these changes were vital for cell activity and metabolites production. Furthermore, the PCN production reached 9.58 ± 0.57 g/L after optimization of the fed-batch fermentation strategy in 1 L bioreactor. Finally, the fermentation scale-up of the optimal medium and optimal feeding strategy were conducted in 30 L bioreactor at the optimal pH, and their PCN production reached 9.17 g/L and 9.62 g/L respectively, which were comparable to that in 1 L bioreactor. In this study, the high PCN production was achieved from the shake-flask fermentation to 30 L bioreactor, and the optimal feeding strategy improved PCN production in bioreactor without increasing total glycerol compared with in shake flask. It provides promising pathways for the optimization of processes for the production of other phenazines.

Activity of bacteria isolated from bats against Pseudogymnoascus destructans in China

White-nose syndrome, a disease that is caused by the psychrophilic fungus Pseudogymnoascus destructans, has threatened several North America bat species with extinction. Recent studies have shown that East Asian bats are infected with P. destructans but show greatly reduced infections. While several factors have been found to contribute to these reduced infections, the role of specific microbes in limiting P. destructans growth remains unexplored. We isolated three bacterial strains with the ability to inhibit P. destructans, namely, Pseudomonas yamanorum GZD14026, Pseudomonas brenneri XRD11711 and Pseudomonas fragi GZD14479, from bats in China. Pseudomonas yamanorum, with the highest inhibition score, was selected to extract antifungal active substance. Combining mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy analyses, we identified the active compound inhibiting P. destructans as phenazine-1-carboxylic acid (PCA), and the minimal inhibitory concentration (MIC) was 50.12 μg ml-1 . Whole genome sequencing also revealed the existence of PCA biosynthesis gene clusters. Gas chromatography-mass spectrometry (GC-MS) analysis identified volatile organic compounds. The results indicated that 10 ppm octanoic acid, 100 ppm 3-tert-butyl-4-hydroxyanisole (isoprenol) and 100 ppm 3-methyl-3-buten-1-ol (BHA) inhibited the growth of P. destructans. These results support that bacteria may play a role in limiting the growth of P. destructans on bats.

Biosynthesis and metabolic engineering of 1-hydroxyphenazine in Pseudomonas chlororaphis H18

Background

1-Hydroxyphenazine (1-OH-PHZ) is a phenazine microbial metabolite with broad-spectrum antibacterial activities against a lot of plant pathogens. However, its use is hampered by the low yield all along. Metabolic engineering of microorganisms is an increasingly powerful method for the production of valuable organisms at high levels. Pseudomonas chlororaphis is recognized as a safe and effective plant rhizosphere growth-promoting bacterium, and faster growth rate using glycerol or glucose as a renewable carbon source. Therefore, Pseudomonas chlororaphis is particularly suitable as the chassis cell for the modification and engineering of phenazines.

Results

In this study, enzyme PhzS (monooxygenase) was heterologously expressed in a phenazine-1-carboxylic acid (PCA) generating strain Pseudomonas chlororaphis H18, and 1-hydroxyphenazine was isolated, characterized in the genetically modified strain. Next, the yield of 1-hydroxyphenazine was systematically engineered by the strategies including (1) semi-rational design remodeling of crucial protein PhzS, (2) blocking intermediate PCA consumption branch pathway, (3) enhancing the precursor pool, (4) engineering regulatory genes, etc. Finally, the titer of 1-hydroxyphenazine reached 3.6 g/L in 5 L fermenter in 54 h.

Conclusions

The 1-OH-PHZ production of Pseudomonas chlororaphis H18 was greatly improved through systematically engineering strategies, which is the highest, reported to date. This work provides a promising platform for 1-hydroxyphenazine engineering and production.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01731-y.

H-NS family protein MvaU downregulates phenazine-1-carboxylic acid (PCA) biosynthesis via binding to an AT-rich region within the promoter of the phz2 gene cluster in the rhizobacterium Pseudomonas strain PA1201

Histone-like nucleoid-structuring (H-NS) proteins are key regulators in gene expression silencing and in nucleoid compaction. The H-NS family member proteins MvaU in Pseudomonas aeruginosa are thought to bind the same AT-rich regions of chromosomes and function to coordinate the control of a common set of genes. Here, we explored the molecular mechanism by which MvaU controls PCA biosynthesis in P. aeruginosa PA1201. We present evidence suggesting that MvaU is self-regulated. Deletion of mvaU significantly increased PCA production, and PCA production sharply decreased when mvaU was over-expressed. MvaU transcriptionally repressed phz2 cluster expression and consequently reduced PCA biosynthesis. β-galactosidase assays confirmed that base pairing near the −35 box is required when MvaU regulates PCA production in PA1201. Electrophoretic mobility shift assays (EMSA) and additional point mutation analysis demonstrated that MvaU directly bound to an AT-rich motif within the promoter of the phz2 cluster. Chromatin immunoprecipitation (ChIP) analysis also indicated that MvaU directly bound to the P5 region of the phz2 cluster promoter. MvaU repression of PCA biosynthesis was independent of QscR and OxyR in PA1201 and neither PCA or H₂O₂ were the environmental signals that induced mvaU expression. These findings detail a new MvaU-dependent regulatory pathway of PCA biosynthesis in PA1201 and provide a foundation to increase PCA fermentation titer by genetic engineering.

