Engineering of Ancestors as a Tool to Elucidate Structure, Mechanism, and Specificity of Extant Terpene Cyclase

The molecular complexity of terpene biosynthesis in red algae: current state and future perspectives

Covering the period 1998-2024Red algae are the largest group of seaweeds and rich sources of bioactive terpenes with broad and significant biotechnological potential. However, the main obstacle to the economic exploitation of these compounds is the difficulty of obtaining them on an industrial and sustainable scale. Genetic engineering and heterologous biosynthesis are promising tools for overcoming this limitation, but little is known about red algal terpene biosynthetic routes. In general, terpene biosynthesis relies on complex mechanisms that produce a wide array of chemically diverse compounds. In this article, we review the main processes that contribute to such chemical diversity of terpenes, which are divided into four biosynthetic steps: (i) biosynthesis of isoprenoid precursors, (ii) linear condensation of precursors to produce polyisoprenyl diphosphate intermediary molecules, (iii) terpene synthase-catalyzed chemical/structural modifications, and (iv) additional chemical/structural modifications on the basic terpene carbon skeleton. Terpene synthase evolution in algae and topics that have only recently been explored, such as terpene synthase catalytic and substrate promiscuity, have also been analyzed in detail. We present a detailed analysis of terpenoid metabolism in red algae, highlighting the mechanisms that generate their chemical diversity and identifying knowledge gaps. Additionally, we provide perspectives to guide future studies, aiming to advance the heterologous biosynthesis of terpenes from red algae for biotechnological development and application.

Ancestral Sequence Reconstruction and Comprehensive Computational Simulations Unmask an Efficient PET Hydrolase with the Wobbled Catalytic Triad

Beyond directed evolution, ancestral sequence reconstruction (ASR) has emerged as a powerful strategy for engineering proteins with superior functional properties. Herein, we harnessed ASR to uncover robust PET hydrolase variants, expanding the repertoire of PET-degrading enzymes and providing deeper insights into the underlying mechanisms of PET hydrolysis. As a result, ASR1-PETase, featuring a unique cysteine catalytic site, was discovered. Despite having only 19.3 % sequence identity with IsPETase, ASR1-PETase demonstrated improved PET degradation efficiency, with a finely-tuned substrate-binding cleft. Comprehensive experimental validation, including mutagenesis studies and comparisons with six state-of-the-art PET hydrolases, combined with microsecond-scale molecular dynamics (MD) simulations and QM-cluster calculations, revealed that ASR1-PETase's C161 catalytic residue assisted with the wobbled H242 can simultaneously cleave both ester bonds of BHET - a feature not commonly observed in other PET hydrolases. This mechanism may serve as the primary driving force for accelerating PET hydrolysis while minimizing the accumulation of the intermediate MHET, thereby enhancing the efficiency of TPA production.

Ancestral Sequence Reconstruction for Designing Biocatalysts and Investigating their Functional Mechanisms

Biocatalysis has emerged as a green approach for efficient and sustainable production in various industries. In recent decades, numerous advancements in computational and predictive approaches, including ancestral sequence reconstruction (ASR) have sparked a new wave for protein engineers to improve and expand biocatalyst capabilities. ASR is an evolution-based strategy that uses phylogenetic relationships among homologous extant sequences to probabilistically infer the most likely ancestral sequences. It has proven to be a powerful tool with applications ranging from creating highly stable enzymes for direct applications to preparing moderately active robust protein scaffolds for further enzyme engineering. Intriguingly, it can also provide insights into fundamental aspects that are challenging to study with extant (current) enzymes. This Perspective discusses a practical strategy for guiding enzyme engineers on how to embrace ASR as a practical or associated protocol for protein engineering and highlights recent examples of using ASR in various applications, including increasing thermostability, expanding promiscuity, fine-tuning selectivity and function, and investigating mechanistic and evolution aspects. We believe that the use of the ASR approach will continue to contribute to the ongoing development of the biocatalysis field. We have been in a "golden era" for biocatalysis in which numerous useful enzymes have been developed through many waves of enzyme engineering via advancements in computational methodologies.

