Sesquarterpenes (C35 Terpenes) Biosynthesized via the Cyclization of a Linear C35 Isoprenoid by a Tetraprenyl-β-curcumene Synthase and a Tetraprenyl-β-curcumene Cyclase: Identification of a New Terpene Cyclase

Structural-model-based genome mining can efficiently discover novel non-canonical terpene synthases hidden in genomes of diverse species

Non-canonical terpene synthases (TPSs) with primary sequences that are unrecognizable as canonical TPSs have evaded detection by conventional genome mining. This study aimed to prove that novel non-canonical TPSs can be efficiently discovered from proteins, hidden in genome databases, predicted to have 3D structures similar to those of class I TPSs. Six types of non-canonical TPS candidates were detected using this search strategy from 268 genome sequences from actinomycetes. Functional analyses of these candidates revealed that at least three types were novel non-canonical TPSs. We propose classifying the non-canonical TPSs as classes ID, IE, and IF. A hypothetical protein MBB6373681 from Pseudonocardia eucalypti (PeuTPS) was selected as a representative example of class ID TPSs and characterized. PeuTPS was identified as a diterpene synthase that forms a 6/6/6-fused tricyclic gersemiane skeleton. Analyses of PeuTPS variants revealed that amino acid residues within new motifs [D(N/D), ND, and RXXKD] located close to the class I active site in the 3D structure were essential for enzymatic activity. The homologs of non-canonical TPSs found in this study exist in bacteria as well as in fungi, protists, and plants, and the PeuTPS gene is not located near terpene biosynthetic genes in the genome. Therefore, structural-model-based genome mining is an efficient strategy to search for novel non-canonical TPSs that are independent of biological species and biosynthetic gene clusters and will contribute to expanding the structural diversity of terpenoids.

Identification and functional/structural analyses of large terpene synthases

Large terpene synthases (large-TSs) are a new family of TSs. The first large-TS discovered was from Bacillus subtilis (BsuTS), which is involved in the biosynthesis of a C35 sesquarterpene. Large-TSs are the only enzymes that enable the biosynthesis of sesquarterpenes and do not share any sequence homology with canonical Class I and II TSs. Thus, the investigation of large-TSs is promising for expanding the chemical space in the terpene field. In this chapter, we describe the experimental methods used for identifying large-TSs, as well as their functional and structural analyses. Additionally, several enzymes related to the biosynthesis of large-TS substrates have been described.

The Bacillus subtilis cell envelope stress-inducible ytpAB operon modulates membrane properties and contributes to bacitracin resistance

Antibiotics that inhibit peptidoglycan synthesis trigger the activation of both specific and general protective responses. σM responds to diverse antibiotics that inhibit cell wall synthesis. Here, we demonstrate that cell wall-inhibiting drugs, such as bacitracin and cefuroxime, induce the σM-dependent ytpAB operon. YtpA is a predicted hydrolase previously proposed to generate the putative lysophospholipid antibiotic bacilysocin (lysophosphatidylglycerol), and YtpB is the branchpoint enzyme for the synthesis of membrane-localized C35 terpenoids. Using targeted lipidomics, we reveal that YtpA is not required for the production of lysophosphatidylglycerol. Nevertheless, ytpA was critical for growth in a mutant strain defective for homeoviscous adaptation due to a lack of genes for the synthesis of branched chain fatty acids and the Des phospholipid desaturase. Consistently, overexpression of ytpA increased membrane fluidity as monitored by fluorescence anisotropy. The ytpA gene contributes to bacitracin resistance in mutants additionally lacking the bceAB or bcrC genes, which directly mediate bacitracin resistance. These epistatic interactions support a model in which σM-dependent induction of the ytpAB operon helps cells tolerate bacitracin stress, either by facilitating the flipping of the undecaprenyl phosphate carrier lipid or by impacting the assembly or function of membrane-associated complexes involved in cell wall homeostasis.IMPORTANCEPeptidoglycan synthesis inhibitors include some of our most important antibiotics. In Bacillus subtilis, peptidoglycan synthesis inhibitors induce the σM regulon, which is critical for intrinsic antibiotic resistance. The σM-dependent ytpAB operon encodes a predicted hydrolase (YtpA) and the enzyme that initiates the synthesis of C35 terpenoids (YtpB). Our results suggest that YtpA is critical in cells defective in homeoviscous adaptation. Furthermore, we find that YtpA functions cooperatively with the BceAB and BcrC proteins in conferring intrinsic resistance to bacitracin, a peptide antibiotic that binds tightly to the undecaprenyl-pyrophosphate lipid carrier that sustains peptidoglycan synthesis.

