Microbial Pyrrolnitrin: Natural Metabolite with Immense Practical Utility.

Pyrrolnitrin (PRN) is a microbial pyrrole halometabolite of immense antimicrobial significance for agricultural, pharmaceutical and industrial implications. The compound and its derivatives have been isolated from rhizospheric fluorescent or non-fluorescent pseudomonads, Serratia and Burkholderia. They are known to confer biological control against a wide range of phytopathogenic fungi, and thus offer strong plant protection prospects against soil and seed-borne phytopathogenic diseases. Although chemical synthesis of PRN has been obtained using different steps, microbial production is still the most useful option for producing this metabolite. In many of the plant-associated isolates of Serratia and Burkholderia, production of PRN is dependent on the quorum-sensing regulation that usually involves N-acylhomoserine lactone (AHL) autoinducer signals. When applied on the organisms as antimicrobial agent, the molecule impedes synthesis of key biomolecules (DNA, RNA and protein), uncouples with oxidative phosphorylation, inhibits mitotic division and hampers several biological mechanisms. With its potential broad-spectrum activities, low phototoxicity, non-toxic nature and specificity for impacts on non-target organisms, the metabolite has emerged as a lead molecule of industrial importance, which has led to developing cost-effective methods for the biosynthesis of PRN using microbial fermentation. Quantum of work narrating focused research efforts in the emergence of this potential microbial metabolite is summarized here to present a consolidated, sequential and updated insight into the chemistry, biology and applicability of this natural molecule.

A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology.

Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species ( Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.

Manzamine Alkaloids from an Acanthostrongylophora sp. Sponge.

Five new manzamine alkaloids (1-5) and new salt forms of two known manzamines (6 and 7), along with seven known compounds (8-14) of the same structural class, were isolated from an Indonesian Acanthostrongylophora sp. sponge. On the basis of the results of combined spectroscopic analyses, the structure of kepulauamine A (1) was determined to possess an unprecedented pyrrolizine moiety, while others were functional group variants of known manzamines. These compounds exhibited weak cytotoxicity, moderate antibacterial activity, and mild inhibition against the enzyme isocitrate lyase.

A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene.

Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria's host is a "farmer" clone of the social amoeba Dictyostelium discoideum that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of Pseudomonas fluorescens, only one of which serves as a food source. The other strain produces diffusible small molecules: pyrrolnitrin, a known antifungal agent, and a chromene that potently enhances the farmer's spore production and depresses a nonfarmer's spore production. Genome sequence and phylogenetic analyses identify a derived point mutation in the food strain that generates a premature stop codon in a global activator (gacA), encoding the response regulator of a two-component regulatory system. Generation of a knockout mutant of this regulatory gene in the nonfood bacterial strain altered its secondary metabolite profile to match that of the food strain, and also, independently, converted it into a food source. These results suggest that a single mutation in an inedible ancestral strain that served a protective role converted it to a "domesticated" food source.

Expression of an entire bacterial operon in plants.

Multigene expression is required for metabolic engineering, i.e. coregulated expression of all genes in a metabolic pathway for the production of a desired secondary metabolite. To that end, several transgenic approaches have been attempted with limited success. Better success has been achieved by transforming plastids with operons. IL-60 is a platform of constructs driven from the geminivirus Tomato yellow leaf curl virus. We demonstrate that IL-60 enables nontransgenic expression of an entire bacterial operon in tomato (Solanum lycopersicum) plants without the need for plastid (or any other) transformation. Delivery to the plant is simple, and the rate of expressing plants is close to 100%, eliminating the need for selectable markers. Using this platform, we show the expression of an entire metabolic pathway in plants and delivery of the end product secondary metabolite (pyrrolnitrin). Expression of this unique secondary metabolite resulted in the appearance of a unique plant phenotype disease resistance. Pyrrolnitrin production was already evident 2 d after application of the operon to plants and persisted throughout the plant's life span. Expression of entire metabolic pathways in plants is potentially beneficial for plant improvement, disease resistance, and biotechnological advances, such as commercial production of desired metabolites.

Further biochemical studies on aminopyrrolnitrin oxygenase (PrnD).

Active site modeling of dimerization interface in combination with site-directed mutagenesis indicates that the electron in the PrnD Rieske oxygenase can be transferred by either of two pathways, one involving Asp183' and the other involving Asn180'. In addition, the overexpression of the isc operon involved in the assembly of iron-sulfur clusters increased the catalytic activity of PrnD in Escherichia coli by a factor of at least 4.

Structure-inhibitory activity relationships of pyrrolnitrin analogues on its biosynthesis.

