Sub-functionalization and epigenetic regulation of a biosynthetic gene cluster inSolanaceae DOI Creative Commons
Santiago Priego‐Cubero, Eva Knoch, Zhidan Wang

et al.

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

Published: Oct. 3, 2024

Abstract Biosynthetic gene clusters (BGCs) are sets of often heterologous genes that genetically and functionally linked. Among eukaryotes, BGCs most common in plants fungi, where they ensure the co-expression different enzymes coordinating biosynthesis specialised metabolites. Here, we report on a newly identified withanolide BGC Physalis grisea (ground-cherry), member nightshade family ( Solanaceae ). A combination transcriptomic, epigenomic metabolic analyses, revealed that, following duplication event, this evolved two tissue-specifically expressed sub-clusters, containing eight pairs paralogs contribute to related but distinct biochemical processes; sub- functionalisation is tightly associated with epigenetic features local chromatin environment. The sub-clusters appear strictly isolated from each other at structural level, forming highly self-interacting domain tissue-dependent levels condensation. This correlates expression exclusively either above- or below-ground tissue, thus spatially separating production compounds. By comparative phylogenomic analysis, show likely before diversification underwent lineage- specific diversifications losses. tissue-specific sub-functionalisation species Physalideae tribe other, independent events outside clade. In sum, our study reports first instance an epigenetically modulated within sheds light withanolides, diverse group steroidal triterpenoids important plant defence amenable pharmaceutical applications due their anti-inflammatory, antibiotic anti- cancer properties.

Language: Английский

Recent advances in triterpenoid pathway elucidation and engineering DOI
Sandeep Dinday, Sumit Ghosh

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 68, P. 108214 - 108214

Published: July 20, 2023

Language: Английский

Citations

38
Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John’s wort DOI
Song Wu, Ana Luísa Malaco Morotti, Jun Yang

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(9), P. 1439 - 1457

Published: Aug. 12, 2024

Language: Английский

Citations

9
Comprehensive mutant chemotyping reveals embedding of a lineage-specific biosynthetic gene cluster in wider plant metabolism DOI Creative Commons
Xue Qiao, Alan Houghton, James Reed

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(12)

Published: March 19, 2025

Plants produce diverse specialized metabolites with important ecological functions. It has recently become apparent that the genes for many of these pathways are not dispersed in plant genomes, but rather arranged like beads on a string biosynthetic gene clusters (BGCs). Pathways encoded by BGCs as rule dedicated linear do form parts wider metabolic networks. In contrast, biosynthesis widely distributed more ancestral such carotenoids and anthocyanins clustered. Little is known about how evolved clustered interact general metabolism. We characterized 12-gene BGC antimicrobial defense compound avenacin A-1, triterpene glycoside produced oats. Avenacin A-1 acylated fluorophore N -methyl anthranilate confers bright blue fluorescence oat root tips under ultraviolet light. Here, we exploit suite >100 avenacin-deficient mutants identified screening reduced to identify required function this paradigm BGC. Using combination mutant chemotyping, biochemical molecular analysis, genome resequencing, two nonclustered ( Sad4 Pal2 ) encoding enzymes synthesize donors glycosylation acylation (recruited from phenylpropanoid tryptophan pathways). Our finding Cluster Auxiliary Enzymes (CAEs) provides insights into interplay between metabolism newly lineage-specific

Language: Английский

Citations

1
Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach DOI
Hongwei Yu,

Yuli Li,

Wentao Han

et al.

Nature Protocols, Journal Year: 2024, Volume and Issue: 19(6), P. 1623 - 1678

Published: March 21, 2024

Language: Английский

Citations

5
Synthesis of polymerizable betulin maleic diester derivative for dental restorative resins with antibacterial activity DOI
Zhiyuan Ma, Yifan Chen, Ruili Wang

et al.

Dental Materials, Journal Year: 2024, Volume and Issue: 40(6), P. 941 - 950

Published: May 7, 2024

Language: Английский

Citations

5
Drought stress-mediated alterations in secondary metabolites and biosynthetic gene expression in cumin plants: Insights from gene-specific and metabolite-level analyses DOI Creative Commons

Sepideh Ghasemi,

Hassan Hassani Kumleh, Mojtaba Kordrostami

et al.

Plant Stress, Journal Year: 2023, Volume and Issue: 10, P. 100241 - 100241

Published: Sept. 27, 2023

In this research, we investigated the impact of drought stress on secondary metabolite production in cumin plants and associated transcriptional changes biosynthetic genes. Drought induced a significant increase levels beta-carotene, lycopene, terpenes, anthocyanin, phenolic compounds, flavonoids, alkaloids, indicating an adaptive metabolic shift response to adverse conditions. Concurrently, there was upregulation expression key genes, including Phenylalanine ammonia-lyase (PAL), 3-deoxy-7-phosphoheptulonate synthase (DAHP synthase), Deoxy xylose phosphate reductase (DXS), 3-hydroxy-3-methylglutaryl-CoA (HMGR), Geranyl diphosphate (GPPS), which corroborated findings. Notably, while most metabolites exhibited increasing trend under stress, flavonoids displayed disproportionate elevation, even as overall decrease compounds other metabolites. This observation suggests potential activation alternative flavonoid synthesis pathways or conversion during stress. Strong correlations were identified between genes their respective concentrations, underscoring central role regulation Collectively, our results provide comprehensive understanding adaptations when exposed Such insights can be pivotal designing drought-resilient crops, with implications for food security amidst escalating climatic challenges.