Class II terpene cyclases: structures, mechanisms, and engineering

Covering: up to July 2023Terpene cyclases (TCs) catalyze some of the most complicated reactions in nature and are responsible for creating the skeletons of more than 95 000 terpenoid natural products. The canonical TCs are divided into two classes according to their structures, functions, and mechanisms. The class II TCs mediate acid-base-initiated cyclization reactions of isoprenoid diphosphates, terpenes without diphosphates (e.g., squalene or oxidosqualene), and prenyl moieties on meroterpenes. The past twenty years witnessed the emergence of many class II TCs, their reactions and their roles in biosynthesis. Class II TCs often act as one of the first steps in the biosynthesis of biologically active natural products including the gibberellin family of phytohormones and fungal meroterpenoids. Due to their mechanisms and biocatalytic potential, TCs elicit fervent attention in the biosynthetic and organic communities and provide great enthusiasm for enzyme engineering to construct novel and bioactive molecules. To engineer and expand the structural diversities of terpenoids, it is imperative to fully understand how these enzymes generate, precisely control, and quench the reactive carbocation intermediates. In this review, we summarize class II TCs from nature, including sesquiterpene, diterpene, triterpene, and meroterpenoid cyclases as well as noncanonical class II TCs and inspect their sequences, structures, mechanisms, and structure-guided engineering studies.

In silico analysis of sporulene biosynthesis pathway genes in the members of the class Bacilli

Sporulene, a pentacyclic triterpenoid, was discovered in Bacillus subtilis and is associated with bacterial endospores. However, the study was not further extended, leaving a trail of questions. One such question is what diversity of sporulenes exists among spore-forming members? Considering the sporulene biosynthesis pathway as a fundamental tool to survey the distribution of this molecule, a genome mining study was conducted. Mining for genes encoding putative proteins of sporulene biosynthesis pathway among the class Bacilli members revealed the presence of hepS, hepT, ytpB, and sqhC genes in the members of the family Bacillaceae, Caryophanaceae, Paenibacillaceae, and Sporolactobacillaceae. However, these genes were completely absent in the members of Staphylococcaceae, Lactobacillaceae, Aerococcaceae, Carnobacteriaceae, and Leuconostocaceae. Unlike other probable pathway related proteins, a conserved amino acid domain of putative terpenoid cyclase (YtpB) appeared deep-rooted among the genus Bacillus members. In-depth analysis showed the constant gene arrangement of hepS, hepT, ytpB, and sqhC genes in these members, there by demonstrating the conserved nature of sporulene biosynthesis pathway in the members of the genus Bacillus. Our study suggests confinement of the sporulene biosynthesis pathway to spore-forming members of the class Bacilli, majorly to the genus Bacillus.

