Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae)

AbstractTropane alkaloids and terpenoids are widely used in the medicine and pharmaceutic industry and evolved as chemical defenses against herbivores and pathogens in the annual herb Datura stramonium (Solanaceae). Here, we present the first draft genomes of two plants from contrasting environments of D. stramonium. Using these de novo assemblies, along with other previously published genomes from 11 Solanaceae species, we carried out comparative genomic analyses to provide insights on the genome evolution of D. stramonium within the Solanaceae family, and to elucidate adaptive genomic signatures to biotic and abiotic stresses in this plant. We also studied, in detail, the evolution of four genes of D. stramonium—Putrescine N-methyltransferase, Tropinone reductase I, Tropinone reductase II and Hyoscyamine-6S-dioxygenase—involved in the tropane alkaloid biosynthesis. Our analyses revealed that the genomes of D. stramonium show signatures of expansion, physicochemical divergence and/or positive selection on proteins related to the production of tropane alkaloids, terpenoids, and glycoalkaloids as well as on R defensive genes and other important proteins related with biotic and abiotic pressures such as defense against natural enemies and drought.

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Tropane alkaloids and terpenes synthase genes of Datura stramonium (Solanaceae)

PeerJ ◽

10.7717/peerj.11466 ◽

2021 ◽

Vol 9 ◽

pp. e11466

Author(s):

Sabina Velázquez-Márquez ◽

Iván M. De-la-Cruz ◽

Rosalinda Tapia-López ◽

Juan Núñez-Farfán

Keyword(s):

Positive Selection ◽

Chemical Defense ◽

Protein Structures ◽

Tropane Alkaloids ◽

Datura Stramonium ◽

Protein Modeling ◽

Terpene Synthases ◽

New Genes ◽

Datura Metel ◽

Tropinone Reductase

Background Plants have evolved physical–chemical defense to prevent/diminish damage by their enemies. Chemical defense involves the synthesis’ pathways of specialized toxic, repellent, or anti-nutritive metabolites to herbivores. Molecular evolutionary studies have revealed the origin of new genes, acquisition and functional diversification along time in different plant lineages. Methods Using bioinformatic tools we analyze gene divergence of tropane alkaloids (TAs) and terpene synthases (TPSs) in Datura stramonium and other species of Solanaceae; compared gene and amino acids sequence of TAs and TPSs on genomes, cDNA and proteins sequences of Viridiplantae. We analyzed two recently assembled genomes of D. stramonium (Ticumán and Teotihuacán), transcriptomes of Datura metel and genomes of other Solanaceae. Hence, we analyzed variation of TAs and TPSs to infer genes involved in plant defense and plant responses before stress. We analyzed protein modeling and molecular docking to predict interactions between H6H and ligand; we translated the sequences (Teo19488, Tic8550 and Tic8549) obtained from the two genomes of D. stramonium by using Swiss-Model and Ramachandran plot and MolProbity structure validation of Teo19488 protein model. Results For TAs, we detected an expansion event in the tropinone reductase II (TRII) and the ratio synonymous/non-synonymous substitutions indicate positive selection. In contrast, a contraction event and negative selection was detected in tropinone reductase I (TRI). In Hy-oscyamine 6 b-hydroxylase (H6H), enzyme involved in the production of tropane alkaloids atropine and scopolamine, the synonymous/non-synonymous substitution ratio in its dominion indicates positive selection. For terpenes (TPS), we found 18 DsTPS in D. stramomiun and seven in D. metel; evolutionary analyses detected positive selection in TPS10.1 and TPS10.2 of D. stramonium and D. metel. Comparison of copies of TPSs in D. stramonium detected variation among them in the binding site. Duplication events and differentiation of TAs and TPSs of D. stramonium, as compared to other Solanaceae, suggest their possible involvement on adaptive evolution of defense to herbivores. Protein modeling and docking show that the three protein structures obtained of DsH6H from Teo19488, Tic-8550 and Tic8549 maintain the same interactions and the union site of 2OG-FeII_Oxy with the Hy-o ligand as in 6TTM of D. metel. Conclusion Our results indicate differences in the number of gene copies involved in the synthesis of tropane alkaloids, between the genomes of D. stramonium from two Mexican populations. More copies of genes related to the synthesis of tropane alkaloids (TRI, TRII, H6H, PMT) are found in D. stramonium as compared to Viridiplantae. Likewise, for terpene synthases (TPS), TPS-10 is duplicated in D. stramonium and D. metel. Further studies should be directed to experimentally assess gain (overexpression) or loss (silencing) of function of duplicated genes.

