Geosmin biosynthesis. Mechanism of the fragmentation-rearrangement in the conversion of germacradienol to geosmin

Enantioselective synthesis of all stereoisomers of geosmin and of biosynthetically related natural products

Synthetic routes to geosmin and its enantiomer are well established, but the enantioselective synthesis of stereoisomers of geosmin is unknown. Here a stereoselective synthesis of all stereoisomers of geosmin is reported, yielding all compounds in high enantiomeric purity. Furthermore, the stereoselective synthesis of a geosmin derivative isolated from a mangrove associated streptomycete was performed, establishing the absolute configuration of the natural product. Finally, a new side product of the geosmin synthase from Streptomyces ambofaciens was isolated and its structure was elucidated by NMR spectroscopy. The absolute configuration of this new compound was determined through a stereoselective synthesis.

Heterologous production of (-)-geosmin in Saccharomyces cerevisiae

(-)-Geosmin has high demand in perfumes and cosmetic products for its earthy congenial aroma. The current production of (-)-geosmin is either by distillation of sun-baked soil or by inefficient chemical synthesis because of the presence of multiple chiral centers. Fermentation processes are not viable as the titers of the Streptomyces sp. based processes are low. This work presents an alternative route by the heterologous synthesis of (-)-geosmin in Saccharomyces cerevisiae. The enzyme involved is the bifunctional geosmin synthase that catalyzes the conversion of farnesyl diphosphate to germacradienol and germacradienol to geosmin. This study evaluated the activity of many orthologs of geosmin synthase when expressed heterologously in S. cerevisiae. When the well-characterized CAB41566 from Streptomyces coelicolor origin was tested, germacradienol and germacrene D were detected but no geosmin. Bioinformatic analysis based on high/low identities to N-terminal and C-terminal domains of CAB41566 was carried out to identify different orthologs of geosmin synthase proteins from different bacterial and fungal origins. ADO68918 of Stigmatella aurantiaca origin showed the best activity among the tested orthologs, not only in terms of geosmin production but also an order of magnitude higher total abundance of the products of geosmin synthase as compared to CAB41566. This study successfully demonstrated the production of (-)-geosmin in S. cerevisiae and offers an alternative, sustainable and environment-friendly approach to producing (-)-geosmin.

Production of non-natural terpenoids through chemoenzymatic synthesis using substrate analogs

Chemoenzymatic synthesis of non-natural terpenes using the promiscuous activity of terpene synthases allows for the expansion of the chemical space of terpenoids with potentially new bioactivities. In this report, we describe protocols for the preparation of a novel aphid attractant, (S)-14,15-dimethylgermacrene D, by exploiting the promiscuity of (S)-germacrene D synthase from Solidago canadensis and using an engineered biocatalytic route to convert prenols to terpenoids. The method uses a combination of five enzymes to carry out the preparation of terpenoid semiochemicals in two steps: (1) diphosphorylation of five or six carbon precursors (prenol, isoprenol and methyl-isoprenol) catalyzed by Plasmodium falciparum choline kinase and Methanocaldococcus jannaschii isopentenyl phosphate kinase to form DMADP, IDP and methyl-IDP, and (2) chain elongation and cyclization catalyzed by Geobacillus stearothermophilus (2E,6E)-farnesyl diphosphate synthase and S. canadensis (S)-germacrene D synthase to produce (S)-germacrene D and (S)-14,15-dimethylgermacrene D. Using this method, new non-natural terpenoids are readily accessible and the approach can be adopted to produce different terpene analogs and terpenoid derivatives with potential novel applications.

The microbial biosynthesis of noncanonical terpenoids

Terpenoids are a class of structurally complex, naturally occurring compounds found predominantly in plant, animal, and microorganism secondary metabolites. Classical terpenoids typically have carbon atoms in multiples of five and follow well-defined carbon skeletons, whereas noncanonical terpenoids deviate from these patterns. These noncanonical terpenoids often result from the methyltransferase-catalyzed methylation modification of substrate units, leading to irregular carbon skeletons. In this comprehensive review, various activities and applications of these noncanonical terpenes have been summarized. Importantly, the review delves into the biosynthetic pathways of noncanonical terpenes, including those with C6, C7, C11, C12, and C16 carbon skeletons, in bacteria and fungi host. It also covers noncanonical triterpenes synthesized from non-squalene substrates and nortriterpenes in Ganoderma lucidum, providing detailed examples to elucidate the intricate biosynthetic processes involved. Finally, the review outlines the potential future applications of noncanonical terpenoids. In conclusion, the insights gathered from this review provide a reference for understanding the biosynthesis of these noncanonical terpenes and pave the way for the discovery of additional unique and novel noncanonical terpenes. KEY POINTS: •The activities and applications of noncanonical terpenoids are introduced. •The noncanonical terpenoids with irregular carbon skeletons are presented. •The microbial biosynthesis of noncanonical terpenoids is summarized.

Volatile sensation: The chemical ecology of the earthy odorant geosmin

Geosmin may be the most familiar volatile compound, as it lends the earthy smell to soil. The compound is a member of the largest family of natural products, the terpenoids. The broad distribution of geosmin among bacteria in both terrestrial and aquatic environments suggests that this compound has an important ecological function, for example, as a signal (attractant or repellent) or as a protective specialized metabolite against biotic and abiotic stresses. While geosmin is part of our everyday life, scientists still do not understand the exact biological function of this omnipresent natural product. This minireview summarizes the current general observations regarding geosmin in prokaryotes and introduces new insights into its biosynthesis and regulation, as well as its biological roles in terrestrial and aquatic environments.

