Insights on the susceptibility of plant pathogenic fungi to phenazine-1-carboxylic acid and its chemical derivatives

Study on the Design, Synthesis, Bioactivity and Translocation of the Conjugates of Phenazine-1-carboxylic Acid and N-Phenyl Alanine Ester

The natural pesticide phenazine-1-carboxylic acid (PCA) is known to lack phloem mobility, whereas Metalaxyl is a representative phloem systemic fungicide. In order to endow PCA with phloem mobility and also enhance its antifungal activity, thirty-two phenazine-1-carboxylic acid-N-phenylalanine esters conjugates were designed and synthesized by conjugating PCA with the active structure N-acylalanine methyl ester of Metalaxyl. All target compounds were characterized by 1H NMR, 13C NMR and HRMS. The antifungal evaluation results revealed that several target compounds exhibited moderate to potent antifungal activities against Sclerotinia sclerotiorum, Bipolaris sorokiniana, Phytophthora parasitica, Phytophthora citrophthora. In particular, compound F7 displayed excellent antifungal activity against S. sclerotiorum with an EC50 value of 6.57 µg/mL, which was superior to that of Metalaxyl. Phloem mobility study in castor bean system indicated good phloem mobility for the target compounds F1-F16. Particularly, compound F2 exhibited excellent phloem mobility; the content of compound F2 in the phloem sap of castor bean was 19.12 μmol/L, which was six times higher than Metalaxyl (3.56 μmol/L). The phloem mobility tests under different pH culture solutions verified the phloem translocation of compounds related to the "ion trap" effect. The distribution of the compound F2 in tobacco plants further suggested its ambimobility in the phloem, exhibiting directional accumulation towards the apical growth point and the root. These results provide valuable insights for developing phloem mobility fungicides mediated by exogenous compounds.

Fe-Based Nanomaterials and Plant Growth Promoting Rhizobacteria Synergistically Degrade Polychlorinated Biphenyls by Producing Extracellular Reactive Oxygen Species

Plant growth promoting rhizobacteria (PGPR) produce extracellular reactive oxygen species (ROS) to protect plants from external stresses. Fe-based nanomaterials can potentially interact with PGPR and synergistically degrade organic pollutants, yet they have received no study. Here, we studied how the interaction between a typical PGPR (Pseudomonas chlororaphis, JD37) and Fe-based nanomaterials facilitated the degradation of 2,4,4'-trichlorobiphenyl (PCB28), by comparing the zerovalent iron of 20 nm (nZVI20), 100 nm (nZVI100), and 5 μm; iron oxide nanomaterials (α-Fe2O3, γ-Fe2O3, and Fe3O4) of ca. 20 nm; and ferrous and ferric salts. Although all Fe materials (0.1 g L-1) alone could not degrade aqueous PCB28 (0.1 mg L-1) under dark or aerobic conditions, nZVI20, nZVI100, α-Fe2O3, and Fe2+ promoted PCB28 degradation by JD37, with the half-life of PCB28 shortened from 16.5 h by JD37 alone to 8.1 h with nZVI100 cotreatment. Mechanistically, the nanomaterials stimulated JD37 to secrete phenazine-1-carboxylic acid and accelerated the NADH/NAD+ conversion, promoting O2*- generation; JD37 increased Fe(II) dissolution from the nanomaterials, facilitating *OH generation; and the ROS gradually degraded PCB28 into benzoic acid through dihydroxy substitution, oxidation to quinone, and Michael addition. These findings provide a new strategy of nanoenabled biodegradation of organic pollutants by applying Fe-based nanomaterials and PGPR.

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.

Specialized Metabolites from the Allelopathic Plant Retama raetam as Potential Biopesticides

To cope with the rising food demand, modern agriculture practices are based on the indiscriminate use of agrochemicals. Although this strategy leads to a temporary solution, it also severely damages the environment, representing a risk to human health. A sustainable alternative to agrochemicals is the use of plant metabolites and plant-based pesticides, known to have minimal environmental impact compared to synthetic pesticides. Retama raetam is a shrub growing in Algeria’s desert areas, where it is commonly used in traditional medicine because of its antiseptic and antipyretic properties. Furthermore, its allelopathic features can be exploited to effectively control phytopathogens in the agricultural field. In this study, six compounds belonging to isoflavones and flavones subgroups have been isolated from the R. raetam dichloromethane extract and identified using spectroscopic and optical methods as alpinumisoflavone, hydroxyalpinumisoflavone, laburnetin, licoflavone C, retamasin B, and ephedroidin. Their antifungal activity was evaluated against the fungal phytopathogen Stemphylium vesicarium using a growth inhibition bioassay on PDA plates. Interestingly, the flavonoid laburnetin, the most active metabolite, displayed an inhibitory activity comparable to that exerted by the synthetic fungicide pentachloronitrobenzene, in a ten-fold lower concentration. The allelopathic activity of R. raetam metabolites against parasitic weeds was also investigated using two independent parasitic weed bioassays to discover potential activities on either suicidal stimulation or radicle growth inhibition of broomrapes. In this latter bioassay, ephedroidin strongly inhibited the growth of Orobanche cumana radicles and, therefore, can be proposed as a natural herbicide.

