Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead

Biosynthesis and recruitment of reactive amino acids in nonribosomal peptide assembly lines

Reactive amino acid side chains play important roles in the binding of peptides to specific targets. In addition, their reactivity enables selective peptide conjugation and functionalization for pharmaceutical purposes. Diverse reactive amino acids are incorporated into nonribosomal peptides, which serve as a source for drug candidates. Notable examples include (poly)unsaturated (enamine, alkyne, and furyl) and halogenated residues, strained carbacycles (cyclopropyl and cyclopropanol), small heterocycles (oxirane and aziridine), and reactive N-N functionalities (hydrazones, diazo compounds, and diazeniumdiolates). Their biosynthesis requires diverse biocatalysts for sophisticated reaction mechanisms. Several avenues have been identified for their incorporation into peptides, the recruitment by adenylation domains or ligases, on-line modifications, and enzymatic tailoring reactions. Combined with protein engineering approaches, this knowledge provides new opportunities in synthetic biology and bioorthogonal chemistry.

Direct α-Hydroxy Acid Loading onto a Bacterial Thiotemplate Assembly Line via a Multienzyme Gateway

Various nonribosomal peptide synthetases (NRPSs) create structural and functional diversity by incorporating α-hydroxy acids into peptide backbones. Trigonic acid, an unusual cyclopropanol-substituted hydroxy acid, is the source of the molecular warhead of malleicyprol, a critical virulence factor of human and animal pathogens of the Burkholderia pseudomallei (BP) group. The process of selecting and loading this building block remained enigmatic as the NRPS module designated for this task is incomplete. Using a combination of bioinformatics, mutational analyses, targeted metabolomics, and in vitro biochemical assays, we show that two trans-acting enzymes are required to load this central building block onto the modular assembly line. An adenylation-thiolation didomain enzyme (BurJ) activates trigonic acid, followed by the translocation of the enzyme-bound α-hydroxy acid thioester by an FkbH-like protein with a mutated phosphatase domain (BurH). This specialized gateway is the first reported direct loading of an α-hydroxy acid onto a bona fide NRPS module in bacteria and expands the synthetic biology toolbox for the site-specific incorporation of non-canonical building blocks. Moreover, insight into the biochemical basis of virulence factor biosynthesis can provide a foundation for developing enzyme inhibitors as anti-virulence therapeutics against BP pathogen infections.

Analysis of the Valgamicin Biosynthetic Pathway Reveals a General Mechanism for Cyclopropanol Formation across Diverse Natural Product Scaffolds

Cyclopropanol rings are highly reactive and may function as molecular "warheads" that affect natural product bioactivity. Yet, knowledge on their biosynthesis is limited. Using gene cluster analyses, isotope labeling, and in vitro enzyme assays, we shed first light on the biosynthesis of the cyclopropanol-substituted amino acid cleonine, a residue in the antimicrobial depsipeptide valgamicin C and the cytotoxic glycopeptide cleomycin A2. We decipher the biosynthetic origin of valgamicin C and show that the cleonine cyclopropanol ring is derived from dimethylsulfoniopropionate (DMSP). Furthermore, we demonstrate that part of the biosynthesis is analogous to the formation of malleicyprol polyketides in pathogenic bacteria. By genome mining and metabolic profiling, we identify the potential to produce cyclopropanol rings in other bacterial species. Our results reveal a general mechanism for cyclopropyl alcohol biosynthesis across diverse natural products that may be harnessed for bioengineering and drug discovery.

Burkholderia pseudomallei and melioidosis

Burkholderia pseudomallei, the causative agent of melioidosis, is found in soil and water of tropical and subtropical regions globally. Modelled estimates of the global burden predict that melioidosis remains vastly under-reported, and a call has been made for it to be recognized as a neglected tropical disease by the World Health Organization. Severe weather events and environmental disturbance are associated with increased case numbers, and it is anticipated that, in some regions, cases will increase in association with climate change. Genomic epidemiological investigations have confirmed B. pseudomallei endemicity in newly recognized regions, including the southern United States. Melioidosis follows environmental exposure to B. pseudomallei and is associated with comorbidities that affect the immune response, such as diabetes, and with socioeconomic disadvantage. Several vaccine candidates are ready for phase I clinical trials. In this Review, we explore the global burden, epidemiology and pathophysiology of B. pseudomallei as well as current diagnostics, treatment recommendations and preventive measures, highlighting research needs and priorities.

Two-step resonance-energy-transfer-based ratiometric biosensor for sensing and annihilation of Staphylococcus aureus

A two-step resonance energy transfer (RET)-based fluorescence/electrochemiluminescence (FL/ECL) biosensor was developed for ratiometric measurement and annihilation of Staphylococcus aureus (S. aureus). Using coupled dual-recognition-triggered target conversion with the catalytic hairpin assembly (CHA) technique, the monitoring of S. aureus was obtained at the single-cell level.

Novel Biocatalysts from Specialized Metabolism

Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.

Tigliane Diterpenoids

The distribution, chemistry, and molecular bioactivity of tiglianes are reviewed from the very beginning of the studies on these diterpenoids, summarizing their clinical and toxicological literature mostly in its more recent and controversial aspects, and critically analyzing various proposals for their biosynthesis.

Bioinformatics-guided discovery of biaryl-linked lasso peptides

Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Using mass spectrometry, stable isotope incorporation, and extensive 2D-NMR spectrometry, we report the structural characterization of two unique examples of (C-N) biaryl-linked lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with a Trp-Tyr crosslink, while longipepetin A, from Longimycelium tulufanense, features a Trp-Trp linkage. Besides the unusual bicyclic frame, a Met of longipepetin A undergoes S-methylation to yield a trivalent sulfonium, a heretofore unprecedented RiPP modification. A bioinformatic survey revealed additional lasso peptide BGCs containing P450 enzymes which await future characterization. Lastly, nocapeptin A bioactivity was assessed against a panel of human and bacterial cell lines with modest growth-suppression activity detected towards Micrococcus luteus.

