Chemoproteomics approach to elucidating biosynthetic pathway of plant natural products DOI Creative Commons

Quanyu Yin,

Mengquan Yang

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Nov. 26, 2024

Natural products derived from medicinal plants are a class of compounds with extensive biological activities, playing crucial role in the pharmaceutical, food, and cosmetics industries. Due to their excellent physiological functions, increasing attention is being paid biosynthesis pathways plant natural (PNPs) (Kawatra et al., 2022;Halder Jha, 2023). However, as market demand continues grow, traditional harvesting extraction methods exert immense pressure on environment (Singh, In recent years, rapid advancement synthetic biology has offered new approaches for producing structurally complex bioactive small-molecule using biotechnology (Hesami Nevertheless, lack knowledge about biosynthetic significantly impedes largescale biomanufacturing plants. Unlike microorganisms, genes relatively dispersed across chromosomes, often efficient genetic manipulation systems, which hinders elucidation pathways.Recently, chemoproteomics based activity probes demonstrated great potential elucidating product (steviol glycosides, camptothecin, chalcomoracin, etc.), it enables identification functional proteins interacting substrates, thereby accelerating discovery (Li 2018;Zhou 2018;Gao 2020;Wong 2020;Zhang 2024) (Figure 1).Traditional have played advancing our understanding pathways, laying foundation emerging technologies like chemoproteomics. Gene knockout RNA interference (RNAi) methods, example, been widely used identify involved by observing phenotypic changes metabolite production when specific silenced (Zhao 2016). Additionally, multi-omics approaches, such transcriptomics, offer insights gene coexpression, though these can be limited need data analysis do not directly enzyme activities (Liu 2024a;Swamidatta Lichman, 2024). Heterologous expression, microbial enabled individual or clusters recreating outside native context (Lau Sattely, 2015;Hong 2022;Yang biochemical assays verify function may require large amounts purified protein, time-intensive process (Tatsis 2017). These while foundational, fall short dissecting within plants, where chemoproteomics, its activity-based annotation capabilities, offers distinct advantages. Consequently, applying technology comprehensively analyze only practical value but also holds strategic significance achieving through (Zhang 2022;Gao 2023;Liu 2023;Zhang 2023;Golubova 2024;Jiang 2024;Liu 2024b). Affinity specialized chemical tools isolate active enzymes samples, particularly those biosynthesis. typically consist binding moiety that targets enzyme's site, reactive tag capture covalent attachment after activation reporter detection.Effective affinity probe design requires specificity mimic stability conditions, controlled reactivity ensure selective durable (Parker Pratt, 2020;Fang 2021) 2). The primary advantage lies ability selectively target proteomes, bypassing purification manipulation. challenges non-specific complexity limit effectiveness (Tabana proven invaluable mapping shown studies synthesizing steviol glycosides other products. Steviol sweetening agents Stevia rebaudiana, studied due non-caloric sweeteners (Masand Recent research utilizing chemoproteomics-based strategy successfully identified UDP-glycosyltransferases (UGTs) SrUGT73E1, AtUGT73C1 AtUGT73C5, play pivotal catalyzing glycosylation form 2018;Wong 2020). use photoaffinity steviol, combined mass spectrometry, allowed researchers profile UGTs responsible final steps.This advances pathway novel platform glycosylation, enabling scalable production.Chalcomoracin, flavonoid isolated mulberry (Morus alba), synthesized highly unique flavin adenine dinucleotide (FAD)-dependent intermolecular Diels-Alder reaction. For this cycloaddition reaction was unknown, despite importance formation chalcomoracin's characteristic cyclohexene ring. enzyme, Morus alba Diels-Alderase (MaDA), intermediate (BIP)-based (Gao MaDA catalyzes the[4+2] high enantioselectivity, marking first stand-alone 2020;Gao characterization had remained inaccessible genomics transcriptomics clustering pathways.Camptothecin, an alkaloid potent anti-cancer properties, Camptotheca acuminata Ophiorrhiza pumila (Yang 2021). camptothecin long subject study, significant gap steps following strictosamide formation. A breakthrough came OpCYP716E111, epoxidase conversion epoxide. Using chemoproteomic approach, designed diazirine-based strictosamide, OpCYP716E111 proteome This fills critical underscores power uncover previously unknown metabolic processes.The discoveries surrounding highlight broad applicability field Traditional nature genes, making difficult pinpoint each step.Chemoproteomics circumvents issue targeting small molecule probes, allowing even non-model approach advantageous secondary metabolism organized into clusters, feature common systems rare Chemoproteomics advantages studying sensitivity detecting low-abundance without needing cloning protein expression steps. It distinguish between closely related isoforms multiple simultaneously, comprehensive view networks systems.These features make valuable biosynthesis.Furthermore, integration promise sustainable compounds. By identifying characterizing biosynthesis, reconstitute hosts, plant-derived 2023).Despite advantages, faces pathways. include optimization reliance high-quality spectrometry accurate identification. arise limitations affect efficiency specificity. Future advancements, improved selectivity omics technologies, hold overcoming obstacles enhancing approach's utility research.Chemoproteomics indispensable tool camptothecin. frontier research, key facilitating application biology. As will likely central unlocking full pharmaceutical industrial applications.MY: Conceptualization, Writing-original draft. MY, QY: Writing-review editing.