Extracts from Environmental Strains of Pseudomonas spp. Effectively Control Fungal Plant Diseases

The use of synthetic chemical products in agriculture is causing severe damage to the environment and human health, but agrochemicals are still widely used to protect our crops. To counteract this trend, we have been looking for alternative strategies to control plant diseases without causing harm to the environment or damage to our health. However, these alternatives are still far from completely replacing chemical products. Microorganisms have been widely known as a biological tool to control plant diseases, but their use is still limited due to the high variability in their efficacy, together with issues in product registration. However, the metabolites produced by these microorganisms can represent a novel tool for the environment-friendly management of plant diseases, while reducing the issues mentioned above. In this study, we explore the soil microbial diversity in natural systems to look for microorganisms with the potential to be used in pre- and post-harvest protection against fungal plant pathogens. Using a simple workflow, we isolated 22 bacterial strains that were tested both in vitro and in vivo for their ability to counteract the growth of common plant pathogens. The three best isolates, identified as members of the bacterial genus Pseudomonas, were used to produce a series of alcoholic extracts, which were then tested for their action against plant pathogens in simulated real-world applications. Results show that extracts from these isolates have an exceptional biocontrol activity and can be successfully used to control plant pathogens in operational setups. Thus, this study shows that the environmental microbiome is an important source of microorganisms producing metabolites that might provide an alternative strategy to synthetic chemical products.

Biosynthetic Pathway Construction and Production Enhancement of 1-Hydroxyphenazine Derivatives in Pseudomonas chlororaphis H18

1-Hydroxyphenazine derivatives are phenazine family chemicals with broad-spectrum antibacterial and potential biological activities. However, the lack of variety and low titer hinder their applications. In this research, three enzymes PhzS (monooxygenase), NaphzNO1 (N-monooxygenase), and LaphzM (methyltransferase) were heterologously expressed in a phenazine-1-carboxylic acid generating strain Pseudomonas chlororaphis H18. Four phenazines, 1-hydroxyphenazine, 1-methoxyphenazine, 1-hydroxyphenazine N' 10-oxide, and a novel phenazine derivative 1-methoxyphenazine N' 10-oxide, were isolated, characterized in the genetically modified strains, and exhibited excellent antimicrobial activities. Next, we verified the hydroxyl methylation activity of LaphzM and elucidated the biosynthetic pathway of 1-methoxyphenazine N' 10-oxide in vitro. Moreover, the titer of 1-hydroxyphenazine derivatives was engineered. The three compounds 1-methoxyphenazine, 1-hydroxyphenazine N' 10-oxide, and 1-methoxyphenazine N' 10-oxide all reach the highest titer reported to date. This work provides a promising platform for phenazine derivatives' combinatorial biosynthesis and engineering.

Pseudomonas fluorescens Showing Antifungal Activity against Macrophomina phaseolina, a Severe Pathogenic Fungus of Soybean, Produces Phenazine as the Main Active Metabolite

Pseudomonas fluorescens 9 and Bacillus subtilis 54, proposed as biofungicides to control Macrophomina phaseolina, a dangerous pathogen of soybean and other crops, were grown in vitro to evaluate their ability to produce metabolites with antifungal activity. The aim of the manuscript was to identify the natural compounds responsible for their antifungal activity. Only the culture filtrates of P. fluorescens 9 showed strong antifungal activity against M. phaseolina. Its organic extract contained phenazine and mesaconic acid (1 and 2), whose antifungal activity was tested against M. phaseolina, as well as Cercospora nicotianae and Colletotrichum truncatum, other pathogens of soybean; however, only compound 1 exhibited activity. The antifungal activity of compound 1 was compared to phenazine-1-carboxylic acid (PCA, 3), 2-hydroxyphenazine (2-OH P, 4), and various semisynthetic phenazine nitro derivatives in order to perform a structure-activity relationship (SAR) study. PCA and phenazine exhibited the same percentage of growth inhibition in M. phaseolina and C. truncatum, whereas PCA (3) showed lower activity against C. nicotianae than phenazine. 2-Hydroxyphenazine (4) showed no antifungal activity against M. phaseolina. The results of the SAR study showed that electron attractor (COOH and NO2) or repulsor (OH) groups significantly affect the antifungal growth, as well as their α- or β-location on the phenazine ring. Both PCA and phenazine could be proposed as biopesticides to control the soybean pathogens M. phaseolina, C. nicotianae, and C. truncatum, and these results should prompt an investigation of their large-scale production and their suitable formulation for greenhouse and field applications.

Phenazine-1-Carboxylic Acid (PCA), Produced for the First Time as an Antifungal Metabolite by Truncatella angustata, a Causal Agent of Grapevine Trunk Diseases (GTDs) in Iran

The phytopathogenic fungus Truncatella angustata, associated with grapevine trunk diseases (GTDs) in Iran, produces the well-known secondary metabolite isocoumumarin (+)-6-hyroxyramulosin and surprisingly also phenazine-1-carboxylic acid (PCA). PCA, identified by spectroscopic (essentially 1H NMR and ESI MS) spectra, is a bacterial metabolite well known for its antifungal activity and was found for the first time in T. angustata culture filtrates. The antifungal activity of PCA was assayed against four different fungi responsible for GTDs, Phaeoacremonium minimum, Phaeoacremonium italicum, Fomitiporia mediterranea, involved in grapevine esca disease, and Neofusicoccum parvum, responsible for Botryosphaeria dieback. The activity was compared with that of the known commercial fungicide, pentachloronitrobenzene, and the close phenazine. PCA and phenazine exhibited strong antifungal activity against all phytopathogenic fungi, inhibiting the fungal growth by about 90-100% and 80-100%, respectively. These results suggested that T. angustata could use PCA to compete with other phytopathogenic fungi that attack grapevine and thus PCA could be proposed as a biofungicide against the fungi responsible for grapevine esca and Botryosphaeria dieback diseases.