Neoroseomonas marina sp. nov., Isolated from a Beach Sand

A pink-pigmented bacterium (strain JC162^T = KCTC 32190^T) was isolated from a beach sand sample. Cells were Gram-stain-negative, coccoid, non-motile, and strictly aerobic. EzBioCloud BLAST search of 16S rRNA gene sequence showed that strain KCTC 32190^T had the highest sequence identity to the members of the genus Neoroseomonas and was closely related to N. oryzicola YC6724^T (99.8%), N. sediminicola FW-3^T (98.5%), N. soli 5N26^T (98.2%), and other members of the genus Neoroseomonas (< 97.9%) in the family Acetobacteriaceae within the class of Alphaproteobacteria. Chemo-organoheterotrophy was the only growth mode and growth was possible on a wide range of organic substrates. Strain KCTC 32190^T was positive for catalase and oxidase. Fatty acid composition of strain KCTC 32190^T includes (in decreasing %) C_18:1ω7c, cyclo-C_19:0ω8c, C_18:02-OH, C_16:0, C_18:03-OH, C_16:1ω7c/C_16:1ω6c, C_16:02-OH and C_16:1ω5c. Polar lipids comprised of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, and three unidentified lipids. The genomic DNA G+C content of the strain KCTC 32190^T was 70.9 mol%. Strain KCTC 32190^T has a low ANI value of < 92.7% and genome reassociation (based on digital DNA-DNA hybridization) value of < 48.8% with the nearest type strains. The genome relatedness is supported by other polyphasic taxonomic data to propose strain KCTC 32190^T as a new species in the genus Neoroseomonas with the name Neoroseomonas marina sp. nov. The type strain is strain JC162^T (KCTC 32190^T = CGMCC1.12364^T).

Insight into the mechanism of geranyl-β-phellandrene formation catalyzed by Class IB terpene synthases

Terpene synthase (TS) from Bacillus alcalophilus (BalTS) is the only Class IB TS for which a 3D structure has been elucidated. Recently, geranyl-β-phellandrene, a novel cyclic diterpene, was identified as a product of BalTS in addition to the acyclic β-springene. In the present study, we have provided insight into the mechanism of geranyl-β-phellandrene formation. Deuterium labeling experiments revealed that the compound is produced via a 1,3-hydride shift. In addition, nonenzymatic reactions using divalent metal ions were performed. The enzyme is essential for the geranyl-β-phellandrene formation. Furthermore, BalTS variants targeting tyrosine residues enhanced the yield of geranyl-β-phellandrene and the proportion of the compound of the total products. It was suggested that the expansion of the active site space may allow the conformation of the intermediates necessary for cyclization. The present study describes the first Class IB TSs to successfully alter product profiles while retaining high enzyme activity.

Alkalihalobacterium elongatum gen. nov. sp. nov.: An Antibiotic-Producing Bacterium Isolated From Lonar Lake and Reclassification of the Genus Alkalihalobacillus Into Seven Novel Genera

A Gram-stain positive, long, rod-shaped, motile, and spore-forming bacterium (MEB199^T) was isolated from a sediment sample collected from Lonar Lake, India. The strain was oxidase and catalase positive. The strain grew optimally at pH 10, NaCl concentration of 3.5% at 37°C. The major fatty acids were iso-C_15:0, iso-C_16:0, anteiso-C_15:0, and iso-C_17:0. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP). Phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol were the major polar lipids of MEB199^T. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MEB199^T belonged to the family Bacillaceae and exhibited a distinctive position among the members of the genus Alkalihalobacillus (Ahb.). Strain MEB199^T shared the highest 16S rRNA gene sequence similarity with Alkalihalobacillus alkalinitrilicus ANL-iso4^T (98.36%), whereas with type species Ahb. alcalophilus DSM 485^T, it is 94.91%, indicating that strain MEB199^T is distinctly related to the genus Alkalihalobacillus. The G + C content of genomic DNA was 36.47 mol%. The digital DNA-DNA hybridization (dDDH) (23.6%) and average nucleotide identity (ANI) (81%) values between strain MEB199^T and Ahb. alkalinitrilicus ANL-iso4^T confirmed the novelty of this new species. The pairwise identity based on the 16S rRNA gene sequence between the species of genus Alkalihalobacillus ranges from 87.4 to 99.81% indicating the heterogeneity in the genus. The different phylogenetic analysis based on the genome showed that the members of the genus Alkalihalobacillus separated into eight distinct clades. The intra-clade average amino acid identity (AAI) and percentage of conserved proteins (POCP) range from 52 to 68% and 37 to 59%, respectively, which are interspersed on the intra-genera cutoff values; therefore, we reassess the taxonomy of genus Alkalihalobacillus. The phenotypic analysis also corroborated the differentiation between these clades. Based on the phylogenetic analysis, genomic indices, and phenotypic traits, we propose the reclassification of the genus Alkalihalobacillus into seven new genera for which the names Alkalihalobacterium gen. nov., Halalkalibacterium gen. nov., Halalkalibacter gen. nov., Shouchella gen. nov., Pseudalkalibacillus gen. nov., Alkalicoccobacillus gen. nov., and Alkalihalophilus gen. nov. are proposed and provide an emended description of Alkalihalobacillus sensu stricto. Also, we propose the Ahb. okuhidensis as a heterotypic synonym of Alkalihalobacillus halodurans. Based on the polyphasic taxonomic analysis, strain MEB199^T represents a novel species of newly proposed genus for which the name Alkalihalobacterium elongatum gen. nov. sp. nov. is proposed. The type strain is MEB199^T (= MCC 2982^T, = JCM 33704^T, = NBRC 114256^T, = CGMCC 1.17254^T).

