Structure of isoprene synthase illuminates the chemical mechanism of teragram atmospheric carbon emission

Enhancing isoprene production by supplementing mevalonate pathway expressed in E. coli with immobilized enzymes

Isoprene is an important component in rubber production, which can be produced using the E. coli mevalonic acid (MVA) pathway, and this method has the advantage of green environmental protection and sustainable. However, due to the excessive accumulation of intermediates, the growth of cells was inhibited and the enzyme activity decreased gradually, so it was difficult to increase the yield of isoprene. The immobilized enzyme has the characteristics of high stability and strong reusability, so in this study, the immobilized enzyme was added to the fermentation process of isoprene production by mevalonate metabolizing bacteria (PT-P), to explore the effect on isoprene synthesis. Under the optimum conditions, compared with PT-P fermentation alone, the enzyme catalyzes the conversion of MVA with an efficiency of up to 50.86%, and the yield of isoprene increased by about 30%, reaching 234.47 mg/L.

Structure and Function of Sabinene Synthase, a Monoterpene Cyclase That Generates a Highly Strained [3.1.0] Bicyclic Product

Sabinene is a plant natural product with a distinctive strained [3.1.0] bicyclic ring system that is used commercially as a spicy and pine-like fragrance with citrus undertones. This unusual monoterpene has also been studied as an antifungal and anti-inflammatory agent as well as a next-generation biofuel. In order to understand the molecular determinants of [3.1.0] bicyclic ring formation in sabinene biosynthesis, we now report three X-ray crystal structures of sabinene synthase from Western red cedar, Thuja plicata (TpSS), with open and partially closed active site conformations at 2.21-2.72 Å resolution. We additionally report the complete biochemical characterization of sabinene synthase, including steady-state kinetics, active site mutagenesis, and product array profiling. The catalytic metal ion requirement is unexpectedly broad for a class I terpene cyclase: optimal catalytic activity was measured using Mn2+ or Co2+, with more modest activity observed using Mg2+ or Ni2+. Kinetic parameters were determined for both full-length TpSS and a deletion variant lacking the putative N-terminal plastidial targeting sequence, designated ΔTpSS. Monoterpene product profiles for both indicated similar product arrays independent of the catalytic metal ion used, with sabinene comprising nearly 90% of the total products generated. Site-directed mutagenesis was utilized to probe the function of active site residues, and several mutants yielded altered product arrays. Most notably, the G458A substitution converted ΔTpSS into a high-activity α-pinene synthase. α-Pinene contains a bicyclic [3.1.1] ring system; structural and mechanistic analyses suggest a molecular rationale for the reprogrammed transannulation reaction, leading to the alternative bicyclic product.

Expanding the structural diversity of terpenes by synthetic biology approaches

Terpenoids display chemical and structural diversities as well as important biological activities. Despite their extreme variability, the range of these structures is limited by the scope of natural products that canonically derive from interconvertible five-carbon (C5) isoprene units. New approaches have recently been developed to expand their structural diversity. This review systematically explores the combinatorial biosynthesis of noncanonical building blocks via the coexpression of the canonical mevalonate (MVA) pathway and C-methyltransferases (C-MTs), or by using the lepidopteran mevalonate (LMVA) pathway. Unnatural terpenoids can be created from farnesyl diphosphate (FPP) analogs by chemobiological synthesis and terpene cyclopropanation by artificial metalloenzymes (ArMs). Advanced technologies to accelerate terpene biosynthesis are discussed. This review provides a valuable reference for increasing the diversity of valuable terpenoids and their derivatives, as well as for expanding their potential applications.

Optimization of IspSib stability through directed evolution to improve isoprene production

Enzyme stability is often a limiting factor in the microbial production of high-value-added chemicals and commercial enzymes. A previous study by our research group revealed that the unstable isoprene synthase from Ipomoea batatas (IspSib) critically limits isoprene production in engineered Escherichia coli. Directed evolution was, therefore, performed in the present study to improve the thermostability of IspSib. First, a tripartite protein folding system designated as lac'-IspSib-'lac, which could couple the stability of IspSib to antibiotic ampicillin resistance, was successfully constructed for the high-throughput screening of variants. Directed evolution of IspSib was then performed through two rounds of random mutation and site-saturation mutation, which produced three variants with higher stability: IspSibN397V A476V, IspSibN397V A476T, and IspSibN397V A476C. The subsequent in vitro thermostability test confirmed the increased protein stability. The melting temperatures of the screened variants IspSibN397V A476V, IspSibN397V A476T, and IspSibN397V A476C were 45.1 ± 0.9°C, 46.1 ± 0.7°C, and 47.2 ± 0.3°C, respectively, each of which was higher than the melting temperature of wild-type IspSib (41.5 ± 0.4°C). The production of isoprene at the shake-flask fermentation level was increased by 1.94-folds, to 1,335 mg/L, when using IspSibN397V A476T. These findings provide insights into the optimization of the thermostability of terpene synthases, which are key enzymes for isoprenoid production in engineered microorganisms. In addition, the present study would serve as a successful example of improving enzyme stability without requiring detailed structural information or catalytic reaction mechanisms.IMPORTANCEThe poor thermostability of IspSib critically limits isoprene production in engineered Escherichia coli. A tripartite protein folding system designated as lac'-IspSib-'lac, which could couple the stability of IspSib to antibiotic ampicillin resistance, was successfully constructed for the first time. In order to improve the enzyme stability of IspSib, the directed evolution of IspSib was performed through error-PCR, and high-throughput screening was realized using the lac'-IspSib-'lac system. Three positive variants with increased thermostability were obtained. The thermostability test and the melting temperature analysis confirmed the increased stability of the enzyme. The production of isoprene was increased by 1.94-folds, to 1,335 mg/L, using IspSibN397V A476T. The directed evolution process reported here is also applicable to other terpene synthases key to isoprenoid production.

Molecular characterization of a moss isoprene synthase provides insight into its evolution

This is the first report on the molecular characterization of isoprene synthase (ISPS) from the moss Calohypnum plumiforme. After isoprene emission from C. plumiforme was confirmed, the cDNA encoding C. plumiforme ISPS (CpISPS) was narrowed down using a genome database associated with protein structure prediction, and a CpISPS gene was identified. The recombinant CpISPS, produced in Escherichia coli, converted dimethylallyl diphosphate to isoprene. Phylogenetic analysis indicated similarity between the amino acid sequences of CpISPS and moss diterpene cyclases (DTCs) but not ISPSs of higher plants, implying that CpISPS is derived from moss DTCs and is evolutionarily unrelated to canonical ISPSs of higher plants. CpISPS is a novel class I cyclase of the terpene synthase-c subfamily harboring αβ domains. This study will help further study of isoprene biosynthesis and the physiological functions of isoprene in mosses.