Pseudomonas chlororaphis metabolites as biocontrol promoters of plant health and improved crop yield

The Pseudomonas fluorescens complex contains at least eight phylogenetic groups and each of these includes several bacterial species sharing ecological and physiological traits. Pseudomonas chlororaphis classified in a separate group is represented by three different subspecies that show distinctive traits exploitable for phytostimulation and biocontrol of phytopathogens. The high level of microbial competitiveness in soil as well as the effectiveness in controlling several plant pathogens and pests can be related to the P. chlororaphis ability to implement different stimulating and toxic mechanisms in its interaction with plants and the other micro- and macroorganisms. Pseudomonas chlororaphis strains produce antibiotics, such as phenazines, pyrrolnitrine, 2-hexyl, 5-propyl resorcinol and hydrogen cyanide, siderophores such as pyoverdine and achromobactine and a complex blend of volatile organic compounds (VOCs) that effectively contribute to the control of several plant pathogens, nematodes and insects. Phenazines and some VOCs are also involved in the induction of systemic resistance in plants. This complex set of beneficial strategies explains the high increasing interest in P. chlororaphis for commercial and biotechnological applications. The aim of this review is to highlight the role of the different mechanisms involved in the biocontrol activity of P. chlororaphis strains.

Fungal-Bacterial Cooccurrence Patterns Differ between Arbuscular Mycorrhizal Fungi and Nonmycorrhizal Fungi across Soil Niches

Soil bacteria and fungi are known to form niche-specific communities that differ between actively growing and decaying roots. Yet almost nothing is known about the cross-kingdom interactions that frame these communities and the environmental filtering that defines these potentially friendly or competing neighbors. We explored the temporal and spatial patterns of soil fungal (mycorrhizal and nonmycorrhizal) and bacterial cooccurrence near roots of wild oat grass, Avena fatua, growing in its naturalized soil in a greenhouse experiment. Amplicon sequences of the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA genes from rhizosphere and bulk soils collected at multiple plant growth stages were used to construct covariation-based networks as a step toward identifying fungal-bacterial associations. Corresponding stable-isotope-enabled metagenome-assembled genomes (MAGs) of bacteria identified in cooccurrence networks were used to inform potential mechanisms underlying the observed links. Bacterial-fungal networks were significantly different in rhizosphere versus bulk soils and between arbuscular mycorrhizal fungi (AMF) and nonmycorrhizal fungi. Over 12 weeks of plant growth, nonmycorrhizal fungi formed increasingly complex networks with bacteria in rhizosphere soils, while AMF more frequently formed networks with bacteria in bulk soils. Analysis of network-associated bacterial MAGs suggests that some of the fungal-bacterial links that we identified are potential indicators of bacterial breakdown and consumption of fungal biomass, while others intimate shared ecological niches.IMPORTANCE Soils near living and decomposing roots form distinct niches that promote microorganisms with distinctive environmental preferences and interactions. Yet few studies have assessed the community-level cooccurrence of bacteria and fungi in these soil niches as plant roots grow and senesce. With plant growth, we observed increasingly complex cooccurrence networks between nonmycorrhizal fungi and bacteria in the rhizosphere, while mycorrhizal fungal (AMF) and bacterial cooccurrence was more pronounced in soil further from roots, in the presence of decaying root litter. This rarely documented phenomenon suggests niche sharing of nonmycorrhizal fungi and bacteria, versus niche partitioning between AMF and bacteria; both patterns are likely driven by C substrate availability and quality. Although the implications of species cooccurrence are fiercely debated, MAGs matching the bacterial nodes in our networks possess the functional potential to interact with the fungi that they are linked to, suggesting an ecological significance of fungal-bacterial cooccurrence patterns.

One-Step Synthesis of Carbon Nanoparticles Capable of Long-Term Tracking Lipid Droplet for Real-Time Monitoring of Lipid Catabolism and Pharmacodynamic Evaluation of Lipid-Lowering Drugs

Lipid droplets (LDs) are intracellular lipid-rich organelles, which not only serve as neutral lipid reservoirs but also involve in many physiological processes and are associated with a variety of metabolic diseases and cancers. Long-term tracking of the state and behavior of LDs is of great significance but challenging. The difficulty is largely due to the lack of low cytotoxicity, high photobleaching resistance, and long intracellular retention probes that are capable of long-term tracking LDs. Herein, we report the discovery of two amphiphilic LD-targeting carbon nanoparticles (CNPs, i.e., CPDs and CDs) prepared by one-step room-temperature and hydrothermal methods. Their high lipid-water partition coefficient (log P > 2.13) and strong positive solvatochromism property ensure the quality of LD imaging. Especially, CDs exhibit favorable biocompatibility (2 mg mL^-1, cell viability >90%), excellent photostability (after continuous laser irradiation on a confocal microscope for 2 h, relative FL intensity >85%), and superior intracellular retention ability, thereby enabling long-term tracking of LDs in hepatocytes for up to six passages. Based on the excellent long-term tracking ability, CDs are successfully applied to observe autophagy in a typical catabolic process and to evaluate the effect of a commonly used lipid-lowering drug atorvastatin on hepatocyte lipid uptake.