Engineering the Substrate Specificity of UDP-Glycosyltransferases for Synthesizing Triterpenoid Glycosides with a Linear Trisaccharide as Aided by Ancestral Sequence Reconstruction

Triterpenoids have wide applications in the pharmaceutical and agricultural industries. The glycosylation of triterpenoids catalyzed by UDP-glycosyltransferases (UGTs) is a crucial method for producing valuable derivatives with enhanced functions. However, only a few UDP-glucosyltransferases have been reported to synthesize the rare triterpenoids with linear-chain trisaccharide at C3-OH. This study revealed that the UGT91H subfamily primarily contributed to the 2"-O-glycosylation of triterpenoids with high regioselectivity, then the substrate scope was further expanded by ancestral sequence reconstruction (ASR). With ancestral enzyme UGT91H_A1 as a model, the sequence-structure-function relationship was explored. A RTAS loop (R212/T213/A214/S215) was identified to affect the substrate specificity of UGT91H_A1. Transferring this RTAS loop to the corresponding position of UGT91H enzymes successfully expanded their substrate spectra. The functional role of RTAS loop was further elucidated by molecular dynamics simulation and quantum mechanical computation. UGT91H_A1 was applied to the low-cost synthesis of terpenoid rhamnosides with a linear trisaccharide in combining with a self-sufficient UDP-rhamnose regeneration system. Finally, we developed a phylogeny-based platform to efficiently mining new UGT91Hs from plant genomic data. This study provided robust biocatalysts for synthesizing various triterpenoid glycosides with a linear trisaccharide and demonstrated ASR as an efficient tool in engineering the function of UDP-glycosyltransferases.

Ancestral Sequence Reconstruction to Enable Biocatalytic Synthesis of Azaphilones

Biocatalysis can be powerful in organic synthesis but is often limited by enzymes' substrate scope and selectivity. Developing a biocatalytic step involves identifying an initial enzyme for the target reaction followed by optimization through rational design, directed evolution, or both. These steps are time consuming, resource-intensive, and require expertise beyond typical organic chemistry. Thus, an effective strategy for streamlining the process from enzyme identification to implementation is essential to expanding biocatalysis. Here, we present a strategy combining bioinformatics-guided enzyme mining and ancestral sequence reconstruction (ASR) to resurrect enzymes for biocatalytic synthesis. Specifically, we achieve an enantioselective synthesis of azaphilone natural products using two ancestral enzymes: a flavin-dependent monooxygenase (FDMO) for stereodivergent oxidative dearomatization and a substrate-selective acyltransferase (AT) for the acylation of the enzymatically installed hydroxyl group. This cascade, stereocomplementary to established chemoenzymatic routes, expands access to enantiomeric linear tricyclic azaphilones. By leveraging the co-occurrence and coevolution of FDMO and AT in azaphilone biosynthetic pathways, we identified an AT candidate, CazE, and addressed its low solubility and stability through ASR, obtaining a more soluble, stable, promiscuous, and reactive ancestral AT (AncAT). Sequence analysis revealed AncAT as a chimeric composition of its descendants with enhanced reactivity likely due to ancestral promiscuity. Flexible receptor docking and molecular dynamics simulations showed that the most reactive AncAT promotes a reactive geometry between substrates. We anticipate that our bioinformatics-guided, ASR-based approach can be broadly applied in target-oriented synthesis, reducing the time required to develop biocatalytic steps and efficiently access superior biocatalysts.

Characterization, structural, and evolutionary analysis of an extremophilic GH5 endoglucanase from Bacillus sp. G131: Insights from ancestral sequence reconstruction

Nature has developed extremozymes that catalyze complex reaction processes in extreme environmental conditions. Accordingly, a combined approach consisting of extremozyme screening, ancestral sequence resurrection (ASR), and molecular dynamic simulation was utilized to construct a developed endoglucanase. The primary experimental and in-silico data led to the prediction of a hypothetical sequence of endoglucanase (EG5-G131) using Bacillus sp. G131 confirmed by amplification and sequencing. EG5-G131 exhibited noticeable stability in a broad-pH range, several detergents, organic solvents, and temperatures up to 80 °C. The molecular weight, Vmax, and Km of the purified endoglucanase were estimated to be 36 kDa, 4.32 μmol/min, and 23.62 mg/ml, respectively. The calculated thermodynamic parameters for EG5-G131 confirmed its intrinsic thermostability. Computational analysis revealed Glu142 and Glu230 as active-site residues of the enzyme. Furthermore, the enzyme remained bound to cellotetraose at 298 K, 333 K, 343 K, and 353 K for 300 ns, consistent with our experimental data. ASR of EG5-G131 led to the introduction of ancestral ANC204 and ANC205, which show similar thermodynamic characteristics with the last Firmicute common ancestor. Finally, truncating loops from the N-terminal of two sequences created two variants with desirable thermal stability, suggesting the evolutionary deciphering of the functional domain of the GH5 family in Bacillus sp. G131.