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Effects of Water Availability in the Soil on Tropane Alkaloid Production in Cultivated Datura stramonium

Metabolites ◽

10.3390/metabo9070131 ◽

2019 ◽

Vol 9 (7) ◽

pp. 131 ◽

Cited By ~ 3

Author(s):

Abigail Moreno-Pedraza ◽

Jennifer Gabriel ◽

Hendrik Treutler ◽

Robert Winkler ◽

Fredd Vergara

Keyword(s):

Mass Spectrometry ◽

Water Availability ◽

Mass Spectra ◽

Tropane Alkaloids ◽

Datura Stramonium ◽

Tropane Alkaloid ◽

Industrial Applications ◽

Cultivated Plants ◽

Irrigation Levels ◽

Different Levels

Background: different Solanaceae and Erythroxylaceae species produce tropane alkaloids. These alkaloids are the starting material in the production of different pharmaceuticals. The commercial demand for tropane alkaloids is covered by extracting them from cultivated plants. Datura stramonium is cultivated under greenhouse conditions as a source of tropane alkaloids. Here we investigate the effect of different levels of water availability in the soil on the production of tropane alkaloids by D. stramonium. Methods: We tested four irrigation levels on the accumulation of tropane alkaloids. We analyzed the profile of tropane alkaloids using an untargeted liquid chromatography/mass spectrometry method. Results: Using a combination of informatics and manual interpretation of mass spectra, we generated several structure hypotheses for signals in D. stramonium extracts that we assign as putative tropane alkaloids. Quantitation of mass spectrometry signals for our structure hypotheses across different anatomical organs allowed us to identify patterns of tropane alkaloids associated with different levels of irrigation. Furthermore, we identified anatomic partitioning of tropane alkaloid isomers with pharmaceutical applications. Conclusions: Our results show that soil water availability is an effective method for maximizing the production of specific tropane alkaloids for industrial applications.

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Facing tropane alkaloid contamination in millet

Quality Assurance and Safety of Crops & Foods ◽

10.15586/qas.v13i2.888 ◽

2021 ◽

Vol 13 (2) ◽

pp. 79-86

Author(s):

Jens Begemann ◽

Saman Ostovar ◽

Christine Schwake-Anduschus

Keyword(s):

Plant Material ◽

Tropane Alkaloids ◽

Datura Stramonium ◽

Tropane Alkaloid ◽

The European Union ◽

Limit Values ◽

Jimson Weed ◽

Seed Content ◽

Maize Cultivation ◽

The Eu

Thorn Apple or Jimson Weed (Datura stramonium) is a tropane alkaloid containing widespread pest plant growing in central Europe. This pest predominantly occurs in millet, buckwheat and maize cultivation. Therefore, sound cleaning of these crops is just as pivotal as reliable analytics. The cleaning of millet at laboratory scale with commercial mechanical cleaning devices, such as sieves, indented separators or table sorters without using colour sorters, reduces the dark coloured Datura seed content by up to 99%. Nevertheless, the few remaining Datura seeds (up to one nut per 30 kg) could lead to an exceedance of the European Union (EU) limit values for tropane alkaloids in baby food. However, plant material other than seeds or even invisible abrasion of Datura seeds can contaminate the millet during harvest, handling, cleaning processes or crop transportation. Contamination originating from adhesive dust can be removed by dehulling the kernels, and a reduction below the EU detection limit could be achieved.

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Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture

BMC Genomics ◽

10.1186/s12864-021-07489-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Alex Rajewski ◽

Derreck Carter-House ◽

Jason Stajich ◽

Amy Litt

Keyword(s):

Tissue Culture ◽

Gene Annotation ◽

Draft Genome ◽

Tropane Alkaloids ◽

Datura Stramonium ◽

Single Copy ◽

Tropane Alkaloid ◽

Biosynthetic Genes ◽

Protein Coding ◽

Culture Process

Abstract Background Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkaloids. Recently, we published a tissue-culture based transformation protocol for D. stramonium that enables more thorough functional genomics studies of this plant. However, the tissue culture process can lead to undesirable phenotypic and genomic consequences independent of the transgene used. Here, we have assembled and annotated a draft genome of D. stramonium with a focus on tropane alkaloid biosynthetic genes. We then use mRNA sequencing and genome resequencing of transformants to characterize changes following tissue culture. Results Our draft assembly conforms to the expected 2 gigabasepair haploid genome size of this plant and achieved a BUSCO score of 94.7% complete, single-copy genes. The repetitive content of the genome is 61%, with Gypsy-type retrotransposons accounting for half of this. Our gene annotation estimates the number of protein-coding genes at 52,149 and shows evidence of duplications in two key alkaloid biosynthetic genes, tropinone reductase I and hyoscyamine 6 β-hydroxylase. Following tissue culture, we detected only 186 differentially expressed genes, but were unable to correlate these changes in expression with either polymorphisms from resequencing or positional effects of transposons. Conclusions We have assembled, annotated, and characterized the first draft genome for this important model plant species. Using this resource, we show duplications of genes leading to the synthesis of the medicinally important alkaloid, scopolamine. Our results also demonstrate that following tissue culture, mutation rates of transformed plants are quite high (1.16 × 10− 3 mutations per site), but do not have a drastic impact on gene expression.

