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

PeerJ ◽  
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.

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
I. M. De-la-Cruz ◽  
A. Hallab ◽  
U. Olivares-Pinto ◽  
R. Tapia-López ◽  
S. Velázquez-Márquez ◽  
...  
Keyword(s):  
Natural Enemies ◽  
De Novo ◽  
Tropane Alkaloids ◽  
Datura Stramonium ◽  
Tropane Alkaloid ◽  
Chemical Defenses ◽  
Comparative Genomic ◽  
Genomic Signatures ◽  
Solanaceae Species ◽  
Tropinone Reductase

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.

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

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

Levels of tropinone-reductase activities influence the spectrum of tropane esters found in transformed root cultures of Datura stramonium L.

Planta ◽  
1992 ◽  
Vol 188 (4) ◽  
Author(s):  
Birgit Dr�ger ◽  
Andreas Portsteffen ◽  
Angela Schaal ◽  
PeterH. McCabe ◽  
AbigaelC.J. Peerless ◽  
...  
Keyword(s):  
Datura Stramonium ◽  
Root Cultures ◽  
Tropinone Reductase ◽  
Transformed Root Cultures

scholarly journals Development of a DNA-based Assay to Detect and Quantify Tropane Alkaloids Producing Thornapple Contaminations in Processed Food

2019 ◽  
Vol 73 (5) ◽  
pp. 422-425 ◽  
Author(s):  
Anna Weston ◽  
Peter Brodmann ◽  
Maximilian Widmer ◽  
Julian Bartel ◽  
Eric Kübler
Keyword(s):  
Genetically Modified Organisms ◽  
Tropane Alkaloids ◽  
Food Product ◽  
Food Products ◽  
Datura Stramonium ◽  
Processed Food ◽  
Panicum Miliaceum ◽  
Main Ingredient ◽  
Nutrient Source ◽  
Specificity And Sensitivity

Contaminates such as pesticides, toxic molecules of natural origin, genetically modified organisms and others can occur in processed food, especially if the main ingredient grows in open fields exposed to the environment. In particular, some health threatening toxic compounds are natural ingredients of plants that grow wild next to vegetables intended for consumption and can therefore enter the crop yield and stay there undetected. The tropane alkaloids-containing nightshade thornapple Datura stramonium, often grows in close vicinity to millet (Panicum miliaceum) a widely cultivated cereal, representing an important nutrient source in different countries of Asia and Africa. Discriminating thornapple from millet during harvest is not easy and consequently, millet-containing food products are often contaminated with tropane alkaloids from thornapple. In this work, two DNA specific hydrolysis probe qPCR methods were developed for Datura stramonium and Panicum miliaceum in order to detect thornapple contamination in millet-containing food products. The specificity and sensitivity of the developed assay system allows for its application in screenings during food product testing.

KORP: knowledge-based 6D potential for fast protein and loop modeling

2019 ◽  
Vol 35 (17) ◽  
pp. 3013-3019 ◽  
Author(s):  
José Ramón López-Blanco ◽  
Pablo Chacón
Keyword(s):  
Structure Prediction ◽  
Protein Structures ◽  
Joint Probability ◽  
Protein Modeling ◽  
Supplementary Information ◽  
Joint Probability Distribution ◽  
Loop Modeling ◽  
Statistical Potentials ◽  
Knowledge Based ◽  
Backbone Atoms

Abstract Motivation Knowledge-based statistical potentials constitute a simpler and easier alternative to physics-based potentials in many applications, including folding, docking and protein modeling. Here, to improve the effectiveness of the current approximations, we attempt to capture the six-dimensional nature of residue–residue interactions from known protein structures using a simple backbone-based representation. Results We have developed KORP, a knowledge-based pairwise potential for proteins that depends on the relative position and orientation between residues. Using a minimalist representation of only three backbone atoms per residue, KORP utilizes a six-dimensional joint probability distribution to outperform state-of-the-art statistical potentials for native structure recognition and best model selection in recent critical assessment of protein structure prediction and loop-modeling benchmarks. Compared with the existing methods, our side-chain independent potential has a lower complexity and better efficiency. The superior accuracy and robustness of KORP represent a promising advance for protein modeling and refinement applications that require a fast but highly discriminative energy function. Availability and implementation http://chaconlab.org/modeling/korp. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals

2020 ◽  
Vol 117 (11) ◽  
pp. 5977-5986 ◽  
Author(s):  
Greg Slodkowicz ◽  
Nick Goldman
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary Biology ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Protein Structures ◽  
Unexpected Finding ◽  
Evolutionary Analysis ◽  
Genomic Scale ◽  
Evolution Of Mammals

Understanding the molecular basis of adaptation to the environment is a central question in evolutionary biology, yet linking detected signatures of positive selection to molecular mechanisms remains challenging. Here we demonstrate that combining sequence-based phylogenetic methods with structural information assists in making such mechanistic interpretations on a genomic scale. Our integrative analysis shows that positively selected sites tend to colocalize on protein structures and that positively selected clusters are found in functionally important regions of proteins, indicating that positive selection can contravene the well-known principle of evolutionary conservation of functionally important regions. This unexpected finding, along with our discovery that positive selection acts on structural clusters, opens previously unexplored strategies for the development of better models of protein evolution. Remarkably, proteins where we detect the strongest evidence of clustering belong to just two functional groups: Components of immune response and metabolic enzymes. This gives a coherent picture of pathogens and xenobiotics as important drivers of adaptive evolution of mammals.

scholarly journals Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions

2017 ◽  
Vol 30 (5) ◽  
pp. 387-394 ◽  
Author(s):  
J.C. Gaines ◽  
A. Virrueta ◽  
D.A. Buch ◽  
S.J. Fleishman ◽  
C.S. O'Hern ◽  
...  
Keyword(s):  
Hard Sphere ◽  
Protein Structures ◽  
Standard Test ◽  
Protein Modeling ◽  
Side Chain ◽  
Hard Sphere Model ◽  
Sphere Model ◽  
Modeling Software ◽  
High Prediction ◽  
Chain Conformations

Abstract Protein core repacking is a standard test of protein modeling software. A recent study of six different modeling software packages showed that they are more successful at predicting side chain conformations of core compared to surface residues. All the modeling software tested have multicomponent energy functions, typically including contributions from solvation, electrostatics, hydrogen bonding and Lennard–Jones interactions in addition to statistical terms based on observed protein structures. We investigated to what extent a simplified energy function that includes only stereochemical constraints and repulsive hard-sphere interactions can correctly repack protein cores. For single residue and collective repacking, the hard-sphere model accurately recapitulates the observed side chain conformations for Ile, Leu, Phe, Thr, Trp, Tyr and Val. This result shows that there are no alternative, sterically allowed side chain conformations of core residues. Analysis of the same set of protein cores using the Rosetta software suite revealed that the hard-sphere model and Rosetta perform equally well on Ile, Leu, Phe, Thr and Val; the hard-sphere model performs better on Trp and Tyr and Rosetta performs better on Ser. We conclude that the high prediction accuracy in protein cores obtained by protein modeling software and our simplified hard-sphere approach reflects the high density of protein cores and dominance of steric repulsion.

Ontogenetic variation of the tropane alkaloids in Datura stramonium

2005 ◽  
Vol 33 (10) ◽  
pp. 1017-1029 ◽  
Author(s):  
Strahil Berkov ◽  
Tsvetelina Doncheva ◽  
Stefan Philipov ◽  
Kiril Alexandrov
Keyword(s):  
Tropane Alkaloids ◽  
Datura Stramonium ◽  
Ontogenetic Variation
Sign in / Sign up

Export Citation Format

Share Document