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

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

New methodological breakthrough in total protein synthesis

Since the first synthesis of an amino acid dimer in the late 19th century, synthetic proteins represented a fascinating goal for generations of chemists. Invented in the 1960s, the solid phase peptide synthesis (SPPS) technology is since used routinely for peptides made up of a few dozen amino acids. The discovery of "chemical ligation" reactions in the 1990s paved the way to the synthesis of proteins of more than one hundred amino acids: extremely selective chemical reactions are used under aqueous conditions to couple peptide segments - themselves synthesized by SPPS -, devoted of side chain protective groups usually required in organic synthesis. Thanks to these methodological breackthroughs, the chemical approach to protein synthesis today advantageously complements biotechnological methods and enable the generation of native or modified proteins, tailor-made tools for deciphering biological processes at atomic resolution.

However, the synthesis of proteins of several hundred amino acids requires numerous successive chemical ligations, and therefore particularly delicate stages of purification of the reaction intermediates. One solution to overcome these steps is to assemble the proteins onto a solid support. Although very attractive, this approach has been limited to proofs of concept: one of the main reasons is the difficulty of grafting on a suitable solid support the first peptide segment through a linker that can be easily cleaved once the ligations carried out. Indeed, the conditions required for cleaving the linkers developed so far are incompatible with many proteins.

To overcome this problem, CBM scientists, in collaboration with colleagues from IC2MP in Poitiers, explored linkers programmed to be cleaved under very mild conditions by an enzymatic reaction. Remarkably, the size of the enzyme directly correlates with the rate at which the arm is cleaved, and therefore with the efficiency of the release of the synthesized protein. The method was applied to the synthesis of a peptide of 160 amino acids, which is to date the longest sequence ever synthesized by solid phase chemical ligations.

Reference of the article : S. A. Abboud, M. Amoura, J.-B. Madinier, B. Renoux, S. Papot, V. Piller, V. Aucagne. Enzyme-cleavable linkers for protein chemical synthesis through solid-phase ligations, Angew. Chem. Int. Ed., 2021, accepted article. https://doi.org/10.1002/anie.202103768

See the news on the website of the CNRS institute of chemistry




J.-M. Bonmatin co-author of a letter in Science (July 16, 2021)

A group of co-authors, specialists in pollinators, has just published a letter in Science (Simon-Delso at al. 2021). The letter is a call to European Ministers to act responsibly and reduce toxic risks to pollinators in pesticide assessments. For example, while the natural mortality of honeybees can reach up to 5%, the scientific community agrees on a maximum "acceptable" rate of 7% for a pesticide. To accept 10% is to take a risk that is far too high in view of the already catastrophic situation regarding the collapse of pollinators. Because of the crucial importance of such decisions for the planet and our future, the authors and publisher have chosen a more direct style than usual to get their message across.

Reference : Simon-Delso N, Aebi A, Arnold G, Bonmatin JM, Hatjina F, Medrzycki P & Sgolastra F (2021) Maximize EU pollinator protection: Minimize risk, Science, 373(5552), 290. DOI: 10.1126/science.abj8116




Biotechnocentre 33rd conference

The 33rd Biotechnocentre conference will be held on October 7 and 8, 2021  at Center Parcs Domaine Les Hauts de Bruyères - Rue Lamotte - 41 600 Chaumont-sur-Tharonne.

With the participation of Doctoral School 549 "Santé, Sciences Biologiques et Chimie du Vivant" (SSBCV).

Among the speakers announced, Vincent Aucagne, head of the thematic group "Synthetic proteins and bioorthogonal chemistry" " will give a conference entitled "Methodological developments for the chemical synthesis of proteins"

Registration before September 3, 2021 at biotechnocentre@sfr.fr

See the poster

Conferences program

When a non-conserved protein domain becomes essential

Rho-dependent termination of transcription is a critical regulatory mechanism specific to bacteria. In a subset of species including most Actinobacteria and Bacteroidetes, the Rho factor contains a large, poorly conserved N-terminal insertion domain (NID) of cryptic function. Through the first characterization of an actinobacterial Rho factor containing a very large NID (~40% of total mass), we show that such a non-conserved protein domain can be essential for activity. Without NID, the Rho factor of Bacteroides fragilis (BfRho) indeed cannot induce transcription termination and displays a reduced affinity for RNA. Intriguingly, the presence of a NID in BfRho is not correlated to the lack of residues or motifs deemed essential in NID-less Rho factors from evolutionary distinct species. The NID requirement is probably linked to the coevolution of partner feature(s) such as lineage-specific RNA polymerase domains and/or low G+C content of the B. fragilis transcriptome. Our data thus highlight that ‘essential function’ does not always rhyme with ‘structural conservation’.

Simon I., Delaleau M., Schwartz A., Boudvillain M.
A Large Insertion Domain in the Rho Factor From a Low G + C, Gram-negative Bacterium is Critical for RNA Binding and Transcription Termination Activity
Journal of Molecular Biology (2021) 433 (15) 167060 - Doi : 10.1016/j.jmb.2021.167060




Biodiversity skepticism?

Biodiversity skepticism?

Based on analysis of time series of abundances of insect species in the United States, Crossley et al. reported in Nature Ecology & Evolution (August 2020) that there is no evidence of a global decline in insect abundance or diversity in the United States, this for both natural and anthropogenic sites. Their study described the apparent robustness of insect populations in the U.S. as reassuring, in contrast to recent studies reporting dramatic declines in their abundance around the world.

However, a multidisciplinary consortium including researchers from INRAE, the University of Rennes and CNRS identified major problems in the Crossley et al. paper concerning: 1) statistical analysis and 2) inconsistencies in data selection. The consortium demonstrates, in a commentary published in Nature Ecology & Evolution Desquilbet et al. , that these biases call into question the conclusions of Crossley et al.

This is the second time (see here) that a high-ranking publication downplaying insect declines has been subject to methodological criticisms. These studies raise the question of a "biodiversity-skepticism" within the scientific community. In order to implement an appropriate protection of biodiversity, public decision-makers need an informed diagnosis that is not clouded by biased studies which slow down decision-making.

Reference :
Desquilbet M, Cornillon PA, Gaume L & Bonmatin JM (2021)
Matters arising: Adequate statistical modelling and data selection are essential when analysing abundance and diversity trends
Nature Ecology & Evolution doi : https://www.nature.com/articles/s41559-021-01427-x