Language: Английский

Biosynthesis of plant neuroactive alkaloids treating Alzheimer’s disease DOI Creative Commons

Quanyu Yin,

Zhen Zhu, Mengquan Yang

et al.

Frontiers in Pharmacology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 5, 2025

Alzheimer's disease (AD) is a debilitating neurodegenerative disorder characterized by cognitive decline and memory impairment. With increasing global prevalence, the need for effective therapeutic interventions critical. Among currently approved treatments, acetylcholinesterase inhibitors (AChEIs) like huperzine A galantamine stand out due to their neuroprotective roles. These plant-derived alkaloids have demonstrated significant efficacy in alleviating symptoms acetylcholine levels brain.While numerous other plant exhibit varying degrees of neuroactive properties, remain only marketed as specific treatments AD diseases. For example, such berberine (from Berberis species) rhynchophylline Uncaria rhynchophylla) shown potential targeting amyloid-beta (Aβ) aggregation, oxidative stress, tau hyperphosphorylation. Similarly, harmine has ability inhibit hyperphosphorylation through dual inhibition glycogen synthase kinase-3 beta (GSK-3β) specificity tyrosine phosphorylation regulated kinase 1A (DYRK1A). However, these metabolites not yet advanced clinical applications (Ng et al., 2015;Rezaul Islam 2024).The elucidation biosynthetic pathways marks advancement understanding biochemistry specialized metabolism. It advances our but also provides opportunities sustainable scalable production synthetic biology approaches. By leveraging this approach, researchers can reconstruct natural products microbial or systems, facilitating efficient reducing reliance on native sources valuable compounds (Liu 2023;Zhang 2023;Bai 2024a;Teng 2024). This opinion highlights implications discoveries future research application treatment.Huperzine A, derived from Huperzia serrata (Lycopodiaceae), well-known AChEI that been widely used traditional Chinese medicine (Ma Gang, 2004;Yang 2017;Wang 2020;Zhang The pathway provided crucial insights into formation Lycopodium uncovered enzymes with novel functions (Li 2022;Ushimaru Abe, 2023;Cheng Recent studies identified three neofunctionalized α-carbonic anhydrase-like (CAL) responsible key Mannich-like condensations form core carbon-carbon bonds alkaloids, steps construction polycyclic skeletons.Through transcriptome analysis enzyme characterization, Nett al. CAL-1 CAL-2, which promote annulation reactions (Nett 2023;Liu 2024a;Zamar proceeds stereospecific modifications scaffold tailoring, involving additional Fe(II)-dependent dioxygenases, introduce oxidation final bioactive (Figure 1) 2021;Nett 2023;Ushimaru 2023). findings shed light complex evolution species, suggesting evolved metabolite defense mechanism. breakthrough deepens opens door bioengineering chassis, resources (Zhang 2022;Gao 2024b;Golubova 2024).Galantamine, an alkaloid plants Amaryllidaceae family, particularly daffodils (Narcissus spp.), another treatment (Prvulovic 2010). Similar was recently elucidated, providing invaluable its (Kilgore 2014;Li 2018;Li 2019;Hu 2021;Mehta discovery began identifying precursor, 4'-O-methylnorbelladine (4OMN), followed coupling catalyzed cytochrome P450 NtCYP96T6. facilitates para-ortho (p-o') necessary produce skeleton. Subsequent methylation reduction steps, NtNMT1 NtAKR1 respectively, complete biosynthesis 2) (Mehta profound metabolic engineering. sourced primarily populations daffodils, biosynthesize it engineered systems holds promise Additionally, galantamine's helps understand how generate chemical diversity simple precursors, foundation engineering related value.The underscores complexity elegance Both share common feature acting inhibitors, though evolutionary origins differ significantly. families, distinct pressures, developed highly allow synthesize intricate structures. While represents advancement, several challenges remain.First, vivo functional roles are fully understood. speculated they serve against herbivores, regulatory mechanisms governing elusive (Chavez Further ecological could provide important medicinal plants, pathways, interactions environment (Szypuła Pietrosiuk, 2024).Second, scalability producing heterologous remains challenge. transient expression N.benthamiana proof-of-concept biosynthesis, translating industrial-scale will require optimization gene expression, precursor supply, enzymatic activity plant-based platforms 2024b;Yang Optimizing enhancing activity, achieving high-yield critical bottlenecks.Microbial platforms, Saccharomyces cerevisiae Pichia pastoris, offer promising avenues large-scale ease genetic manipulation 2023;Yang On hand, chassis Nicotiana benthamiana unique advantages, including environments compartmentalized cells conducive 2023;Golubova 2024;Liu 2024b). Advances CRISPR-based genome editing, multi-gene assembly, flux pivotal overcoming current limitations (Liao 2023;Xie 2023;Teng tools, create paving way accessible therapeutics disease.Finally, discovering new species should be overlooked. likely represent fraction produce. Systematic exploration yield AChE diseases.The moment neuropharmacology. deepen metabolism practical treatments. As population ages burden diseases grows, plantderived continue play essential role treatment. lies intersection biology, engineering, sciences, innovative solutions neurological disorders.MY: Conceptualization, Writing-original draft. MY, QY, ZZ: Writing-review editing.