Inactivation of fungal spores by performic acid in water: Comparisons with peracetic acid

Performic acid (PFA) has received increasing attention in water disinfection due to its high disinfection efficiency and fewer formation of disinfection by-products. However, the inactivation of fungal spores by PFA has not been investigated. In this study, the results showed that the log-linear regression plus tail model adequately described the inactivation kinetic of fungal spores with PFA. The k values of A. niger and A. flavus with PFA were 0.36 min^-1 and 0.07 min^-1, respectively. Compared to peracetic acid, PFA was more efficient in inactivating fungal spores and caused more serious damage on cell membrane. Compared to neutral and alkaline conditions, acidic environments demonstrated a greater inactivation efficiency for PFA. The increase of PFA dosage and temperature had a promoting effect on the inactivation efficiency of fungal spores. PFA could kill the fungal spores by damaging cell membrane and penetration of cell membranes. In real water, the inactivation efficiency declined as a result of the existence of background substances such as dissolved organic matter. Moreover, the regrowth potential of fungal spores in R2A medium were severely inhibited after inactivation. This study provides some information for PFA to control fungi pollution and explores the mechanism of PFA inactivation.

Molecular networking-guided isolation of undescribed antifungal odoriferous sesquiterpenoids from a marine mesophotic zone sponge-associated Streptomyces sp. NBU3428

Under the guidance of MS/MS-based molecular networking, eight odoriferous sesquiterpenes including two undescribed geosmin-type sesquiterpenoid degradations, odoripenoid A (1) and odoripenoid B (2), and two undescribed germacrane-type sesquiterpenoids, odoripenoid C (3) and odoripenoid (4), together with four known related compounds (5-8) were isolated from the EtOAc extract of the marine mesophotic zone sponge-associated Streptomyces sp. NBU3428. All chemical structures including absolute configurations of these compounds were elucidated by means of HRESIMS, NMR, ECD calculations and single-crystal X-ray diffraction experiments. Compounds 1 and 2 represent the rarely geosmin-related metabolites directly as natural products from actinomycetes. The isolated compounds (1-8) were assayed in a range of biological activities. Compounds 1 and 2 showed anti-Candida albicans activity with MIC values of 16 and 32 μg/mL, respectively, representing potential antifungal agents.

Occurrence of fungal spores in drinking water: A review of pathogenicity, odor, chlorine resistance and control strategies

Fungi in drinking water have been long neglected due to the lack of convenient analysis methods, widely accepted regulations and efficient control strategies. However, in the last few decades, fungi in drinking water have been widely recognized as opportunity pathogens that cause serious damage to the health of immune-compromised individuals. In drinking water treatment plants, fungal spores are more resistant to chlorine disinfection than bacteria and viruses, which can regrow in drinking water distribution systems and subsequently pose health threats to water consumers. In addition, fungi in drinking water may represent an ignored source of taste and odor (T&O). This review identified 74 genera of fungi isolated from drinking water and presented their detailed taxonomy, sources and biomass levels in drinking water systems. The typical pathways of exposure of water-borne fungi and the main effects on human health are clarified. The fungi producing T&O compounds and their products are summarized. Data on free chlorine or monochloramine inactivation of fungal spores and other pathogens are compared. At the first time, we suggested four chlorine-resistant mechanisms including aggregation to tolerate chlorine, strong cell walls, cellular responses to oxidative stress and antioxidation of melanin, which are instructive for the future fungi control attempts. Finally, the inactivation performance of fungal spores by various technologies are comprehensively analyzed. The purpose of this study is to provide an overview of fungi distribution and risks in drinking water, provide insight into the chlorine resistance mechanisms of fungal spores and propose approaches for the control of fungi in drinking water.

Phylogenetic Analysis and Characterization of Odorous Compound-Producing Actinomycetes in Sediments in the Sanbe Reservoir, A Drinking Water Reservoir in Japan

Odor caused by the presence of geosmin and 2-methylisoborneol (2-MIB) in aquatic ecosystems leads to considerable economic loss worldwide. The odorous compounds are primarily produced by cyanobacteria and actinomycetes. While the contribution of odorous compounds-producing cyanobacteria has been thoroughly investigated, the production of geosmin and 2-MIB by actinomycetes in aquatic ecosystems is poorly understood. In this study, we isolated geosmin and/or 2-MIB-producing actinomycetes in sediments collected from the Sanbe Reservoir, Japan, identified the biosynthetic gene of geosmin and 2-MIB, and investigated the production of the odorous compounds by the isolated strains. Partial sequence of 16S rRNA and the biosynthetic genes was determined to analyze the phylogenetic relationship among the strains. The geosmin and 2-MIB concentrations in the culture of the isolated strains were measured using gas chromatography mass spectrometry. Fifty-four strains of odorous compounds-producing and non-geosmin-producing actinomycetes were isolated from sediments from the Sanbe Reservoir. Diverse actinomycetes were identified and many of them produced geosmin and/or 2-MIB. Many odorous compounds-producing actinomycetes were phylogenetically different from previously reported producing actinomycetes. The producing ability of the odorous compounds of the isolated strains in this study was not significantly related with the phylogenetic groups of 16S rRNA and the biosynthetic genes. The findings suggest that the odorous compounds-producing actinomycetes in the sediments are diverse and different from previously reported strains.

High Versatility of IPP and DMAPP Methyltransferases Enables Synthesis of C6, C7 and C8 Terpenoid Building Blocks

The natural substance class of terpenoids covers an extremely wide range of different structures, although their building block repertoire is limited to the C₅ compounds DMAPP and IPP. This study aims at the characterization of methyltransferases (MTases) that modify these terpene precursors and the demonstration of their suitability for biotechnological purposes. All seven enzymes tested accepted IPP as substrate and altogether five C₆ compounds and six C₇ compounds were formed within the reactions. A high selectivity for the deprotonation site as well as high stereoselectivity could be observed for most of the biocatalysts. Only the enzyme from Micromonospora humi also accepted DMAPP as substrate, converting it into (2R)‐2‐methyl‐IPP in vitro. In vivo studies demonstrated the production of a C₈ compound and a hydride shift step within the MTase‐catalyzed reaction. Our study presents IPP/DMAPP MTases with very different catalytic properties, which provide biosynthetic access to many novel terpene‐derived structures.

