Typologie d'actualités: Team Molecular, Structural and Chemical Biology

Identification of a ‘double‘ protein post-translational modification

Proteins are the main ‘molecular machines’ of the cell. To efficiently perform their tasks, they have to be dynamically switched on and off, recruited to specific cellular locations, and degraded in a timely manner. One of the main mechanisms that regulate these processes is temporary covalent attachment, to a protein, of extra regulatory elements known as protein post-translational modifications. The modification reaction is catalysed by specific enzymes and can lead to changes in protein activity, localisation, or half-life. Two of the common protein modifications are ubiquitin and ADP-ribose, each of which can be linked directly to a protein substrate.

In the study published in Science Advances, an international team of researchers, including Vincent Aucagne, Marcin Suskiewicz, and Hervé Meudal from the CBM in Orléans, led by Ivan Ahel and Dragana Ahel groups at the University of Oxford, have demonstrated that these two individual modifications can be joined together, producing a ‘double’ protein modification. The enzymes responsible for this process are DELTEX E3 ligases, which can efficiently attach ubiquitin to protein-linked ADP-ribose. A key contribution of Orléans scientists to the project was the analysis of the ubiquitin-ADP-ribose linkage performed using mass spectrometry (MS) and nuclear magnetic resonance (NMR) equipment of the new MOV2ING platform in Orléans.

The study shows that different protein modifications can be joined together to either combine two regulatory signals or produce a third, distinct signal, with a specific function. This shows previously unappreciated level of complexity in protein regulation.

While the role of ubiquitin-ADP-ribose in cells remains unclear, DELTEX enzymes have previously been linked to both development and antiviral response. The authors showed that the SARS-CoV-2 virus possesses enzymes that can remove the new modification, possibly allowing the virus to inhibit the host immune response.

References :
Kang Zhu, Marcin J. Suskiewicz, Hloušek-Kasun, Hervé Meudal, Andreja Mikoč, Vincent Aucagne, Dragana Ahel and Ivan Ahel
DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on protein substrates
Science Advances, 5 Oct 2022, Vol 8, Issue 40 DOI: 10.1126/sciadv.add4253

A versatile new approach to seek constitutive or conditional helicase substrates at global scale

Helicases are ubiquitous ‘molecular motor’ enzymes that disrupt nucleic acid (NA) helices and NA-protein interactions. Despite the key roles of helicases in many cellular processes and diseases, their target repertoires and the determinants of their functional specialization are often unknown. Scientists from the ‘RNA remodeling’ group of CBM have developed a new screening scheme, Helicase-SELEX, to elucidate helicase substrate requirements and find natural or synthetic helicase substrates in large NA sequence libraries. Using the transcription termination Rho helicase as prototype, the CBM scientists have discovered ~3300 functional substrate sequences in Escherichia coli, thereby providing the first detailed map of Rho utilization (Rut) sites at genome scale. Further, they have shown that inclusion of a Rho cofactor (NusG) in the selection scheme can modulate the H-SELEX outcome and help probe specificity determinants at global scale. Finally, they have used H-SELEX to evolve synthetic Rut sequences operating as riboswitches able to elicit Rho activity in vitro and in vivo only in presence of an orthogonal cofactor (serotonin). Thus, Helicase-SELEX is a versatile new approach to characterize or exploit helicases for fundamental or biotechnology purposes.

The CNRS Institute of Chemistry has reported this new original screening approach on its website

Référence

Delaleau M., Eveno E., Simon I., Schwartz A & Boudvillain M.
A scalable framework for the discovery of functional helicase substrates and helicase-driven regulatory switches
PNAS 2022

https://www.pnas.org/doi/10.1073/pnas.2209608119

7th Biotechnocentre theme day – June 17, 2022

Researchers in biosciences and life chemistry met "face-to-face" for the Biotechnocentre's thematic day on "Exposome and Epigenetics: how does the environment play with our genes?" ". Renowned speakers declined the different facets of the exposome: physical or chemical exposure or exposure to different pathogens, stress, diet, social inequalities... They also highlighted the impact of the exposome on the environment and on our health, which can have different consequences depending on gender, age, genetic heritage and on its regulation by reversible epigenetic modifications.
See the Booklet of the day (poster, program, summaries).

A new mechanism of antiobiotic resistance

The bacterial Rho factor is a molecular motor that induces genome-wide transcription termination. Rho is essential in many species, including in Mycobacterium tuberculosis where inactivation of the rho gene leads to rapid death. Nevertheless, the Rho factor of M. tuberculosis [MtbRho] displays idiosyncrasies, including resistance to the antibiotic bicyclomycin [BCM], which remain unexplained. To identify the molecular origin of these idiosyncrasies, we solved the structure of MtbRho by cryo-EM at 3.3 Å. This atomic structure notably reveals a leucine → methionine substitution that creates steric hindrance in the binding pockets of BCM, close to the ATPase sites, thereby conferring resistance to BCM at the expanse of molecular motor efficiency. Our work contributes to explain the unusual properties of MtbRho and provides groundwork for the development of new antibiotics.

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J.-M. Bonmatin co-authored an article linking neonicotinoid insecticides to chronic kidney disease of undetermined etiology (CKDu)

Chronic Kidney Diseases (CKD) are a growing scourge worldwide, particularly in less developed countries with intensive agriculture. Several risk factors have been identified, but an undetermined etiology (CKDu) remains which may be linked to pesticides (Floris et al., 2021).

J.-M. Bonmatin participated in a study in Sri Lanka published in Scientific Reports late 2021 (Taira et al., 2021). Although the size of the study remains statistically modest, the authors (members of the Task Force on Systemic Pesticide) showed that the concentrations of several neonicotinoids measured in urine were related to the biomarkers Cystatin-C and L-FABP as well as to the neurophysiological symptoms observed. The authors conclude that the urinary concentrations of these neonicotinoids are a risk factor for tubular disorders of the kidney. This is another element that adds to our previous publications (e.g., Ichikawa et al., 2019 and Bonmatin et al., 2021) on the human health effects of these insecticides.

Neonicotinoids, known as "bee killers" and which are the source of major impacts on biodiversity (invertebrates and vertebrates) are still widely used for rice cultivation in Asia (Prihandiani et al., 2021).  These insecticides have been banned in France since 2018 (except for sugar beet). They are in the process of being banned in Sri Lanka.

Référence :  Taira K, Kawakami T, Weragoda SK, Herath HMAS, Ikenaka Y, Fujioka K, Hemachandra M, Pallewatta N, Aoyama Y, Ishizuka M, Bonmatin JM & Komori M (2021) Scientific Reports, 11, 22484.

https://doi-org.inc.bib.cnrs.fr/10.1038/s41598-021-01732-2