Language: Английский

Citations

1

Semi‐automated workflow for high‐throughput Agrobacterium‐mediated plant transformation DOI Creative Commons
Davide Annese, Facundo Romani, Carolina Grandellis

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(1)

Published: April 1, 2025

High-throughput experiments in plants are hindered by long generation times and high costs. To address these challenges, we present an optimized pipeline for Agrobacterium tumefaciens transformation a simplified protocol to obtain stable transgenic lines of the model liverwort Marchantia polymorpha, paving way efficient high-throughput plant synthetic biology other applications. Our involves freeze-thaw method six-well plates that can be adapted robotic automation. Using Opentrons open-source platform, implemented semi-automated showing similar efficiency compared manual manipulation. Additionally, have streamlined process selection M. reducing cost, time, labor without compromising efficiency. The addition sucrose media significantly enhances production gemmae, accelerating isogenic plants. We believe protocols potential facilitate screenings diverse species represent significant step towards full automation pipelines. This approach allows testing ~100 constructs per month, using conventional tissue culture facilities. recently demonstrated successful implementation this screening hundreds fluorescent reporters gemmae.

Language: Английский

Citations

1

Localising enzymes to biomolecular condensates increases their accumulation and benefits engineered metabolic pathway performance in Nicotiana benthamiana DOI Creative Commons
Anya Lindström Battle, A. John Barrett, Mark D. Fricker

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

Summary Establishment of N. benthamiana as a robust biofactory is complicated by issues such product toxicity and proteolytic degradation target proteins / introduced enzymes. Here we investigate whether biomolecular condensates can be used to address these problems. We engineered in leaves using transient expression synthetic modular scaffolds. The vivo properties the that resulted were consistent with them being liquid-like bodies thermodynamic features typical multicomponent phase-separating systems. show recruitment enzymes led several fold yield increases one- three-step metabolic pathways (citramalate biosynthesis poly-3-hydroxybutyrate (PHB) biosynthesis, respectively). This enhanced could for reasons including improved enzyme kinetics, metabolite channelling or avoidance cytotoxicity retention pathway within condensate, which was demonstrated PHB. However, also observed several-fold increase amount accumulated when they targeted condensates. suggests more stable localised condensate than freely diffusing cytosol. hypothesise this stability likely main driver increased production. Our findings provide foundation leveraging plant engineering advance versatile industrial applications.

