Biology subjects

Lichman, B. R.

Publications and source records attributed to Lichman, B. R..

8 recordsLinked to original sources

bioRxiv2025

Nicotine biosynthesis completed by cryptic activating glucosylation

Nicotine is a neuroactive alkaloid produced by tobacco (Nicotiana tabacum) as a defense against herbivory, and an addictive stimulant that has been used by humans for millennia. Despite its significance, the core steps of its biosynthesis have remained elusive. Here, we demonstrate in vitro reconstruction of nicotine synthase, a four-enzyme stereoselective biocatalytic cascade that forms (S)-nicotine from nicotinic acid and N-methylpyrrolinium. This cascade includes two glucose-processing enzymes that participate in a cryptic activating glucosylation step. We also reconstruct this pathway in planta and present high resolution X-ray structures of the key oxidoreductases A622 and BBL bound to their substrate and product, respectively. This work establishes the complete biosynthetic pathway to nicotine, providing new gene targets for controlling alkaloid production in Nicotiana and unlocking enzymatic routes to pyridine alkaloids.

biochemistry↗

bioRxiv2025

Artemether and Euphorbia Factor L9 suppress kynurenine production through distinct effects on Tryptophan metabolism.

L-Tryptophan (Trp) is an essential amino acid, catabolised through the kynurenine pathway, which is mediated by the enzymes indoleamine-2,3-dioxygenase 1 (IDO1), IDO2, or Trp-2,3-deoxygenase (TDO). Therapeutic targeting of Trp metabolism could be relevant to several pathologies. In cancer, IDO1 acts as an immune checkpoint suppressing effector T cell function. Yet, direct inhibition of IDO1 has had limited success in clinical trials. Therefore, alternative approaches to Trp metabolism therapeutic targeting are needed. We screened a library of 597 natural products (NPs) or NP derivatives for their effect on kynurenine production in triple negative breast cancer cells. This revealed 24 candidate inhibitors of kynurenine production. Amongst them, artemether, a member of the artemisinin family of anti-malarial drugs, suppressed kynurenine production, likely via an endoperoxide bridge-dependent mechanism. The Euphorbia factor L9 (EFL9) inhibited kynurenine production likely via a C7-benzoylation-dependent mechanism. Neither artemether nor EFL9 affected JAK/STAT signaling or IDO1 levels. Targeted metabolomics analyses demonstrated that artemether suppressed kynurenine production through heme sequestration, a mechanism that would affect all members of the IDO/TDO family of metalloenzymes. EFL9 affected purine and amino acid metabolism and the cellular redox balance. Comparisons to the effects of ouabain, a NP regulator of IDO1 levels, and Linrodostat, a clinically used small molecule IDO1 inhibitor, revealed distinct metabolic profiles, with ouabain and EFL9 showing the largest overlap. Importantly, the kynurenine-suppressing activity of artemether and EFL9 is not cancer cell-specific. Overall, our findings set the foundation for the use of derivatives of artemether or EFL9 as novel Trp metabolism-targeting therapeutics.

cancer biology↗

bioRxiv2024

Divergent biosynthesis of monoterpene indole alkaloids from geissoschizine

Plants can generate structural diversity by enzymatic rearrangement of a central intermediate. 19E-geisssochizine is one such chemically versatile intermediate that plays a central role in the biosynthesis of monoterpene indole alkaloids such as strychnine, ibogaine and vinblastine. Here we report how 19E-geissoschizine undergoes oxidative transformations to generate four distinct alkaloid scaffolds through the action of three biosynthetic enzymes. Using in vitro enzymatic assays and gene silencing, we demonstrate how these three cytochrome P450 enzymes in the medicinal plant Catharanthus roseus transform 19E-geisssochzine into strychnos, sarpagan, akuammiline-type, and mavacurane-type alkaloids. We use mutational analysis to show how minimal changes to the active site of these similar enzymes modulate product specificity. This work highlights how substrate reactivity and enzyme mutations work synergistically to generate chemical diversity.

biochemistry↗

bioRxiv2024

Streamlined screening platforms lead to the discovery of pachysiphine synthase from Tabernanthe iboga

Plant-specialized metabolism is largely driven by the oxidative tailoring of key chemical scaffolds catalyzed by cytochrome P450 (CYP450s) enzymes. The monoterpene indole alkaloids tabersonine and pseudo-tabersonine, found in the medicinal plant Tabernanthe iboga, are extensively modified by oxidative reactions. Here we developed a streamlined screening strategy to screen the activity of T. iboga CYP450s in Nicotiana benthamiana. Using multigene constructs encoding the biosynthesis of tabersonine and pseudo-tabersonine scaffolds, we set out to uncover the CYP450s responsible for oxidative transformations of these scaffolds. Our approach identified two T. iboga cytochrome P450 enzymes: pachysiphine synthase (PS) and 16-hydroxy-tabersonine synthase (T16H). These enzymes catalyze an epoxidation and site-specific hydroxylation of tabersonine to produce pachysiphine and 16-OH-tabersonine, respectively. We further demonstrated that these genes produced the expected products when expressed in Catharanthus roseus flowers. This work provides new insights into the biosynthetic pathways of MIAs and underscores the utility of N. benthamiana and C. roseus as platforms for the functional characterization of plant enzymes.

