Production of the Antifungal Isochromanone Ajudazols A and B inChondromyces crocatus Cm c5: Biosynthetic Machinery and Cytochrome P450 Modifications

Myxobacteria: biology and bioactive secondary metabolites

Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.

Chitinolyticbacter albus sp. Nov., A Novel Chitin-Degrading Bacterium Isolated from Ancient Wood Rhizosphere Soil

In this study, a novel aerobic mesophilic bacterial strain with capable of degrading chitin, designated YIM B06366^T, was isolated and classified. The rod-shaped, Gram-stain-negative, on-spore-forming bacterium originated from rhizosphere soil sample collected in Kunming City, Yunnan Province, southwest PR China. Strain YIM B06366^T exhibited growth at temperatures between 20 and 35 °C (optimum, 30 °C) and at pH 6.0-8.0 (optimum, pH 6.0). The analysis of 16S rRNA gene sequence similarity revealed that strain YIM B06366^T was most closely related to type strain Chitinolyticbacter meiyuanensis SYBC-H1^T (98.9%). Phylogenetic analysis based on genome data indicated that strain YIM B06366^T should be assigned to the genus Chitinolyticbacter. The Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) values between strain YIM B06366^T and the reference strain Chitinolyticbacter meiyuanensis SYBC-H1^T were 84.4% and 27.7%, respectively. The major fatty acids included Summed Feature 3 (C_16:1 ω6c/C_16:1 ω7c), Summed Feature 8 (C_18:1 ω6c/C_18:1 ω7c), and C_16:0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipids, and two unidentified phospholipids. The predominant menaquinone was Q-8, and the genomic DNA G + C content was 64.1%. Considering the polyphasic taxonomic evidence, strain YIM B06366^T is proposed as a novel species within the genus Chitinolyticbacter, named Chitinolyticbacter albus sp. nov. (type strain YIM B06366^T = KCTC 92434^T = CCTCC AB 2022163^T).

Synthesis of isochromanone containing natural products from myxobacteria

This review details the biological activity, biosynthesis and synthesis of isochromanone metabolites isolated from myxobacteria. Strategies towards the synthesis of the isochomanone and oxazole fragments of these natural products are highlighted.

Expanding the Ajudazol Cytotoxin Scaffold: Insights from Genome Mining, Biosynthetic Investigations, and Novel Derivatives

Myxobacteria have proven to be a rich source of natural products, but their biosynthetic potential seems to be underexplored given the high number of biosynthetic gene clusters present in their genomes. In this study, a truncated ajudazol biosynthetic gene cluster in Cystobacter sp. SBCb004 was identified using mutagenesis and metabolomics analyses and a set of novel ajudazols (named ajudazols C-J, 3-10, respectively) were detected and subsequently isolated. Their structures were elucidated using comprehensive HR-MS and NMR spectroscopy. Unlike the known ajudazols A (1) and B (2), which utilize acetyl-CoA as the biosynthetic starter unit, these novel ajudazols were proposed to incorporate 3,3-dimethylacrylyl CoA as the starter. Ajudazols C-J (3-10, respectively) are characterized by varying degrees of hydroxylation, desaturation, and different glycosylation patterns. Two P450-dependent enzymes and one glycosyltransferase are shown to be responsible for the hydroxylation at C-8, the desaturation at C-15 and C-33, and the transfer of a d-β-glucopyranose, respectively, based on mutagenesis results. One of the cytochrome P450-dependent enzymes and the glycosyltransferase were found to be encoded by genes located outside the biosynthetic gene cluster. Ajudazols C-H (3-8, respectively) exhibit cytotoxicity against various cancer cell lines.

3-Hydroxy-3-methylisochroman-1-one–2-(carboxymethyl)benzoic acid (1/1)

The title co-crystalline compound, C10H10O3·C9H8O4, has been synthesized and characterized in a single-crystal X-ray diffraction study. In the 3-hydroxy-3-methylisochroman-1-one molecule, the six-membered heterocyclic ring lies between an envelope and a screw-boat conformation. In the 2-carboxymethylbenzoic acid, molecule, the 2-carboxymethyl substituent is almost planar (r.m.s deviation = 0.048 Å) and makes a dihedral angle of 79.59 (7)° with the planar benzene ring. In this molecule, intramolecular C—H...O contacts generate five- and six-membered rings, forming a tricyclic ring system. In the crystal, classical O—H...O and C—H...O hydrogen bonds combine with C—H...π(ring) and unusual C=O...π(ring) contacts to generate a three-dimensional network.