Enhanced recovery of nitrous oxide from incineration leachate in a microbial electrolysis cell inoculated with a nosZ-deficient strain of Pseudomonas aeruginosa

High concentrations of nitrous oxide were recovered from partial nitrification treated leachate in a microbial electrolysis cell (MEC) inoculated with a nosZ-deficient strain of Pseudomonas aeruginosa. N₂O conversion efficiencies > 90% were achieved when a potential of 0.8 V was applied to the MEC. The ΔnosZ strain was enriched in the 0.8 V MEC, but Achromobacter dominated the non-current control. Nitric oxide reductase genes were highly expressed by ΔnosZ cells growing in the 0.8 V MEC, consistent with enhanced nitrous oxide production rates. Concentrations of phenazine derivatives and transcripts from phenazine biosynthesis genes were also high in the 0.8 V MEC. Phenazine derivatives are known to act as electron shuttles, enhance biofilm formation, and help ward off competitors, thereby increasing the survivability of the ΔnosZ strain in the MEC. These results show that applied current stabilized growth of the ΔnosZ strain in the reactor and allowed it to sustainably generate high concentrations of nitrous oxide.

Identification and evaluation of a panel of strong constitutive promoters in Listeria monocytogenes for improving the expression of foreign antigens

Attenuated Listeria monocytogenes could be a potential vaccine vector for the immunotherapy of tumors or pathogens. However, the lack of reliable promoters has limited its ability to express foreign antigens. In the present study, 21 promoters were identified from Listeria monocytogenes through RNA-seq analysis under two pH conditions of pH 7.4 and pH 5.5. Based on the constructed fluorescence report system, 7 constitutive promoters exhibited higher strength than P_help (1.8-fold to 5.4-fold), a previously reported strong promoter. Furthermore, the selected 5 constitutive promoters exhibited higher UreB production activity than P_help (1.1-fold to 8.3-fold). Notably, a well-characterized constitutive promoter P₁₈ was found with the highest activity of fluorescence intensity and UreB production. In summary, the study provides a panel of strong constitutive promoters for Listeria monocytogenes and offers a theoretical basis for mining constitutive promoters in other organisms. KEY POINTS: • Twenty-one promoters were identified from L. monocytogenes through RNA-seq. • Fluorescent tracer of L. monocytogenes (P₁₈) was performed in vitro and in vivo. • A well-characterized constitutive promoter P₁₈ could improve the expression level of a foreign antigen UreB in L. monocytogenes.

Highly Regioselective and Chemoselective [3 + 3] Annulation of Enaminones with ortho-Fluoronitrobenzenenes: Divergent Synthesis of Aposafranones and Their N-Oxides

A base-promoted unprecedented strategy for the regioselective and chemoselective divergent synthesis of highly functionalized aposafranones and their N-oxides has been developed from the [3 + 3] annulation of enaminones with o-fluoronitrobenzenenes. This novel synthetic strategy offers an alternative method for the construction of aposafranones and their N-oxides are meaningful in the fields of both biology and organic synthesis. The established protocol explores the annulation scope of enaminones, and it expands the application of nitro-based cyclization.

Effect of culture medium optimization on the secondary metabolites activity of Lysobacter antibioticus 13-6

Fermentation products of Lysobacter antibioticus 13-6 have antagonistic activity against devastating phytopathogenic bacerium Xanthomonas oryzae pv. oryzicola. The production of Lysobacter antibioticus 13-6 secondary metabolites was increased by optimizing the fermentation medium; using a single-factor screening test, Plackett-Burman Design, and Box-Behnken Design. The medium's final formulation for active secondary metabolites high-yield included peptone 5 g/L, glucose 4.73 g/L, MgSO₄·7H₂O 2.33 g/L, and K₂HPO₄ 2.21 g/L. We compared phenazine-1-carboxylic acid (PCA) contents of L. antibioticus 13-6 in the initial and optimized mediums through HPLC. It was found PCA contents of the optimized medium are two folds more than in the initial medium. We also detected the relative expression of five phenazine genes of L. antibioticus 13-6 via RT-qPCR, and it was found that genes: phzB, C, S, and NO1 have more significant expression compared with the initial medium, while gene phzD has found just significant. Further, we revealed that the optimal fermentation conditions for secondary metabolites were: fermentation time 60 hours, shaking speed 160 rpm, inoculum size 3%, and the initial pH = 7.0. In the end, it was determined that the antimicrobial activity and quality of L. antibioticus 13-6 secondary metabolites were increased by about 41.75% and 2-times, respectively, after the optimization of the fermentation medium.

Metabolic Engineering of Pseudomonas chlororaphis Qlu-1 for the Enhanced Production of Phenazine-1-carboxamide

Phenazine-1-carboxylic acid (PCA), the primary active ingredient of Shenqinmycin, was awarded the China Pesticide Certificate in 2011 due to its excellent antibacterial action. Phenazine-1-carboxamide (PCN) is a derivative of PCA, which is modified by the phzH gene, and its anti-bacterial effect is better than that of PCA. At present, PCN can be produced via Pseudomonas fermentation using an opportunistic pathogen, Pseudomonas aeruginosa. Qlu-1 is an environmentally friendly strain of Pseudomonas chlororaphis that can produce phenazine derivatives. We replaced the phzO gene with the phzH gene from P. aeruginosa to achieve PCN accumulation. Different strategies were used to enhance PCN production: knocking out of negative regulatory factors, enhancing the shikimate pathway by gene overexpression and gene knocking, and using fed-batch fermentation. Finally, an engineered strain of P. chlororaphis was produced, which produced 11.45 g/L PCN. This achievement indicates that Qlu-1 could be modified as a potential microbial cell factory for PCN production by metabolic engineering.