Molecular characteristics of isoprene synthase and its control effects on isoprene emissions from tropical trees

The isoprene emission rate from plants is simulated by a function of light intensity and leaf temperature, and the G-93 formula is the most extensively applied algorithm for this purpose. Isoprene is biosynthesized by the enzyme isoprene synthase (IspS), and instantly emitted from the leaf. Enzyme kinetics of IspS and substrate availability are important factors involved in the short-term leaf-level control of isoprene emissions. It is thus assumed that the parameters of G-93 may correlate with the kinetics of IspSs, however, at present there is no data available on the relationship between these two parameters. In this investigation, six IspS genes from tropical trees were cloned, their properties characterized, and the relationship between the enzyme kinetics of IspSs and the parameters of G-93 examined. There was a negative correlation between the enzyme kinetics of IspS K_m and parameter C_T1 of G93, which is used to define the temperature dependency of isoprene emissions. However, performance constant of IspS (k_cat/K_m) only showed slight positive correlation with C_T1.suggesting that the enzyme kinetics of IspS has limited significance in controlling the temperature response of isoprene emissions. The molecular structure of IspS was further elucidated using a molecular dynamics simulation with a focus on the active site in the 6 α-helices bundle. The simulation of the enzyme-substrate complex of IspS from B. variegata predicted a new metal binding domain in helix F (E383) and catalytic motif FXRDRLXE in the A-C loop that could involve the deprotonation of dimethylallyl diphosphate (DMADP) to form a carbocation. Notably, after the binding of a metal ion and DMADP, the active-site closure mechanism was found to involve conformational alterations in the helix H-α1 and transition from a loose to tight enclosure of the 6 α-helices bundles to tune the active pocket size. The characteristics identified for the IspSs from tropical trees could help to explain regional isoprene emissions in tropical areas.

Role of regulatory pathways and multi-omics approaches for carbon capture and mitigation in cyanobacteria

Cyanobacteria are known for their metabolic potential and carbon capture and sequestration capabilities. These cyanobacteria are not only an effective source for carbon minimization and resource mobilization into value-added products for biotechnological gains. The present review focuses on the detailed description of carbon capture mechanisms exerted by the various cyanobacterial strains, the role of important regulatory pathways, and their subsequent genes responsible for such mechanisms. Moreover, this review will also describe effectual mechanisms of central carbon metabolism like isoprene synthesis, ethylene production, MEP pathway, and the role of Glyoxylate shunt in the carbon sequestration mechanisms. This review also describes some interesting facets of using carbon assimilation mechanisms for valuable bio-products. The role of regulatory pathways and multi-omics approaches in cyanobacteria will not only be crucial towards improving carbon utilization but also will give new insights into utilizing cyanobacterial bioresource for carbon neutrality.

Microbial (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate reductase (IspH) and its biotechnological potential: A mini review

(E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) reductase (IspH) is a [4Fe-4S] cluster-containing enzyme, involved in isoprenoid biosynthesis as the final enzyme of the methylerythritol phosphate (MEP) pathway found in many bacteria and malaria parasites. In recent years, many studies have revealed that isoprenoid compounds are an alternative to petroleum-derived fuels. Thus, ecofriendly methods harnessing the methylerythritol phosphate pathway in microbes to synthesize isoprenoid compounds and IspH itself have received notable attention from researchers. In addition to its applications in the field of biosynthesis, IspH is considered to be an attractive drug target for infectious diseases such as malaria and tuberculosis due to its survivability in most pathogenic bacterium and its absence in humans. In this mini-review, we summarize previous reports that have systematically illuminated the fundamental and structural properties, substrate binding and catalysis, proposed catalytic mechanism, and novel catalytic activities of IspH. Potential bioengineering and biotechnological applications of IspH are also discussed.

Non-enzymatic formation of isoprene and 2-methyl-3-buten-2-ol (2-MBO) by manganese

It has been suggested that isoprene synthesis by isoprene synthase (IspS) proceeds via a substrate-assisted mechanism. The authors observed a non-enzymatic isoprene formation by Mn²⁺, which represents the basis of IspS enzyme reaction. Because IspS and many other terpene synthases require Mn²⁺ metal ions as cofactor, this study characterized the formation reaction for the first time. Metal ions including Mn²⁺ non-enzymatically produced both isoprene and 2-methyl-3-buten-2-ol (2-MBO) from dimethylallyl pyrophosphate (DMADP). Isoprene formation was most enhanced by Fe²⁺ and, to a lesser extent, by Mn²⁺ or Cu²⁺. Ni²⁺, Co²⁺, Mg²⁺, and Ba²⁺ exhibited a low activity to generate both isoprene and 2-MBO. The proportion of isoprene and 2-MBO varied with the Mn²⁺ concentration: isoprene predominated over 2-MBO at a higher Mn²⁺ concentration. Similarly, isoprene formation by Mn²⁺ increased exponentially as temperature increased with predominance of isoprene over 2-MBO at higher temperature. Both isoprene and 2-MBO formation was enhanced by acidic and neutral pH compared to alkaline conditions. Molecular dynamic simulation of DMADP suggested that the formation reaction is initiated by deprotonation of hydrogen on allyl terminal carbon by phosphate oxygen and generates carbocation and allyl anion intermediates. This is followed by quenching to produce isoprene or by hydroxyl addition to form 2-MBO. Thus, this study provided an insight into reaction mechanism of isoprene and 2-MBO biosynthesis and highlighted some parts of isoprene emission from terrestrial plants, which could be formed by non-enzymatic mechanism.

Integrated Four Comparative-Omics Reveals the Mechanism of the Terpenoid Biosynthesis in Two Different Overwintering Cryptomeria fortunei Phenotypes

Chinese cedar (Cryptomeria fortunei) is a tree species with important ornamental, medicinal, and economic value. Terpenoids extracted from the essential oil of C. fortunei needles have been considered valuable ingredients in the pharmaceutical and cosmetic industries. However, the possible gene regulation mechanisms that limit terpenoid biosynthesis in this genus are poorly understood. Here, we adopted integrated metabolome analysis, transcriptome, small-RNA (sRNA), and degradome sequencing to analyze the differences in terpenoid regulatory mechanisms in two different overwintering C. fortunei phenotypes (wild-type and an evergreen mutant). A total of 1447/6219 differentially synthesized metabolites (DSMs)/unigenes (DEGs) were detected through metabolome/transcriptome analyses, and these DSMs/DEGs were significantly enriched in flavonoid and diterpenoid biosynthesis pathways. In C. fortunei needles, 587 microRNAs (miRNAs), including 67 differentially expressed miRNAs (DERs), were detected. Among them, 8346 targets of 571 miRNAs were predicted using degradome data, and a 72-miRNA-target regulatory network involved in the metabolism of terpenoids and polyketides was constructed. Forty-one targets were further confirmed to be involved in terpenoid backbone and diterpenoid biosynthesis, and target analyses revealed that two miRNAs (i.e., aly-miR168a-5p and aof-miR396a) may be related to the different phenotypes and to differential regulation of diterpenoid biosynthesis. Overall, these results reveal that C. fortunei plants with the evergreen mutation maintain high terpenoid levels in winter through miRNA-target regulation, which provides a valuable resource for essential oil-related bioengineering research.