Undesirable odour substances (geosmin and 2-methylisoborneol) in water environment: Sources, impacts and removal strategies

Off-flavours in fish products generated from recirculating aquaculture systems (RAS) are a major problem in the fish farming industry affecting the market demand and prices. A particular concern is the muddy or musty odour and taste in fish due to the presence of secondary metabolites geosmin and 2-methylisoborneol (2-MIB), produced by actinobacteria (mainly Streptomyces), myxobacteria and cyanobacteria. Off-flavours have deteriorated the quality of fish, rendering their products unfit for human consumption. The process of odour removal requires purification for several days to weeks in clean water; thus this leads to additional production costs. Geosmin and 2-MIB, detected at extremely low odour thresholds, are the most widespread off-flavour metabolites in aquaculture, entering through fish gills and accumulating in the fish adipose tissues. In this review, we aimed to determine the diversity and identity of geosmin- and 2-MIB-producing bacteria in aquaculture and provide possible strategies for their elimination.

Structures, Occurrences and Biosynthesis of 11,12,13-Tri-nor-Sesquiterpenes, an Intriguing Class of Bioactive Metabolites

The compounds 11,12,13-tri-nor-sesquiterpenes are degraded sesquiterpenoids which have lost the C₃ unit of isopropyl or isopropenyl at C-7 of the sesquiterpene skeleton. The irregular C-backbone originates from the oxidative removal of a C₃ side chain from the C₁₅ sesquiterpene, which arises from farnesyl diphosphate (FDP). The C₁₂-framework is generated, generally, in all families of sesquiterpenes by oxidative cleavage of the C₃ substituent, with the simultaneous introduction of a double bond. This article reviews the isolation, biosynthesis and biological activity of this special class of sesquiterpenes, the 11,12,13-tri-nor-sesquiterpenes.

Temperature affects growth, geosmin/2-methylisoborneol production, and gene expression in two cyanobacterial species

Cyanobacterial blooms accompanied by taste and odor (T&O) compounds affect the recreational function and safe use of drinking water. Geosmin and 2-methylisoborneol (2-MIB) are the most common T&O compounds. In this study, we investigated the effect of temperature on geosmin and 2-MIB production in Dolichospermum smithii and Pseudanabaena foetida var. intermedia. More specifically, transcription of one geosmin synthase gene (geoA) and two 2-MIB synthase genes (mtf and mtc) was explored. Of the three temperatures (15, 25, and 35 °C) tested, the maximum Chl-a content was determined at 25 °C in both D. smithii and P. foetida var. intermedia. The maximum total geosmin concentration (19.82 μg/L) produced by D. smithii was detected at 25 °C. The total 2-MIB concentration (82.5 μg/L) produced by P. foetida var. intermedia was the highest at 35 °C. Besides, the lowest Chl-a content and minimum geosmin/2-MIB concentration were observed at 15 °C. There was a good positive correlation between geosmin/2-MIB concentration and Chl-a content. The expression levels of the geoA, mtf, and mtc genes at 15 °C were significantly higher than those at 25 and 35 °C. The transcription of the mtf and mtc genes in P. foetida var. intermedia was higher at 35 °C than at 25 °C. The results highlight unfavorable temperature can increase the potential of geosmin/2-MIB synthesis from the gene expression level in cyanobacteria. This study could provide basic knowledge of geosmin/2-MIB production by cyanobacteria for better understanding and management of T&O problems in drinking water.

The complemented mutant complΔBcstc7niaD, in the STC7 of Botrytis cinerea led to the characterization of 11,12,13-tri-nor-eremophilenols derivatives

Botrytis cinerea has high potential for the production of specialized metabolites. The recent resequencing of the genome of the B05.10 strain using PacBio technology and the resulting update of the Ensembl Fungi (2017) database in the genome sequence have been instrumental in identifying new genes that could be involved in secondary metabolism. Thus, a new sesquiterpene cyclase (STC) coding gene (Bcstc7) has been included in the gene list from this phytopathogenic fungus. We recently constructed the null and complement transformants in STC7 which enabled us to functionally characterize this STC. Deletion of the Bcstc7 gene abolished (+)-4-epi-eremophilenol biosynthesis, and could then be re-established by complementing the null mutant with the Bcstc7 gene. Chemical analysis of the complemented transformant suggests that STC7 is the principal enzyme responsible for the key cyclization step of farnesyl diphosphate (FDP) to (+)-4-epi-eremophil-9-en-11-ols. A thorough analysis of the metabolites produced by two wild-type strains, B05.10 and UCA992, and the complemented mutant ^complΔBcstc7^niaD, revealed the isolation and structural characterization of six 11,12,13-tri-nor-eremophilene derivatives, in addition to a large number of known eremophilen-11-ol derivatives. The structural characterization was carried out by extensive spectroscopic techniques. The biosynthesis of these compounds is explained by a retroaldol reaction or by dehydration and oxidative cleavage of C11-C13 carbons. This is the first time that this interesting family of degraded eremophilenols has been isolated from the phytopathogenous fungus B. cinerea.

Non-canonical substrates for terpene synthases in bacteria are synthesized by a new family of methyltransferases

The 'biogenetic isoprene rule', formulated in the mid 20th century, predicted that terpenoids are biosynthesized via polymerization of C5 isoprene units. The polymerizing enzymes have been identified to be isoprenyl diphosphate synthases, products of which are catalyzed by terpene synthases (TPSs) to achieve vast structural diversity of terpene skeletons. Irregular terpenes (e.g, C11, C12, C16, C17) are also frequently observed, and they have presumed to be synthesized by the modification of terpene skeletons. This review highlights the exciting discovery of an additional route to the biosynthesis of irregular terpenes which involves the action of a newly discovered enzyme family of isoprenyl diphosphate methyltransferases (IDMTs). These enzymes methylate, and sometimes cyclize, the classical isoprenyl diphosphate substrates to produce modified, non-canonical substrates for specifically evolved TPSs. So far, this new pathway has been found only in bacteria. Structure and sequence comparisons of the IDMTs strongly indicate a conservation of their active pockets and overall topologies. Some bacterial IDMTs and TPSs appear in small gene clusters, which may facilitate future mining of bacterial genomes for identification of irregular terpene-producing enzymes. The IDMT-TPS route for terpenoid biosynthesis presents another example of nature's ingenuity in creating chemical diversity, particularly terpenoids, for organismal fitness. IDMT isoprenyl diphosphate methyltransferases IDPMT isopentenyl diphosphate methyltransferase GDPMT geranyl diphosphate methyltransferase FDPMT farnesyl diphosphate methyltransferases BGC biosynthetic gene cluster TPS terpene synthase MIBS 2-methylisoborneol synthase MBS 2-methylenebornane synthase DMADP Dimethylallyl diphosphate SAM S-adenosyl-L-methionine.

