Production of tailored hydroxylated prodiginine showing combinatorial activity with rhamnolipids against plant-parasitic nematodes

Bacterial secondary metabolites exhibit diverse remarkable bioactivities and are thus the subject of study for different applications. Recently, the individual effectiveness of tripyrrolic prodiginines and rhamnolipids against the plant-parasitic nematode Heterodera schachtii, which causes tremendous losses in crop plants, was described. Notably, rhamnolipid production in engineered Pseudomonas putida strains has already reached industrial implementation. However, the non-natural hydroxyl-decorated prodiginines, which are of particular interest in this study due to a previously described particularly good plant compatibility and low toxicity, are not as readily accessible. In the present study, a new effective hybrid synthetic route was established. This included the engineering of a novel P. putida strain to provide enhanced levels of a bipyrrole precursor and an optimization of mutasynthesis, i.e., the conversion of chemically synthesized and supplemented monopyrroles to tripyrrolic compounds. Subsequent semisynthesis provided the hydroxylated prodiginine. The prodiginines caused reduced infectiousness of H. schachtii for Arabidopsis thaliana plants resulting from impaired motility and stylet thrusting, providing the first insights on the mode of action in this context. Furthermore, the combined application with rhamnolipids was assessed for the first time and found to be more effective against nematode parasitism than the individual compounds. To obtain, for instance, 50% nematode control, it was sufficient to apply 7.8 μM hydroxylated prodiginine together with 0.7 μg/ml (~ 1.1 μM) di-rhamnolipids, which corresponded to ca. ¼ of the individual EC₅₀ values. In summary, a hybrid synthetic route toward a hydroxylated prodiginine was established and its effects and combinatorial activity with rhamnolipids on plant-parasitic nematode H. schachtii are presented, demonstrating potential application as antinematodal agents. Graphical Abstract.

Mechanisms underlying the inhibitory effects of Cd2+ on prodigiosin synthesis in Serratia marcescens KMR-3

Prodigiosin (2-methyl-3-pentyl-6-methoxyprodiginine), a red-colored microbial pigment, is produced in large quantities by Serratia marcescens KMR-3. This bacterium can grow in a medium with a Cd²⁺ concentration of 500 mg/L, but it does not produce prodigiosin when the Cd²⁺ concentration in the medium is higher than 140 mg/L. Therefore, we investigated the mechanisms by which Cd²⁺ inhibits prodigiosin synthesis. Upon addition of Cd²⁺ to the medium, the expression of the prodigiosin (pig) gene cluster was significantly downregulated. Simultaneously, genes encoding proteins related to the synthesis of arginine and proline(prodigiosin precursors) were significantly downregulated, while the degradation-related genes were upregulated. Furthermore, PigF, which encodes a key enzyme involved in the synthesis of 4-methoxy-2,2'-bipyrrole-5-carboxaldehyde and PigC, which encodes a key enzyme involved in the last step of prodigiosin synthesis, were downregulated by 80% and 55%, respectively, following Cd²⁺ treatment. As PigC and PigF are located on the cell membrane and are involved in the final steps of prodigiosin synthesis, the cell membrane might be presumed to be the site of prodigiosin synthesis. The bacterial membrane exhibited different degrees of elongation, folding, fragmentation, and sagging after the addition of Cd²⁺, while likely destroying the site of prodigiosin synthesis.

Transcriptomic Analysis Reveals Competitive Growth Advantage of Non-pigmented Serratia marcescens Mutants

Serratia marcescens is a common bacterium well-known for the red secondary metabolite prodigiosin. However, color mutants have long been described. Non-pigmented strains can be found to exist both naturally and under laboratory conditions. It is unclear why S. marcescens loses prodigiosin synthesis capacity in certain conditions. In the present study, we find that the spontaneous color mutants arise within a few generations (about five passages) and rapidly replace the wild-type parent cells (about 24 passages), which indicates a growth advantage of the former. Although, the loss of prodigiosin synthesis genes (pigA-N) is frequently reported as the major reason for pigment deficiency, it was unexpected that the whole gene cluster is completely preserved in the different color morphotypes. Comparative transcriptomic analysis indicates a dramatic variation at the transcriptional level. Most of the pig genes are significantly downregulated in the color morphotypes which directly lead to prodigiosin dyssynthesis. Besides, the transcriptional changes of several other genes have been noticed, of which transcriptional regulators, membrane proteins, and nearly all type VI secretion system (T6SS) components are generally downregulated, while both amino acid metabolite and transport systems are activated. In addition, we delete the transcription regulator slyA to generate a non-pigmented mutant. The ΔslyA strain loses prodigiosin synthesis capacity, but has a higher cell density, and surprisingly enhances the virulence as an entomopathogen. These data indicate that S. marcescens shuts down several high-cost systems and activates the amino acid degradation and transport pathways at the transcriptional level to obtain extra resources, which provides new insights into the competitive growth advantage of bacterial spontaneous color mutants.