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.

Mini Review: Bacterial Membrane Composition and Its Modulation in Response to Stress

Antibiotics and other agents that perturb the synthesis or integrity of the bacterial cell envelope trigger compensatory stress responses. Focusing on Bacillus subtilis as a model system, this mini-review summarizes current views of membrane structure and insights into how cell envelope stress responses remodel and protect the membrane. Altering the composition and properties of the membrane and its associated proteome can protect cells against detergents, antimicrobial peptides, and pore-forming compounds while also, indirectly, contributing to resistance against compounds that affect cell wall synthesis. Many of these regulatory responses are broadly conserved, even where the details of regulation may differ, and can be important in the emergence of antibiotic resistance in clinical settings.

Mesobacillus aurantius sp. nov., isolated from an orange-colored pond near a solar saltern

An endospore producing, strict aerobic, Gram-stain-positive, orange-colored colony forming bacterium designated as strain JC1013^T was isolated from an orange pond near a solar saltern of Tamil Nadu, India. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain was affiliated to the family Bacillaceae of the phylum Firmicutes. Strain showed highest 16S rRNA gene sequence identity of 98.7% with Mesobacillus selenatarsenatis SF-1 ^T and below 98.3% with other members of the genus Mesobacillus. Strain JC1013^T produced carotenoid pigments and indole compounds. Major cellular fatty acids of strain JC1013^T were iso-C_15:0, anteiso-C_15:0, C_16:0 3-OH, iso-C_17:0ω10c and summed feature 4 (iso-C_17:1 I/ anteisoB). Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and four unidentified phospholipids. Strain JC1013^T constituted m-diaminopimelic acid as diagnostic cell wall amino acids. MK-7 is the predominant menaquinone of strain JC1013^T. The genome size of strain JC1013^T was 4.6 Mbp and its G + C content was 42.7 mol%. For the affirmation of strain's taxonomic status, a detailed phylogenomic study was done. Based on the phylogenetic analyses, low ANI (84.6%), AAI (88.5%) values, in-silico DDH (< 29%) value, morphological, physiological and chemo-taxonomical characteristics, strain JC1013^T was clearly distinguished from the nearest phylogenetic neighbor, Mesobacillus selenatarsenatis SF-1^T to conclude that it is a new species of the genus Mesobacillus. We propose the name as Mesobacillus aurantius with type strain JC1013^T (= NBRC 114146^T = KACC 21451 ^T).

Mini Review: Bacterial Membrane Composition and Its Modulation in Response to Stress

Antibiotics and other agents that perturb the synthesis or integrity of the bacterial cell envelope trigger compensatory stress responses. Focusing on Bacillus subtilis as a model system, this mini-review summarizes current views of membrane structure and insights into how cell envelope stress responses remodel and protect the membrane. Altering the composition and properties of the membrane and its associated proteome can protect cells against detergents, antimicrobial peptides, and pore-forming compounds while also, indirectly, contributing to resistance against compounds that affect cell wall synthesis. Many of these regulatory responses are broadly conserved, even where the details of regulation may differ, and can be important in the emergence of antibiotic resistance in clinical settings.