Crocadepsins-Depsipeptides from the Myxobacterium Chondromyces crocatus Found by a Genome Mining Approach

Analysis of the genome sequence of the myxobacterium Chondromyces crocatus Cm c5 revealed the presence of numerous cryptic megasynthetase gene clusters, one of which we here assign to two previously unknown chlorinated metabolites by a comparative gene inactivation and secondary metabolomics approach. Structure elucidation of these compounds revealed a unique cyclic depsipeptide skeleton featuring β- and δ-amide bonds of aspartic acid and 3-methyl ornithine moieties, respectively. Insights into their biosynthesis were obtained by targeted gene inactivation and feeding experiments employing isotope-labeled precursors. The compounds were produced ubiquitously by the species Chondromyces crocatus and were found to inhibit the carbon storage regulator-RNA interaction.

Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis

Here, we report the complete genome sequence of the type strain of the myxobacterial genus Chondromyces, Chondromyces crocatus Cm c5. It presents one of the largest prokaryotic genomes featuring a single circular chromosome and no plasmids. Analysis revealed an enlarged set of tRNA genes, along with reduced pressure on preferred codon usage compared to that of other bacterial genomes. The large coding capacity and the plethora of encoded secondary metabolite biosynthetic gene clusters are in line with the capability of Cm c5 to produce an arsenal of antibacterial, antifungal, and cytotoxic compounds. Known pathways of the ajudazol, chondramide, chondrochloren, crocacin, crocapeptin, and thuggacin compound families are complemented by many more natural compound biosynthetic gene clusters in the chromosome. Whole-genome comparison of the fruiting-body-forming type strain (Cm c5, DSM 14714) to an accustomed laboratory strain which has lost this ability (nonfruiting phenotype, Cm c5 fr-) revealed genetic changes in three loci. In addition to the low synteny found with the closest sequenced representative of the same family, Sorangium cellulosum, extensive genetic information duplication and broad application of eukaryotic-type signal transduction systems are hallmarks of this 11.3-Mbp prokaryotic genome.

Biosynthesis of crocacin involves an unusual hydrolytic release domain showing similarity to condensation domains

The crocacins are potent antifungal and cytotoxic natural compounds from myxobacteria of the genus Chondromyces. Although total synthesis approaches have been reported, the molecular and biochemical basis guiding the formation of the linear crocacin scaffold has remained unknown. Along with the identification and functional analysis of the crocacin biosynthetic gene cluster from Chondromyces crocatus Cm c5, we here present the identification and biochemical characterization of an unusual chain termination domain homologous to condensation domains responsible for hydrolytic release of the product from the assembly line. In particular, gene inactivation studies and in vitro experiments using the heterologously produced domain CroK-C2 confirm this surprising role giving rise to the linear carboxylic acid. Additionally, we determined the kinetic parameters of CroK-C2 by monitoring hydrolytic cleavage of the substrate mimic N-acetylcysteaminyl-crocacin B using an innovative high-performance liquid chromatography mass spectrometry-based assay.

Antibiotics from myxobacteria

Covering: up to the end of 2013. Myxobacteria produce a vast range of structurally diverse natural products with prominent biological activities. Here, we provide a detailed description and judge the potential of all antibiotically active myxobacterial compounds as lead structures, pointing out their particularities and, if known, their mode of action. Thus, the review provides an overview of the potential of specific compounds, suitable for future investigations and possible clinical applications.

Gold Catalysis: Biarylphosphine Ligands as Key for the Synthesis of Dihydroisocoumarins

A gold-catalyzed phenol synthesis was successfully used in the synthesis of dihydroisocoumarins for the first time. A large number of gold(i) complexes were prepared and tested; only complexes based on the biarylphosphine motif were successful.

Structure and noncanonical chemistry of nonribosomal peptide biosynthetic machinery

Structural biology has provided significant insights into the complex chemistry and macromolecular organization of nonribosomal peptide synthetases. In addition, novel pathways are continually described, expanding the knowledge of known biosynthetic chemistry.

Synthesis of myxobacteria metabolites

Myxobacteria are an excellent source of novel secondary metabolites with a range of biological activities. This review details the synthesis of several examples of these natural products. The total synthesis of all the members of the crocacin family is presented where the stereochemistry of the stereotetrad was set via a tin-mediated syn-aldol reaction followed by selective anti-reduction. The other key step in the route to crocacins A, B, and D was the introduction of the enamide functionality by acylation of an enecarbamate. A formal synthesis of apicularen A is also discussed, which involved a base-induced macrolactonization reaction and a transannular oxy-Michael cyclization to secure the tetrahydropyran ring. Finally, the total synthesis of deshydroxyajudazol B is summarized. This route details a modified approach to the 2,4-disubstituted oxazole, and a Diels–Alder reaction followed by aromatization was utilized to form the isochromanone moiety. A highly efficient Sonogashira coupling followed by partial reduction then gave deshydroxyajudazol B.