KnowVolution of prodigiosin ligase PigC towards condensation of short-chain prodiginines

One round of KnowVolution enhanced the catalytic activity of prodigiosin ligase PigC with short-chain monopyrroles, opening access to anticancer prodiginines.

Understanding substrate binding and the role of gatekeeping residues in PigC access tunnels

Prodigiosin ligase PigC has been engineered by semi-rational design to accept short chain-pyrroles, providing molecular understanding of access tunnels and the substrate-binding pocket.

Ambigols from the Cyanobacterium Fischerella ambigua Increase Prodigiosin Production in Serratia spp

When a library of 573 cyanobacteria extracts was screened for inhibition of the quorum sensing regulated prodigiosin production of Serratia marcescens, an extract of the cyanobacterium Fischerella ambigua (Näg.) Gomont 108b was found to drastically increase prodigiosin production. Bioactivity-guided isolation of the active compounds resulted in the two new natural products ambigol D and E along with the known ambigols A and C. Ambigol C treatment increased prodiginine production of Serratia sp. ATCC 39006 (S39006) by a factor of 10, while ambigols A and D were found to have antibiotic activity against this strain. The RNA-Seq of S39006 treated with ambigol C and subsequent differential gene expression and functional enrichment analyses indicated a significant downregulation of genes associated with the translation machinery and fatty acid biosynthesis in Serratia, as well as increased expression of genes related to the uptake of l-proline. These results suggest that the ambigols increase prodiginine production in S39006 not by activating the SmaIR quorum sensing system but possibly by increasing the precursor supply of l-proline and malonyl-CoA.

Genetic Analysis and Immunoelectron Microscopy of Wild and Mutant Strains of the Rubber Tree Endophytic Bacterium Serratia marcescens Strain ITBB B5-1 Reveal Key Roles of a Macrovesicle in Storage and Secretion of Prodigiosin

Rubber tree is an economically important tropical crop. Its endophytic bacterial strain Serratia marcescens ITBB B5-1 contains an intracellular macrovesicle and red pigment. In this research, the red pigment was identified as prodigiosin by quadrupole time-of-flight mass spectrometry. Prodigiosin has a wide range of potential medical values such as anticancer and antiorgan transplant rejection. The strain ITBB B5-1 accumulated prodigiosin up to 2000 mg/L, which is higher production compared to most known Serratia strains. The formation of the macrovesicle and prodigiosin biosynthesis were highly associated and were both temporal- and temperature-dependent. A mutant strain B5-1mu that failed to produce prodigiosin was obtained by ultraviolet mutagenesis. Whole genome sequencing of wild-type and mutant strains indicated that the PigC gene encoding the last-step enzyme in the prodigiosin biosynthesis pathway was mutated in B5-1mu by a 17-bp deletion. Transmission electron microscopy analysis showed that the macrovesicle was absent in the mutant strain, indicating that formation of the macrovesicle relied on prodigiosin biosynthesis. Immunoelectron microscopy using prodigiosin-specific antiserum showed the presence of prodigiosin in the macrovesicle, the cell wall, and the extracellular vesicles, while immuno-reaction was not observed in the mutant cell. These results indicate that the macrovesicle serves as a storage organelle of prodigiosin, and secretes prodigiosin into cell envelop and culture medium as extracellular vesicles.