Language: Английский

Citations

0

Localising enzymes to biomolecular condensates increase their accumulation and benefits engineered metabolic pathway performance in Nicotiana benthamiana DOI Creative Commons
Anya Lindström Battle, A. John Barrett, Mark D. Fricker

et al.

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

Summary The establishment of Nicotiana benthamiana as a robust biofactory is complicated by issues such product toxicity and proteolytic degradation target proteins/introduced enzymes. Here we investigate whether biomolecular condensates can be used to address these problems. We engineered in N. leaves using transient expression synthetic modular scaffolds. vivo properties the that resulted were consistent with them being liquid‐like bodies thermodynamic features typical multicomponent phase‐separating systems. show recruitment enzymes led several‐fold yield increases one‐ three‐step metabolic pathways (citramalate biosynthesis poly‐3‐hydroxybutyrate (PHB) biosynthesis, respectively). This enhanced could for several reasons including improved enzyme kinetics, metabolite channelling or avoidance cytotoxicity retention pathway within condensate, which was demonstrated PHB. However, also observed increase amount accumulated when they targeted condensates. suggests more stable localised condensate than freely diffusing cytosol. hypothesise this stability likely main driver increased production. Our findings provide foundation leveraging plant engineering advance versatile industrial applications.

Language: Английский

Citations

0

UGT73FB1 contributes to scaffold‐selective biosynthesis of triterpenoid glucosyl esters in saponin‐rich bark of arjuna tree DOI

Poonam Vyas,

Payal Srivastava,

Gaurav Srivastava

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(1)

Published: April 1, 2025

SUMMARY Plants make structurally diverse triterpenoids for their physiological needs, which have shown numerous therapeutic applications. Arjuna tree ( Terminalia arjuna ) produces bioactive oleanane (β‐amyrin‐derived) arjunic acid, arjungenin, and arjunolic the respective C28‐ O ‐glucopyranosyl esters arjunetin, arjunglucoside I, II. Arjunic acid arjunetin are major oleananes in bark, while II found minor levels. Although arjungenin was detected at a considerable level, I only trace suggesting selective biosynthesis and/or accumulation of triterpenoid glucosyl bark. However, enzyme contributing to ‐glucosylation not characterized. We mined RNA‐sequencing data identified UDP‐glucosyltransferase (UGT) transcripts that were enriched bark transcriptome. Further, biochemical screening UGTs UGT73FB1, catalyzed scaffold‐selective manner. Recombinant UGT73FB1 produced Escherichia coli or Nicotiana benthamiana formed II, but ester (arjunglucoside I). Interestingly, showed better activity using than ursanes (α‐amyrin‐derived), it did show various lupane (lupeol‐derived). Overall, spatial patterns transcript expression suggested role arjuna. Moreover, co‐expression with β‐amyrin synthase C2, C23, C28 hydroxylases/oxidases led complete reconstruction pathway N. , utility enzymes rare glucopyranosyl heterologous hosts.

Language: Английский

Citations

0

Navigating the challenges of engineering composite specialized metabolite pathways in plants DOI Creative Commons
Sachin A. Gharat, Vaijayanti A. Tamhane, Ashok P. Giri

et al.

The Plant Journal, Journal Year: 2025, Volume and Issue: 121(6)

Published: March 1, 2025

SUMMARY Plants are a valuable source of diverse specialized metabolites with numerous applications. However, these compounds often produced in limited quantities, particularly under unfavorable ecological conditions. To achieve sufficient levels target metabolites, alternative strategies such as pathway engineering heterologous systems like microbes (e.g., bacteria and fungi) or cell‐free can be employed. Another approach is plant engineering, which aims to either enhance the native production original reconstruct model system. Although increasing metabolite promising strategy, plants exotic pose significant challenges for genetic manipulation. Effective requires comprehensive prior knowledge genes enzymes involved, well precursor, intermediate, branching, final metabolites. Thus, thorough elucidation biosynthetic closely linked successful metabolic host systems. In this review, we highlight recent advances engineering. We focus on efforts engineer complex, multi‐step pathways that require expression at least eight transient three stable transformation. Reports complex stably transformed remain relatively scarce. discuss major hurdles overcoming them, followed by an overview achievements, challenges, solutions reconstitution through Recent including computer‐based predictions offer platforms sustainable plants.