A Functional Switch Between Asperfumene and Fusicoccadiene Synthase and Entrance to Asperfumene Biosynthesis through a Vicinal Deprotonation-Reprotonation Process

The diterpene synthase AfAS was identified from Aspergillus fumigatiaffinis. Its amino acid sequence and-according to a structural model-active site architecture are highly similar to those of the fusicocca-2,10(14)-diene synthase PaFS, but AfAS produces a structurally much more complex diterpene with a novel 6-5-5-5 tetracyclic skeleton called asperfumene. The cyclisation mechanism of AfAS was elucidated through isotopic labelling experiments and DFT calculations. The reaction cascade proceeds in its initial steps through similar intermediates as for the PaFS cascade, but then diverges through an unusual vicinal deprotonation-reprotonation process that triggers a skeletal rearrangement at the entrance to the steps leading to the unique asperfumene skeleton. The structural model revealed only one major difference between the active sites: The PaFS residue F65 is substituted by I65 in AfAS. Intriguingly, site-directed mutagenesis experiments with both diterpene synthases revealed that position 65 serves as a bidirectional functional switch for the biosynthesis of tetracyclic asperfumene versus structurally less complex diterpenes.

Engineering the next-generation synthetic cell factory driven by protein engineering

Synthetic cell factory offers substantial advantages in economically efficient production of biofuels, chemicals, and pharmaceutical compounds. However, to create a high-performance synthetic cell factory, precise regulation of cellular material and energy flux is essential. In this context, protein components including enzymes, transcription factor-based biosensors and transporters play pivotal roles. Protein engineering aims to create novel protein variants with desired properties by modifying or designing protein sequences. This review focuses on summarizing the latest advancements of protein engineering in optimizing various aspects of synthetic cell factory, including: enhancing enzyme activity to eliminate production bottlenecks, altering enzyme selectivity to steer metabolic pathways towards desired products, modifying enzyme promiscuity to explore innovative routes, and improving the efficiency of transporters. Furthermore, the utilization of protein engineering to modify protein-based biosensors accelerates evolutionary process and optimizes the regulation of metabolic pathways. The remaining challenges and future opportunities in this field are also discussed.

Ancestral terpene cyclases: From fundamental science to applications in biosynthesis

Terpenes constitute one of the largest family of natural products with potent applications as renewable platform chemicals and medicines. The low activity, selectivity and stability displayed by terpene biosynthetic machineries can constitute an obstacle towards achieving expedient biosynthesis of terpenoids in processes that adhere to the 12 principles of green chemistry. Accordingly, engineering of terpene synthase enzymes is a prerequisite for industrial biotechnology applications, but obstructed by their complex catalysis that depend on reactive carbocationic intermediates that are prone to undergo bifurcation mechanisms. Rational redesign of terpene synthases can be tedious and requires high-resolution structural information, which is not always available. Furthermore, it has proven difficult to link sequence space of terpene synthase enzymes to specific product profiles. Herein, the author shows how ancestral sequence reconstruction (ASR) can favorably be used as a protein engineering tool in the redesign of terpene synthases without the need of a structure, and without excessive screening. A detailed workflow of ASR is presented along with associated limitations, with a focus on applying this methodology on terpene synthases. From selected examples of both class I and II enzymes, the author advocates that ancestral terpene cyclases constitute valuable assets to shed light on terpene-synthase catalysis and in enabling accelerated biosynthesis.

Engineering Biocatalysts for the C-H Activation of Fatty Acids by Ancestral Sequence Reconstruction

Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids, but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the subterminal positions of fatty acids. Herein we show that ancestral sequence reconstruction (ASR) is an effective tool to explore the sequence-activity landscape of a family of multidomain, self-sufficient P450 monooxygenases. We resurrected 11 catalytically active CYP116B ancestors, each with a unique regioselectivity fingerprint that varied from subterminal in the older ancestors to mid-chain in the lineage leading to the extant, P450-TT. In lineages leading to extant enzymes in thermophiles, thermostability increased from ancestral to extant forms, as expected if thermophily had arisen de novo. Our studies show that ASR can be applied to multidomain enzymes to develop active, self-sufficient monooxygenases as regioselective biocatalysts for fatty acid hydroxylation.