Phytohormones and volatile organic compounds, like geosmin, in the ectomycorrhiza of Tricholoma vaccinum and Norway spruce (Picea abies)

The ectomycorrhizospheric habitat contains a diverse pool of organisms, including the host plant, mycorrhizal fungi, and other rhizospheric microorganisms. Different signaling molecules may influence the ectomycorrhizal symbiosis. Here, we investigated the potential of the basidiomycete Tricholoma vaccinum to produce communication molecules for the interaction with its coniferous host, Norway spruce (Picea abies). We focused on the production of volatile organic compounds and phytohormones in axenic T. vaccinum cultures, identified the potential biosynthesis genes, and investigated their expression by RNA-Seq analyses. T. vaccinum released volatiles not usually associated with fungi, like limonene and β-barbatene, and geosmin. Using stable isotope labeling, the biosynthesis of geosmin was elucidated. The geosmin biosynthesis gene ges1 of T. vaccinum was identified, and up-regulation was scored during mycorrhiza, while a different regulation was seen with mycorrhizosphere bacteria. The fungus also released the volatile phytohormone ethylene and excreted salicylic and abscisic acid as well as jasmonates into the medium. The tree excreted the auxin, indole-3-acetic acid, and its biosynthesis intermediate, indole-3-acetamide, as well as salicylic acid with its root exudates. These compounds could be shown for the first time in exudates as well as in soil of a natural ectomycorrhizospheric habitat. The effects of phytohormones present in the mycorrhizosphere on hyphal branching of T. vaccinum were assessed. Salicylic and abscisic acid changed hyphal branching in a concentration-dependent manner. Since extensive branching is important for mycorrhiza establishment, a well-balanced level of mycorrhizospheric phytohormones is necessary. The regulation thus can be expected to contribute to an interkingdom language.

Redesigning the Molecular Choreography to Prevent Hydroxylation in Germacradien-11-ol Synthase Catalysis

Natural sesquiterpene synthases have evolved to make complex terpenoids by quenching reactive carbocations either by proton transfer or by hydroxylation (water capture), depending on their active site. Germacradien-11-ol synthase (Gd11olS) from Streptomyces coelicolor catalyzes the cyclization of farnesyl diphosphate (FDP) into the hydroxylated sesquiterpene germacradien-11-ol. Here, we combine experiment and simulation to guide the redesign of its active site pocket to avoid hydroxylation of the product. Molecular dynamics simulations indicate two regions between which water molecules can flow that are responsible for hydroxylation. Point mutations of selected residues result in variants that predominantly form a complex nonhydroxylated product, which we identify as isolepidozene. Our results indicate how these mutations subtly change the molecular choreography in the Gd11olS active site and thereby pave the way for the engineering of terpene synthases to make complex terpenoid products.

Effects of elevated nitrogen on the growth and geosmin productivity of Dolichospermum smithii

Geosmin is one of the most common earthy-musty odor compounds, which is mainly produced by cyanobacteria in surface water. Nitrogen (N) is an important factor affecting the growth of cyanobacteria and its secondary metabolites production due to the eutrophication. In this study, we compared the effects of elevated N on the growth and geosmin productivity of Dolichospermum smithii NIES-824 (synonym Anabaena smithii NIES-824), aiming to better understand the mechanisms involved and give an important and fundamental knowledge to solve off-flavor problem. Results show that elevated N concentration promoted more chlorophyll a (Chl-a) production, whereas the geosmin synthesis decreased, revealing a possible competitive correlation between the Chl-a concentration and geosmin production of D. smithii NIES-824. The majority of geosmin (> 90%) was retained intracellularly during the 28 days of cultivation. The qRT-PCR analysis demonstrates that the expression level of the geosmin synthase gene (geoA) was constitutive and decreased at the higher N concentration during the exponential growth phase of cyanobacterial cells. Furthermore, the decrease of geoA expression during the decline phase suggested that geoA transcription was closely related to cell activity and isoprenoid productivity.

Immunomodulatory Constituents of Conocephalum conicum (Snake Liverwort) and the Relationship of Isolepidozenes to Germacranes and Humulanes

Structural elucidation of three new sesquiterpenoids, namely, (1Z,4E)-lepidoza-1(10),4-dien-14-ol (1), rel-(1(10)Z,4S,5E,7R)-germacra-1(10),6 diene-11,14-diol (2), and rel-(1(10)Z,4S,5E,7R)-humula-1(10),5-diene-7,14-diol (3), isolated from the liverwort Conocephalum conicum, was accomplished by a combination of extensive NMR experiments, ¹H NMR simulation, and other means. Additionally, the change of the identity of bicyclogermacren-14-al, previously reported as a C. conicum constituent, to isolepidozen-14-al is proposed. Compounds 2 and 3 appear to be related to 1 via hydration involving a shared intermediate, a substituted cyclopropylmethyl cation, formed by a highly regio- and stereoselective protonation of 1, followed by a stereospecific fission of the three-membered ring. In other words, an isolepidozene derivative might be a branchpoint to humulanes and germacranes; this transformation could be of, up to now, unknown, biosynthetic and/or synthetic relevance. Multivariate statistical analysis of the compositional data of C. conicum extract constituents was used to probe the hypothesized biochemical relations. The immunomodulatory effect of 1-3 and conocephalenol (4) was evaluated in an in vitro model on both nonstimulated and mitogen-stimulated rat splenocytes. The compounds displayed varying degrees of cytotoxicity to nonstimulated splenocytes, whereas 2 and 3 were found to exert immunosuppressive effects on concanavalin A-stimulated splenocytes while not being cytotoxic at the same concentrations.