S-Adenosylmethionine: more than just a methyl donor

Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.

Bacterial Pathogen Channels Medium-Sized Fatty Acids into Malleicyprol Biosynthesis

Bacterial pathogens of the Burkholderia pseudomallei (BP) group cause life-threatening infections in both humans and animals. Critical for the virulence of these often antibiotic-resistant pathogens is the polyketide hybrid metabolite malleicyprol, which features two chains, a short cyclopropanol-substituted chain and a long hydrophobic alkyl chain. The biosynthetic origin of the latter has remained unknown. Here, we report the discovery of novel overlooked malleicyprol congeners with varied chain lengths and identify medium-sized fatty acids as polyketide synthase (PKS) starter units that constitute the hydrophobic carbon tails. Mutational and biochemical analyses show that a designated coenzyme A-independent fatty acyl-adenylate ligase (FAAL, BurM) is essential for recruiting and activating fatty acids in malleicyprol biosynthesis. In vitro reconstitution of the BurM-catalyzed PKS priming reaction and analysis of ACP-bound building blocks reveal a key role of BurM in the toxin assembly. Insights into the function and role of BurM hold promise for the development of enzyme inhibitors as novel antivirulence therapeutics to combat infections with BP pathogens.

Dual DNA recycling amplifications coupled with Au NPs@ZIF-MOF accelerator for enhanced electrochemical ratiometric sensing of pathogenic bacteria

Sensitive and accurate quantification of pathogenic bacteria is vastly significant to the related food safety. Herein, a sensitive ratiometric electrochemical biosensor was developed for the detection of Staphylococcus aureus (S. aureus) based on dual DNA recycling amplifications and Au NPs@ZIF-MOF accelerator. Gold nanoparticles-loaded Zeolitic imidazolate metal-organic framework (Au NPs@ZIF-MOF) as electrode substrate possessed a large specific surface area for nucleic acid adsorption, and as an accelerator promoted the transfer of electrons. The strong recognition of aptamer to target S. aureus could initiate the padlock probe-based exponential rolling circle amplification (P-ERCA, as the first DNA recycling amplification), generating large numbers of trigger DNA strands. The released trigger DNA further activated the catalytic hairpin assembly (CHA, as the second DNA recycling amplification) on electrode surface. Consequently, P-ERCA and CHA continuously brought about one target to many signal transduction, leading to an exponential amplification. To achieve the accuracy of detection, the signal ratio of methylene blue (MB) and ferrocene (Fc) (I_MB/I_Fc) was applied for intrinsic self-calibrating. Taking advantages of dual DNA recycling amplifications and Au NPs@ZIF-MOF, the proposed sensing system displayed high sensitivity for S. aureus quantification with a linear range of 5-10⁸ CFU/mL, and the limit of detection was 1 CFU/mL. Moreover, this system represented excellent reproducibility, selectivity, and practicability for S. aureus analysis in foods.

An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity

The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP+/NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.

Post-Cyclization Skeletal Rearrangements in Plant Triterpenoid Biosynthesis by a Pair of Branchpoint Isomerases

Triterpenoids possess potent biological activities, but their polycyclic skeletons are challenging to synthesize. The skeletal diversity of triterpenoids in plants is generated by oxidosqualene cyclases based on epoxide-triggered cationic rearrangement cascades. Normally, triterpenoid skeletons then remain unaltered during subsequent tailoring steps. In contrast, the highly modified triterpenoids found in Sapindales plants imply the existence of post-cyclization skeletal rearrangement enzymes that have not yet been found. We report here a biosynthetic pathway in Sapindales plants for the modification of already cyclized tirucallane triterpenoids, controlling the pathway bifurcation between different plant triterpenoid classes. Using a combination of bioinformatics, heterologous expression in plants and chemical analyses, we identified a cytochrome P450 monooxygenase and two isomerases which harness the epoxidation-rearrangement biosynthetic logic of triterpene cyclizations for modifying the tirucallane scaffold. The two isomerases share the same epoxide substrate made by the cytochrome P450 monooxygenase CYP88A154, but generate two different rearrangement products, one containing a cyclopropane ring. Our findings reveal a process for skeletal rearrangements of triterpenoids in nature that expands their scaffold diversity after the initial cyclization. In addition, the enzymes described here are crucial for the biotechnological production of limonoid, quassinoid, apoprotolimonoid, and glabretane triterpenoids.

Bioinformatics-Guided Discovery of Biaryl-Tailored Lasso Peptides

Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Here, we report the structural characterization of two unique examples of (C-N) biaryl-containing lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with Trp-Tyr crosslink while longipepetin A, from Longimycelium tulufanense, features Trp-Trp linkage. Besides the unusual bicyclic frame, longipepetin A receives an S-methylation by a new Met methyltransferase resulting in unprecedented sulfonium-bearing RiPP. Our bioinformatic survey revealed P450(s) and further maturating enzyme(s)-containing lasso BGCs awaiting future characterization.

Hot off the Press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as hyjapone A from Hypericum japonicum.

An intramodular thioesterase domain catalyses chain release in the biosynthesis of a cytotoxic virulence factor

The bimodular PKS-NRPS BurA has two unusual non-C-terminal thioesterase domains. We show that the intramodular TE-B is responsible for the hydrolytic release of gonyol, an intermediate for the biosynthesis of the virulence factor malleicyprol.