Confirmation of the stereochemistry of spiroviolene

We confirm the previously revised stereochemistry of spiroviolene by X-ray crystallographically characterizing a hydrazone derivative of 9-oxospiroviolane, which is synthesized by hydroboration/oxidation of spiroviolene followed by oxidation of the resultant hydroxy group. An unexpected thermal boron migration occurred during the hydroboration process of spiroviolene that resulted in the production of a mixture of 1α-hydroxyspiroviolane, 9α- and 9β-hydroxyspiroviolane after oxidation. The assertion of the cis-orientation of the 19- and 20-methyl groups provided further support for the revised cyclization mechanism of spiroviolene.

Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat

To understand the origin and early evolution of life it is crucial to establish characteristics of the primordial environment that facilitated the emergence and evolution of life. One important environmental factor is the pH of the primordial environment. Here, we assessed the pH-dependent thermal stabilities of previously reconstructed ancestral nucleoside diphosphate kinases and ribosomal protein uS8s. The selected proteins were likely to be present in ancient organisms such as the last common ancestor of bacteria and that of archaea. We also assessed the thermal stability of homologous proteins from extant acidophilic, neutralophilic, and alkaliphilic microorganisms as a function of pH. Our results indicate that the reconstructed ancestral proteins are more akin to those of extant alkaliphilic bacteria, which display greater stability under alkaline conditions. These findings suggest that the common ancestors of bacterial and archaeal species thrived in an alkaline environment. Moreover, we demonstrate the reconstruction method employed in this study is a valuable technique for generating alkali-tolerant proteins that can be used in a variety of biotechnological and environmental applications.

Strategies for modulating transglycosylation activity, substrate specificity, and product polymerization degree of engineered transglycosylases

Glycosides are widely used in many fields due to their favorable biological activity. The traditional plant extractions and chemical methods for glycosides production are limited by environmentally unfriendly, laborious protecting group strategies and low yields. Alternatively, enzymatic glycosylation has drawn special attention due to its mild reaction conditions, high catalytic efficiency, and specific stereo-/regioselectivity. Glycosyltransferases (GTs) and retaining glycoside hydrolases (rGHs) are two major enzymes for the formation of glycosidic linkages. Therein GTs generally use nucleotide phosphate activated donors. In contrast, GHs can use broader simple and affordable glycosyl donors, showing great potential in industrial applications. However, most rGHs mainly show hydrolysis activity and only a few rGHs, namely non-Leloir transglycosylases (TGs), innately present strong transglycosylation activities. To address this problem, various strategies have recently been developed to successfully tailor rGHs to alleviate their hydrolysis activity and obtain the engineered TGs. This review summarizes the current modification strategies in TGs engineering, with a special focus on transglycosylation activity enhancement, substrate specificity modulation, and product polymerization degree distribution, which provides a reference for exploiting the transglycosylation potentials of rGHs.

Rational Design of Taxadiene Hydroxylase by Ancestral Enzyme Construction and the Elucidation of Key Amino Acids

Cytochrome P450 monooxygenases (CYP450s) play an important role in the biosynthesis of natural products by activating inert C-H bonds and inserting hydroxyl groups. However, the activities of most plant-derived CYP450s are extremely low, limiting the heterologous biosynthesis of natural products. Traditional enzyme engineering methods, either rational or screening-based, are not suitable for CYP450s because of the lack of crystal structures and high-throughput screening methods for this class of enzymes. CYP725A4 is the first hydroxylase involved in the biosynthesis pathway of Taxol. Its low activity, promiscuity, and multispecificity make it a bottleneck in Taxol biosynthesis. Here, we identified key amino acids that affect the in vivo activity of CYP725A4 by constructing the ancestral enzymes of CYP725A4. We obtained positive mutants that showed an improved yield of hydroxylated products based on the key amino acids identified, providing guidance for the modification of other CYP450s involved in the biosynthesis of natural products.

