The Structure-Based Three-Dimensional Pharmacophore Models for Arabidopsis thaliana HPPD inhibitors as Herbicide

Arabidopsis thaliana genome encodes two POLE2 homologs known as polymerase epsilon catalytic subunit A (POLE2A) and polymerase epsilon catalytic subunit B (POLE2B). They play a very important role in DNA repair mechanisms. In this study, bioinformatics tools were used to understand DNA repair mechanisms in A. thaliana in which POLE2A and POLE2B proteins are involved. Through interactome analysis of POLE2A and POLE2B homolog proteins in A. thaliana, their additional roles in DNA repair were explored. The most important proteins that are participating in DNA repairs, like MSH2, MSH5, PCNA1, PCNA2, PRL, and CDC45 were identified as interactors of both POLE2A and POLE2B. The three-dimensional structure of POLE2 proteins was identified to decipher the complexity of NER, GG-NER, MMR, TFIIH, and TC-NER repair mechanisms through the identification of docking sites. The interaction complex of POLE2A and POLE2B with six proteins was confirmed and found to have a significant role in DNA repair processes and UV-B tolerance. The interactome analysis of POLE2A and POLE2B performed here once again confirms the complexity of the DNA repair mechanism in plants.

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A CLEM approach to access to the ultrastructure at the graft interface in Arabidopsis thaliana

10.1101/2021.07.13.452258 ◽

2021 ◽

Author(s):

Clément Chambaud ◽

Sarah Jane Cookson ◽

Nathalie Ollat ◽

Emmanuelle M. F. Bayer ◽

Lysiane Brocard

Keyword(s):

Electron Microscopy ◽

Arabidopsis Thaliana ◽

Endoplasmic Reticulum ◽

Cell Wall ◽

Light And Electron Microscopy ◽

Three Dimensional ◽

Cellular Events ◽

Membrane Tethering ◽

Secondary Plasmodesmata ◽

Graft Interface

Despite recent progress in our understanding of the graft union formation, we still know little about the cellular events underlying the grafting process. This is partially due to the difficulty of reliably targeting the graft interface in electron microscopy to study its ultrastructure and three-dimensional architecture. To overcome this technological bottleneck, we developed a correlative light electron microscopy approach (CLEM) to study the graft interface with high ultrastructural resolution. Grafting hypocotyls of Arabidopsis thaliana lines expressing YFP or mRFP in the endoplasmic reticulum allowed the efficient targeting of the grafting interface for under light and electron microscopy. To explore the potential of our method to study sub-cellular events at the graft interface, we focused on the formation of secondary plasmodesmata (PD) between the grafted partners. We showed that 4 classes of PD were formed at the interface and that PD introgression into the call wall was initiated equally by both partners. Moreover, the success of PD formation appeared not systematic with a third of PD not spanning the cell wall entirely. Characterizing the ultrastructural characteristics of these failed PD gives us insights into the process of secondary PD biogenesis. We showed that the thinning of the cell wall and the endoplasmic reticulum-plasma membrane tethering seem to be required for the establishment of symplastic connections between the scion and the rootstock. The resolution reached in this work shows that our CLEM method offer a new scale to the study for biological processes requiring the combination of light and electron microscopy.

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Virtual Screening Using Pharmacophore Models Retrieved from Molecular Dynamic Simulations

International Journal of Molecular Sciences ◽

10.3390/ijms20235834 ◽

2019 ◽

Vol 20 (23) ◽

pp. 5834 ◽

Cited By ~ 5

Author(s):

Pavel Polishchuk ◽

Alina Kutlushina ◽

Dayana Bashirova ◽

Olena Mokshyna ◽

Timur Madzhidov

Keyword(s):

Virtual Screening ◽

Molecular Dynamic ◽

Complex Structure ◽

Three Dimensional ◽

Cyclin Dependent Kinase ◽

Dynamic Simulations ◽

Crystal Complex ◽

Pharmacophore Models ◽

Selection And Ranking ◽

Selection Of

Pharmacophore models are widely used for the identification of promising primary hits in compound large libraries. Recent studies have demonstrated that pharmacophores retrieved from protein-ligand molecular dynamic trajectories outperform pharmacophores retrieved from a single crystal complex structure. However, the number of retrieved pharmacophores can be enormous, thus, making it computationally inefficient to use all of them for virtual screening. In this study, we proposed selection of distinct representative pharmacophores by the removal of pharmacophores with identical three-dimensional (3D) pharmacophore hashes. We also proposed a new conformer coverage approach in order to rank compounds using all representative pharmacophores. Our results for four cyclin-dependent kinase 2 (CDK2) complexes with different ligands demonstrated that the proposed selection and ranking approaches outperformed the previously described common hits approach. We also demonstrated that ranking, based on averaged predicted scores obtained from different complexes, can outperform ranking based on scores from an individual complex. All developments were implemented in open-source software pharmd.

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Mitochondrial Arabidopsis thaliana TRXo Isoforms Bind an Iron–Sulfur Cluster and Reduce NFU Proteins In Vitro

Antioxidants ◽

10.3390/antiox7100142 ◽

2018 ◽

Vol 7 (10) ◽

pp. 142 ◽

Cited By ~ 8

Author(s):

Flavien Zannini ◽

Thomas Roret ◽

Jonathan Przybyla-Toscano ◽

Tiphaine Dhalleine ◽

Nicolas Rouhier ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Protein Interactions ◽

Function Analysis ◽

Active Form ◽

Three Dimensional ◽

Dimensional Structure ◽

Regulation Mechanism ◽

Iron Sulfur Cluster ◽

Iron Sulfur

In plants, the mitochondrial thioredoxin (TRX) system generally comprises only one or two isoforms belonging to the TRX h or o classes, being less well developed compared to the numerous isoforms found in chloroplasts. Unlike most other plant species, Arabidopsis thaliana possesses two TRXo isoforms whose physiological functions remain unclear. Here, we performed a structure–function analysis to unravel the respective properties of the duplicated TRXo1 and TRXo2 isoforms. Surprisingly, when expressed in Escherichia coli, both recombinant proteins existed in an apo-monomeric form and in a homodimeric iron–sulfur (Fe-S) cluster-bridged form. In TRXo2, the [4Fe-4S] cluster is likely ligated in by the usual catalytic cysteines present in the conserved Trp-Cys-Gly-Pro-Cys signature. Solving the three-dimensional structure of both TRXo apo-forms pointed to marked differences in the surface charge distribution, notably in some area usually participating to protein–protein interactions with partners. However, we could not detect a difference in their capacity to reduce nitrogen-fixation-subunit-U (NFU)-like proteins, NFU4 or NFU5, two proteins participating in the maturation of certain mitochondrial Fe-S proteins and previously isolated as putative TRXo1 partners. Altogether, these results suggest that a novel regulation mechanism may prevail for mitochondrial TRXs o, possibly existing as a redox-inactive Fe-S cluster-bound form that could be rapidly converted in a redox-active form upon cluster degradation in specific physiological conditions.

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