Transcriptomic, Biochemical, and Morphological Study Reveals the Mechanism of Inhibition of Pseudopestalotiopsis camelliae-sinensis by Phenazine-1-Carboxylic Acid

Gray blight disease is one of the most destructive diseases of tea plants and occurs widely in the tea-growing areas of the world. It is caused by several fungal phytopathogens, of which Pseudopestalotiopsis camelliae-sinensis is the main pathogen in China. The environmentally friendly antimicrobial, phenazine-1-carboxylic acid (PCA), a metabolite of the natural soil-borne bacteria Pseudomonas spp., can inhibit a range of fungal crop diseases. In this study, we determined that PCA was active against Ps. camelliae-sinensis in vitro. We studied the mode of action of PCA on hyphae using a microscopic investigation, transcriptomics, biochemical methods, and molecular docking. The results of scanning and transmission electron microscopy indicated that PCA caused developmental deformity of mycelia and organelle damage, and it significantly decreased the accumulation of exopolysaccharides on the hyphal surface. The transcriptome revealed that 1705 and 1683 differentially expressed genes of Ps. camelliae-sinensis treated with PCA were up-regulated or down-regulated, respectively, with genes associated with ribosome biogenesis, oxidative phosphorylation, and encoding various proteins of N-glycan biosynthesis being significantly up-regulated. Up-regulation of nine genes related to N-glycan biosynthesis of Ps. camelliae-sinensis in response to PCA treatment was confirmed by reverse transcription qPCR. The enzymatic activity of catalase and superoxide dismutase of hyphae was significantly decreased by PCA treatment. Our results indicated that exposure to PCA resulted in expression changes in oxidoreductase genes, accumulation of reactive oxygen species, and decreased activity of catalase, with concomitant damage to the fungal cell membrane and cell wall.

Discovery of novel obovatol-based phenazine analogs as potential antifungal agents: synthesis and biological evaluation in vitro

To explore candidate fungicides from plant secondary metabolites, 16 novel obovatol-type phenazine derivatives were semi-synthesized from obovatol isolated from the leaves of Magnolia obovata Thunb. The antifungal activity of synthesized compounds was investigated in vitro against four phytopathogenic fungi using the spore germination method. The bioassay results showed that eight derivatives (8b, 8g, 8h–k, 8i′, and 8k′) exhibited better antifungal activity against Fusarium solani than two positive controls, especially compounds 8b (IC50 = 64.61 μg mL−1) and 8i′ (IC50 = 79.97 μg mL−1) showed pronounced inhibition of spore germination activity against F. solani. They could be used as lead compounds for further structural optimization. Additionally, the preliminary structure-activity relationships (SARs) illustrated that the introduction of a benzene ring monosubstituted with electron-withdrawing groups into the obovatol scaffold could lead to potentially antifungal compounds.

Quorum Sensing Inhibitors against Chromobacterium violaceum CV026 Derived from an Actinomycete Metabolite Library

Quorum sensing (QS) is a microbial signaling system that regulates the expression of many virulence genes. Herein, we studied five compounds-No. 1: (E)-2-methyl-3- (4-nitro-phenyl)-acrylaldehyde; No. 29-2: pimprinine [5-(1H-indol-3-yl)-2-methyloxazole]; No. 48: (2E,4E)-2-methyl-5-phenyl-2,4-pentadienoic acid; No. 74: (3E,5E)-5-methyl-6-(4-nitrophenyl)-hexa-3,5-dien-2-ol; and No. 130: methyphenazine-1-carboxylate-derived from an actinomycete metabolite library. These compounds were confirmed to be QS inhibitors that reduced violacein production in Chromobacterium violaceum CV026. Additionally, compounds No. 1, No. 74, and No. 130 significantly reduced fluorescent pigment production in Pseudomonas aeruginosa ATCC 27853.

Relevance of Plant Growth Promoting Microorganisms and Their Derived Compounds, in the Face of Climate Change

Climate change has already affected food security in many parts of the world, and this situation will worsen if nothing is done to combat it. Unfortunately, agriculture is a meaningful driver of climate change, through greenhouse gas emissions from nitrogen-based fertilizer, methane from animals and animal manure, as well as deforestation to obtain more land for agriculture. Therefore, the global agricultural sector should minimize greenhouse gas emissions in order to slow climate change. The objective of this review is to point out the various ways plant growth promoting microorganisms (PGPM) can be used to enhance crop production amidst climate change challenges, and effects of climate change on more conventional challenges, such as: weeds, pests, pathogens, salinity, drought, etc. Current knowledge regarding microbial inoculant technology is discussed. Pros and cons of single inoculants, microbial consortia and microbial compounds are discussed. A range of microbes and microbe derived compounds that have been reported to enhance plant growth amidst a range of biotic and abiotic stresses, and microbe-based products that are already on the market as agroinputs, are a focus. This review will provide the reader with a clearer understanding of current trends in microbial inoculants and how they can be used to enhance crop production amidst climate change challenges.

