3-O-isobutyrylkinamycin C and 4-deacetyl-4-O-isobutyrylkinamycin C, new antibiotics produced by a Saccharothrix species

Discovering the secondary metabolic potential of Saccharothrix

Rare actinomycetes are highly valued as potential sources of novel bioactive secondary metabolites. Among these rare actinomycetes, the genus Saccharothrix is particularly noteworthy due to its ability to produce a diverse range of bioactive secondary metabolites. With the continuous sequencing of bacterial genomes and the rapid development of bioinformatics technologies, our knowledge of the secondary metabolic potential of Saccharothrix can become more comprehensive, but this space has not been reviewed or explored. This review presents a detailed overview of the chemical structures and bioactivities of 138 Saccharothrix-derived secondary metabolites, which are classified into five distinct groups based on their biosynthetic pathways. Furthermore, we delve into experimentally characterized biosynthetic pathways of nine bioactive metabolites. By utilizing a combination of cheminformatic and bioinformatic approaches, we attempted to establish connections between the metabolite families and the biosynthetic gene cluster families encoded by Saccharothrix strains. Our analysis provides a comprehensive perspective on the secondary metabolites that can be linked to corresponding BGCs and highlights the underexplored biosynthetic potential of Saccharothrix. This review also provides guidance for the targeted discovery and biosynthesis of novel natural products from Saccharothrix.

Bioprospecting of Soil-Derived Actinobacteria Along the Alar-Hotan Desert Highway in the Taklamakan Desert

Taklamakan desert is known as the largest dunefield in China and as the second largest shifting sand desert in the world. Although with long history and glorious culture, the Taklamakan desert remains largely unexplored and numerous microorganisms have not been harvested in culture or taxonomically identified yet. The main objective of this study is to explore the diversity, novelty, and pharmacological potential of the cultivable actinomycetes from soil samples at various sites along the Alar-Hotan desert highway in the Taklamakan desert. A total of 590 actinobacterial strains were recovered by the culture-dependent approach. Phylogenetic analysis based on 16S ribosomal RNA (rRNA) gene sequences unveiled a significant level of actinobacterial diversity with 55 genera distributed in 27 families of 12 orders. Thirty-six strains showed relatively low 16S rRNA similarities (<98.65%) with validly described species, among which four strains had already been characterized as novel taxa by our previous research. One hundred and forty-six actinobacterial isolates were selected as representatives to evaluate the antibacterial activities and mechanism of action by the paper-disk diffusion method and a double fluorescent protein reporter "pDualrep2" system, respectively. A total of 61 isolates exhibited antagonistic activity against the tested "ESKAPE" pathogens, among which seven strains could produce bioactive metabolites either to be able to block translation machinery or to induce SOS-response in the pDualrep2 system. Notably, Saccharothrix sp. 16Sb2-4, harboring a promising antibacterial potential with the mechanism of interfering with protein translation, was analyzed in detail to gain deeper insights into its bioactive metabolites. Through ultra-performance liquid chromatography (UPLC)-quadrupole time-of-flight (QToF)-MS/MS based molecular networking analysis and databases identification, four families of compounds (1-16) were putatively identified. Subsequent bioassay-guided separation resulted in purification of four 16-membered macrolide antibiotics, aldgamycin H (8), aldgamycin K (9), aldgamycin G (10), and swalpamycin B (11), and their structures were elucidated by HR-electrospray ionization source (ESI)-MS and NMR spectroscopy. All compounds 8-11 displayed antibacterial activities by inhibiting protein synthesis in the pDualrep2 system. In conclusion, this work demonstrates that Taklamakan desert is a potentially unique reservoir of versatile actinobacteria, which can be a promising source for discovery of novel species and diverse bioactive compounds.

Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis

Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.

A photo-induced C–C bond formation methodology to construct tetrahydrofluorenones and their related structures

A metal-free, photo-induced C–C bond formation methodology was developed to construct tetrahydrofluorenones and their related structures.

Nocardiopsis and Saccharothrix genera in Saharan soils in Algeria: isolation, biological activities and partial characterization of antibiotics