Structure, catalysis, and inhibition mechanism of prenyltransferase

Isoprenoids, also known as terpenes or terpenoids, represent a large family of natural products composed of five‐carbon isopentenyl diphosphate or its isomer dimethylallyl diphosphate as the building blocks. Isoprenoids are structurally and functionally diverse and include dolichols, steroid hormones, carotenoids, retinoids, aromatic metabolites, the isoprenoid side‐chain of ubiquinone, and isoprenoid attached signaling proteins. Productions of isoprenoids are catalyzed by a group of enzymes known as prenyltransferases, such as farnesyltransferases, geranylgeranyltransferases, terpenoid cyclase, squalene synthase, aromatic prenyltransferase, and cis‐ and trans‐prenyltransferases. Because these enzymes are key in cellular processes and metabolic pathways, they are expected to be potential targets in new drug discovery. In this review, six distinct subsets of characterized prenyltransferases are structurally and mechanistically classified, including (1) head‐to‐tail prenyl synthase, (2) head‐to‐head prenyl synthase, (3) head‐to‐middle prenyl synthase, (4) terpenoid cyclase, (5) aromatic prenyltransferase, and (6) protein prenylation. Inhibitors of those enzymes for potential therapies against several diseases are discussed. Lastly, recent results on the structures of integral membrane enzyme, undecaprenyl pyrophosphate phosphatase, are also discussed.

Origin and Evolution of Polycyclic Triterpene Synthesis

Polycyclic triterpenes are members of the terpene family produced by the cyclization of squalene. The most representative polycyclic triterpenes are hopanoids and sterols, the former are mostly found in bacteria, whereas the latter are largely limited to eukaryotes, albeit with a growing number of bacterial exceptions. Given their important role and omnipresence in most eukaryotes, contrasting with their scant representation in bacteria, sterol biosynthesis was long thought to be a eukaryotic innovation. Thus, their presence in some bacteria was deemed to be the result of lateral gene transfer from eukaryotes. Elucidating the origin and evolution of the polycyclic triterpene synthetic pathways is important to understand the role of these compounds in eukaryogenesis and their geobiological value as biomarkers in fossil records. Here, we have revisited the phylogenies of the main enzymes involved in triterpene synthesis, performing gene neighborhood analysis and phylogenetic profiling. Squalene can be biosynthesized by two different pathways containing the HpnCDE or Sqs proteins. Our results suggest that the HpnCDE enzymes are derived from carotenoid biosynthesis ones and that they assembled in an ancestral squalene pathway in bacteria, while remaining metabolically versatile. Conversely, the Sqs enzyme is prone to be involved in lateral gene transfer, and its emergence is possibly related to the specialization of squalene biosynthesis. The biosynthesis of hopanoids seems to be ancestral in the Bacteria domain. Moreover, no triterpene cyclases are found in Archaea, invoking a potential scenario in which eukaryotic genes for sterol biosynthesis assembled from ancestral bacterial contributions in early eukaryotic lineages.

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.

Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases

Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.

BceAB-Type Antibiotic Resistance Transporters Appear To Act by Target Protection of Cell Wall Synthesis

Resistance against cell wall-active antimicrobial peptides in bacteria is often mediated by transporters. In low-GC-content Gram-positive bacteria, a common type of such transporters is BceAB-like systems, which frequently provide high-level resistance against peptide antibiotics that target intermediates of the lipid II cycle of cell wall synthesis. How a transporter can offer protection from drugs that are active on the cell surface, however, has presented researchers with a conundrum.

