The structure of (E)-biformene synthase provides insights into the biosynthesis of bacterial bicyclic labdane-related diterpenoids

Actinomycetes as Producers of Biologically Active Terpenoids: Current Trends and Patents

Terpenes and their derivatives (terpenoids and meroterpenoids, in particular) constitute the largest class of natural compounds, which have valuable biological activities and are promising therapeutic agents. The present review assesses the biosynthetic capabilities of actinomycetes to produce various terpene derivatives; reports the main methodological approaches to searching for new terpenes and their derivatives; identifies the most active terpene producers among actinomycetes; and describes the chemical diversity and biological properties of the obtained compounds. Among terpene derivatives isolated from actinomycetes, compounds with pronounced antifungal, antiviral, antitumor, anti-inflammatory, and other effects were determined. Actinomycete-produced terpenoids and meroterpenoids with high antimicrobial activity are of interest as a source of novel antibiotics effective against drug-resistant pathogenic bacteria. Most of the discovered terpene derivatives are produced by the genus Streptomyces; however, recent publications have reported terpene biosynthesis by members of the genera Actinomadura, Allokutzneria, Amycolatopsis, Kitasatosporia, Micromonospora, Nocardiopsis, Salinispora, Verrucosispora, etc. It should be noted that the use of genetically modified actinomycetes is an effective tool for studying and regulating terpenes, as well as increasing productivity of terpene biosynthesis in comparison with native producers. The review includes research articles on terpene biosynthesis by Actinomycetes between 2000 and 2022, and a patent analysis in this area shows current trends and actual research directions in this field.

Diterpenoids from Streptomyces: Structures, Biosyntheses and Bioactivities

Bacteria, especially Streptomyces spp., have been emerging as rich sources of natural diterpenoids with diverse structures and broad bioactivities. Here, we review diterpenoids biosynthesized by Streptomyces , with an emphasis on their structures, biosyntheses, and bioactivities. Although diterpenoids from Streptomyces are relatively rare compared to those from plants and fungi, their novel skeletons, biosyntheses and bioactivities present opportunities for discovering new drugs, enzyme mechanisms, and applications in bio-catalysis and metabolic pathway engineering.

Insights into Enzymatic Catalytic Mechanism of bCinS: The Importance of Protein Conformational Change

Although the available crystal structures of BCinS (Streptomyces clavuligerus 1,8-cineole synthase), a typic class I terpene cyclases (TPCs), have shown notable protein conformational flexibility once binding with the substrate, the...

Functional characterization and structural bases of two class I diterpene synthases in pimarane-type diterpene biosynthesis

Pimarane-type diterpenoids are widely distributed in all domains of life, but no structures or catalytic mechanisms of pimarane-type diterpene synthases (DTSs) have been characterized. Here, we report that two class I DTSs, Sat1646 and Stt4548, each accept copalyl diphosphate (CPP) as the substrate to produce isopimara-8,15-diene (1). Sat1646 can also accept syn-CPP and produce syn-isopimaradiene/pimaradiene analogues (2-7), among which 2 possesses a previously unreported "6/6/7" ring skeleton. We solve the crystal structures of Sat1646, Sat1646 complexed with magnesium ions, and Stt4548, thereby revealing the active sites of these pimarane-type DTSs. Substrate modeling and subsequent site-directed mutagenesis experiments demonstrate different structural bases of Sat1646 and Stt4548 for 1 production. Comparisons with previously reported DTSs reveal their distinct carbocation intermediate stabilization mechanisms, which control the conversion of a single substrate CPP into structurally diverse diterpene products. These results illustrate the structural bases for enzymatic catalyses of pimarane-type DTSs, potentially facilitating future DTS engineering and combinatorial biosynthesis.

Residue-Orientation-Dependent Dynamics and Selectivity of Active Pocket in Microbe Class I Terpene Cyclases

Microbe class I terpene cyclases (TPCs) are responsible for deriving numerous functionally and structurally diverse groups of terpenoid natural products. The conformational change of their active pockets from "open" state to "closed" state upon substrate binding has been clarified. However, the key structural basis relevant to this active pocket dynamics and its detailed molecular mechanism are still unclear. In this work, on the basis of the molecular dynamics (MD) on two microbe class I TPCs (SdS and bCinS), we propose that the active pocket dynamics is highly dependent on the residue orientation of two conserved structural bases R-D dyad and X-R-D triad, rather than the previously suggested flexibility of kink region. Actually, we considered that the flexibility of kink region is synchronous with the R residue orientation of the X-R-D triad, which could regulate the entrance size of active pocket and thus affect the substrate selectivity of active pocket by utilizing the promiscuity of the X-R-D triad. Furthermore, to better understand the function of the two structural bases, two intelligible models of "PPi catcher-locker" and "selector-PPi sensor-orienter" are proposed to, respectively, describe the R-D dyad and X-R-D triad and broadened to more microbe class I TPCs. These findings exhibit the dynamics of active pocket inaccessible in static crystal structures and provide useful structural basis knowledge for further design of microbe class I TPCs with different cyclization ability.

Current understanding and biotechnological application of the bacterial diterpene synthase CotB2

CotB2 catalyzes the first committed step in cyclooctatin biosynthesis of the soil bacterium Streptomyces melanosporofaciens. To date, CotB2 represents the best studied bacterial diterpene synthase. Its reaction mechanism has been addressed by isoptope labeling, targeted mutagenesis and theoretical computations in the gas phase, as well as full enzyme molecular dynamic simulations. By X-ray crystallography different snapshots of CotB2 from the open, inactive, to the closed, active conformation have been obtained in great detail, allowing us to draw detailed conclusions regarding the catalytic mechanism at the molecular level. Moreover, numerous alternative geranylgeranyl diphosphate cyclization products obtained by CotB2 mutagenesis have exciting applications for the sustainable production of high value bioactive substances.