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Jacobsen syndrome and neonatal bleeding: report on two unrelated patients

Italian Journal of Pediatrics ◽

10.1186/s13052-021-01108-2 ◽

2021 ◽

Vol 47 (1) ◽

Author(s):

Gregorio Serra ◽

Luigi Memo ◽

Vincenzo Antona ◽

Giovanni Corsello ◽

Valentina Favero ◽

...

Keyword(s):

Developmental Delay ◽

De Novo ◽

Comparative Genomic ◽

Fish Analysis ◽

Variable Degree ◽

Jacobsen Syndrome ◽

Contiguous Gene ◽

Clinical Consequences ◽

11Q Deletion

Abstract Introduction In 1973, Petrea Jacobsen described the first patient showing dysmorphic features, developmental delay and congenital heart disease (atrial and ventricular septal defect) associated to a 11q deletion, inherited from the father. Since then, more than 200 patients have been reported, and the chromosomal critical region responsible for this contiguous gene disorder has been identified. Patients’ presentation We report on two unrelated newborns observed in Italy affected by Jacobsen syndrome (JBS, also known as 11q23 deletion). Both patients presented prenatal and postnatal bleeding, growth and developmental delay, craniofacial dysmorphisms, multiple congenital anomalies, and pancytopenia of variable degree. Array comparative genomic hybridization (aCGH) identified a terminal deletion at 11q24.1-q25 of 12.5 Mb and 11 Mb, in Patient 1 and 2, respectively. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletion for Patient 1; parents of Patient 2 refused further genetic investigations. Conclusions Present newborns show the full phenotype of JBS including thrombocytopenia, according to their wide 11q deletion size. Bleeding was particularly severe in one of them, leading to a cerebral hemorrhage. Our report highlights the relevance of early diagnosis, genetic counselling and careful management and follow-up of JBS patients, which may avoid severe clinical consequences and lower the mortality risk. It may provide further insights and a better characterization of JBS, suggesting new elements of the genotype-phenotype correlations.

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Tropane alkaloid biosynthesis: a centennial review

Natural Product Reports ◽

10.1039/d0np00076k ◽

2021 ◽

Author(s):

Jian-Ping Huang ◽

Yong-Jiang Wang ◽

Tian Tian ◽

Li Wang ◽

Yijun Yan ◽

...

Keyword(s):

De Novo ◽

Tropane Alkaloid ◽

Alkaloid Biosynthesis

From the first ambitious imagination of tropinone biosynthesis mechanism in plants published in 1917 to the de novo production of scopolamine in yeast realized in 2020, what did we learn from this long story of more than 100 years old?

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Analytical and in silico study of the inclusion complexes between tropane alkaloids atropine and scopolamine with cyclodextrins

Chemical Papers ◽

10.1007/s11696-021-01742-4 ◽

2021 ◽

Author(s):

Monica Butnariu ◽

Massimiliano Peana ◽

Ioan Sarac ◽

Salvatore Chirumbolo ◽

Haralampos Tzoupis ◽

...

Keyword(s):

Molecular Modeling ◽

Test Performance ◽

Tropane Alkaloids ◽

Datura Stramonium ◽

In Silico Study ◽

Modeling Techniques ◽

Poorly Soluble ◽

Application Potential ◽

Ft Ir ◽

Allelopathic Compounds

AbstractDatura stramonium L. (Solanaceae) possesses a rich tropane alkaloids (TAs) spectrum. The plant contains, in particular, the allelopathic compounds scopolamine and atropine, which are poorly soluble in water, thus limiting their use in agrochemical formulations as biocidal and deterrent agents against herbivore insects. The efficacy of the hydrophobic TAs extracts could be increased with the improvement of their dissolution/leaching properties. This is important for improving screening and test performance and for elucidating the activity of environmentally friendly agricultural approaches, with new perspectives for the production and use of those biodegradable insecticidal products. The present study explores the aspects of atropine and scopolamine complexation with cyclodextrin (CDs) through FT-IR and UV–Vis spectroscopies. In addition, the structures of the inclusion complex of atropine, scopolamine and β-CD have been investigated by molecular modeling techniques. The results obtained indicate that β-CDs are a promising carriers for improving the properties of TAs, therefore increasing their application potential in agrochemical formulations. Graphic abstract

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