Resistance against cell wall-active antimicrobial peptides in bacteria is often mediated by transporters. In low-GC-content Gram-positive bacteria, a common type of such transporters is BceAB-like systems, which frequently provide high-level resistance against peptide antibiotics that target intermediates of the lipid II cycle of cell wall synthesis. How a transporter can offer protection from drugs that are active on the cell surface, however, has presented researchers with a conundrum. Multiple theories have been discussed, ranging from removal of the peptides from the membrane and internalization of the drug for degradation to removal of the cellular target rather than the drug itself. To resolve this much-debated question, we here investigated the mode of action of the transporter BceAB of Bacillus subtilis. We show that it does not inactivate or import its substrate antibiotic bacitracin. Moreover, we present evidence that the critical factor driving transport activity is not the drug itself but instead the concentration of drug-target complexes in the cell. Our results, together with previously reported findings, lead us to propose that BceAB-type transporters act by transiently freeing lipid II cycle intermediates from the inhibitory grip of antimicrobial peptides and thus provide resistance through target protection of cell wall synthesis. Target protection has so far only been reported for resistance against antibiotics with intracellular targets, such as the ribosome. However, this mechanism offers a plausible explanation for the use of transporters as resistance determinants against cell wall-active antibiotics in Gram-positive bacteria where cell wall synthesis lacks the additional protection of an outer membrane.

Identification and Characterization of a Membrane-Bound Sesterterpene Cyclase from Streptomyces somaliensis

Sesterterpenes are usually found in plants and fungi, but are rare in bacteria. Here, we present the identification of StsC from Streptomyces somaliensis, a member of the UbiA superfamily, as a membrane-bound sesterterpene cyclase in bacteria. The cyclized products for StsC, somaliensenes A (1) and B (2), were identified by expressing the corresponding gene in an engineered Escherichia coli strain. The structures of 1 and 2 were determined by analysis of the NMR and MS spectroscopic data.

Crystal structure and functional analysis of large-terpene synthases belonging to a newly found subclass

The first crystal structure of a large-terpene synthase elucidated two novel Asp rich motifs and a new subclass of terpene synthases.

Thousands of terpenes have been identified to date. However, only two classes of enzymes are known to be involved in their biosynthesis, and each class has characteristic amino-acid motifs. We recently identified a novel large-terpene (C₂₅/C₃₀/C₃₅) synthase, which shares no motifs with known enzymes. To elucidate the molecular mechanism of this enzyme, we determined the crystal structure of a large-β-prene synthase from B. alcalophilus (BalTS). Surprisingly, the overall structure of BalTS is similar to that of the α-domain of class I terpene synthases although their primary structures are totally different from each other. Two novel aspartate-rich motifs, DYLDNLxD and DY(F,L,W)IDxxED, are identified, and mutations of any one of the aspartates eliminate its enzymatic activity. The present work leads us to propose a new subclass of terpene synthases, class IB, which is probably responsible for large-terpene biosynthesis.

Protonation-Initiated Cyclization by a Class II Terpene Cyclase Assisted by Tunneling

Terpenes represent one of the most diversified classes of natural products with potent biological activities. The key to the myriad of polycyclic terpene skeletons with crucial functions in organisms from all kingdoms of life are terpene cyclase enzymes. These biocatalysts enable stereospecific cyclization of relatively simple, linear, prefolded polyisoprenes by highly complex, partially concerted, electrophilic cyclization cascades that remain incompletely understood. Herein, additional mechanistic light is shed on terpene biosynthesis by kinetic studies in mixed H2 O/D2 O buffers of a class II bacterial ent-copalyl diphosphate synthase. Mass spectrometry determination of the extent of deuterium incorporation in the bicyclic product, reminiscent of initial carbocation formation by protonation, resulted in a large kinetic isotope effect of up to seven. Kinetic analysis at different temperatures confirmed that the isotope effect was independent of temperature, which is consistent with hydrogen tunneling.

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.