Active Site Loop Engineering Abolishes Water Capture in Hydroxylating Sesquiterpene Synthases

Terpene synthases (TS) catalyze complex reactions to produce a diverse array of terpene skeletons from linear isoprenyl diphosphates. Patchoulol synthase (PTS) from Pogostemon cablin converts farnesyl diphosphate into patchoulol. Using simulation-guided engineering, we obtained PTS variants that eliminate water capture. Further, we demonstrate that modifying the structurally conserved Hα-1 loop also reduces hydroxylation in PTS, as well as in germacradiene-11-ol synthase (Gd11olS), leading to cyclic neutral intermediates as products, including α-bulnesene (PTS) and isolepidozene (Gd11olS). Hα-1 loop modification could be a general strategy for engineering sesquiterpene synthases to produce complex cyclic hydrocarbons without the need for structure determination or modeling.

Decoding Catalysis by Terpene Synthases

The review by Christianson, published in 2017 on the twentieth anniversary of the emergence of the field, summarizes the foundational discoveries and key advances in terpene synthase/cyclase (TS) biocatalysis (Christianson, D. W. Chem Rev2017, 117 (17), 11570-11648. DOI: 10.1021/acs.chemrev.7b00287). Here, we review the TS literature published since then, bringing the field up to date and looking forward to what could be the near future of TS rational design. Many revealing discoveries have been made in recent years, building on the knowledge and fundamental principles uncovered during those initial two decades of study. We use these to explore TS reaction chemistry and see how a combined experimental and computational approach helps to decipher the complexities of TS catalysis. Revealed are a suite of catalytic motifs which control product outcome in TSs, some obvious, some more subtle. We examine each in detail, using the most recent papers and insights to illustrate how exactly this fascinating class of enzymes takes a single acyclic substrate and turns it into the many thousands of complex terpenoids found in Nature. We then explore some of the recent strategies for TS engineering, including machine learning and other data-driven approaches. From this, rational and predictive engineering of TSs, "designer terpene synthases", will begin to emerge as a realistic goal.

Molecular insights into the catalytic promiscuity of a bacterial diterpene synthase

Diterpene synthase VenA is responsible for assembling venezuelaene A with a unique 5-5-6-7 tetracyclic skeleton from geranylgeranyl pyrophosphate. VenA also demonstrates substrate promiscuity by accepting geranyl pyrophosphate and farnesyl pyrophosphate as alternative substrates. Herein, we report the crystal structures of VenA in both apo form and holo form in complex with a trinuclear magnesium cluster and pyrophosphate group. Functional and structural investigations on the atypical 115DSFVSD120 motif of VenA, versus the canonical Asp-rich motif of DDXX(X)D/E, reveal that the absent second Asp of canonical motif is functionally replaced by Ser116 and Gln83, together with bioinformatics analysis identifying a hidden subclass of type I microbial terpene synthases. Further structural analysis, multiscale computational simulations, and structure-directed mutagenesis provide significant mechanistic insights into the substrate selectivity and catalytic promiscuity of VenA. Finally, VenA is semi-rationally engineered into a sesterterpene synthase to recognize the larger substrate geranylfarnesyl pyrophosphate.

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes' innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.

Engineering the Thermostability of a d-Carbamoylase Based on Ancestral Sequence Reconstruction for the Efficient Synthesis of d-Tryptophan

Employing ancestral sequence reconstruction and consensus sequence analysis, the thermostability of a novel d-carbamoylase derived from Nitratireductor indicus (NiHyuC) was engineered through greedy-oriented iterative combinatorial mutagenesis. A mutant S202P/E208D/R277L (M4Th3) was obtained with significantly elevated thermostability. M4Th3 has a half-life of 36.5 h at 40 °C, about 28.5 times of 1.3 h of its parent M4. For the reaction at 40 °C, M4Th3 can catalyze 10 mM N-carbamoyl-d-tryptophan to produce d-tryptophan with a conversion ratio of 96.4% after 12 h, which is significantly higher than 64.1% of M4. MD simulation reveals that new hydrogen bonds emerging from E208D on the surface can increase the hydrophobicity of the protein, leading to improved stability. More importantly, R277L could contribute to enhanced interface stability of homodimeric M4. This study provides a thermostable d-carbamoylase for the "hydantoinase process", which has potential in the industrial synthesis of optically pure natural and non-natural amino acids.