Substrate Flexibility of the Flavin-Dependent Dihydropyrrole Oxidases PigB and HapB Involved in Antibiotic Prodigiosin Biosynthesis

In the biosynthesis of the tripyrrolic pigment prodigiosin, PigB is a predicted flavin-dependent oxidase responsible for the formation of 2-methyl-3-amylpyrrole (MAP) from a dihydropyrrole. To prove which dihydropyrrole is the true intermediate, both possibilities, 5-methyl-4-pentyl-3,4-dihydro-2H-pyrrole (5 a, resulting from transamination of the aldehyde of 3-acetyloctanal) and 2-methyl-3-pentyl-3,4-dihydro-2H-pyrrole (6, resulting from transamination of the ketone), were synthesised. Only 5 a restored pigment production in a strain of Serratia sp. ATCC 39006 blocked earlier in MAP biosynthesis. PigB is membrane-associated and inactive when its transmembrane domain was deleted, but HapB, its homologue in Hahella chejuensis, lacks the transmembrane domain and is active in solution. Two colourimetric assays for PigB and HapB were developed, and the HapB-catalysed reaction was kinetically characterised. Ten analogues of 5 a were synthesised, varying in the C2 and C3 side chains, and tested as substrates of HapB in vitro and for restoration of pigment production in Serratia ΔpigD in vivo. All lengths of side chain tested at C3 were accepted, but only short side chains at C2 were accepted. The knowledge that 5 a is an intermediate in prodigiosin biosynthesis and the ease of synthesis of analogues of 5 a makes a range of prodigiosin analogues readily available by mutasynthesis.

RedH and PigC Catalyze the Biosynthesis of Hybrubins via Phosphorylation of 4'-Methoxy-2,2'-Bipyrrole-5'-Carbaldehyde

Hybrubins are "unnatural" alkaloids with the same 4'-methoxy-2,2'-bipyrrole-5'-methine moiety found in prodiginines and a different ring derived from tetramic acids. Here, we demonstrated that RedH, a homologue of prodigiosin synthetase PigC, was responsible for the biosynthesis of hybrubins A and B in Streptomyces lividans In vitro reactions indicated that RedH and PigC catalyzed the intermolecular condensation between 4'-methoxy-2,2'-bipyrrole-5'-carbaldehyde (MBC) and (Z)-5-ethylidenetetramic acid (ETA) to produce hybrubin B. Moreover, we demonstrated that RedH and PigC activated MBC via phosphorylation of the aldehyde group to form an intermediate P_i-MBC and that the subsequent condensation between P_i-MBC and (Z)-5-ethylidenetetramic acid occurs in a nonenzymatic way.IMPORTANCE Hybrubins are an emerging class of prodiginines possessing a new C ring derived from 5'-substituted tetramic acids and the methylene bridge connecting the C ring at a different position. We have supposed that condensation between 4'-methoxy-2,2'-bipyrrole-5'-carbaldehyde (MBC) and 5-ethylidenetetramic acid (ETA) yields the hybrid natural products hybrubins, which was proposed to be catalyzed by the undecylprodigiosin synthetase RedH. However, it is doubted whether RedH is able to catalyze another type of condensation between MBC and tetramic acids. In this study, we have demonstrated that the MBC-ETA condensation proceeds through RedH/PigC-catalyzed enzymatic activation of MBC via phosphorylation and a nonenzymatic condensation of P_i-MBC with ETA. Since MBC analogues have been shown to be accepted by PigC, more hybrubin analogues might be produced by using combinations of MBC analogues and other tetramic acids in future studies.

A colourimetric high-throughput screening system for directed evolution of prodigiosin ligase PigC

A colourimetric high-throughput screening system was developed for the first directed evolution campaign on PigC towards production of artificial prodiginines.

Isolation and characterization of tambjamine MYP1, a macrocyclic tambjamine analogue from marine bacterium Pseudoalteromonas citrea

Tambjamines are natural products that consist of a conserved bipyrrole core functionalized with different imines giving rise to many derivatives. The core structure of tambjamines allows ion coordination through the nitrogen atoms, which is a key aspect in many of their observed antimicrobial, anticancer, and antimalarial bioactivities. Minor variances in the compound structure have a considerable impact on the potency of these activities, so identifying new analogues is valuable for maximizing tambjamine biological potential. In this work, we describe the isolation and structure elucidation of the first naturally occurring macrocyclized tambjamine, tambjamine MYP1, from the marine microbe Pseudoalteromonas citrea. We also compare the apparent pK _a of cyclic and linear tambjamine analogues and discuss how structural strain may effect the compound's ion coordination abilities.