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

Terpenoids are the largest and structurally most diverse class of natural products. They possess potent and specific biological activity in multiple assays and against diseases, including cancer and malaria as notable examples. Although the number of characterized terpenoid molecules is huge, our knowledge of how they are biosynthesized is limited, particularly when compared to the well-studied thiotemplate assembly lines. Bacteria have only recently been recognized as having the genetic potential to biosynthesize a large number of complex terpenoids, but our current ability to associate genetic potential with molecular structure is severely restricted. The canonical terpene biosynthetic pathway uses a single enzyme to form a cyclized hydrocarbon backbone followed by modifications with a suite of tailoring enzymes that can generate dozens of different products from a single backbone. This functional promiscuity of terpene biosynthetic pathways renders terpene biosynthesis susceptible to rational pathway engineering using the latest developments in the field of synthetic biology. These engineered pathways will not only facilitate the rational creation of both known and novel terpenoids, their development will deepen our understanding of a significant branch of biosynthesis. The biosynthetic insights gained will likely empower a greater degree of engineering proficiency for non-natural terpene biosynthetic pathways and pave the way towards the biotechnological production of high value terpenoids.

Phylogenomic analyses and distribution of terpene synthases among Streptomyces

Terpene synthases are widely distributed among microorganisms and have been mainly studied in members of the genus Streptomyces. However, little is known about the distribution and evolution of the genes for terpene synthases. Here, we performed whole-genome based phylogenetic analysis of Streptomyces species, and compared the distribution of terpene synthase genes among them. Overall, our study revealed that ten major types of terpene synthases are present within the genus Streptomyces, namely those for geosmin, 2-methylisoborneol, epi-isozizaene, 7-epi-α-eudesmol, epi-cubenol, caryolan-1-ol, cyclooctat-9-en-7-ol, isoafricanol, pentalenene and α-amorphene. The Streptomyces species divide in three phylogenetic groups based on their whole genomes for which the distribution of the ten terpene synthases was analysed. Geosmin synthases were the most widely distributed and were found to be evolutionary positively selected. Other terpene synthases were found to be specific for one of the three clades or a subclade within the genus Streptomyces. A phylogenetic analysis of the most widely distributed classes of Streptomyces terpene synthases in comparison to the phylogenomic analysis of this genus is discussed.

Identification of geosmin biosynthetic gene in geosmin-producing colonial cyanobacteria Coelosphaerium sp. and isolation of geosmin non-producing Coelosphaerium sp. from brackish Lake Shinji in Japan

Geosmin is an earthy-muddy smelling compound produced in aquatic ecosystems by microorganisms including cyanobacteria. An increase in geosmin levels affecting the local fishery occurred in May 2007 in Lake Shinji, Japan, and geosmin-producing colonial cyanobacterium, Coelosphaerium sp. G2, was isolated from a water sample from the lake and identified. Cyanobacteria Coelosphaerium sp. is commonly found in Lake Shinji; however, prior to 2007, earthy-muddy odors were not a frequent issue. Further, there was no information regarding the geosmin biosynthetic gene in colonial cyanobacteria. Here, the geosmin biosynthetic gene (geoA) in strain G2 was identified and its nucleotide sequence was determined. It was found that geoA had 79% and 78% identity with geoA from filamentous geosmin-producing cyanobacteria Fischerella sp. PCC 9431 and geoA2 from Phormidium sp. P2r, respectively. The deduced amino acid sequence of GeoA consisted of two domains that were annotated as terpene cyclase. In 2015, geosmin non-producing Coelosphaerium sp. S3C5 was isolated from Lake Shinji and identified by morphological and genetic analyses. There was no difference in morphology or nucleotide sequences of 16S rRNA and 16S-23S internal transcribed spacer (ITS) between geosmin-producing and non-producing strains, which are therefore closely related and can exist in Lake Shinji. Distinguishing the two strains by observation under a microscope and sequencing of 16S rRNA and 16S-23S ITS have proven difficult. Inconsistency between the appearance of Coelosphaerium cells and the detection of the odor in water samples could therefore be attributed to dominance by the geosmin-producing strain or the non-producing strain. The increase in earthy smell is assumed to be caused by an increase in the geosmin-producing strain in Lake Shinji. Genetic analysis of geoA in Coelosphaerium sp. and the relative abundances of geosmin-producing and non-producing Coelosphaerium strains in Lake Shinji can be used to mitigate the economic damages caused by geosmin. Development of a molecular method to monitor the geosmin-producing strain in water ecosystems is equally important to alleviate the earthy smell caused by this particular strain.

Retracted Article: Synthesis of deuterated isopentyl pyrophosphates for chemo-enzymatic labelling methods: GC-EI-MS based 1,2-hydride shift in epicedrol biosynthesis

A sesquiterpene epicedrol cyclase mechanism was elucidated based on the gas chromatography coupled to electron impact mass spectrometry fragmentation data of deuterated (²H) epicedrol analogues. The chemo-enzymatic method was applied for the specific synthesis of 8-position labelled farnesyl pyrophosphate and epicedrol. EI-MS fragmentation ions compared with non-labelled and isotopic mass shift fragments suggest that the ²H of C6 migrates to the C7 position during the cyclization mechanism.

The cyclisation mechanism of epicedrol cyclase elucidated based on GC-EI-MS fragmentation of specific deuterated (²H) epicedrol analogues. The chemo-enzymatic method was applied for the synthesis 8-position-²H-farnesyl pyrophosphate synthesis.