An angular dioxygenase gene cluster responsible for the initial phenazine-1-carboxylic acid degradation step in Rhodococcus sp. WH99 can protect sensitive organisms from toxicity

A bacterial strain, Rhodococcus sp. WH99, capable of degrading phenazine-1-carboxylic acid (PCA) was isolated and characterized. Genome comparison revealed that a 21499-bp DNA fragment containing a putative angular dioxygenase gene cluster consisting of the dioxygenase-, ferredoxin reductase- and ferredoxin-encoding genes (pzcA1A2, pzcC and pzcD) is missed in the PCA degradation-deficient mutant WH99M. The pzcA1A2CD genes were expressed in Escherichia coli respectively and hydroxylation of PCA to 1,2-dihydroxyphenazine occurred in vitro only when all components were present. However, in vivo analyses showed that pzcA1A2 and pzcD were indispensable for PCA degradation, while PzcC can be partially replaced by other ferredoxin reductases. Hydroxylation of PCA not only initiates degradation of PCA in strain WH99 but also provides protection to sensitive organisms that would otherwise be inhibited by PCA toxicity. This study illustrates a new initial PCA degradation step in Gram-positive bacteria and enhances our understanding of the genes responsible for PCA hydroxylation, thus enabling targeted studies on protection by PCA degradation in diverse environments.

Root colonization by Pseudomonas chlororaphis primes tomato (Lycopersicum esculentum) plants for enhanced tolerance to water stress

Previous research demonstrated that Pseudomonas chlororaphis subsp. aureofaciens strain M71, a plant growth promoting bacterium (PGPB), exerts beneficial effects on plant metabolism and primes tolerance mechanisms against biotic stresses in tomatoes. We designed an experiment to assess whether root colonization with P. chlororaphis is also able to improve tolerance to water stress in tomatoes. Our results show that inoculation with P. chlororaphis stimulates the antioxidant activity of well-watered tomatoes while maintaining a steady-state level of reactive oxygen species (ROS), increases the expression of genes encoding for the biosynthesis of leaf terpenes, stimulates the production of both the phytohormones ABA and IAA, in turn affecting plant shape (number of leaves) and height (length of internodes), without altering photosynthesis. Upon exposure to mild water stress conditions, an improved antioxidant activity in tomatoes 'primed' by P. chlororaphis inoculation limited the accumulation of reactive oxygen species (ROS) in leaves and thus enhanced tolerance, also through increase of the (osmolyte) proline content. Moreover, P. chlororaphis inoculation further enhanced the ABA level in leaves of water-stressed tomatoes allowing a more efficient modulation of stomatal closure that resulted in an improved water use efficiency (WUE) and biomass accumulation.

Design, synthesis and biological activity of hydroxybenzoic acid ester conjugates of phenazine-1-carboxylic acid

We prepared 16 novel hydroxybenzoic acid ester conjugates of phenazine-1-carboxylic acid (PCA) and investigated their biological activity. Most of the synthesized conjugates displayed some level of fungicidal activities in vitro against five phytopathogenic fungi. Nine conjugates 5b, 5c, 5d, 5e, 5h, 5i, 5m, 5n and 5o (EC50 between 3.2 μg/mL and 14.1 μg/mL) were more active than PCA (EC50 18.6 μg/mL) against Rhizoctonia solani. Especially conjugate 5c showed the higher fungicidal activity against Rhizoctonia solani which is 6.5-fold than PCA. And the results of the bioassay indicated that the fungicidal activity of conjugates was associated with their LogP, and the optimal LogP values of the more potent fungicidal activities within these conjugates ranged from 4.42 to 5.08. The systemic acquired resistance induced by PCA-SA ester conjugate 5c against rice sheath blight disease in rice seedlings was evaluated. The results revealed that PCA-SA ester conjugate 5c retained the resistance induction activity of SA against rice sheath blight.

Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments

Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods. Metabolic engineering allows elevated shikimate production titer by inactivating the competing pathways, increasing intracellular level of key precursors, and overexpressing rate-limiting enzymes. The development of synthetic and systems biology-based novel technologies have revealed a new roadmap for the construction of high shikimate-producing strains. This review elaborates the enhanced biosynthesis of shikimate by utilizing an array of traditional metabolic engineering along with novel advanced technologies. The first part of the review is focused on the mechanistic pathway for shikimate production, use of recombinant and engineered strains, improving metabolic flux through the shikimate pathway, chemically inducible chromosomal evolution, and bioprocess engineering strategies. The second part discusses a variety of industrially pertinent compounds derived from shikimate with special reference to aromatic amino acids and phenazine compound, and main engineering strategies for their production in diverse bacterial strains. Towards the end, the work is wrapped up with concluding remarks and future considerations.

Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

Background

Phytophthora infestans is responsible for late blight, one of the most important potato diseases. Phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 isolated in our laboratory shows biocontrol potential against various plant pathogens. To characterize the effect of LBUM223 on the transcriptome of P. infestans, we conducted an in vitro time-course study. Confrontational assay was performed using P. infestans inoculated alone (control) or with LBUM223, its phzC- isogenic mutant (not producing PCA), or exogenically applied PCA. Destructive sampling was performed at 6, 9 and 12 days and the transcriptome of P. infestans was analysed using RNA-Seq. The expression of a subset of differentially expressed genes was validated by RT-qPCR.