The complex resistomes of Paenibacillaceae reflect diverse antibiotic chemical ecologies

The ecology of antibiotic resistance involves the interplay of a long natural history of antibiotic production in the environment, and the modern selection of resistance in pathogens through human use of these drugs. Important components of the resistome are intrinsic resistance genes of environmental bacteria, evolved and acquired over millennia, and their mobilization, which drives dissemination in pathogens. Understanding the dynamics and evolution of resistance across bacterial taxa is essential to address the current crisis in drug-resistant infections. Here we report the exploration of antibiotic resistance in the Paenibacillaceae prompted by our discovery of an ancient intrinsic resistome in Paenibacillus sp. LC231, recovered from the isolated Lechuguilla cave environment. Using biochemical and gene expression analysis, we have mined the resistome of the second member of the Paenibacillaceae family, Brevibacillus brevis VM4, which produces several antimicrobial secondary metabolites. Using phylogenomics, we show that Paenibacillaceae resistomes are in flux, evolve mostly independent of secondary metabolite biosynthetic diversity, and are characterized by cryptic, redundant, pseudoparalogous, and orthologous genes. We find that in contrast to pathogens, mobile genetic elements are not significantly responsible for resistome remodeling. This offers divergent modes of resistome development in pathogens and environmental bacteria.

Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme

Prodiginines, which are tripyrrole alkaloids displaying a wide array of bioactivities, occur as linear and cyclic congeners. Identification of an unclustered biosynthetic gene led to the discovery of the enzyme responsible for catalyzing the regiospecific C-H activation and cyclization of prodigiosin to cycloprodigiosin in Pseudoalteromonas rubra. This enzyme is related to alkylglycerol monooxygenase and unrelated to RedG, the Rieske oxygenase that produces cyclized prodiginines in Streptomyces, implying convergent evolution.

New Prodigiosin Derivatives Obtained by Mutasynthesis in Pseudomonas putida

The deeply red-colored natural compound prodigiosin is a representative of the prodiginine alkaloid family, which possesses bioactivities as antimicrobial, antitumor, and antimalarial agents. Various bacteria including the opportunistic human pathogen Serratia marcescens and different members of the Streptomycetaceae and Pseudoalteromonadaceae produce prodiginines. In addition, these microbes generally accumulate many structurally related alkaloids making efficient prodiginine synthesis and purification difficult and expensive. Furthermore, it is known that structurally different natural prodiginine variants display differential bioactivities. In the herein described mutasynthesis approach, 13 different derivatives of prodigiosin were obtained utilizing the GRAS (generally recognized as safe) classified strain Pseudomonas putida KT2440. Genetic engineering of the prodigiosin pathway together with incorporation of synthetic intermediates thus resulted in the formation of a so far unprecedented structural diversity of new prodiginine derivatives in P. putida. Furthermore, the formed products allow reliable conclusions regarding the substrate specificity of PigC, the final condensing enzyme in the prodigiosin biosynthesis pathway of S. marcescens. The biological activity of prodigiosin toward modulation of autophagy was preserved in prodiginine derivatives. One prodiginine derivative displayed more potent autophagy inhibitory activity than the parent compound or the synthetic clinical candidate obatoclax.

MarH, a Bifunctional Enzyme Involved in the Condensation and Hydroxylation Steps of the Marineosin Biosynthetic Pathway

A novel bifunctional enzyme, MarH, has been identified, and its key functional role in the marineosin biosynthesis successfully probed. MarH catalyzes (1) a condensation step between 4-methoxy-2,2'-bipyrrole-5-carboxaldehyde (MBC) and 2-undecylpyrrole (UP) to form undecylprodiginine (UPG) and (2) hydroxylation of the alkyl chain of UPG to form the (S)-23-hydroxyundecylprodiginine (HUPG), which is essential for MarG catalyzed bicyclization toward the formation of an unusual spiro-tetrahydropyran-aminal ring of marineosins. The final enigmatic steps in the marineosin biosynthesis have now been deciphered.