Catégorie d'actualités: significant publications

A review on ADP-ribosylation appeared in the journal Cell

ADP-ribosylation is a biochemical reaction in which the ADP-ribose group from NAD+ becomes covalently attached to various substrates. As such, ADP-ribosylation represents a ubiquitous modification of proteins and other biomolecules (e.g., nucleic acids). Catalysed by a range of specific enzymes, the most important of which in humans is PARP1, ADP-ribosylation serves as a regulatory mechanism influencing a wide array of cellular processes in all domains of life. This new review, published in the authoritative Leading Edge series of reviews of the journal Cell, covers the state of the art on this subject spanning structural biology, biochemistry, cell biology, and the clinical facets of ADP-ribosylation. In addition to Marcin Suskiewicz from the CBM as the first author, the review was co-authored by Ivan Ahel and members of his group at the University of Oxford.

Suskiewicz M., Prokhlrova E., Rack J.G.M., Ahel I.
ADP-ribosylation from molecular mechanisms to therapeutic implications
Cell Review, Volume 186, Issue 21, pages 4475-4495, October 12, 2023 - doi: 10.1016/j.cell.2023.08.03

The work of CBM researchers on the epidermis highlighted by the CNRS Institute of Chemistry

L'Institut de Chimie du CNRS a publié dans sa rubrique "Actualités" un article signalant les recherches sur l'épiderme de l'équipe "Biologie cutanée et microenvironnement", dirigée par le Docteur Catherine Grillon.

Actuellement, les modèles 3D de peau, en culture in vitro, sont développés dans les conditions d’oxygène de l’air ambiant, soit 18 à 20%. Pourtant, à l’intérieur de la peau, le taux d’oxygène physiologique est beaucoup plus bas, notamment dans la couche basale de l’épiderme où il descend entre 1 et 3%. Dans ces conditions les modèles actuels sont-ils véritablement représentatifs de l’état physiologique de notre peau ?

Pour répondre à cette question, les scientifiques de l'équipe "Biologie cutanée et microenvironnement" ont reconstruit de nouveaux modèles 3D d’épiderme respectant le taux réel d’oxygène physiologique dans la peau. Ils ont montré que le taux d’oxygène influe sur l'épaisseur de la peau et qu'il contrôle les défenses antioxydantes des cellules de l'épiderme.

Ce travail démontre qu’il est important de prendre en compte le taux réel d'oxygène physiologique pour comprendre le fonctionnement des cellules de l’épiderme en condition in vitro.

Voir l'actualité sur le site de l'Institut de Chimie du CNRS

Référence

Chettouh-Hammas N, Fasani F, Boileau A, Gosset D, Busco G & Grillon C.
Improvement of Antioxidant Defences in Keratinocytes Grown in Physioxia: Comparison of 2D and 3D Models.
Oxid Med Cell Longev. 2023

https://doi.org/10.1155/2023/6829931

The CNRS Institute of Chemistry reports on its website the work of CBM researchers

Understanding the function of proteins requires knowing their structures.
To do this, scientists used artificial intelligence to predict the shape of a class of "PARP" type proteins that regulate DNA repair, gene transcription, and antiviral response, but are also potential targets for new cancer therapies. This approach, published in the journal Nucleic Acids Research, could be extended to many other families of proteins.

Voir l'actualité sur le site de l'Institut de Chimie du CNRS

Référence

Updated protein domain annotation of the PARP protein family sheds new light on biological function
Marcin J. Suskiewicz, Deeksha Munnur, Øyvind Strømland, Ji-Chun Yang, Laura E. Easton, Chatrin Chatri , Kang Zhu, Domagoj Baretić, Stéphane Goffinont, Marion Schuller, Wing-Fung Wu, Jonathan M Elkins, Dragana Ahel, Sumana Sanyal, David Neuhaus & Ivan Ahel
Journal Nucleic Acids Research

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad514/7199335?login=true

Oxygen impact on our skin antioxidant defences: a new epidermis 3D model that is closer to physiology

Skin in vitro 3D models, with varying degrees of complexity, are all developed under ambient air oxygen conditions, i.e. 18-20%, and are widely used to study the mechanisms governing skin functions or to screen numerous molecules for pharmaceutical or cosmetic purposes. However, in the skin, the physiological oxygen level is much lower, particularly in the basal layer of the epidermis where it falls to between 1 and 3%. In in vitro culture, skin cells are therefore in hyperoxia. Are these models representative of the physiological state of our skin?

To investigate this, researchers in the "Skin Biology and Microenvironment" team have developed new 2D and 3D in vitro models under the oxygen conditions of the skin's physiological microenvironment. They have shown that oxygen levels influence keratinocyte proliferation, leading to morphological differences in reconstructed epidermis. As oxygen levels are important in the production of free radicals, molecules that accelerate skin ageing, the researchers studied the antioxidant defences of the cells in these cultures. They showed that antioxidant activity was increased in physiological conditions, either by over-expression or over-activation of enzymes.

This work shows that oxygen levels control the antioxidant defences of skin cells, and that it is important to take this parameter into account in order to reproduce physiological conditions as closely as possible.