CO2 -responsiveness of leaf isoprene emission: Why do species differ?

Leaf isoprene emission rate, I, decreases with increasing atmospheric CO₂ concentration with major implications for global change. There is a significant interspecific variability in [CO₂ ]-responsiveness of I, but the extent of this variation is unknown and its reasons are not understood. We hypothesized that the magnitude of emission reduction reflects the size and changeability of precursor pools responsible for isoprene emission (dimethylallyl diphosphate, DMADP and 2-methyl-erythritol 2,4-cyclodiphosphate, MEcDP). Changes in I and intermediate pool sizes upon increase of [CO₂ ] from 400 to 1500 μmol/mol were studied in nine woody species spanning boreal to tropical ecosystems. I varied 10-fold, total substrate pool size 37-fold and the ratio of DMADP/MEcDP pool sizes 57-fold. At higher [CO₂ ], I was reduced on average by 65%, but [CO₂ ]-responsiveness varied an order of magnitude across species. The increase in [CO₂ ] resulted in concomitant reductions in both substrate pools. The variation in [CO₂ ]-responsiveness across species scaled with the reduction in pool sizes, the substrate pool size supported and the share of DMADP in total substrate pool. This study highlights a major interspecific variation in [CO₂ ]-responsiveness of isoprene emission and conclusively links this variation to interspecific variability in [CO₂ ] effects on substrate availability and intermediate pool size.

Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus

Linalool and nerolidol are terpene alcohols that occur naturally in many aromatic plants and are commonly used in food and cosmetic industries as flavors and fragrances. In plants, linalool and nerolidol are biosynthesized as a result of respective linalool synthase and nerolidol synthase, or a single linalool/nerolidol synthase. In our previous work, we have isolated a linalool/nerolidol synthase (designated as PamTps1) from a local herbal plant, Plectranthus amboinicus, and successfully demonstrated the production of linalool and nerolidol in an Escherichia coli system. In this work, the biochemical properties of PamTps1 were analyzed, and its 3D homology model with the docking positions of its substrates, geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15) in the active site were constructed. PamTps1 exhibited the highest enzymatic activity at an optimal pH and temperature of 6.5 and 30 °C, respectively, and in the presence of 20 mM magnesium as a cofactor. The Michaelis-Menten constant (Km) and catalytic efficiency (kcat/Km) values of 16.72 ± 1.32 µM and 9.57 × 10-3 µM-1 s-1, respectively, showed that PamTps1 had a higher binding affinity and specificity for GPP instead of FPP as expected for a monoterpene synthase. The PamTps1 exhibits feature of a class I terpene synthase fold that made up of α-helices architecture with N-terminal domain and catalytic C-terminal domain. Nine aromatic residues (W268, Y272, Y299, F371, Y378, Y379, F447, Y517 and Y523) outlined the hydrophobic walls of the active site cavity, whilst residues from the RRx8W motif, RxR motif, H-α1 and J-K loops formed the active site lid that shielded the highly reactive carbocationic intermediates from the solvents. The dual substrates use by PamTps1 was hypothesized to be possible due to the architecture and residues lining the catalytic site that can accommodate larger substrate (FPP) as demonstrated by the protein modelling and docking analysis. This model serves as a first glimpse into the structural insights of the PamTps1 catalytic active site as a multi-substrate linalool/nerolidol synthase.

Assessment of Isoprene as a Possible Biosignature Gas in Exoplanets with Anoxic Atmospheres

The search for possible biosignature gases in habitable exoplanet atmospheres is accelerating, although actual observations are likely years away. This work adds isoprene, C₅H₈, to the roster of biosignature gases. We found that isoprene geochemical formation is highly thermodynamically disfavored and has no known abiotic false positives. The isoprene production rate on Earth rivals that of methane (CH₄; ∼500 Tg/year). Unlike methane, on Earth isoprene is rapidly destroyed by oxygen-containing radicals. Although isoprene is predominantly produced by deciduous trees, isoprene production is ubiquitous to a diverse array of evolutionary distant organisms, from bacteria to plants and animals-few, if any, volatile secondary metabolites have a larger evolutionary reach. Although non-photochemical sinks of isoprene may exist, such as degradation of isoprene by life or other high deposition rates, destruction of isoprene in an anoxic atmosphere is mainly driven by photochemistry. Motivated by the concept that isoprene might accumulate in anoxic environments, we model the photochemistry and spectroscopic detection of isoprene in habitable temperature, rocky exoplanet anoxic atmospheres with a variety of atmosphere compositions under different host star ultraviolet fluxes. Limited by an assumed 10 ppm instrument noise floor, habitable atmosphere characterization when using James Webb Space Telescope (JWST) is only achievable with a transit signal similar or larger than that for a super-Earth-sized exoplanet transiting an M dwarf star with an H₂-dominated atmosphere. Unfortunately, isoprene cannot accumulate to detectable abundance without entering a run-away phase, which occurs at a very high production rate, ∼100 times the Earth's production rate. In this run-away scenario, isoprene will accumulate to >100 ppm, and its spectral features are detectable with ∼20 JWST transits. One caveat is that some isoprene spectral features are hard to distinguish from those of methane and also from other hydrocarbons containing the isoprene substructure. Despite these challenges, isoprene is worth adding to the menu of potential biosignature gases.

Bacterial terpenome

Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.

Evolution of isoprene emission in Arecaceae (palms)

Isoprene synthase (IspS) is the sole enzyme in plants responsible for the yearly emission in the atmosphere of thousands of tonnes of the natural hydrocarbon isoprene worldwide. Species of the monocotyledonous family Arecaceae (palms) are among the highest plant emitters, but to date no IspS gene from this family has been identified. Here, we screened with PTR-ToF-MS 18 genera of the Arecaceae for isoprene emission and found that the majority of the sampled species emits isoprene. Putative IspS genes from six different genera were sequenced and three of them were functionally characterized by heterologous overexpression in Arabidopsis thaliana, demonstrating that they encode functional IspS genes. Site-directed mutagenesis and expression in Arabidopsis demonstrated the functional relevance of a novel IspS diagnostic tetrad from Arecaceae, whose most variable amino acids could not preserve catalytic function when substituted by a putatively dicotyledonous-specific tetrad. In particular, mutation of threonine 479 likely impairs the open-closed transition of the enzyme by altering the network of hydrogen bonds between helices H1α, H, and I. These results shed new light on the evolution of IspS in monocots, suggesting that isoprene emission is an ancestral trait within the Arecaceae family. The identification of IspS from Arecaceae provides promising novel enzymes for the production of isoprene in heterologous systems and allows the screening and selection of commercially relevant palm varieties with lower environmental impact.