The complete genome sequence of Streptomyces albolongus YIM 101047, the producer of novel bafilomycins and odoriferous sesquiterpenoids

Streptomyces albolongus YIM 101047 produces novel bafilomycins and odoriferous sesquiterpenoids with cytotoxic and antimicrobial activities. Here, we report the complete genome sequence of S. albolongus YIM 101047, which consists of an 8,027,788bp linear chromosome. Forty-six putative biosynthetic gene clusters of secondary metabolites were found. The sesquiterpenoid gene cluster was on the left arm (0.09-0.10Mb), and the bafilomycin biosynthetic gene cluster was on the right arm (7.46-7.64Mb) of the chromosome. Twenty-two putative gene clusters with high or moderate similarity to important antibiotic biosynthetic gene clusters were found, including the antitumor agents bafilomycin, epothilone and hedamycin; the antibacterial/antifungal agents clavulanic acid, collismycin A, frontalamides, kanamycin, streptomycin and streptothricin; the protein phosphatase inhibitor RK-682; and the acute iron poisoning medication desferrioxamine B. The genome sequence reported here will enable us to study the biosynthetic mechanism of these important antibiotics and will facilitate the discovery of novel secondary metabolites with potential applications to human health.

Structural and Chemical Biology of Terpenoid Cyclases

The year 2017 marks the twentieth anniversary of terpenoid cyclase structural biology: a trio of terpenoid cyclase structures reported together in 1997 were the first to set the foundation for understanding the enzymes largely responsible for the exquisite chemodiversity of more than 80000 terpenoid natural products. Terpenoid cyclases catalyze the most complex chemical reactions in biology, in that more than half of the substrate carbon atoms undergo changes in bonding and hybridization during a single enzyme-catalyzed cyclization reaction. The past two decades have witnessed structural, functional, and computational studies illuminating the modes of substrate activation that initiate the cyclization cascade, the management and manipulation of high-energy carbocation intermediates that propagate the cyclization cascade, and the chemical strategies that terminate the cyclization cascade. The role of the terpenoid cyclase as a template for catalysis is paramount to its function, and protein engineering can be used to reprogram the cyclization cascade to generate alternative and commercially important products. Here, I review key advances in terpenoid cyclase structural and chemical biology, focusing mainly on terpenoid cyclases and related prenyltransferases for which X-ray crystal structures have informed and advanced our understanding of enzyme structure and function.

Geosmin as a source of the earthy-musty smell in fruits, vegetables and water: Origins, impact on foods and water, and review of the removing techniques

The earthy-musty smell produced by Streptomyces sp. is assigned to geosmin and is responsible for the major organoleptic defects found in drinking water, fruits and vegetables such as grapes, mushrooms, carrots, and beet. Geosmin is also found in juices and musts before fermentation and its presence has been associated with partial presence of Botrytis cinerea. It has a variable detection threshold depending on the matrix and the detection level ranges from 5 to 50 ng/L. On the sensory level, very few individuals are immune to geosmin and although the intensity of the defect caused by this molecule decreases rapidly in the nose, a bad taste is very persistent in the mouth. As the origin of geosmin is fungal, conventional control techniques used for geosmin prevention are limited to ventilation, improving the integrity of plants and use of storage temperatures around 1 °C in a humidity-controlled environment. However, it has been demonstrated that only the combination of different prophylactic and preventive measures provide a relatively sufficient efficacy. Therefore, prevention of factors favoring the formation of geosmin is still topical. Some chemical treatments showed relatively good results against Botrytis cinerea. However, there is a requirement that must be met, namely that only one chemical per family per year must be used. Moreover, a multi-year alternation of chemical families is a strong agronomic recommendation. Regarding Penicillium, no active material is 100% approved and it negative effects plants such as beet and grapes. Consequently, the importance of finding effective ways to fight against geosmin formation is still relevant. From analytical point of view, measurement of geosmin is mainly based on gas chromatography.

Multi-domain terpenoid cyclase architecture and prospects for proximity in bifunctional catalysis

Crystal structures of terpenoid cyclases reveal assemblies of three basic domains designated α, β, and γ. While the biosynthesis of cyclic monoterpenes (C₁₀) and sesquiterpenes (C₁₅) most often involves enzymes with α or αβ domain architecture, the biosynthesis of cyclic diterpenes (C₂₀), sesterterpenes (C₂₅), and triterpenes (C₃₀) can involve enzymes with α, αα, βγ, or αβγ domain architecture. Indeed, some enzymes of terpenoid biosynthesis are bifunctional, with distinct active sites that catalyze sequential reactions. Interestingly, some of these enzymes oligomerize to form dimers, tetramers, and hexamers. Not only can such assemblies enable enzyme regulation by allostery, but they can also provide a modest enhancement of terpenoid product flux through proximity channeling or cluster channeling. The mixing and matching of functional terpenoid cyclase domains through tertiary and/or quaternary structure may also comprise an evolutionary strategy for facile product diversification.

Bafilomycins and Odoriferous Sesquiterpenoids from Streptomyces albolongus Isolated from Elephas maximus Feces

From a fermentation broth of Streptomyces albolongus obtained from Elephas maximus feces, nine bafilomycins (1-9) and seven odoriferous sesquiterpenoids (10-16) were isolated. The structures of the new compounds, including three bafilomycins, 19-methoxybafilomycin C1 amide (1), 21-deoxybafilomycin A1 (2), and 21-deoxybafilomycin A2 (3), and two sesquiterpenoid degradation products, (1β,4β,4aβ,8aα)-4,8a-dimethyloctahydronaphthalene-1,4a(2H)-diol (10) and (1β,4β,4aβ,7α,8aα)-4,8a-dimethyloctahydronaphthalene-1,4a,7(2H)-triol (11), were elucidated by comprehensive spectroscopic data analysis. The cytotoxicity activity against four human cancer cell lines and antimicrobial activities against a panel of bacteria and fungi of all compounds isolated were evaluated. Compounds 1, 7, and 8 were cytotoxic, with IC50 values ranging from 0.54 to 5.02 μM. Compounds 2, 7, 8, and 10 showed strong antifungal activity against Candida parapsilosis, with MIC values of 3.13, 1.56, 1.56, and 3.13 μg/mL respectively.