A squalene synthase-like enzyme initiates production of tetraterpenoid hydrocarbons in Botryococcus braunii Race L

The green microalga Botryococcus braunii is considered a promising biofuel feedstock producer due to its prodigious accumulation of hydrocarbon oils that can be converted into fuels. B. braunii Race L produces the C₄₀ tetraterpenoid hydrocarbon lycopadiene via an uncharacterized biosynthetic pathway. Structural similarities suggest this pathway follows a biosynthetic mechanism analogous to that of C₃₀ squalene. Confirming this hypothesis, the current study identifies C₂₀ geranylgeranyl diphosphate (GGPP) as a precursor for lycopaoctaene biosynthesis, the first committed intermediate in the production of lycopadiene. Two squalene synthase (SS)-like complementary DNAs are identified in race L with one encoding a true SS and the other encoding an enzyme with lycopaoctaene synthase (LOS) activity. Interestingly, LOS uses alternative C₁₅ and C₂₀ prenyl diphosphate substrates to produce combinatorial hybrid hydrocarbons, but almost exclusively uses GGPP in vivo. This discovery highlights how SS enzyme diversification results in the production of specialized tetraterpenoid oils in race L of B. braunii.

The green microalga Botryococcus braunii is a promising biofuel producer due to its ability to produce large amounts of hydrocarbon oils that can be converted into fuels. Here the authors implicate lycopaoctaene synthase, a squalene synthases-like enzyme, in the first step towards the biosynthesis of the C40 tetraterpenoid hydrocarbon lycopadiene.

Bacillus subtilis extracytoplasmic function (ECF) sigma factors and defense of the cell envelope

Bacillus subtilis provides a model for investigation of the bacterial cell envelope, the first line of defense against environmental threats. Extracytoplasmic function (ECF) sigma factors activate genes that confer resistance to agents that threaten the integrity of the envelope. Although their individual regulons overlap, σ(W) is most closely associated with membrane-active agents, σ(X) with cationic antimicrobial peptide resistance, and σ(V) with resistance to lysozyme. Here, I highlight the role of the σ(M) regulon, which is strongly induced by conditions that impair peptidoglycan synthesis and includes the core pathways of envelope synthesis and cell division, as well as stress-inducible alternative enzymes. Studies of these cell envelope stress responses provide insights into how bacteria acclimate to the presence of antibiotics.

Metabolic engineering of Bacillus subtilis for terpenoid production

Terpenoids are the largest group of small-molecule natural products, with more than 60,000 compounds made from isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). As the most diverse group of small-molecule natural products, terpenoids play an important role in the pharmaceutical, food, and cosmetic industries. For decades, Escherichia coli (E. coli) and Saccharomyces cerevisiae (S. cerevisiae) were extensively studied to biosynthesize terpenoids, because they are both fully amenable to genetic modifications and have vast molecular resources. On the other hand, our literature survey (20 years) revealed that terpenoids are naturally more widespread in Bacillales. In the mid-1990s, an inherent methylerythritol phosphate (MEP) pathway was discovered in Bacillus subtilis (B. subtilis). Since B. subtilis is a generally recognized as safe (GRAS) organism and has long been used for the industrial production of proteins, attempts to biosynthesize terpenoids in this bacterium have aroused much interest in the scientific community. This review discusses metabolic engineering of B. subtilis for terpenoid production, and encountered challenges will be discussed. We will summarize some major advances and outline future directions for exploiting the potential of B. subtilis as a desired "cell factory" to produce terpenoids.

Terpenoid biosynthesis off the beaten track: unconventional cyclases and their impact on biomimetic synthesis

Terpene and terpenoid cyclizations are counted among the most complex chemical reactions occurring in nature and contribute crucially to the tremendous structural diversity of this largest family of natural products. Many studies were conducted at the chemical, genetic, and biochemical levels to gain mechanistic insights into these intriguing reactions that are catalyzed by terpene and terpenoid cyclases. A myriad of these enzymes have been characterized. Classical textbook knowledge divides terpene/terpenoid cyclases into two major classes according to their structure and reaction mechanism. However, recent discoveries of novel types of terpenoid cyclases illustrate that nature's enzymatic repertoire is far more diverse than initially thought. This Review outlines novel terpenoid cyclases that are out of the ordinary.

Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach

Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products. To predict functions and specificity of triterpenoid synthases, a mechanism-based, multi-intermediate docking approach is proposed. In addition to enzyme function prediction, other potential applications of the current approach, such as enzyme mechanistic studies and enzyme redesign by mutagenesis, are discussed.

The rapid growth in the number of protein sequences presents challenges for enzyme function assignment. Computational methods, such as bioinformatics, homology modeling and docking, are becoming increasingly important for predicting of enzyme functions from protein sequences. Terpenoids are one of largest classes of natural products, and many drugs (e.g. taxol) consist of terpenoids or terpenoid derivatives. Understanding the biosynthesis of the terpenoids is of great interest. Terpenoid synthases catalyze the key cyclization steps of the biosynthesis of terpenoids via carbocation rearrangements, generating numerous multiple-ring carbon skeletons. Triterpenoid synthases, as an important class of terpenoid synthases, catalyze the cyclization of either squalene or oxido-squalene into cyclized products such as sterols (e.g. lanosterol). In this work, we propose a computational approach that can be used to predict product specificity of the triterpenoid synthases. Our approach provides insight into the ‘design principles’ of these fascinating enzymes, and may become a practical approach for function prediction and enzyme engineering.

Accumulation of heptaprenyl diphosphate sensitizes Bacillus subtilis to bacitracin: implications for the mechanism of resistance mediated by the BceAB transporter

Heptaprenyl diphosphate (C35 -PP) is an isoprenoid intermediate in the synthesis of both menaquinone and the sesquarterpenoids. We demonstrate that inactivation of ytpB, encoding a C35 -PP utilizing enzyme required for sesquarterpenoid synthesis, leads to an increased sensitivity to bacitracin, an antibiotic that binds undecaprenyl pyrophosphate (C55 -PP), a key intermediate in cell wall synthesis. Genetic studies indicate that bacitracin sensitivity is due to accumulation of C35 -PP, rather than the absence of sesquarterpenoids. Sensitivity is accentuated in a ytpB menA double mutant, lacking both known C35 -PP consuming enzymes, and in a ytpB strain overexpressing the HepST enzyme that synthesizes C35 -PP. Conversely, sensitivity in the ytpB background is suppressed by mutation of hepT or by supplementation with 1,4-dihydroxy-2-naphthoate, a co-substrate with C35 -PP for MenA. Bacitracin sensitivity results from impairment of the BceAB and BcrC resistance mechanisms by C35 -PP: in a bceAB bcrC double mutant disruption of ytpB no longer increases bacitracin sensitivity. These results suggest that C35 -PP inhibits both BcrC (a C55 -PP phosphatase) and BceAB (an ABC transporter that confers bacitracin resistance). These findings lead to a model in which BceAB protects against bacitracin by transfer of the target, C55 -PP, rather than the antibiotic across the membrane.

Terpenoid synthase structures: a so far incomplete view of complex catalysis

The complexity of terpenoid natural products has drawn significant interest, particularly since their common (poly)isoprenyl origins were discovered. Notably, much of this complexity is derived from the highly variable cyclized and/or rearranged nature of the observed hydrocarbon skeletal structures. Indeed, at least in some cases it is difficult to immediately recognize their derivation from poly-isoprenyl precursors. Nevertheless, these diverse structures are formed by sequential elongation to acyclic precursors, most often with subsequent cyclization and/or rearrangement. Strikingly, the reactions used to assemble and diversify terpenoid backbones share a common carbocationic driven mechanism, although the means by which the initial carbocation is generated does vary. High-resolution crystal structures have been obtained for at least representative examples from each of the various types of enzymes involved in producing terpenoid hydrocarbon backbones. However, while this has certainly led to some insights into the enzymatic structure-function relationships underlying the elongation and simpler cyclization reactions, our understanding of the more complex cyclization and/or rearrangement reactions remains limited. Accordingly, selected examples are discussed here to demonstrate our current understanding, its limits, and potential ways forward.