Language: Английский

Citations

0

Recent trends in human milk oligosaccharides: New synthesis technology, regulatory effects, and mechanisms of non‐intestinal functions DOI

Qingxue Chen,

Xiangxin Wang, Peng Zhang

et al.

Comprehensive Reviews in Food Science and Food Safety, Journal Year: 2025, Volume and Issue: 24(2)

Published: March 1, 2025

Abstract Recently, the non‐intestinal functions of human milk oligosaccharides (HMOs) have been widely documented, including their roles in promoting brain development and growth, as well ameliorating anxiety, allergies, obesity. Understanding mechanisms action is becoming increasingly critical. Furthermore, these effects are frequently associated with type structure HMOs. As an innovative technology, “plant factory” expected to complement traditional synthesis technology. This study reviews novel techniques. Particular emphasis placed on processes, advantages, limitations technology can express genes related HMO instantaneously plant leaves, thereby enabling rapid cost‐effective generation However, remains underdeveloped, challenges low yield unsustainable production must be addressed. we present overview most recent clinical preclinical studies review emphasizes underlying HMOs primarily exert through cleavage beneficial monomer components, metabolism produce advantageous metabolites, regulation immune responses.

Language: Английский

Citations

0

Harnessing plant biosynthesis for the development of next-generation therapeutics DOI Creative Commons
Philip Spence, James Reed, Anne Osbourn

et al.

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(11), P. e3002886 - e3002886

Published: Nov. 5, 2024

Genomics-based predictions indicate that plants harbor the ability to make a vast array of as yet undiscovered chemistry. Recent advances open up potential harness this capability at unprecedented scale for discovery and development new therapeutics.

Language: Английский

Citations

1

Semi-automated workflow for high-throughput Agrobacterium-mediated plant transformation DOI Creative Commons
Davide Annese, Facundo Romani, Carolina Grandellis

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 10, 2024

ABSTRACT High-throughput experiments in plants are hindered by long generation times and high costs. To address these challenges, we present an optimized pipeline for Agrobacterium tumefaciens transformation simplified a protocol to obtain stable transgenic lines of the model liverwort Marchantia polymorpha , paving way efficient high-throughput plant synthetic biology other applications. Our involves freeze-thaw method 6-well plates that can be adapted robotic automation. Using Opentrons open-source platform, implemented semi-automated showing similar efficiency compared manual manipulation. Additionally, have streamlined process selection M. reducing cost, time, labour without compromising efficiency. The addition sucrose media significantly enhances production gemmae, accelerating isogenic plants. We believe protocols potential facilitate screenings diverse species represent significant step towards full automation pipelines. This approach allows testing ∼100 constructs per month, using conventional tissue culture facilities. recently demonstrated successful implementation this screening hundreds fluorescent reporters gemmae.

Language: Английский

Citations

0

De Novo Synthesis of Anticholinergic Hyoscyamine and Scopolamine in Nicotiana benthamiana Based on Elucidating Tropane Alkaloid Biosynthetic Pathway of Anisodus luridus DOI Creative Commons

Mengling Wen,

Junlan Zeng, Fei Qiu

et al.

Agronomy, Journal Year: 2024, Volume and Issue: 14(11), P. 2460 - 2460

Published: Oct. 22, 2024

Anisodus luridus, a perennial herb belonging to the genus of Solanaceae family, is an important Tibetan medicinal plant that produces pharmaceutical tropane alkaloids (TAs) including hyoscyamine and scopolamine. Its high yield makes A. luridus valuable source for commercially producing TAs. In this study, we conduct homologous gene research across transcriptome data different tissues together with functionally tested sequences in Atropa belladonna as reference identify 13 candidate genes TAs biosynthesis luridus. The results show these identified were highly conserved terms sequence similarity expression patterns compared belladonna, suggesting two species may share same biosynthetic pathway biosynthesis. Furthermore, scopolamine was detected Nicotiana benthamiana leaves when enzymes co-expressed N. benthamiana, which confirmed are involved our study not only systematically elucidate alkaloid but also realize de novo synthesis first time. It now possible make potential production through synthetic biology techniques.

Language: Английский

Citations

0