Improvement of Antioxidant Defences in Keratinocytes Grown in Physioxia: Comparison of 2D and 3D Models.
Chettouh-Hammas N, Fasani F, Boileau A, Gosset D, Busco G, Grillon C.
Oxid Med Cell Longev. 2023 Jun 17;2023:6829931. doi: https://doi.org/10.1155/2023/6829931

Structural insights into the SUMOylation reaction

SUMOylation and ubiquitylation are related protein modifications where small proteins (SUMO or ubiquitin) become covalently attached to protein substrates to regulate their function. Both these protein modifications are essential for viability and are strongly implicated in human disease, but SUMOylation remains less studied than ubiquitylation. A key step in both SUMOylation and ubiquitylation reactions is the formation of a reactive thioester molecule in which SUMO or ubiquitin becomes linked to a cysteine residue on proteins called E2. It is from there that SUMO/ubiquitin is transferred onto the final protein substrate. In the study just published in Journal of Biological Chemistry, the researchers from the CBM used site-directed mutagenesis to create a version of the human E2-SUMO thioester that – unlike the native reactive thioester – is chemically stable and can be studied with structural biology methods. The crystal structure of this molecule revealed potential regulatory mechanisms for the SUMOylation process. The mutagenesis approach was inspired by a method developed for the yeast SUMOylation pathway by the group of Chris Lima.

The article, authored by the CBM engineer Stéphane Goffinont and other members of the team “Protein Post-Translational Modifications and DNA Repair: Structure, Function, and Dynamics”, is the first publication from the project “SUMOwriteNread”. The project is led by the CBM researcher Marcin J. Suskiewicz and funded by the Horizon Europe programme of the European Union (European Research Council Starting Grant no 101078837).

Stéphane Goffinont, Franck Coste, Pierre Prieu-Serandon, Lucija Mance, Virginie Gaudon, Norbert Garnier, Bertrand Castaing and Marcin Józef Suskiewicz
Structural insights into the regulation of the human E2∼SUMO conjugate through analysis of its stable mimetic.
Journal of Biological Chemistry, Volume 299, Issue 7, 2023, 104870 - https://www.sciencedirect.com/science/article/pii/S0021925823018987

Combining computers and experiments to study the domain composition and function of the PARP protein family

Prediction of protein structure with the artificial intelligence (AI)-powered program AlphaFold2 – hailed by the Science magazine, the biggest scientific breakthrough in 2021 – has rapidly revolutionised protein science. Trained on a large dataset of experimentally determined protein structures, AlphaFold2 can generate a model of a protein’s three-dimensional (tertiary) structure given its amino-acid sequence (primary structure). AlphaFold2 models are highly reliable, thus offering a good basis for understanding the function of proteins whose experimental structure is not available or is not complete.

In the present article, published in the journal Nucleic Acids Research, a collaborative team composed of researchers from Orléans, Oxford, and Cambridge, carefully examined AlphaFold2 models of an important group of proteins called the PARP protein family, which includes 17 proteins in human. These proteins regulate DNA repair and many other cellular pathways by catalysing a protein post-translational modification called protein (ADP-ribosyl)ation. The analysis of AlphaFold2 models allowed annotating all protein domains in this family, several of which have not been annotated before. This analysis served as a starting point for various accompanying experiments which validated some of the insights gained from the predicted models. Featuring an accessible introduction into the new computational approaches, the study can serve as a blueprint for scientists studying other protein families.

Two of the CBM members involved in the study are Marcin J. Suskiewicz and Stéphane Goffinont, both from the group “Protein Post-Translational Modifications: Structure, Function, and Dynamics”. This work is linked to a grant from Ligue contre le Cancer CSIRGO 2023.

References :
Marcin J Suskiewicz and others, Updated protein domain annotation of the PARP protein family sheds new light on biological function, Nucleic Acids Research, 2023;, gkad514,
https://doi.org/10.1093/nar/gkad514

Truly life materials?

Physiological characterization of life in Engineered Living Materials by confocal microscopy at single cell resolution.

The CNRS Institute of Chemistry reported this remarkable research on its site. See the article

Engineered Living Materials (ELMs) combine living cells with non-living scaffolds to get life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs are 3D-printed, and called bio-ink. For ELMs to be functional, cells in ELMs has to remain alive and active. However, currently, microorganism physiology in ELMs is still elusive and restrict their use.

Researchers of the team "Cell signalling and neurofibromatosis" reconstituted such bioprinted ELMs by associating the yeast Saccharomyces cerevisiae with the hydrogel Pluronic F-127. Theydeveloped genetically engineered yeast by integrating fluorescent gene whose expression is correlated to a physiological parameter: ATP concentration (metabolism), intracellular pH (growth phase), morphology … These engineered and ratiometric biosensors are effective and allow to assess yeast physiological status in ELM directly in situ by confocal microscopy at single cell scale level. They constitute a valuable tool easy to adapt to any other system by associating them to other materials to evaluate their biocompatibility.

Furthermore, the researchers tested their recently developed copper biosensor embedded into this hydrogel F-127, and showed it is fully functional into this ELM. Yeast biosensor association with hydrogel provides several very interesting advantages such as protecting yeast from contaminations and supplying them with nutrients.

This work allows to establish the proof of concept that F127 associated with engineered yeast S. cerevisiae is a promising ELM in order to develop easy to use whole-cell biosensors able to detect copper directly on samples collected in the environment.

Bojan Žunar B., Ito T., Mosrin C., Sugahara Y., Bénédetti H., Guégan R. and Vallée B.
Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae.
Biomater Res 26, 85 (2022). https://doi.org/10.1186/s40824-022-00337-8