Characterization and Engineering of Pseudomonas chlororaphis LX24 with High Production of 2-Hydroxyphenazine

Metabolic engineering of Pseudomonas chlororaphis P3 for high-level and directed production of phenazine-1,6-dicarboxylic acid from crude glycerol

Phenazine-1,6-dicarboxylic acid (PDC) is a precursor of complex substituted phenazines used as pesticides and pharmaceuticals. The PDC biosynthesis exists the low production and the high proportion of by-products phenazine-1-carboxylic acid (PCA) derivatives in Pseudomonas P3△A. Herein, PDC production were improved by systematic metabolic engineering and synthetic regulation. The directed PDC biosynthesis was achieved by introducing the isozymes of PhzF', and PCA derivatives was barely detectable. Subsequently, a high-level PDC-producing strain P3FK2E-aF'EC was obtained by co-overexpression of aroE, phzE, phzC, and aphzF' in a multi-knockout strain. Through scale-up culture, the highest PDC production and proportion reached 6,447.05 mg/L and 99.68 %, with the productivity of 89.54 mg/L·h using KB. Economically, PDC production achieved 5,584.35 mg/L accounting for 99.43 % with the highest productivity of 108.32 mg/L·h from crude glycerol. This study first achieved the directed high-level production of PDC from renewable energy, and presented a potential biosynthesis platform for PDC derivatives in Pseudomonas.

Recent Advances in Phenazine Natural Products: Chemical Structures and Biological Activities

Phenazine natural products are a class of colored nitrogen-containing heterocycles produced by various microorganisms mainly originating from marine and terrestrial sources. The tricyclic ring molecules show various chemical structures and the decorating groups dedicate extensive pharmacological activities, including antimicrobial, anticancer, antiparasitic, anti-inflammatory, and insecticidal. These secondary metabolites provide natural materials for screening and developing medicinal compounds in the field of medicine and agriculture due to biological activities. The review presents a systematic summary of the literature on natural phenazines in the past decade, including over 150 compounds, such as hydroxylated, O-methylated, N-methylated, N-oxide, terpenoid, halogenated, glycosylated phenazines, saphenic acid derivatives, and other phenazine derivatives, along with their characterized antimicrobial and anticancer activities. This review may provide guidance for the investigation of phenazines in the future.

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.

Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis

The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis. Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling the identification of targets for metabolic engineering of bioproduction hosts.

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.

Pyocyanin Modulates Gastrointestinal Transformation and Microbiota

Phenazines are ubiquitously produced by Pseudomonas spp. in the environment and are widely used in agriculture and clinical therapies, making their accumulation through the food chain cause potential risks to human health. Here, we utilized pyocyanin (PYO) as a representative to study the effects of phenazines on digestive tracts. Pharmacokinetic analysis showed that PYO exhibited low systemic exposure, slow elimination, and low accumulation in both rat and pig models. PYO was subsequently found to induce intestinal microbiota dysbiosis, destroy the mucus layer and physical barrier, and even promote gut vascular barrier (GVB) impairment, consequently increasing the gut permeability. Additionally, integral and metabolomic analyses of the liver demonstrated that PYO induced liver inflammation and metabolic disorders. The metabolic analysis further confirmed that all of the metabolites of PYO retain the nitrogen-containing tricyclic structural skeleton of phenazines, which was the core bioactivity of phenazine compounds. These findings elucidated that PYO could be metabolized by animals. Meanwhile, high levels of PYO could induce intestinal barrier impairment and liver damage, suggesting that we should be alert to the accumulation of phenazines.

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.