Biochemistry and genetics of taste- and odor-producing cyanobacteria

Cyanobacteria are one of the principal sources of volatile organic compounds (VOCs) which cause offensive taste and odor (T&O) in drinking and recreational water, fish, shellfish and other seafood. Although non-toxic to humans, these T&O compounds severely undermine public trust in these commodities, resulting in substantial costs in treatment, and lost revenue to drinking water, aquaculture, food and beverage and tourist/hospitality industries. Mitigation and control have been hindered by the complexity of the communities and processes which produce and modify T&O events, making it difficult to source-track the major producer(s) and the factors governing VOC production and fate. Over the past decade, however, advances in bioinformatics, enzymology, and applied detection technologies have greatly enhanced our understanding of the pathways, the enzymes and the genetic coding for some of the most problematic VOCs produced by cyanobacteria. This has led to the development of tools for rapid and sensitive detection and monitoring for the VOC production at source, and provided the basis for further diagnostics of endogenous and exogenous controls. This review provides an overview of current knowledge of the major cyanobacterial VOCs, the producers, the biochemistry and the genetics and highlight the current applications and further research needs in this area.

Bacterial terpene cyclases

This review summarises the characterised bacterial terpene cyclases and their products and discusses the enzyme mechanisms.

Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with αα Domain Architecture That Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence

Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg(2+) for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with three Mg(2+) ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed on the basis of ∼36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low-resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis.

Community of environmental streptomyces related to geosmin development in Chinese liquors

Diverse Streptomyces species act as geosmin producers in the Chinese liquor-making process. In this paper, the ecology of these Streptomyces species was analyzed using denaturing gradient gel electrophoresis (DGGE) of amplified Actinobacteria -specified rDNA. The result showed that Streptomyces were widely distributed during Daqu incubation, and multiple processing, geographic, and climate factors can affect their distribution and diversity. The genes associated with geosmin production were characterized in four geosmin-producing Streptomyces strains, all of which were isolated from geosmin-contaminated Daqu. On the basis of this information, a real-time PCR method was developed, enabling the detection of traces of Streptomyces in complex solid-state matrices. The primer was targeted at the gene coding for geosmin synthase (geoA). The real-time PCR method was found to be specific for geosmin-producing Streptomyces and did not show any cross-reactivity with geosmin-negative isolates, which are frequently present in the Chinese liquor-brewing process. Quantification of geoA in the Chinese liquor-making process could permit the monitoring of the level of geosmin producers prior to the occurrence of geosmin production. Comparison of the qPCR results based on the gene encoding geosmin synthase and Actinobacteria-specified rDNA showed that about 1-10% of the Actinobacteria carry the geosmin synthesis gene.

Identification and characterization of xiamycin A and oxiamycin gene cluster reveals an oxidative cyclization strategy tailoring indolosesquiterpene biosynthesis

Xiamycin A (XMA) and oxiamycin (OXM) are bacterial indolosesquiterpenes featuring rare pentacyclic ring systems and are isolated from a marine-derived Streptomyces sp. SCSIO 02999. The putative biosynthetic gene cluster for XMA/OXM was identified by a partial genome sequencing approach. Eighteen genes were proposed to be involved in XMA/OXM biosynthesis, including five genes for terpene synthesis via a non-mevalonate pathway, eight genes encoding oxidoreductases, and five genes for regulation and resistance. Targeted disruptions of 13 genes within the xia gene cluster were carried out to probe their encoded functions in XMA/OXM biosynthesis. The disruption of xiaK, encoding an aromatic ring hydroxylase, led to a mutant producing indosespene and a minor amount of XMA. Feeding of indosespene to XMA/OXM nonproducing mutants revealed indosespene as a common precursor for XMA/OXM biosynthesis. Most notably, the flavin dependent oxygenase XiaI was biochemically characterized in vitro to convert indosespene to XMA, revealing an unusual oxidative cyclization strategy tailoring indolosesquiterpene biosynthesis.

Structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor and implications for the mechanism of isoprenoid modification

Geranyl diphosphate C-methyltransferase (GPPMT) from Streptomyces coelicolor A3(2) is the first methyltransferase discovered that modifies an acyclic isoprenoid diphosphate, geranyl diphosphate (GPP), to yield a noncanonical acyclic allylic diphosphate product, 2-methylgeranyl diphosphate, which serves as the substrate for a subsequent cyclization reaction catalyzed by a terpenoid cyclase, methylisoborneol synthase. Here, we report the crystal structures of GPPMT in complex with GPP or the substrate analogue geranyl S-thiolodiphosphate (GSPP) along with S-adenosyl-L-homocysteine in the cofactor binding site, resulting from in situ demethylation of S-adenosyl-L-methionine, at 2.05 or 1.82 Å resolution, respectively. These structures suggest that both GPP and GSPP can undergo catalytic methylation in crystalline GPPMT, followed by dissociation of the isoprenoid product. S-Adenosyl-L-homocysteine remains bound in the active site, however, and does not exchange with a fresh molecule of cofactor S-adenosyl-L-methionine. These structures provide important clues about the molecular mechanism of the reaction, especially with regard to the face of the 2,3 double bond of GPP that is methylated as well as the stabilization of the resulting carbocation intermediate through cation-π interactions.