Twenty-five soil samples were collected in the Algerian Sahara and analyzed to isolate rare actinomycetes. Eighty-six isolates with the same Nocardiopsis or Saccharothrix morphology were isolated on humic-vitamin B agar medium using dilution techniques and several antibiotics as selective agents. Certain of these antibiotics seemed to be very selective for some phenotypes. Morphological and chemotaxonomic characteristics led to identifying 54 isolates belonging to the Nocardiopsis genus and 32 isolates belonging to the Saccharothrix genus. An assessment of the antimicrobial properties of the isolates showed activities against Gram-positive bacteria, fungi and yeasts. Saccharothrix isolates possessed better antifungal activity than Nocardiopsis. One of them, labeled SA 103, was therefore selected for identification of its antifungal antibiotic activities. Production of overall antifungal and antibacterial activities was checked on the complex medium ISP2 and a synthetic medium (SM) that contains glucose or starch as carbon source, and ammonium or nitrate as nitrogen source. The SM medium containing ammonium sulfate (0.2%), supplemented with starch (0.5%) and yeast extract (0.3%), was retained for production of antibiotics. Active substances were purified by a G25-80 Sephadex column and reverse phase HPLC. Two pure substances were obtained and named ZA01 and ZA02; they were characterized on the basis of combined data resulting from chemical tests, UV visibile and IR spectra and mass spectrometry. The two antibiotics were found to be related and were partially characterized as nucleotidic or nucleosidic antibiotics. Their structures consisted of a chain of three sugar units linked to an aromatic base containing a phosphate residue.

Thiobutacin, a novel antifungal and antioomycete antibiotic from Lechevalieria aerocolonigenes

A novel butanoic acid, thiobutacin (1), 4-(2-aminophenyl)-4-oxo-2-methylthiobutanoic acid (C11H13NO3S), was isolated from the culture broth of a soil actinomycete, Lechevalieria aerocolonigenes strain VK-A9. The structure of thiobutacin (1) was elucidated on the basis of the extensive 2D NMR spectral data including 1H-1H COSY, HMBC, HMQC, ROESY, and NOESY. Thiobutacin (1) showed antioomycete and antifungal activity against phytopathogenic Phytophthora capsici and Botrytis cinerea and the yeast Saccharomyces cerevisiae.

Cycloaddition reactions of alkoxy alkynyl Fischer carbene complexes with o-quinodimethanes (oQDMs)

[reaction: see text] The reaction of o-quinodimethanes (oQDMs) with alkoxy alkynyl Fischer carbene complexes is highly dependent on the carbene complex. Thus, for arylalkynyl carbene complexes, the initial [4 + 2]-cycloadduct evolves opening a new entry to the benzo[b]fluorene skeleton, which is present in many natural products. However, for alkenylalkynyl carbene complexes, the reaction takes place through the double bond, instead of the triple bond, in an unprecedented fashion, leading to new functionalized alkynyl carbene complexes.

Kinamycin Biosynthesis. Synthesis, Isolation, and Incorporation of Stealthin C, an Aminobenzo[b]fluorene

A new intermediate in the biosynthesis of the benzo[b]fluorene antibiotic, kinamycin D, has been identified. 11-Amino-4,5,9-trihydroxy-2-methyl-10H-benzo[b]fluoren-10-one was synthesized and shown to be present in extracts of Streptomyces murayamaensisfermentations. A deuterated sample was prepared and shown to be specifically incorporated into kinamycin D. This new intermediate, now named stealthin C, is also the probable hydroxylation substrate for the biosynthesis of stealthin A by S. viridochromogenes.

Kinamycin acetyltransferase I from Streptomyces murayamaensis, an apparently large, membrane-associated enzyme

Identification and initial characterization of an apparently large, membrane-associated multifunctional enzyme, kinamycin acetyltransferase I (KAT I), is described. KAT I activity was enriched 29-fold over the level in cell-free extracts of Streptomyces murayamaensis. Two acetyltransferase activities catalyzing acetyl coenzyme A dependent conversion of kinamycin F and E to kinamycin E and D, respectively, were inseparable in the course of the partial purification. Partial purification involved separation of KAT I from cytosolic proteins by differential ultracentrifugation, solubilization with 0.5% CHAPS zwitterionic detergent followed by ultracentrifugation, and Sephacryl S400 gel filtration chromatography of the resulting supernatant.

Detection of novel secondary metabolites

The study of antibiotics and other fermentation products has shown that a seemingly unlimited number of compounds with diverse structures are produced by microorganisms. The continued high rate of discovery of new chemical entities, in the light of the abundance of microbial products already described, is due to creative screening procedures that incorporate such features as the emphasis on unusual microorgnaisms, their special propagation and fermentation requirements, supersensitive and highly selective assays, genetic engineering both for the biosynthesis of new compounds and in the development of screening systems, early in vivo evaluation, improved isolation techniques, modern procedures for structure determination, computer-assisted identification, and an efficient multidisciplinary approach. This review focuses on the genesis and development of the gamut of methodologies that have led to the successful detection of the wide variety of novel secondary metabolites that include antibacterial, antigungal, antiviral and antitumour antibiotics, enzyme inhibitors, pharmacologically and immunologically active agents, products useful in agriculture and animal husbandry, microbial regulators, and other compounds for which no bioactive role has yet been found.