Pyrrolnitrin is a bacterial metabolite, served as a natural lead of agricultural fungicides. In a previous study, fenpiclonil was proven to inhibit the oxidative transformation of aminopyrrolnitrin to pyrrolnitrin, catalyzed by aminopyrrolnitrin oxidase (PrnD). This monooxygenase has an interesting catalytic activity of selective oxidation of aromatic amines, rather than aliphatic amines. However, its structural details are not well understood. In this study, various analogues of pyrrolnitrin were prepared to elucidate the structures of active site of PrnD through structure-activity relationships. In vivo pyrrolnitrin biosynthesis inhibition was determined with Burkholderia sp. O33 and Pseudomonas fluorescens Pf-5. Quantitative analysis of pyrrolnitrin and precursors indicates that 2,3-disubstituted phenyl at 3rd carbon and small substituents at 4th carbon of pyrrole are strictly required to give strong inhibitory effects. In addition, dissociable proton of pyrrole is also critical for inhibitory activity. Molecular simulation with homology-based PrnD model suggests a highly restricted conformational space in active site. The results may help more detailed understanding of this unusual enzyme. In addition, the information will be useful for the development of novel fungicide, compatible with pyrrolnitrin-producing bacterium.

Design, synthesis, and fungicidal activity of novel analogues of pyrrolnitrin.

A series of novel analogues of pyrrolnitrin containing a thiophene moiety were designed and synthesized by a facile method, and their structures were characterized by (1)H nuclear magnetic resonance (NMR) and high-resolution mass spectrometry. The isomers IV-h and V-h were isolated, and their structures were identified by 2D NMR, including heteronuclear multiple-quantum coherence (HMQC), heteronuclear multiple-bond correlation (HMBC), and nuclear Overhauser effect spectrometry (NOESY) spectra. Their fungicidal activities against five fungi were evaluated, and the results indicated that some of the title compounds showed excellent fungicidal activities in vitro against Alternaria solani , Gibberella zeae , Physalospora piricola , Fusarium omysporum , and Cercospora arachidicola at the dosage of 50 microg mL(-1). Some compounds shown moderate activity at low dosage. Compound V-h could be considered as a leading structure for further design of agricultural fungicides.

Synthesis of pyrrolnitrin and related halogenated phenylpyrroles.

A general approach to halogenated arylpyrroles, including the antifungal natural product pyrrolnitrin, is described using newly synthesized halogenated pyrroles and 2,6-disubstituted nitrobenzenes or 2,6-disubstituted anilines.

Novel oxidized derivatives of antifungal pyrrolnitrin from the bacterium Burkholderia cepacia K87.

The screening of antifungal active compounds from the fermentation extracts of soil-borne bacterium Burkholderia cepacia K87 afforded pyrrolnitrin (1) and two new pyrrolnitrin analogs, 3-chloro-4-(3-chloro-2-nitrophenyl)-5-methoxy-3-pyrrolin-2-one (2) and 4-chloro-3-(3-chloro-2-nitrophenyl)-5-methoxy-3-pyrrolin-2-one (3). Pyrrolnitrin showed strong antifungal activity against Rhizoctonia solani but the analogs (2 and 3) were found to be marginally active. The isolates, 2 and 3, are believed to be biodegraded derivatives of pyrrolnitrin.

Characterization of a new isolate of Pseudomonas fluorescens strain Psd as a potential biocontrol agent.

AIMS: Evaluation of a new isolate of Pseudomonas fluorescens for its biocontrol properties. METHODS AND RESULTS: Strain Psd identified as Ps. fluorescens, produces secondary metabolites that are toxic to some plant-pathogenic fungi. Inhibition of fungal growth of Fusarium oxysporum and Verticillium dahliae in the presence of bacterial culture filtrate provided the first clue to its biocontrol properties. In order to determine the basis for antifungal properties, antibiotics were extracted and analysed by TLC. Both pyrrolnitrin and phenazines could be detected in the culture of Psd. Presence of response regulator gene gacA of the two component regulatory system (GacS/GacA) was established by PCR amplification and sequencing. Sequence comparison of gacA justified the taxonomic position of this strain among the known members of Pseudomonadaceae. Synthesis of other compounds like toxic lipodepsipeptide, siderophores, and HCN was also confirmed by appropriate biochemical tests. CONCLUSION: Characterization of strain Psd by various biochemical/plate tests followed by chromatographic identification of antibiotics, demonstrates its multifunctional biocontrol property. Response regulator gene gacA provides an additional genetic marker for the phylogenetic studies. SIGNIFICANCE AND IMPACT OF THE STUDY: Ps. fluorescens strain Psd with its multifunctional biocontrol property can be used to bioprotect the crop plants from phytopathogens.

Crystallization and X-ray diffraction of a halogenating enzyme, tryptophan 7-halogenase, from Pseudomonas fluorescens.

Chlorination of natural products is often required for their biological activity; notable examples include vancomycin, the last-ditch antibiotic. It is now known that many chlorinated natural products are made not by haloperoxidases, but by FADH2-dependent halogenases. The mechanism of the flavin-containing enzymes is obscure and there are no structural data. Here, crystals of PrnA (tryptophan 7-halogenase), an enzyme that regioselectively chlorinates tryptophan, cocrystallized with tryptophan and FAD are reported. The crystals belong to the tetragonal space group P4(3)2(1)2 or P4(1)2(1)2, with unit-cell parameters a = b = 67.8, c = 276.9 A. A data set to 1.8 A with 93% completeness and an Rmerge of 7.1% has been collected from a single flash-cooled crystal. A method for incorporating selenomethionine in a Pseudomonas fluorescens expression system also is reported.