The Biosynthesis Related Enzyme, Structure Diversity and Bioactivity Abundance of Indole-Diterpenes: A Review

Indole diterpenes are a large class of secondary metabolites produced by fungi, possessing a cyclic diterpenoid backbone and an indole moiety. Novel structures and important biological activity have made indole diterpenes one of the focuses of synthetic chemists. Although the discovery, identification, structural diversity, biological activity and especially structure-activity relationship of indole diterpenes have been reported in some papers in recent years, they are absent of a systematic and comprehensive analysis, and there is no elucidation of enzymes related to this kind of natural product. Therefore, it is necessary to summarize the relevant reports to provide new perspectives for the following research. In this review, for the first time, the function of related synthases and the structure-activity relationship of indole diterpenes are expounded, and the recent research advances of them are emphasized.

Engineering functional thermostable proteins using ancestral sequence reconstruction

Natural proteins are often only slightly more stable in the native state than the denatured state, and an increase in environmental temperature can easily shift the balance toward unfolding. Therefore, the engineering of proteins to improve protein stability is an area of intensive research. Thermostable proteins are required to withstand industrial process conditions, for increased shelf-life of protein therapeutics, for developing robust 'biobricks' for synthetic biology applications, and for research purposes (e.g., structure determination). In addition, thermostability buffers the often destabilizing effects of mutations introduced to improve other properties. Rational design approaches to engineering thermostability require structural information, but even with advanced computational methods, it is challenging to predict or parameterize all the relevant structural factors with sufficient precision to anticipate the results of a given mutation. Directed evolution is an alternative when structures are unavailable but requires extensive screening of mutant libraries. Recently, however, bioinspired approaches based on phylogenetic analyses have shown great promise. Leveraging the rapid expansion in sequence data and bioinformatic tools, ancestral sequence reconstruction can generate highly stable folds for novel applications in industrial chemistry, medicine, and synthetic biology. This review provides an overview of the factors important for successful inference of thermostable proteins by ancestral sequence reconstruction and what it can reveal about the determinants of stability in proteins.

Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes

The crystal structures of cattleyene synthase (apo-CyS), and CyS complexed with geranylgeranyl pyrophosphate (GGPP) were solved. The CySC59A variant exhibited an increased production of cattleyene and other diterpenes with diverse skeletons. Its structure showed a widened active site cavity explaining the relaxed selectivity. Isotopic labeling experiments revealed a remarkable cyclization mechanism involving several skeletal rearrangements for one of the novel diterpenes.

Thermoadaptation in an Ancestral Diterpene Cyclase by Altered Loop Stability

Thermostability is the key to maintain the structural integrity and catalytic activity of enzymes in industrial biotechnological processes, such as terpene cyclase-mediated generation of medicines, chiral synthons, and fine chemicals. However, affording a large increase in the thermostability of enzymes through site-directed protein engineering techniques can constitute a challenge. In this paper, we used ancestral sequence reconstruction to create a hyperstable variant of the ent-copalyl diphosphate synthase PtmT2, a terpene cyclase involved in the assembly of antibiotics. Molecular dynamics simulations on the μs timescale were performed to shed light on possible molecular mechanisms contributing to activity at an elevated temperature and the large 40 °C increase in melting temperature observed for an ancestral variant of PtmT2. In silico analysis revealed key differences in the flexibility of a loop capping the active site, between extant and ancestral proteins. For the modern enzyme, the loop collapses into the active site at elevated temperatures, thus preventing biocatalysis, whereas the loop remains in a productive conformation both at ambient and high temperatures in the ancestral variant. Restoring a Pro loop residue introduced in the ancestral variant to the corresponding Gly observed in the extant protein led to reduced catalytic activity at high temperatures, with only moderate effects on the melting temperature, supporting the importance of the flexibility of the capping loop in thermoadaptation. Conversely, the inverse Gly to Pro loop mutation in the modern enzyme resulted in a 3-fold increase in the catalytic rate. Despite an overall decrease in maximal activity of ancestor compared to wild type, its increased thermostability provides a robust backbone amenable for further enzyme engineering. Our work cements the importance of loops in enzyme catalysis and provides a molecular mechanism contributing to thermoadaptation in an ancestral enzyme.