Validation of an insertion-engineered isoprene synthase as a strategy to functionalize terpene synthases

Terpene synthases are biotechnologically-relevant enzymes with a variety of applications. However, they are typically poor catalysts and have been difficult to engineer. Structurally, most terpene synthases share two conserved domains (α- and β-domains). Some also contain a third domain containing a second active site (γ-domain). Based on the three-domain architecture, we hypothesized that αβ terpene synthases could be engineered by insertion of a heterologous domain at the site of the γ-domain (an approach we term “Insertion-engineering terpene synthase”; Ie-TS). We demonstrate that by mimicking the domain architecture of αβγ terpene synthases, we can redesign isoprene synthase (ISPS), an αβ terpene synthase, while preserving enzymatic activity. Insertion of GFP or a SpyCatcher domain within ISPS introduced new functionality while maintaining or increasing catalytic turnover. This insertion-engineering approach establishes that the γ-domain position is accessible for incorporation of additional sequence features and enables the rational engineering of terpene synthases for biotechnology.

“Insertion-engineering” approach allows for the modification of αβ terpene synthases.

Functional Characterization of Terpene Synthases Accounting for the Volatilized-Terpene Heterogeneity in Lathyrus odoratus Cultivar Flowers

Lathyrus odoratus (sweet pea) is an ornamental plant with exceptional floral scent, previously used as an experimental organism in the early development of Mendelian genetics. However, its terpene synthases (TPSs), which act as metabolic gatekeepers in the biosynthesis of volatile terpenoids, remain to be characterized. Auto-Headspace Solid-phase Microextraction/Gas chromatography-mass spectrometry analysis of floral volatile terpene constituents from seven sweet pea cultivars identified α-bergamotene, linalool, (-)-α-cubebene, geraniol, β-caryophyllene and β-sesquiphellandrene as the dominant compounds. RNA sequencing was performed to profile the transcriptome of L. odoratus flowers. Bioinformatic analysis identified eight TPS genes (acronymed as LoTPS) that were successfully cloned, heterologously expressed and functionally analyzed. LoTPS4 and LoTPS7, belonging to the TPS-b clade, biochemically catalyzed the formation of monoterpenes and sesquiterpenes. LoTPS3 and LoTPS8, placed in the TPS-a clade, also generated monoterpenes and sesquiterpenes, while LoTPS12 belonging to the TPS-g clade showed linalool/nerolidol synthase activity. Notably, biochemical assays of the recombinant LoTPS proteins revealed their catalytic promiscuity, and the enzymatic products were basically consistent with major volatile compounds released from sweet pea flowers. The data from our study lay the foundation for the chemical ecology, molecular genetics and biotechnological improvement of sweet pea and other legumes (Fabaceae).

Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate

Terpene synthases (TS) are classified into two broad types, Class I and II, based on the chemical strategy for initial carbocation formation and motif sequences of the catalytic site. We have recently identified a new class of enzymes, Class IB, showing the acceptability of long (C₂₀-C₃₅) prenyl-diphosphates as substrates and no amino acid sequence homology with known TS. Conversion of long prenyl-diphosphates such as heptaprenyl-diphosphate (C₃₅) is unusual and has never been reported for Class I and II enzymes. Therefore, the characterization of Class IB enzymes is crucial to understand the reaction mechanism of the extensive terpene synthesis. Here, we report the crystal structure bound with a substrate surrogate and biochemical analysis of a Class IB TS, using the enzyme from Bacillus alcalophilus (BalTS). The structure analysis revealed that the diphosphate part of the substrate is located around the two characteristic Asp-rich motifs, and the hydrophobic tail is accommodated in a unique hydrophobic long tunnel, where the C₃₅ prenyl-diphosphate, the longest substrate of BalTS, can be accepted. Biochemical analyses of BalTS showed that the enzymatic property, such as Mg²⁺ dependency, is similar to those of Class I enzymes. In addition, a new cyclic terpene was identified from BalTS reaction products. Mutational analysis revealed that five of the six Asp residues in the Asp-rich motifs and two His residues are essential for the formation of the cyclic skeleton. These results provided a clue to consider the application of the unusual large terpene synthesis by Class IB enzymes.

The complete functional characterisation of the terpene synthase family in tomato

Analysis of the updated reference tomato genome found 34 full-length TPS genes and 18 TPS pseudogenes. Biochemical analysis has now identified the catalytic activities of all enzymes encoded by the 34 TPS genes: one isoprene synthase, 10 exclusively or predominantly monoterpene synthases, 17 sesquiterpene synthases and six diterpene synthases. Among the monoterpene and sesquiterpene and diterpene synthases, some use trans-prenyl diphosphates, some use cis-prenyl diphosphates and some use both. The isoprene synthase is cytosolic; six monoterpene synthases are plastidic, and four are cytosolic; the sesquiterpene synthases are almost all cytosolic, with the exception of one found in the mitochondria; and three diterpene synthases are found in the plastids, one in the cytosol and two in the mitochondria. New trans-prenyltransferases (TPTs) were characterised; together with previously characterised TPTs and cis-prenyltransferases (CPTs), tomato plants can make all cis and trans C₁₀ , C₁₅ and C₂₀ prenyl diphosphates. Every type of plant tissue examined expresses some TPS genes and some TPTs and CPTs. Phylogenetic comparison of the TPS genes from tomato and Arabidopsis shows expansions in each clade of the TPS gene family in each lineage (and inferred losses), accompanied by changes in subcellular localisations and substrate specificities.

Microbial metabolism of isoprene: a much-neglected climate-active gas

The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.

