Catégorie d'actualités: significant publications

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

Milk thistle, a plant extract with promising –green- medicinal properties against psoriasis

Considering the relative low efficacy and high toxicity of current drug treatments against psoriasis, new therapeutic strategies are needed.

Scientists from CBM have searched for natural products unable to modulate the TGFb/miRNA-21-5p pathway in keratinocyte cells. This axis of regulation was chosen not only because it plays a pivotal role in epidermal haemostasis but also because its dysregulation is systematically associated with skin disorders including psoriasis.

To identify such bioactive compounds, a library of medicinal plant extracts was screened using the miR-ON RILES screening system placed under the control of the miRNA-21-5p in keratinocytes treated with TGFb. Silymarin, a mixture of flavonolignans extracted from Silybum marianum (L.) Gaertn., was identified as the most potent regulator of miRNA-21-5p expression. RNA-sequencing analysis revealed three unexpected transcriptomic signatures associated with keratinocyte differentiation, cell cycle, and lipid metabolism.

Mechanistically, Silymarin blocks cell cycle progression, inhibits keratinocyte differentiation through repression of Notch3 expression, stimulates lipid synthesis via activation of PPARg signaling and inhibits inflammatory responses by suppressing the transcriptional activity of NF-kB. Notably, the topical application of silymarin alleviates the development of psoriasiform lesions in mice by abrogating the altered expression levels of markers involved in inflammation, proliferation, differentiation, and lipid metabolism without inducing toxicity.

Therefore this plant extract might represent a promising "green" alternative to current pharmacological treatments for the management of this pathology.


Elodie Henriet,Florence Abdallah, Yoan Laurent, Cyril Guimpied, Emily Clement, Michel Simon, Chantal Pichon and Patrick BarilTargeting TGF-β1/miR-21 Pathway in Keratinocytes Reveals Protective Effects of Silymarin on Imiquimod-Induced Psoriasis Mouse ModelVolume 3, ISSUE 3, 100175, May 2023 - DOI:https://doi.org/10.1016/j.xjidi.2022.100175

Raman spectroscopy for detecting biomolecules below surface of Mars

Chlorophyllin, beta-carotene, melanin, chitin, cellulose, naringenin and quercetin: these exotic-sounding compounds are biomolecules that allow certain organisms to live in extreme environments. They are thus prime targets for the search for life on Mars. In order to assess their resistance to Martian conditions, an experiment called BIOMEX, for BIOlogy and Mars EXperiment, was carried out on the exterioir of the International Space Station (ISS).

The molecules were mixed with Martian soil analogs before being exposed to solar radiation outside the ISS for 469 days. Back on Earth, they were   analyzed by Raman spectroscopy at the German Aerospace Center (DLR) in Berlin.

Raman spectroscopy analyses the molecular and mineralogical composition of a sample. Compatible with robotic space missions, it is one of the key techniques for searching for traces of life on Mars. NASA's Perseverance rover currently exploring Jezero Crater is equipped with two Raman spectrometers, and ESA's future ExoMars mission will also use one to aid detection of possible biosignatures on Mars in 2030.

The BIOMEX experiment involved many researchers, including members of the Exobiology team at CBM, Olréans. The results, published in the Science Advances, reveal that these biomolecules are resistant to Mars conditions because the minerals composing the Martian soil have a protective effect against UV. Most importantly, the study shows that these molecules could be identified without difficulty on Mars by Raman spectroscopy.

Biosignature stability in space enables their use for life detection on Mars
Mickael Baqué,Theresa Backhaus et al.
Science Advances, Vol 8 -DOI: 10.1126/sciadv.abn7412

Setting the geological scene for the origin of life and continuing open questions about its emergence

The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. However, what is missing from the prebiotic chemical experiments is precise information about the environment and the conditions reigning on the early Earth during the Hadean Era (4.5-4.0 Ga). In particular, there is a lack of understanding about the inorganic ingredients that were available, the stability and longevity of the various environments suggested as locations for the emergence of life, as well the kinetics and rates of the prebiotic steps leading to life.

This contribution reviews our current understanding of the geology of the early Earth at the time when life emerged. Having set the geological scenario, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium cycling of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.

Setting the geological scene for the origin of life and continuing open questions about its emergence
Frances Westall1, André Brack, Alberto G. Fairén and Mitchell D. Schulte
Frontiers in Astronomy and Space Sciences - 05 January 2023 - Volume 9 - doi : 10.3389/fspas.2022.1095701 9:1095701

Bispidines and manganese: a winning couple

As an essential metal ion and an efficient relaxation agent, Mn2+ holds great promise as a substitute for Gd3+ in MRI contrast agent applications, if its stable and inert complexation can be achieved. To achieve this goal, the “Metal complexes and MRI” team of CBM and their collaborators from the University of Heidelberg, Germany, created a Mn2+ selective chelator by introducing four pyridine and one carboxylate donors on a bispidine skeleton. Thanks to a highly rigid and preorganized structure and perfect size-match for Mn2+, the new ligand L provides not only remarkably high thermodynamic stability, but also excellent selectivity over the major biological competitor Zn2+, as well as kinetic inertness. The unusual eight-coordinate structure of the Mn2+ complex, in contrast to the six-coordinate structure of the Zn2+ analogue, underlines that the coordination cavity is perfectly adapted for Mn2+, while it is too large for Zn2+. The MRI efficiency of this MnL complex is about 30% higher than that of typical Mn2+ systems. In vivo MRI experiments realized in control mice at a very low dose (0.02 mmol/kg) indicate good signal enhancement and fast renal clearance. Taken together, MnL is the first chelate that combines such excellent stability, selectivity, inertness and relaxation properties, all of primary importance for MRI use.

D. Ndiaye, P. Cieslik, H. Wadepohl, A. Pallier, S. Même, P. Comba, and É. Tóth, Mn2+ bispidine complex combining exceptional stability, inertness and MRI efficiency, J. Am. Chem. Soc. 2022, doi : 10.1021/jacs.2c10108
JACS spotlight sur cet article : https://pubs.acs.org/doi/pdf/10.1021/jacs.2c12719