Hedycaryol - Central Intermediates in Sesquiterpene Biosynthesis, Part II

The known sesquiterpenes that arise biosynthetically from hedycaryol are summarised. Reasonings for the assignments of their absolute configurations are discussed. The analysis provided here suggests that reprotonations at the C1=C10 double bond of hedycaryol are directed toward C1 and generally lead to 6-6 bicyclic compounds, while reprotonations at the C4=C5 double bond occur at C4 and result in 5-7 bicyclic compounds. Read more in the Review by H. Xu and J. S. Dickschat (DOI: 10.1002/chem.202200405).

Biotechnological potential and initial characterization of two novel sesquiterpene synthases from Basidiomycota Coniophora puteana for heterologous production of δ-cadinol

Background

Terpene synthases are versatile catalysts in all domains of life, catalyzing the formation of an enormous variety of different terpenoid secondary metabolites. Due to their diverse bioactive properties, terpenoids are of great interest as innovative ingredients in pharmaceutical and cosmetic applications. Recent advances in genome sequencing have led to the discovery of numerous terpene synthases, in particular in Basidiomycota like the wood rotting fungus Coniophora puteana, which further enhances the scope for the manufacture of terpenes for industrial purposes.

Results

In this study we describe the identification of two novel (+)-δ-cadinol synthases from C. puteana, Copu5 and Copu9. The sesquiterpene (+)-δ-cadinol was previously shown to exhibit cytotoxic activity therefore having an application as possible, new, and sustainably sourced anti-tumor agent. In an Escherichia coli strain, optimized for sesquiterpene production, titers of 225 mg l⁻¹ and 395 mg l⁻¹, respectively, could be achieved. Remarkably, both enzymes share the same product profile thereby representing the first two terpene synthases from Basidiomycota with identical product profiles. We solved the crystal structure of Copu9 in its closed conformation, for the first time providing molecular details of sesquiterpene synthase from Basidiomycota. Based on the Copu9 structure, we conducted structure-based mutagenesis of amino acid residues lining the active site, thereby altering the product profile. Interestingly, the mutagenesis study also revealed that despite the conserved product profiles of Copu5 and Copu9 different conformational changes may accompany the catalytic cycle of the two enzymes. This observation suggests that the involvement of tertiary structure elements in the reaction mechanism(s) employed by terpene synthases may be more complex than commonly expected.

Conclusion

The presented product selectivity and titers of Copu5 and Copu9 may pave the way towards a sustainable, biotechnological production of the potentially new bioactive (+)-δ-cadinol. Furthermore, Copu5 and Copu9 may serve as model systems for further mechanistic studies of terpenoid catalysis.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01791-8.

Recreating the natural evolutionary trend in key microdomains provides an effective strategy for engineering of a thermomicrobial N-demethylase

N-demethylases have been reported to remove the methyl groups on primary or secondary amines, which could further affect the properties and functions of biomacromolecules or chemical compounds; however, the substrate scope and the robustness of N-demethylases have not been systematically investigated. Here we report the recreation of natural evolution in key microdomains of the Thermomicrobium roseum sarcosine oxidase (TrSOX), an N-demethylase with marked stability (melting temperature over 100 °C) and enantioselectivity, for enhanced substrate scope and catalytic efficiency on -C-N- bonds. We obtained the structure of TrSOX by crystallization and X-ray diffraction (XRD) for the initial framework. The natural evolution in the nonconserved residues of key microdomains-including the catalytic loop, coenzyme pocket, substrate pocket, and entrance site-was then identified using ancestral sequence reconstruction (ASR), and the substitutions that accrued during natural evolution were recreated by site-directed mutagenesis. The single and double substitution variants catalyzed the N-demethylation of N-methyl-L-amino acids up to 1800- and 6000-fold faster than the wild type, respectively. Additionally, these single substitution variants catalyzed the terminal N-demethylation of non-amino-acid compounds and the oxidation of the main chain -C-N- bond to a -C=N- bond in the nitrogen-containing heterocycle. Notably, these variants retained the enantioselectivity and stability of the initial framework. We conclude that the variants of TrSOX are of great potential use in N-methyl enantiomer resolution, main-chain Schiff base synthesis, and alkaloid modification or degradation.