Environmental and physiological controls on diurnal and seasonal patterns of biogenic volatile organic compound emissions from five dominant woody species under field conditions

Biogenic volatile organic compounds (BVOCs) play essential roles in tropospheric chemistry, on both regional and global scales. The emissions of large quantities of species-specific BVOC depend not only on environmental (temperature, T; photosynthetically active radiation, PAR), but also physiological parameters (i.e. net photosynthetic rate, P_n; transpiration rate, T_r; stomatal conductance, g_s and intercellular CO₂ concentration, C_i). Here, isoprene, monoterpene and sesquiterpene emissions were determined from five dominant mature woody tree species in northern China, which are two evergreen conifers (Pinus tabuliformis and Platycladus orientalis) and three broad-leaved deciduous trees (Quercus variabilis, Populus tomentosa and Robinia pseudoacacia). A dynamic enclosure technique combined with GC-MS was used to sample BVOCs and analyse their fractional composition at daily and annual scales. The diurnal data showed that both isoprene and monoterpene emissions increased with increasing temperature, and reached their maximum emission rates in the peak of growing season for both coniferous and broad-leaved species. The emissions of individual compound within the monoterpenes and sesquiterpenes were statistically correlated with each other for all species. Furthermore, some oxygenated monoterpene emissions were highly correlated to sesquiterpenes in all tree species. Linking BVOC emissions to environmental and leaf physiological parameters exhibited that monoterpene emissions were linearly and positively correlated to the variation of T, PAR, P_n and T_r, while their relationship to g_s and C_i is more complex. Collectively, these findings provided important information for improving current model estimations in terms of the linkage between BVOC emissions and plant physiological traits. The data presented in this study can be used to update emission capacity used in models, as this is the first time of reporting BVOC emissions from five dominant species in this region. The whole-year measurement of leaf-level BVOCs can also advance our understanding of seasonal variation in BVOC emissions.

The production of isoprene from cellulose using recombinant Clostridium cellulolyticum strains expressing isoprene synthase

Isoprene is an important bulk chemical which is mostly derived from fossil fuels. It is used primarily for the production of synthetic rubber. Sustainable, biotechnology‐based alternatives for the production of isoprene rely on the fermentation of sugars from food and feed crops, creating an ethical dilemma due to the competition for agricultural land. This issue could be addressed by developing new approaches based on the production of isoprene from abundant renewable waste streams. Here, we describe a proof‐of‐principle approach for the production of isoprene from cellulosic biomass, the most abundant polymer on earth. We engineered the mesophilic prokaryote Clostridium cellulolyticum, which can degrade cellulosic biomass, to utilize the resulting glucose monomers as a feedstock for the production of isoprene. This was achieved by integrating the poplar gene encoding isoprene synthase. The presence of the enzyme was confirmed by targeted proteomics, and the accumulation of isoprene was confirmed by GC‐MS/MS. We have shown for the first time that engineered C. cellulolyticum can be used as a metabolic chassis for the sustainable production of isoprene.

Structure of Sesquisabinene Synthase 1, a Terpenoid Cyclase That Generates a Strained [3.1.0] Bridged-Bicyclic Product

The natural product sesquisabinene is a key component of the fragrant essential oil of the sandalwood tree, currently valued at $5,000/L. Sesquisabinene contains a highly strained [3.1.0] bicyclic ring system and is generated from farnesyl diphosphate in a reaction catalyzed by a class I terpenoid cyclase. To understand how the enzyme directs the formation of a strained hydrocarbon ring system, we now report the X-ray crystal structure of sesquisabinene synthase 1 (SQS1) from the Indian sandalwood tree ( Santalum album). Specifically, we report the structure of unliganded SQS1 at 1.90 Å resolution and the structure of its complex with three Mg²⁺ ions and the inhibitor ibandronate at 2.10 Å resolution. The bisphosphonate group of ibandronate coordinates to all three metal ions and makes hydrogen bond interactions with basic residues at the mouth of the active site. These interactions are similarly required for activation of the substrate diphosphate group to initiate catalysis, although partial occupancy binding of the Mg²⁺_B ion suggests that this structure represents the penultimate metal coordination complex just prior to substrate activation. The structure of the liganded enzyme enables a precise definition of the enclosed active site contour that serves as a template for the cyclization reaction. This contour is very product-like in shape and readily fits an extended conformation of sesquisabinene and its precursor, the homobisabolyl cation. Structural comparisons of SQS1 with epi-isozizaene synthase mutants that also generate sesquisabinene suggest that [3.1.0] ring formation is not dependent on the isoprenoid tail conformation of the homobisabolyl cation.

Enhanced Isoprene Production by Reconstruction of Metabolic Balance between Strengthened Precursor Supply and Improved Isoprene Synthase in Saccharomyces cerevisiae

Isoprene, as a versatile bulk chemical, has wide industrial applications. Here, we attempted to improve isoprene biosynthesis in Saccharomyces cerevisiae by simultaneous strengthening of precursor supply and conversion via a combination of pathway compartmentation and protein engineering. At first, a superior isoprene synthase mutant ISPSLN was created by saturation mutagenesis, leading to almost 4-fold improvement in isoprene production. Subsequent introduction of ISPSLN to strains with strengthened precursor supply in either cytoplasm or mitochondria implied an imperfect match between the synthesis and conversion of the isopentenyl pyrophosphate (IPP)/dimethylallyl diphosphate (DMAPP) pool. To reconstruct metabolic balance between the upstream and downstream flux, additional copies of diphosphomevalonate decarboxylase gene ( MVD1) and isopentenyl-diphosphate delta-isomerase gene ( IDI1) were introduced into the cytoplasmic and mitochondrial engineered strains. Finally, the diploid strain created by mating the above haploid strains produced 11.9 g/L of isoprene, the highest ever reported in eukaryotic cells.

Biochemical characterization of isoprene synthase from Ipomoea batatas

The bio-production process of isoprene, an essential chemical used in industry, is strongly limited by isoprene synthase. In our previous work, relatively high isoprene production was observed with isoprene synthase from Ipomoea batatas (IspS_ib). In this work the biochemical properties of IspS_ib were analyzed and compared with those of isoprene synthase from Populus alba (IspS_pa) and other species. Firstly, IspS_ib and IspS_pa were expressed, purified, and identified by SDS-PAGE and western blot analysis. Secondly, pH and temperature dependence of IspS_ib were performed and an optimum pH of 8.6 and an optimum temperature of 42 °C were resulted. Mg²⁺ with optimum concentration of 56 mM was proved to be needed for enzyme activation. In addition, in vivo and in vitro study of the thermostabilities of IspS_ib and IspS_pa were performed. The enzyme activity of IspS_ib and IspS_pa dropped very rapidly after incubation at 30 °C; almost 80% enzyme activity of IspS_ib was lost after 20 min of incubation. Moreover, the Michaelis-Menten constant was measured. IspS_ib showed a lower K_m, 0.2 mM, and a higher k_cat, 0.37 s^-1, as compared with IspS_pa. The high catalytic efficiency, which was reflected by the high k_cat/K_m ratio, indicates that IspS_ib is a good candidate for the bio-isoprene production, while its thermal instability remains as a challenge. Enzyme engineering efforts, such as direction evolution or semi-rational evolution, are planned for further research.