biochemistry↗

bioRxiv2024

Nonsymmetric formation of Δ1-piperideine from lysine in plants via a bacterial-like PLP-dependent enzyme

Alkaloids are nitrogen-containing natural products derived from amino acids. The basic amino acids lysine and ornithine are precursors to a wide range of alkaloids including the bioactive compounds nicotine, hyoscyamine and securinine. Feeding experiments have shown that the amino acids can be incorporated into alkaloids in a symmetric or nonsymmetric manner. The symmetric pathway is catalysed by two enzymes, a decarboxylase and oxidase, forming a cyclic iminium which acts as the electrophile in the scaffold forming step. Here, we describe the ornithine/lysine/arginine decarboxylase-oxidases (OLADOs), PLP-dependent enzymes responsible for the nonsymmetric pathway, catalysing the single step decarboxylative oxidative deamination of lysine, ornithine or arginine. These enzymes are group III ornithine/lysine/arginine decarboxylases (OLADs), an enzyme class previously exclusively associated with prokaryotes. We reveal OLADs to be widespread in plants and show that OLADOs have repeatedly emerged through parallel evolution from OLADs, via similar active site substitutions. This investigation introduces a new class of eukaryotic decarboxylases, and describes enzymes involved in multiple alkaloid biosynthesis pathways. It furthermore demonstrates how the principle of parallel evolution at a genomic and enzymatic level can be leveraged for gene discovery across multiple lineages.

biochemistry↗

bioRxiv2024

Genome Report: Pseudomolecule-scale genome assemblies of Drepanocaryum sewerzowii and Marmoritis complanata

The Nepetoideae, a subfamily of Lamiaceae (mint family), is rich in aromatic plants, many of which are sought after for their use as flavours and fragrances or for their medicinal properties. Here we present genome assemblies for two species in Nepetiodeae: Drepanocaruym sewerzowii and Marmoritis complanata. Both assemblies were generated using Oxford Nanopore Q20+ reads with contigs anchored to nine pseudomolecules that resulted in 335 Mb and 305 Mb assemblies, respectively, and BUSCO scores above 95% for both the assembly and annotation. We furthermore provide a species tree for the Lamiaceae using only genome derived gene models, complementing existing transcriptome and marker-based phylogenies.

genomics↗

bioRxiv2022

Recycling upstream redox enzymes expands the regioselectivity of cycloaddition in pseudo-aspidosperma alkaloid biosynthesis

Nature uses cycloaddition reactions to generate complex natural product scaffolds. Dehydrosecodine is a highly reactive biosynthetic intermediate that undergoes cycloaddition to generate several alkaloid scaffolds that are the precursors to pharmacologically important compounds such as vinblastine and ibogaine. Here we report how dehydrosecodine can be subjected to redox chemistry, which in turn allows cycloaddition reactions with alternative regioselectivity. By incubating dehydrosecodine with reductase and oxidase biosynthetic enzymes that act upstream in the pathway, we can access the rare pseudo-aspidosperma alkaloids, pseudo-tabersonine and pseudo-vincadifformine, both in vitro and by reconstitution in the plant Nicotiana benthamiana from an upstream intermediate. We propose a stepwise mechanism to explain the formation of the pseudo-tabersonine scaffold by structurally characterizing enzyme intermediates, and by monitoring the incorporation of deuterium labels. This discovery highlights how plants use redox enzymes to enantioselectively generate new scaffolds from common precursors.

biochemistry↗

bioRxiv2022

Integrative metabolomics reveal the organisation of alkaloid biosynthesis in Daphniphyllum macropodum

Daphniphyllum alkaloids are structurally diverse nitrogen-containing compounds with polycyclic, stereochemically rich carbon skeletons. Understanding how plants biosynthesise these compounds may lead to greater access to allow exploration of bioactivities; however, very little is known about their biosynthetic origins. Here, we integrated metabolomics approaches to map alkaloid distribution across Daphniphyllum macropodum plants and tissues. We generated a novel untargeted metabolomics workflow to highlight trends in alkaloid distribution across tissues, using a holistic approach that does not rely on ambiguous peak annotations. Both liquid-chromatography-mass spectrometry and mass-spectrometry imaging analyses independently revealed that alkaloids have a pattern of spatial distribution based on their skeletal subtypes. The distinct alkaloid subtype localisation suggests the biosynthetic pathway is controlled spatially with intermediates transported from the phloem to the epidermis where they undergo additional derivatization. This study sets the stage for the future work on Daphniphyllum alkaloid biosynthesis and highlights how integrating different metabolomics strategies can reveal valuable insights on these compounds distribution within the plant.

plant biology↗