Combining Ancestral Reconstruction with Folding-Landscape Simulations to Engineer Heterologous Protein Expression

Obligate symbionts typically exhibit high evolutionary rates. Consequently, their proteins may differ considerably from their modern and ancestral homologs in terms of both sequence and properties, thus providing excellent models to study protein evolution. Also, obligate symbionts are challenging to culture in the lab and proteins from uncultured organisms must be produced in heterologous hosts using recombinant DNA technology. Obligate symbionts thus replicate a fundamental scenario of metagenomics studies aimed at the functional characterization and biotechnological exploitation of proteins from the bacteria in soil. Here, we use the thioredoxin from Candidatus Photodesmus katoptron, an uncultured symbiont of flashlight fish, to explore evolutionary and engineering aspects of protein folding in heterologous hosts. The symbiont protein is a standard thioredoxin in terms of 3D-structure, stability and redox activity. However, its folding outside the original host is severely impaired, as shown by a very slow refolding in vitro and an inefficient expression in E. coli that leads mostly to insoluble protein. By contrast, resurrected Precambrian thioredoxins express efficiently in E. coli, plausibly reflecting an ancient adaptation to unassisted folding. We have used a statistical-mechanical model of the folding landscape to guide back-to-ancestor engineering of the symbiont protein. Remarkably, we find that the efficiency of heterologous expression correlates with the in vitro (i.e., unassisted) folding rate and that the ancestral expression efficiency can be achieved with only 1-2 back-to-ancestor replacements. These results demonstrate a minimal-perturbation, sequence-engineering approach to rescue inefficient heterologous expression which may potentially be useful in metagenomics efforts targeting recent adaptations.

Mechanistic Insights into the Formation of the 6,10-Bicyclic Eunicellane Skeleton by the Bacterial Diterpene Synthase Bnd4

The eunicellane diterpenoids are a unique family of natural products seen in marine organisms, plants, and bacteria. We used a series of biochemical, bioinformatics, and theoretical experiments to investigate the mechanism of the first diterpene synthase known to form the eunicellane skeleton. Deuterium labeling studies and quantum chemical calculations support that Bnd4, from Streptomyces sp. (CL12-4), forms the 6,10-bicyclic skeleton through a 1,10-cyclization, 1,3-hydride shift, and 1,14-cyclization cascade. Bnd4 also demonstrated sesquiterpene cyclase activity and the ability to prenylate small molecules. Bnd4 possesses a unique D94 NxxxD motif and mutation experiments confirmed an absolute requirement for D94 as well as E169.

Advancements in macromolecular crystallography: from past to present

Protein Crystallography or Macromolecular Crystallography (MX) started as a new discipline of science with the pioneering work on the determination of the protein crystal structures by John Kendrew in 1958 and Max Perutz in 1960. The incredible achievements in MX are attributed to the development of advanced tools, methodologies, and automation in every aspect of the structure determination process, which have reduced the time required for solving protein structures from years to a few days, as evident from the tens of thousands of crystal structures of macromolecules available in PDB. The advent of brilliant synchrotron sources, fast detectors, and novel sample delivery methods has shifted the paradigm from static structures to understanding the dynamic picture of macromolecules; further propelled by X-ray Free Electron Lasers (XFELs) that explore the femtosecond regime. The revival of the Laue diffraction has also enabled the understanding of macromolecules through time-resolved crystallography. In this review, we present some of the astonishing method-related and technological advancements that have contributed to the progress of MX. Even with the rapid evolution of several methods for structure determination, the developments in MX will keep this technique relevant and it will continue to play a pivotal role in gaining unprecedented atomic-level details as well as revealing the dynamics of biological macromolecules. With many exciting developments awaiting in the upcoming years, MX has the potential to contribute significantly to the growth of modern biology by unraveling the mechanisms of complex biological processes as well as impacting the area of drug designing.

Protein engineering for natural product biosynthesis and synthetic biology applications

As protein engineering grows more salient, many strategies have emerged to alter protein structure and function, with the goal of redesigning and optimizing natural product biosynthesis. Computational tools, including machine learning and molecular dynamics simulations, have enabled the rational mutagenesis of key catalytic residues for enhanced or altered biocatalysis. Semi-rational, directed evolution and microenvironment engineering strategies have optimized catalysis for native substrates and increased enzyme promiscuity beyond the scope of traditional rational approaches. These advances are made possible using novel high-throughput screens, including designer protein-based biosensors with engineered ligand specificity. Herein, we detail the most recent of these advances, focusing on polyketides, non-ribosomal peptides and isoprenoids, including their native biosynthetic logic to provide clarity for future applications of these technologies for natural product synthetic biology.