Metabolic engineering for the production of isoprene and isopentenol by Escherichia coli

The biotechnological production of isoprene and isopentenol has recently been studied. Isoprene, which is currently made mainly from petroleum, is an important platform chemical for synthesizing pesticides, medicines, oil additives, fragrances, and more and is especially important in the rubber production industry. Isopentenols, which have better combustion properties than well-known biofuels (ethanol), have recently received more attention. Supplies of petroleum, the conventional source of isoprene and isopentenols, are unsustainable, and chemical synthesis processes could cause serious environmental problems. As an alternative, the biosynthesis of isoprene and isopentenols in cell factories is more sustainable and environmentally friendly. With a number of advantages over other microorganisms, Escherichia coli is considered to be a powerful workhorse organism for producing these compounds. This review will highlight the recent advances in metabolic engineering for isoprene and isopentenol production, especially using E. coli cell factories.

Engineering isoprene synthesis in cyanobacteria

The renewable production of isoprene (Isp) hydrocarbons, to serve as fuel and synthetic chemistry feedstock, has attracted interest in the field recently. Isp (C₅ H₈ ) is naturally produced from sunlight, CO₂ and H₂ O photosynthetically in terrestrial plant chloroplasts via the terpenoid biosynthetic pathway and emitted in the atmosphere as a response to heat stress. Efforts to institute a high capacity continuous and renewable process have included heterologous expression of the Isp synthesis pathway in photosynthetic microorganisms. This review examines the premise and promise emanating from this relatively new research effort. Also examined are the metabolic engineering approaches applied in the quest of renewable Isp hydrocarbons production, the progress achieved so far, and barriers encountered along the way.

Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth

Isoprene (2-methyl-1,3-butadiene), the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, is highly reactive and can have diverse and often detrimental atmospheric effects, which impact on climate and health. Most isoprene is produced by terrestrial plants, but (micro)algal production is important in aquatic environments, and the relative bacterial contribution remains unknown. Soils are a sink for isoprene, and bacteria that can use isoprene as a carbon and energy source have been cultivated and also identified using cultivation-independent methods from soils, leaves and coastal/marine environments. Bacteria belonging to the Actinobacteria are most frequently isolated and identified, and Proteobacteria have also been shown to degrade isoprene. In the freshwater-sediment isolate, Rhodococcus strain AD45, initial oxidation of isoprene to 1,2-epoxy-isoprene is catalyzed by a multicomponent isoprene monooxygenase encoded by the genes isoABCDEF. The resultant epoxide is converted to a glutathione conjugate by a glutathione S-transferase encoded by isoI, and further degraded by enzymes encoded by isoGHJ. Genome sequence analysis of actinobacterial isolates belonging to the genera Rhodococcus, Mycobacterium and Gordonia has revealed that isoABCDEF and isoGHIJ are linked in an operon, either on a plasmid or the chromosome. In Rhodococcus strain AD45 both isoprene and epoxy-isoprene induce a high level of transcription of 22 contiguous genes, including isoABCDEF and isoGHIJ. Sequence analysis of the isoA gene, encoding the large subunit of the oxygenase component of isoprene monooxygenase, from isolates has facilitated the development of PCR primers that are proving valuable in investigating the ecology of uncultivated isoprene-degrading bacteria.

A novel DMAPP-responding genetic circuit sensor for high-throughput screening and evolving isoprene synthase

High-throughput screening is a popular tool for collating biological data which would otherwise require the use of excessive resources. In this study, an artificial genetic circuit sensor responding to dimethylallyl diphosphate (DMAPP) was constructed based on a modified L-arabinose operon for high-throughput screening and isoprene synthase (ispS) evolution in Escherichia coli (E. coli). As a first step, the DNA sequence of the L-arabinose ligand-binding domain (LBD) was replaced with an ispS gene to enable the AraC operon responding to DMAPP, which is the substrate of the IspS enzyme. Then, an enhanced GFP (eGFP) was also introduced as a reporter for pBAD promoter. The expression level of the reporter was monitored using either of the two tools: flow cytometer (FCM) and microplate reader. Sequentially, we observed that a high DMAPP concentration led to low eGFP fluorescence, and the overexpression of ispS gene, which consumes DMAPP, resulted in a high eGFP expression. These results demonstrated that the artificial genetic circuit sensor responded directly to the intracellular concentration of DMAPP, and the expression of IspS enzyme could be positively correlated to the expression level of eGFP. Finally, we identified two IspS mutants with different activities from an ispS gene library and further validated the screening method.

Evolution of catalytic microenvironment governs substrate and product diversity in trichodiene synthase and other terpene fold enzymes

Trichodiene synthase, a terpene fold enzyme catalyzes the first reaction of trichodermin biosynthesis that is an economically important secondary metabolite. Sequence search analysis revealed that the proteins containing terpene fold are present in bacteria, fungi and plants. Terpene fold protein from Selaginella moellendorffii, a lycophyte, appeared at the interface of the microbes and plants in the evolutionary scale. Amino acid residues present around the catalytic pocket determines the size of the substrate as well as product molecules. It has been observed that the overall molecular evolution of the catalytic pockets dictates the choice of substrates/products of the proteins. It was further observed that N-terminus of multi-domain terpene fold proteins may assist in the interactions with the pyrophosphate part of the substrates. The phylogenetic analysis of these proteins further revealed that the enzymes are clustered into groups based on the domains present additional to the catalytic domains. We have also observed inter-domain 'puckering forceps' type motions in the multi-domains using normal mode analysis which were further correlated with their functions. The evolutionary clustering of these proteins was also influenced by the presence/absence of cofactor interacting motifs. These results may be used to modify/enhance the functions of these enzymes using protein engineering methods.

In Planta Recapitulation of Isoprene Synthase Evolution from Ocimene Synthases

Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases. Site-directed mutagenesis demonstrated invivo the functional and evolutionary relevance of the residues considered diagnostic for IspS function. One of these positions was identified by saturating mutagenesis as a major determinant of substrate specificity in AdoIspS able to cause invivo a dramatic change in total volatile emission from hemi- to monoterpenes and supporting evolution of isoprene synthases from ocimene synthases. The mechanism responsible for IspS neofunctionalization by active site size modulation by a single amino acid mutation demonstrated in this study might be general, as the very same amino acidic position is implicated in the parallel evolution of different short-chain terpene synthases from both angiosperms and gymnosperms. Based on these results, we present a model reconciling in a unified conceptual framework the apparently contrasting patterns previously observed for isoprene synthase evolution in plants. These results indicate that parallel evolution may be driven by relatively simple biophysical constraints, and illustrate the intimate molecular evolutionary links between the structural and functional bases of traits with global relevance.

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.