Results

Both LBUM223 and exogenically applied PCA significantly repressed P. infestans’ growth at all times. Compared to the control treatment, transcriptomic analyses showed that the percentages of all P. infestans’ genes significantly altered by LBUM223 and exogenically applied PCA increased as time progressed, from 50 to 61% and from to 32 to 46%, respectively. When applying an absolute cut-off value of 3 fold change or more for all three harvesting times, 207 genes were found significantly differentially expressed by PCA, either produced by LBUM223 or exogenically applied. Gene ontology analysis revealed that both treatments altered the expression of key functional genes involved in major functions like phosphorylation mechanisms, transmembrane transport and oxidoreduction activities. Interestingly, even though no host plant tissue was present in the in vitro system, PCA also led to the overexpression of several genes encoding effectors. The mutant only slightly repressed P. infestans’ growth and barely altered its transcriptome.

Conclusions

Our study suggests that PCA is involved in P. infestans’ growth repression and led to important transcriptomic changes by both up- and down-regulating gene expression in P. infestans over time. Different metabolic functions were altered and many effectors were found to be upregulated, suggesting their implication in biocontrol.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4852-1) contains supplementary material, which is available to authorized users.

Investigating the antifungal activity and mechanism of a microbial pesticide Shenqinmycin against Phoma sp

Tea white scab (TWS) is a major disease affecting tea trees in mid-elevation regions and often occurs during rainy seasons with low temperatures. This disease is caused by the fungal pathogen Phoma sp. TWS can infect young stems, tender leaves, and tender shoots and lead to the production of low-quality tea. Owing to the absence of an effective control, TWS can result in substantial loss in tea production. In this study, we isolated and identified the pathogen from tea leaves infected by TWS and then evaluated in vitro the antifungal activity of Shenqinmycin, polyoxin, azoxystrobin, oligosaccharins, and tebuconazole against Phoma sp. Our results indicated that Shenqinmycin can inhibit the growth of Phoma sp. mycelia, with the EC₅₀ value of 0.74μg/mL. After Phoma sp. being incubated in PDB liquid medium with Shenqinmycin, its mycelia were distorted and distended at 1.56μg/mL of minimum inhibitory concentration for 6h. Crucial genes associated with cell redox homeostasis, proteins synthesis, energy metabolism, and cytoskeleton were studied at mRNA and protein levels through RT-qPCR and Nano-LC-MS/MS. The results showed that the genes of 3-phosphate-glyceraldehyde dehydrogenase, citrate synthase, NADH-ubiquinone oxidoreductase subunit (NADH-subunit), ribosomal protein, eukaryotic initiation factor 4A-I, β-tubulin, and α-tubulin were up-regulated. Meanwhile, the genes of formate dehydrogenase (FDH), malate dehydrogenase, mitochondrial heat shock protein, and protein disulfide-isomerase (PDI) were up-regulated at mRNA level but down-regulated at protein level. These results indicated that Shenqinmycin contribute to cell redox homeostasis by up- or down-regulating NADH-subunit, FDH, and PDI.

Synthesis and bioactivities of diamide derivatives containing a phenazine-1-carboxamide scaffold

Taking natural product phenazine-1-carboxamide (PCN) as a lead compound, a series of novel phenazine-1-carboxylic acid diamide derivatives were designed and synthesised. Their structures were confirmed by ¹H-NMR and HRMS. The bioassays showed that some of the target compounds exhibited promising in vitro fungicidal activities, and exhibited excellent and selective herbicidal activities. Particularly, compounds c, h, o and s displayed root length inhibition activities against barnyard grass with the rate of more than 80%. Compound c exhibited the best activity among all the target compounds against barnyard grass stalk length with the IC₅₀ value of 0.158 mmol/L, and compound o exhibited the best and wide spectrum inhibition against barnyard grass root length and rape in both root length and stalk length herbicidal activities with its IC₅₀ values of 0.067, 0.048 and 0.059 mmol/L respectively. The analysis of preliminary Structure-Activity Relationships provides the theoretical basis for further design of phenazine-1-carboxylic acid.

Screening and characterization of Xanthomonas oryzae pv. oryzae strains with resistance to pheazine-1-carboxylic acid

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight (BLB) and can be effectively controlled by phenazine-1-carboxylic acid (PCA), an antibiotic secreted by Pseudomonas spp. PCA resistance in Xoo was investigated in this research. Only four PCA-resistant strains were obtained by extensive screening, and the resistance was genetically stable in only one of them (P4). P4 was also resistant to phenazine and 1-hydroxyphezine but not to captan, bismerthiazol, or streptomycin. The following were reduced in P4 relative to the parental wild type: growth, virulence, EPS production, extracellular cellulase production and activity, biofilm formation, and swimming ability. ROS accumulation was reduced, resistance to exogenous H2O2 was increased, and expression of catalase genes and catalase activities were increased in P4, suggesting that PCA resistance in P4 results from a reduction in ROS production and/or an increased ability to metabolize ROS following PCA treatment. Given the low risk of Xoo developing PCA resistance and the reduced virulence and fitness of the resistant strain, PCA can be used in alternation with other common bactericides to control BLB in rice fields.