Language: Английский

Citations

13
Navigating Amaryllidaceae Alkaloids: Bridging Gaps and Charting Biosynthetic Territories – A Comprehensive Review DOI Creative Commons
Nuwan Sameera Liyanage, Fatima Awwad, Karen Cristine Gonçalves dos Santos

et al.

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: unknown

Published: April 23, 2024

Amaryllidaceae alkaloid (AAs) biosynthesis has garnered significant attention in recent years, particularly with the commercialisation of galanthamine as a treatment for symptoms Alzheimer's disease. A amount research work over last 8 decades focused on understanding AA biosynthesis, starting from early radiolabelling studies to multi-omics analysis modern biotechnological advancements. Those enabled identification hundreds metabolites, characterisation biochemical pathway, an environmental stimuli, and molecular regulation these pharmaceutically agriculturally important metabolites. Despite numerous works there remain gaps their plants. As such, further is needed fully elucidate metabolic pathway facilitate production. This review aims provide comprehensive overall summary current state knowledge AAs elicitation transcription factors expression cell nucleus transport apoplast, highlight challenges that need be overcome advancement.

Language: Английский

Citations

4
The root of plant-plant interactions: Belowground special cocktails DOI Creative Commons
Laura Mathieu, Elsa Ballini,

Jean-Benoit Morel

et al.

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 80, P. 102547 - 102547

Published: May 14, 2024

Plants interact with each other via a multitude of processes among which belowground communication facilitated by specialized metabolites plays an important but overlooked role. Until now, the exact targets, modes action, and resulting phenotypes that these induce in neighboring plants have remained largely unknown. Moreover, positive interactions driven release root exudates are prevalent both natural field conditions controlled laboratory environments. In particular, intraspecific suggest genotypic recognition mechanism addition to non-self perception plant roots. This review concentrates on recent discoveries regarding how one another through signals intra- interspecific mixtures. Furthermore, we elaborate enhanced understanding can propel agroecology forward.

Language: Английский

Citations

4
Haplotype-resolved genome of Agastache rugosa (Huo Xiang) provides insight into monoterpenoid biosynthesis and gene cluster evolution DOI Creative Commons
Chanchan Liu, Dishuai Li,

Jingjie Dang

et al.

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(5)

Published: Feb. 1, 2025

Abstract Monoterpenoids are small volatile molecules produced by many plants that have applications in consumer products and healthcare. Plants from the mint family (Lamiaceae) prodigious producers of monoterpenoids, including a chemotype Agastache rugosa (Huo Xiang), which produces pulegone isomenthone. We sequenced, assembled annotated haplotype-resolved chromosome-scale genome assembly A. with monoterpene chemotype. This revealed biosynthesis genes biosynthetic gene cluster, shares common origin cluster Schizonepeta tenuifolia. Using phylogenetics synteny analysis, we describe how clusters these two species diverged through inversions duplications. Hi-C identified tentative evidence contact between an array reductases, both regions also enriched retrotransposons. its analysis add valuable novel insights to organization evolution terpenoid Lamiaceae.

Language: Английский

Citations

0
Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster in Solanaceae DOI Creative Commons
Santiago Priego‐Cubero, Eva Knoch, Zhidan Wang

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(8)

Published: Feb. 20, 2025

Biosynthetic gene clusters (BGCs) are sets of often heterologous genes that genetically and functionally linked. Among eukaryotes, BGCs most common in plants fungi ensure the coexpression different enzymes coordinating biosynthesis specialized metabolites. Here, we report identification a withanolide BGC Physalis grisea (ground-cherry), member nightshade family (Solanaceae). A combination transcriptomic, epigenomic, metabolic analyses revealed that, following duplication event, this evolved two tissue-specifically expressed subclusters, containing several pairs paralogs contribute to related but distinct biochemical processes; subfunctionalization is tightly associated with epigenetic features local chromatin environment. The subclusters appear strictly isolated from each other at structural level, forming highly self-interacting domain tissue-dependent levels condensation. This correlates expression either above- or below-ground tissue, thus spatially separating production compounds. By comparative phylogenomics, show likely before diversification Solanaceae underwent lineage-specific diversifications losses. tissue-specific species Physalideae tribe other, independent events outside clade. In sum, our study reports on an instance epigenetically modulated within sheds light withanolides, diverse group steroidal triterpenoids important plant defense amenable pharmaceutical applications due their anti-inflammatory, antibiotic, anticancer properties.

Language: Английский

Citations

0