Cloning and sequencing of the gene of tryptophan-7-halogenase from Pseudomonas fluorescens strain CHA0.

The gene of tryptophan-7-halogenase from the Pseudomonas fluorescens strain CHA0, a producer of the halogenated antibiotic pyrrolnitrin, has been cloned and sequenced.

Synergistic antimicrobial activity of metabolites produced by a nonobligate bacterial predator.

A naturally occurring, gram-negative, nonobligate predator bacterial strain 679-2, exhibits broad-spectrum antimicrobial activity that is due, in part, to the production of three extracellular compounds. Antimicrobial-activity-directed fractionation of a culture of strain 679-2 against a panel of microorganisms has led to the isolation of three compounds: pyrrolnitrin, maculosin, and a new compound, which we have named banegasine. Although pyrrolnitrin is well known in the literature, it has not been found in cells with the herbicide maculosin. Further, this is the first report of production of maculosin by a prokaryote. Both maculosin and banegasine, which displayed no antimicrobial activities alone, were found to potentiate the antimicrobial activity of pyrrolnitrin. Based on 16S rRNA sequence, cellular fatty acid composition, and biochemical and cultural characteristics, strain 679-2 appears to represent a new genus and species of eubacteria, Aristabacter necator. The potent, broad-spectrum antimicrobial activity of predator strain 679-2 may be due to synergism between metabolites.

Novel photodegradation of the antifungal antibiotic pyrrolnitrin in anhydrous and aqueous aprotic solvents.

The UV irradiation of pyrrolnitrin (1a), which is an antibiotic clinically useful against dermatophytosis and possesses a unique 2-(pyrrol-3-yl)nitrobenzene moiety in the molecule, in an anhydrous aprotic solvent resulted in the exclusive formation of transient 7,4'-dichlorospiro[1,3-dihydrobenzo(c)isoxazole-3,3'-pyrrolin-2'-one] (2a) via the intramolecular oxidation of the juxtaposed pyrrole ring by the triplet-excited nitro group. The irradiation in an aqueous aprotic solvent, however, allowed the concurrent occurrence of intramolecular cyclization by the singlet-excited nitro group in 1a and the hydroxylation at the 2-position of the pyrrole ring by water to afford 3,7-dichloro-8-hydroxy-8,8a-dihydropyrrolo[2,3-b]indol-2-one (3a), accompanied by the formation of 2a. Elongation of the irradiation time in these photoreactions caused a rapid consumption of the products, 2a and 3a, to give undetermined polar polymeric products. The present results indicate that the photodegradation of 1a is significantly influenced by the presence of water in the reaction media and by the nature of its excited state. Thus, the loss of the antifungal activities by the photosensitive antibiotic 1a was chemically proved.

Pyrrolnitrin from Burkholderia cepacia: antibiotic activity against fungi and novel activities against streptomycetes.

A bacterial strain identified as Burkholderia cepacia NB-1 was isolated from water ponds in the botanical garden in Tübingen, Germany, and was found to produce a broad spectrum phenylpyrrole antimicrobial substance active against filamentous fungi, yeasts and Gram-positive bacteria. In batch culture containing glycerol and L-glutamic acid, the isolate NB-1 produced the antibiotic optimally late in the growth phase and accumulated a main portion in their cells. Isolation and purification of the antibiotic from Burkholderia (Pseudomonas) cepacia NB-1 by acetone extraction, gel filtration on Sephadex LH-20 and preparative HPLC yielded 0.54 mg l-1 of a pure substance. Spectroscopic data (HPLC, MS and NMR) confirmed that the compound was pyrrolnitrin [3-chloro-4-(2'-nitro-3'-chloro-phenyl) pyrrole]. Pyrrolnitrin has an inhibitory effect on the electron transport system, as demonstrated by isolated mitochondria from Neurospora crassa 74 A. This inhibition was relieved by N,N,N',N'-tetramethyl-p-phenylenediamine dihydrochloride (TMPD), indicating that pyrrolnitrin blocked the electron transfer between the dehydrogenases and the cytochrome components of the respiratory chain. Among Gram-positive bacteria, pyrrolnitrin was most active against certain Streptomyces species, especially S. antibioticus, which has not previously been described in the literature. In the presence of pyrrolnitrin, aerial mycelium and spore formation of Strep. antibioticus was suppressed, although growth continued via substrate mycelium. The new findings of inhibition of streptomycetes and their secondary metabolism by pyrrolnitrin may contribute to the fact that Pseudomonas species predominate in soil and compete even with antibiotic-producing Streptomyces.