The Effect of Phenazine-1-Carboxylic Acid on Mycelial Growth of Botrytis cinerea Produced by Pseudomonas aeruginosa LV Strain

One of the most important postharvest plant pathogens that affect strawberries, grapes and tomatoes is Botrytis cinerea, known as gray mold. The fungus remains in latent form until spore germination conditions are good, making infection control difficult, causing great losses in the whole production chain. This study aimed to purify and identify phenazine-1-carboxylic acid (PCA) produced by the Pseudomonas aeruginosa LV strain and to determine its antifungal activity against B. cinerea. The compounds produced were extracted with dichloromethane and passed through a chromatographic process. The purity level of PCA was determined by reversed-phase high-performance liquid chromatography semi-preparative. The structure of PCA was confirmed by nuclear magnetic resonance and electrospray ionization mass spectrometry. Antifungal activity was determined by the dry paper disk and minimum inhibitory concentration (MIC) methods and identified by scanning electron microscopy and confocal microscopy. The results showed that PCA inhibited mycelial growth, where MIC was 25 μg mL-1. Microscopic analysis revealed a reduction in exopolysaccharide (EPS) formation, showing distorted and damaged hyphae of B. cinerea. The results suggested that PCA has a high potential in the control of B. cinerea and inhibition of EPS (important virulence factor). This natural compound is a potential alternative to postharvest control of gray mold disease.

A genetic screen in combination with biochemical analysis in Saccharomyces cerevisiae indicates that phenazine-1-carboxylic acid is harmful to vesicular trafficking and autophagy

The environmentally friendly antibiotic phenazine-1-carboxylic acid (PCA) protects plants, mammals and humans effectively against various fungal pathogens. However, the mechanism by which PCA inhibits or kills fungal pathogens is not fully understood. We analyzed the effects of PCA on the growth of two fungal model organisms, Saccharomyces cerevisiae and Candida albicans, and found that PCA inhibited yeast growth in a dose-dependent manner which was inversely dependent on pH. In contrast, the commonly used antibiotic hygromycin B acted in a dose-dependent manner as pH increased. We then screened a yeast mutant library to identify genes whose mutation or deletion conferred resistance or sensitivity to PCA. We isolated 193 PCA-resistant or PCA-sensitive mutants in clusters, including vesicle-trafficking- and autophagy-defective mutants. Further analysis showed that unlike hygromycin B, PCA significantly altered intracellular vesicular trafficking under growth conditions and blocked autophagy under starvation conditions. These results suggest that PCA inhibits or kills pathogenic fungi in a complex way, in part by disrupting vesicular trafficking and autophagy.

Novel Three-Component Phenazine-1-Carboxylic Acid 1,2-Dioxygenase in Sphingomonas wittichii DP58

Phenazine-1-carboxylic acid, the main component of shenqinmycin, is widely used in southern China for the prevention of rice sheath blight. However, the fate of phenazine-1-carboxylic acid in soil remains uncertain. Sphingomonas wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources for growth. In this study, dioxygenase-encoding genes, pcaA1A2, were found using transcriptome analysis to be highly upregulated upon phenazine-1-carboxylic acid biodegradation. PcaA1 shares 68% amino acid sequence identity with the large oxygenase subunit of anthranilate 1,2-dioxygenase from Rhodococcus maanshanensis DSM 44675. The dioxygenase was coexpressed in Escherichia coli with its adjacent reductase-encoding gene, pcaA3, and ferredoxin-encoding gene, pcaA4, and showed phenazine-1-carboxylic acid consumption. The dioxygenase-, ferredoxin-, and reductase-encoding genes were expressed in Pseudomonas putida KT2440 or E. coli BL21, and the three recombinant proteins were purified. A phenazine-1-carboxylic acid conversion capability occurred in vitro only when all three components were present. However, P. putida KT2440 transformed with pcaA1A2 obtained phenazine-1-carboxylic acid degradation ability, suggesting that phenazine-1-carboxylic acid 1,2-dioxygenase has low specificities for its ferredoxin and reductase. This was verified by replacing PcaA3 with RedA2 in the in vitro enzyme assay. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) analysis showed that phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation, indicating that PcaA1A2A3A4 constitutes the initial phenazine-1-carboxylic acid 1,2-dioxygenase. This study fills a gap in our understanding of the biodegradation of phenazine-1-carboxylic acid and illustrates a new dioxygenase for decarboxylation.IMPORTANCE Phenazine-1-carboxylic acid is widely used in southern China as a key fungicide to prevent rice sheath blight. However, the degradation characteristics of phenazine-1-carboxylic acid and the environmental consequences of the long-term application are not clear. S. wittichii DP58 can use phenazine-1-carboxylic acid as its sole carbon and nitrogen sources. In this study, a three-component dioxygenase, PcaA1A2A3A4, was determined to be the initial dioxygenase for phenazine-1-carboxylic acid degradation in S. wittichii DP58. Phenazine-1-carboxylic acid was converted to 1,2-dihydroxyphenazine through decarboxylation and hydroxylation. This finding may help us discover the pathway for phenazine-1-carboxylic acid degradation.

The Effect of Phenazine-1-Carboxylic Acid on the Morphological, Physiological, and Molecular Characteristics of Phellinus noxius

In this study, the effect of phenazine-1-carboxylic acid (PCA) on morphological, physiological, and molecular characteristics of Phellinus noxius has been investigated, and the potential antifungal mechanism of PCA against P. noxius was also explored. The results revealed that PCA showed in vitro antifungal potential against P. noxius and completely inhibited P. noxius hyphae at concentrations >40 μg/mL. PCA inhibited both mycelial growth and the loss of mycelial biomass in vitro in a dose-dependent manner. Morphological changes in PCA-treated P. noxius hyphae, such as irregularly swollen mycelia as well as short hyphae with increased septation and less branching, were observed by optical microscopy. The intracellular reactive oxygen species (ROS) levels were significantly increased in PCA-treated P. noxius cells as compared to control groups. Induced hyperpolarization of the mitochondrial membrane potential (MMP), repressed superoxide dismutase (SOD) activity and up-regulated gene expression of seven tested genes were also found in PCA-treated P. noxius groups. Thus, the present results suggested that the mechanism of action of PCA against P. noxius might be attributed to direct damage of mycelium and high intracellular ROS production, and indirect induction of genes involved in cell detoxification, oxidation-reduction process, and electron transport of the respiratory chain.