Exploration and mining of the bacterial terpenome

Tens of thousands of terpenoids are present in both terrestrial and marine plants, as well as fungi. In the last 5-10 years, however, it has become evident that terpenes are also produced by numerous bacteria, especially soil-dwelling Gram-positive organisms such as Streptomyces and other Actinomycetes. Although some microbial terpenes, such as geosmin, the degraded sesquiterpene responsible for the smell of moist soil, the characteristic odor of the earth itself, have been known for over 100 years, few terpenoids have been identified by classical structure- or activity-guided screening of bacterial culture extracts. In fact, the majority of cyclic terpenes from bacterial species have only recently been uncovered by the newly developed techniques of "genome mining". In this new paradigm for biochemical discovery, bacterial genome sequences are first analyzed with powerful bioinformatic tools, such as the BLASTP program or Profile Hidden Markov models, to screen for and identify conserved protein sequences harboring a characteristic set of universally conserved functional domains typical of all terpene synthases. Of particular importance is the presence of variants of two universally conserved domains, the aspartate-rich DDXX(D/E) motif and the NSE/DTE triad, (N/D)DXX(S/T)XX(K/R)(D/E). Both domains have been implicated in the binding of the essential divalent cation, typically Mg(2+), that is required for cyclization of the universal acyclic terpene precursors, such as farnesyl and geranyl diphosphate. The low level of overall sequence similarity among terpene synthases, however, has so far precluded any simple correlation of protein sequence with the structure of the cyclized terpene product. The actual biochemical function of a cryptic bacterial (or indeed any) terpene synthase must therefore be determined by direct experiment. Two common approaches are (i) incubation of the expressed recombinant protein with acyclic allylic diphosphate substrates and identification of the resultant terpene hydrocarbon or alcohol and (ii) in vivo expression in engineered bacterial hosts that can support the production of terpene metabolites. One of the most attractive features of the coordinated application of genome mining and biochemical characterization is that the discovery of natural products is directly coupled to the simultaneous discovery and exploitation of the responsible biosynthetic genes and enzymes. Bacterial genome mining has proved highly rewarding scientifically, already uncovering more than a dozen newly identified cyclic terpenes (many of them unique to bacteria), as well as several novel cyclization mechanisms. Moreover, bioinformatic analysis has identified more than 120 presumptive genes for bacterial terpene synthases that are now ripe for exploration. In this Account, we review a particularly rich vein we have mined in the genomes of two model Actinomycetes, Streptomyces coelicolor and Streptomyces avermitilis, from which the entire set of terpenoid biosynthetic genes and pathways have now been elucidated. In addition, studies of terpenoid biosynthetic gene clusters have revealed a wealth of previously unknown oxidative enzymes, including cytochromes P450, non-heme iron-dependent dioxygenases, and flavin monooxygenases. We have shown that these enzymes catalyze a variety of unusual biochemical reactions, including two-step ketonization of methylene groups, desaturation-epoxidation of secondary methyl groups, and pathway-specific Baeyer-Villiger oxidations of cyclic ketones.

Diversity and analysis of bacterial terpene synthases

Terpenoid compounds are generally considered to be plant or fungal metabolites, although a small number of odorous terpenoid metabolites of bacterial origin have been known for many years. Recently, extensive bacterial genome sequencing and bioinformatic analysis of deduced bacterial proteins using a profile hidden Markov model have revealed more than a hundred distinct predicted terpene synthase genes. Although some of these synthase genes might be silent in the parent microorganisms under normal laboratory culture conditions, the controlled overexpression of these genes in a versatile heterologous host has made it possible to identify the biochemical function of cryptic genes and isolate new terpenoid metabolites.

Terpenoids are widespread in actinomycetes: a correlation of secondary metabolism and genome data

The genomes of all bacteria with publicly available sequenced genomes have been screened for the presence of sesquiterpene cyclase homologues, resulting in the identification of 55 putative geosmin synthases, 23 homologues of 2-methylisoborneol synthases, and 98 other sesquiterpene cyclase homologues. Most of these enzymes by far were found in actinomycetes. The terpenoid volatiles from 35 strains, including 31 actinomycetes and four strains from other taxa, were collected by using a closed-loop stripping apparatus and identified by GC-MS. All of these bacteria apart from one strain encode sesquiterpene cyclase homologues in their genomes. The identified volatile terpenoids were grouped according to structural similarities and their biosynthetic relationship, and the results of these analyses were correlated to the available genome information, resulting in valuable new insights into bacterial terpene biosynthesis.

[Advances on actinomycetic terpenoid biosynthesis]

Terpenoids are the most diverse class of natural products. Recently, a series of terpenoids with novel structures have been isolated from actinomyces. Their biosynthetic gene clusters have been identified and characterized either by direct cloning or genomic mining, which promoted investigations of their biosynthetic pathways, as well as the key enzymatic mechanisms. This paper provides a brief overview of the major research published in the last five years.

Biosynthesis of 2-methylisoborneol in cyanobacteria

The production of odiferous metabolites, such as 2-methlyisoborneol (MIB), is a major concern for water utilities worldwide. Although MIB has no known biological function, the presence of the earthy/musty taste and odor attributed to this compound result in the reporting of numerous complaints by consumers, which undermines water utility performance and the safe and adequate provision of potable waters. Cyanobacteria are the major producers of MIB in natural waters, by mechanisms that have heretofore remained largely unstudied. To investigate the fundamental biological mechanism of MIB biosynthesis in cyanobacteria, the genome of a MIB-producing Pseudanabaena limnetica was sequenced using Next Generation Sequencing, and the recombinant proteins derived from the putative MIB biosynthetic genes were biochemically characterized. We demonstrate that the biosynthesis of MIB in cyanobacteria is a result of 2 key reactions: 1) a S-adenosylmethionine-dependent methylation of the monoterpene precursor geranyl diphosphate (GPP) to 2-methyl-GPP catalyzed by geranyl diphosphate 2-methyltransferase (GPPMT) and 2) further cyclization of 2-methyl-GPP to MIB catalyzed by MIB synthase (MIBS) as part of a MIB operon. Based on a comparison of the component MIB biosynthetic genes in actinomycetes and cyanobacterial organisms, we hypothesize that there have been multiple rearrangements of the genes in this operon.