Exploring the Influence of Domain Architecture on the Catalytic Function of Diterpene Synthases

Terpenoid synthases catalyze isoprenoid cyclization reactions underlying the generation of more than 80,000 natural products. Such dramatic chemodiversity belies the fact that these enzymes generally consist of only three domain folds designated as α, β, and γ. Catalysis by class I terpenoid synthases occurs exclusively in the α domain, which is found with α, αα, αβ, and αβγ domain architectures. Here, we explore the influence of domain architecture on catalysis by taxadiene synthase from Taxus brevifolia (TbTS, αβγ), fusicoccadiene synthase from Phomopsis amygdali (PaFS, (αα)₆), and ophiobolin F synthase from Aspergillus clavatus (AcOS, αα). We show that the cyclization fidelity and catalytic efficiency of the α domain of TbTS are severely compromised by deletion of the βγ domains; however, retention of the β domain preserves significant cyclization fidelity. In PaFS, we previously demonstrated that one α domain similarly influences catalysis by the other α domain [ Chen , M. , Chou , W. K. W. , Toyomasu , T. , Cane , D. E. , and Christianson , D. W. ( 2016 ) ACS Chem. Biol. 11 , 889 - 899 ]. Here, we show that the hexameric quaternary structure of PaFS enables cluster channeling. We also show that the α domains of PaFS and AcOS can be swapped so as to make functional chimeric αα synthases. Notably, both cyclization fidelity and catalytic efficiency are altered in all chimeric synthases. Twelve newly formed and uncharacterized C₂₀ diterpene products and three C₂₅ sesterterpene products are generated by these chimeras. Thus, engineered αβγ and αα terpenoid cyclases promise to generate chemodiversity in the greater family of terpenoid natural products.

Spectacular Oscillations in Plant Isoprene Emission under Transient Conditions Explain the Enigmatic CO2 Response

Plant isoprene emissions respond to light and temperature similarly to photosynthesis, but CO₂ dependencies of isoprene emission and photosynthesis are profoundly different, with photosynthesis increasing and isoprene emission decreasing with increasing CO₂ concentration due to reasons not yet understood. We studied isoprene emission, net assimilation rate, and chlorophyll fluorescence under different CO₂ and O₂ concentrations in the strong isoprene emitter hybrid aspen (Populus tremula × Populus tremuloides), and used rapid changes in ambient CO₂ or O₂ concentrations or light level to induce oscillations. As isoprene-emitting species support very high steady-state chloroplastic pool sizes of the primary isoprene substrate, dimethylallyl diphosphate (DMADP), which can mask the effects of oscillatory dynamics on isoprene emission, the size of the DMADP pool was experimentally reduced by either partial inhibition of isoprenoid synthesis pathway by fosmidomycin-feeding or by changes in ambient gas concentrations leading to DMADP pool depletion in intact leaves. In feedback-limited conditions observed at low O₂ and/or high CO₂ concentration under which the rate of photosynthesis is governed by the limited rate of ATP and NADPH formation due to low chloroplastic phosphate levels, oscillations in photosynthesis and isoprene emission were repeatedly induced by rapid environmental modifications in both partly fosmidomycin-inhibited leaves and in intact leaves with in vivo reduced DMADP pools. The oscillations in net assimilation rate and isoprene emission in feedback-inhibited leaves were in the same phase, and relative changes in the pools of photosynthetic metabolites and DMADP estimated by in vivo kinetic methods were directly proportional through all oscillations induced by different environmental perturbations. We conclude that the oscillations in isoprene emission provide direct experimental evidence demonstrating that the response of isoprene emission to changes in ambient gas concentrations is controlled by the chloroplastic reductant supply.

Multi-Substrate Terpene Synthases: Their Occurrence and Physiological Significance

Terpene synthases are responsible for synthesis of a large number of terpenes in plants using substrates provided by two distinct metabolic pathways, the mevalonate-dependent pathway that is located in cytosol and has been suggested to be responsible for synthesis of sesquiterpenes (C15), and 2-C-methyl-D-erythritol-4-phosphate pathway located in plastids and suggested to be responsible for the synthesis of hemi- (C5), mono- (C10), and diterpenes (C20). Recent advances in characterization of genes and enzymes responsible for substrate and end product biosynthesis as well as efforts in metabolic engineering have demonstrated existence of a number of multi-substrate terpene synthases. This review summarizes the progress in the characterization of such multi-substrate terpene synthases and suggests that the presence of multi-substrate use might have been significantly underestimated. Multi-substrate use could lead to important changes in terpene product profiles upon substrate profile changes under perturbation of metabolism in stressed plants as well as under certain developmental stages. We therefore argue that multi-substrate use can be significant under physiological conditions and can result in complicate modifications in terpene profiles.

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.

Two unexpected promiscuous activities of the iron-sulfur protein IspH in production of isoprene and isoamylene

Background

Bacillus species, possessing the methylerythritol phosphate (MEP) pathway for the synthesis of isoprenoid feedstock, are the highest producers of isoprene among bacteria; however, the enzyme responsible for isoprene synthesis has not been identified. The iron–sulfur protein IspH is the final enzyme of the MEP pathway and catalyses the reductive dehydration of (E)-4-hydroxy-3-methyl-2-butenyl diphosphate (HMBPP) to form isopentenyl diphosphate and dimethylallyl diphosphate (DMAPP). In this study, we demonstrated two unexpected promiscuous activities of IspH from alkaliphilic Bacillus sp. N16-5, which can produce high levels of isoprene.

Results

Bacillus sp. N16-5 IspH could catalyse the formation of isoprene from HMBPP and the conversion of DMAPP into a mixture of 2-methyl-2-butene and 3-methyl-1-butene. Both reactions require an electron transfer system, such as that used for HMBPP dehydration. Isoprene and isoamylene synthesis in Bacillus sp. N16-5 was investigated and the reaction system was reconstituted in vitro, including IspH, ferredoxin and ferredoxin-NADP⁺-reductase proteins and NADPH. The roles of specific IspH protein residues were also investigated by site-directed mutagenesis experiments; two variants (H131N and E133Q) were found to have lost the HMBPP reductase activity but could still catalyse the formation of isoprene. Overexpression of IspH H131N in Bacillus sp. N16-5 resulted in a twofold enhancement of isoprene production, and the yield of isoprene from the strain expressing E133Q was increased 300 % compared with the wild-type strain.

Conclusions

IspH from Bacillus sp. N16-5 is a promiscuous enzyme that can catalyse formation of isoprene and isoamylene. This enzyme, especially the H131N and E133Q variants, could be used for the production of isoprene from HMBPP.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0476-9) contains supplementary material, which is available to authorized users.