Enzymatic Degradation of Phenazines Can Generate Energy and Protect Sensitive Organisms from Toxicity

Diverse bacteria, including several Pseudomonas species, produce a class of redox-active metabolites called phenazines that impact different cell types in nature and disease. Phenazines can affect microbial communities in both positive and negative ways, where their presence is correlated with decreased species richness and diversity. However, little is known about how the concentration of phenazines is modulated in situ and what this may mean for the fitness of members of the community. Through culturing of phenazine-degrading mycobacteria, genome sequencing, comparative genomics, and molecular analysis, we identified several conserved genes that are important for the degradation of three Pseudomonas-derived phenazines: phenazine-1-carboxylic acid (PCA), phenazine-1-carboxamide (PCN), and pyocyanin (PYO). PCA can be used as the sole carbon source for growth by these organisms. Deletion of several genes in Mycobacterium fortuitum abolishes the degradation phenotype, and expression of two genes in a heterologous host confers the ability to degrade PCN and PYO. In cocultures with phenazine producers, phenazine degraders alter the abundance of different phenazine types. Not only does degradation support mycobacterial catabolism, but also it provides protection to bacteria that would otherwise be inhibited by the toxicity of PYO. Collectively, these results serve as a reminder that microbial metabolites can be actively modified and degraded and that these turnover processes must be considered when the fate and impact of such compounds in any environment are being assessed.

IMPORTANCE

Phenazine production by Pseudomonas spp. can shape microbial communities in a variety of environments ranging from the cystic fibrosis lung to the rhizosphere of dryland crops. For example, in the rhizosphere, phenazines can protect plants from infection by pathogenic fungi. The redox activity of phenazines underpins their antibiotic activity, as well as providing pseudomonads with important physiological benefits. Our discovery that soil mycobacteria can catabolize phenazines and thereby protect other organisms against phenazine toxicity suggests that phenazine degradation may influence turnover in situ. The identification of genes involved in the degradation of phenazines opens the door to monitoring turnover in diverse environments, an essential process to consider when one is attempting to understand or control communities influenced by phenazines.

Effects of phenazine-1-carboxylic acid on the biology of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) is the casual agent of bacterial blight, which is one of the most serious diseases of rice. The antibiotic phenazine-1-carboxylic acid (PCA), which is primarily produced by Pseudomonas spp., was found and previously reported very effective against Xoo. However, the biological effects of PCA on Xoo remain unclear. In this study, we found that PCA increased the accumulation of reactive oxygen species (ROS) and reduced the activities of catalase (CAT) and superoxide dismutase (SOD) in Xoo. Xoo was more sensitive to H2O2 than Xanthomonas oryzae pv. oryzicola (Xoc), and had a much lower expression of CAT genes. In addition, proteomic analysis indicated that PCA inhibited carbohydrate metabolism and nutrient uptake in Xoo, and analysis of carbon source utilization further confirmed that carbohydrate metabolism in Xoo was repressed by PCA. In conclusion, PCA acted as a redox-cycling agent that disturbed the redox balance in Xoo and reduced CAT and SOD activities, resulting in higher accumulation of ROS, altered carbohydrate metabolism, and lower energy production and nutrient uptake. Moreover, a deficient antioxidant system in Xoo made it very sensitive to PCA.

Community profiling of culturable fluorescent pseudomonads in the rhizosphere of green gram (Vigna radiata L.)

Study on microbial diversity in the unexplored rhizosphere is important to understand their community structure, biology and ecological interaction with the host plant. This research assessed the genetic and functional diversity of fluorescent pseudomonads [FP] in the green gram rhizophere. One hundred and twenty types of morphologically distinct fluorescent pseudomonads were isolated during vegetative as well as reproductive growth phase of green gram. Rep PCR, ARDRA and RISA revealed two distinct clusters in each case at 75, 61 and 70% similarity coefficient index respectively. 16S rRNA partial sequencing analysis of 85 distantly related fluorescent pseudomonads depicted Pseudomonas aeruginosa as the dominant group. Out of 120 isolates, 23 (19%) showed antagonistic activity towards phytopathogenic fungi. These bacterial isolates showed varied production of salicylic acid, HCN and chitinase, 2, 4-diacetylphloroglucinol (DAPG), phenazine-1-carboxylic acid (PCA) and pyoluteorin (PLT). Production efficiency of inherent level of plant growth promoting (PGP) traits among the 120 isolates demonstrated that 10 (8%) solubilised inorganic phosphates, 25 (20%) produced indoles and 5 (4%) retained ACC deaminase activity. Pseudomonas aeruginosa GGRJ21 showed the highest production of all antagonistic and plant growth promoting (PGP) traits. In a greenhouse experiment, GGRJ21 suppressed root rot disease of green gram by 28-93% (p = 0.05). Consistent up regulation of three important stress responsive genes, i.e., acdS, KatA and gbsA and elevated production efficiency of different PGP traits could promote GGRJ21 as a potent plant growth regulator.