4-[(4-Chlorophenyl)(hydroxy)methylidene]isochromane-1,3-dione

In the title compound, C₁₆H₉ClO₄, the six-membered heterocyclic ring adopts a screw-boat conformation. The benzene rings are oriented to each other at a dihedral angle of 59.26 (9)°. The mol­ecular structure exhibits a ring motif, viz. S(6), owing to an intra­molecular O—H⋯O hydrogen bond. The presence of C—H⋯O contacts generates an infinite chain along [001]. Also present are π–π stacking inter­actions between neighbouring isochromanedione benzene rings [centroid–centroid distance = 3.746 (1) Å], and C—O⋯π inter­actions [O⋯centroid = 3.934 (2) Å].

Insights into an unusual nonribosomal peptide synthetase biosynthesis: identification and characterization of the GE81112 biosynthetic gene cluster

The GE81112 tetrapeptides (1-3) represent a structurally unique class of antibiotics, acting as specific inhibitors of prokaryotic protein synthesis. Here we report the cloning and sequencing of the GE81112 biosynthetic gene cluster from Streptomyces sp. L-49973 and the development of a genetic manipulation system for Streptomyces sp. L-49973. The biosynthetic gene cluster for the tetrapeptide antibiotic GE81112 (getA-N) was identified within a 61.7-kb region comprising 29 open reading frames (open reading frames), 14 of which were assigned to the biosynthetic gene cluster. Sequence analysis revealed the GE81112 cluster to consist of six nonribosomal peptide synthetase (NRPS) genes encoding incomplete di-domain NRPS modules and a single free standing NRPS domain as well as genes encoding other biosynthetic and modifying proteins. The involvement of the cloned gene cluster in GE81112 biosynthesis was confirmed by inactivating the NRPS gene getE resulting in a GE81112 production abolished mutant. In addition, we characterized the NRPS A-domains from the pathway by expression in Escherichia coli and in vitro enzymatic assays. The previously unknown stereochemistry of most chiral centers in GE81112 was established from a combined chemical and biosynthetic approach. Taken together, these findings have allowed us to propose a rational model for GE81112 biosynthesis. The results further open the door to developing new derivatives of these promising antibiotic compounds by genetic engineering.

Genome mining in Sorangium cellulosum So ce56: identification and characterization of the homologous electron transfer proteins of a myxobacterial cytochrome P450

Myxobacteria, especially members of the genus Sorangium, are known for their biotechnological potential as producers of pharmaceutically valuable secondary metabolites. The biosynthesis of several of those myxobacterial compounds includes cytochrome P450 activity. Although class I cytochrome P450 enzymes occur wide-spread in bacteria and rely on ferredoxins and ferredoxin reductases as essential electron mediators, the study of these proteins is often neglected. Therefore, we decided to search in the Sorangium cellulosum So ce56 genome for putative interaction partners of cytochromes P450. In this work we report the investigation of eight myxobacterial ferredoxins and two ferredoxin reductases with respect to their activity in cytochrome P450 systems. Intriguingly, we found not only one, but two ferredoxins whose ability to sustain an endogenous So ce56 cytochrome P450 was demonstrated by CYP260A1-dependent conversion of nootkatone. Moreover, we could demonstrate that the two ferredoxins were able to receive electrons from both ferredoxin reductases. These findings indicate that S. cellulosum can alternate between different electron transport pathways to sustain cytochrome P450 activity.

3-(1-Adamant-yl)-6-methyl-3-(3-methyl-benz-yl)isochroman-1-one

In the title compound, C₂₈H₃₂O₂, the oxanone ring adopts distorted half-boat conformation with the following Cremer and Pople puckering parameters: Q = 0.619 (2) Å, θ = 0.75 (19) and ϕ = 172 (13)°. The dihedral angle betwen two benzene rings is 21.32 (7)°. The adamantane unit consists of three fused cyclo­hexane rings in classical chair conformations, with absolute values of C—C—C—C torsion angles in the range 57.5 (2)–60.9 (2)°. Weak inter­actions of the type C—H⋯O link mol­ecules of each enanti­omer into chains parallel to the b axis and lying about inversion centers. The crystal packing is also stabilized by inter­molecular π-π stacking inter­actions [centroid–centroid distance of 3.8566 (11) Å].

Myxobacteria--'microbial factories' for the production of bioactive secondary metabolites

In this article, we briefly review the potential of myxobacteria as 'natural product factories' by highlighting results from the recently sequenced myxobacterial model strain Myxococcus xanthus. We will focus on the production of polyketides, non-ribosomally-made peptides, and their hybrids, and discuss the evaluation of biosynthetic potential using genome-based methods, as well as biosynthetic process engineering.