General base-general acid catalysis by terpenoid cyclases

Terpenoid cyclases catalyze the most complex reactions in biology, in that more than half of the substrate carbon atoms often undergo changes in bonding during the course of a multistep cyclization cascade that proceeds through multiple carbocation intermediates. Many cyclization mechanisms require stereospecific deprotonation and reprotonation steps, and most cyclization cascades are terminated by deprotonation to yield an olefin product. The first bacterial terpenoid cyclase to yield a crystal structure was pentalenene synthase from Streptomyces exfoliatus UC5319. This cyclase generates the hydrocarbon precursor of the pentalenolactone family of antibiotics. The structures of pentalenene synthase and other terpenoid cyclases reveal predominantly nonpolar active sites typically lacking amino acid side chains capable of serving general base-general acid functions. What chemical species, then, enables the Brønsted acid-base chemistry required in the catalytic mechanisms of these enzymes? The most likely candidate for such general base-general acid chemistry is the co-product inorganic pyrophosphate. Here, we briefly review biological and nonbiological systems in which phosphate and its derivatives serve general base and general acid functions in catalysis. These examples highlight the fact that the Brønsted acid-base activities of phosphate derivatives are comparable to the Brønsted acid-base activities of amino acid side chains.

Moenomycin Biosynthesis: Structure and Mechanism of Action of the Prenyltransferase MoeN5

The structure of MoeN5, a unique prenyltransferase involved in the biosynthesis of the antibiotic moenomycin, is reported. MoeN5 catalyzes the reaction of geranyl diphosphate (GPP) with the cis-farnesyl group in phosphoglycolipid 5 to form the (C25) moenocinyl-sidechain-containing lipid 7. GPP binds to an allylic site (S1) and aligns well with known S1 inhibitors. Alkyl glycosides, glycolipids, can bind to both S1 and a second site, S2. Long sidechains in S2 are "bent" and co-locate with the homoallylic substrate isopentenyl diphosphate in other prenyltransferases. These observations support a MoeN5 mechanism in which 5 binds to S2 with its C6-C11 group poised to attack C1 in GPP to form the moenocinyl sidechain, with the more distal regions of 5 aligning with the distal glucose in decyl maltoside. The results are of general interest because they provide the first structures of MoeN5 and a structural basis for its mechanism of action, results that will facilitate the design of new antibiotics.

Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase

We report the first X-ray structure of the unique "head-to-middle" monoterpene synthase, lavandulyl diphosphate synthase (LPPS). LPPS catalyzes the condensation of two molecules of dimethylallyl diphosphate (DMAPP) to form lavandulyl diphosphate, a precursor to the fragrance lavandulol. The structure is similar to that of the bacterial cis-prenyl synthase, undecaprenyl diphosphate synthase (UPPS), and contains an allylic site (S1) in which DMAPP ionizes and a second site (S2) which houses the DMAPP nucleophile. Both S-thiolo-dimethylallyl diphosphate and S-thiolo-isopentenyl diphosphate bind intact to S2, but are cleaved to (thio)diphosphate, in S1. His78 (Asn in UPPS) is essential for catalysis and is proposed to facilitate diphosphate release in S1, while the P1 phosphate in S2 abstracts a proton from the lavandulyl carbocation to form the LPP product. The results are of interest since they provide the first structure and structure-based mechanism of this unusual prenyl synthase.

Expression, crystallization and structure elucidation of γ-terpinene synthase from Thymus vulgaris

The biosynthesis of γ-terpinene, a precursor of the phenolic isomers thymol and carvacrol found in the essential oil from Thymus sp., is attributed to the activitiy of γ-terpinene synthase (TPS). Purified γ-terpinene synthase from T. vulgaris (TvTPS), the Thymus species that is the most widely spread and of the greatest economical importance, is able to catalyze the enzymatic conversion of geranyl diphosphate (GPP) to γ-terpinene. The crystal structure of recombinantly expressed and purified TvTPS is reported at 1.65 Å resolution, confirming the dimeric structure of the enzyme. The putative active site of TvTPS is deduced from its pronounced structural similarity to enzymes from other species of the Lamiaceae family involved in terpenoid biosynthesis: to (+)-bornyl diphosphate synthase and 1,8-cineole synthase from Salvia sp. and to (4S)-limonene synthase from Mentha spicata.

Controls of the quantum yield and saturation light of isoprene emission in different-aged aspen leaves

Leaf age alters the balance between the use of end-product of plastidic isoprenoid synthesis pathway, dimethylallyl diphosphate (DMADP), in prenyltransferase reactions leading to synthesis of pigments of photosynthetic machinery and in isoprene synthesis, but the implications of such changes on environmental responses of isoprene emission have not been studied. Because under light-limited conditions, isoprene emission rate is controlled by DMADP pool size (SDMADP ), shifts in the share of different processes are expected to particularly strongly alter the light dependency of isoprene emission. We examined light responses of isoprene emission in young fully expanded, mature and old non-senescent leaves of hybrid aspen (Populus tremula x P. tremuloides) and estimated in vivo SDMADP and isoprene synthase activity from post-illumination isoprene release. Isoprene emission capacity was 1.5-fold larger in mature than in young and old leaves. The initial quantum yield of isoprene emission (αI ) increased by 2.5-fold with increasing leaf age primarily as the result of increasing SDMADP . The saturating light intensity (QI90 ) decreased by 2.3-fold with increasing leaf age, and this mainly reflected limited light-dependent increase of SDMADP possibly due to feedback inhibition by DMADP. These major age-dependent changes in the shape of the light response need consideration in modelling canopy isoprene emission.

Identification, Functional Characterization, and Evolution of Terpene Synthases from a Basal Dicot

Bay laurel (Laurus nobilis) is an agriculturally and economically important dioecious tree in the basal dicot family Lauraceae used in food and drugs and in the cosmetics industry. Bay leaves, with their abundant monoterpenes and sesquiterpenes, are used to impart flavor and aroma to food, and have also drawn attention in recent years because of their potential pharmaceutical applications. To identify terpene synthases (TPSs) involved in the production of these volatile terpenes, we performed RNA sequencing to profile the transcriptome of L. nobilis leaves. Bioinformatic analysis led to the identification of eight TPS complementary DNAs. We characterized the enzymes encoded by three of these complementary DNAs: a monoterpene synthase that belongs to the TPS-b clade catalyzes the formation of mostly 1,8-cineole; a sesquiterpene synthase belonging to the TPS-a clade catalyzes the formation of mainly cadinenes; and a diterpene synthase of the TPS-e/f clade catalyzes the formation of geranyllinalool. Comparison of the sequences of these three TPSs indicated that the TPS-a and TPS-b clades of the TPS gene family evolved early in the evolution of the angiosperm lineage, and that geranyllinalool synthase activity is the likely ancestral function in angiosperms of genes belonging to an ancient TPS-e/f subclade that diverged from the kaurene synthase gene lineages before the split of angiosperms and gymnosperms.