Study published in PLoS Pathogens of molecular features of phage receptor SlpA protein demonstrated the complexity of the interactions between human enteropathogen C. difficile and its phages

The emergence of Clostridioides difficile as a leading cause of healthcare-associated nosocomial intestinal infections calls for novel therapeutic strategies, particularly in the context of antibiotic resistance and recurrent disease. Phage therapy is a promising approach, but its clinical application against C. difficile remains hindered by our lack of understanding of the factors driving host specificity. Indeed, it is crucial to understand how phages specifically interact with their host to be able to select the best candidates for cocktail preparation. The main surface layer protein SlpA is a key phage receptor, but the molecular details governing phage-receptor interactions remain unclear. By dissecting the structural features of SlpA required for phage infection through engineered SlpA isoforms and domain modifications, in collaboration with our Canadian collegues from Sherbrooke University, we reveal how specific regions of SlpA mediate phage adsorption and infection. These new insights into phage–receptor interactions will be instrumental in guiding the future engineering of broad-host-range therapeutic phages.

More information : https://doi. org/10.1371/journal.ppat.1013724 

Contact : Olga Soutourina olga.soutourina@i2bc.paris-saclay.fr

https://www.i2bc.paris-saclay.fr/regulatory-rnas-in-clostridia/

Insects choose their bacterial gut symbionts by creating a multifactorial selective environment that promotes competition among symbiont candidates and colonization by the single, best-adapted strain

Funded by the European Research Council (ERC synergy 2025), the project “3Stops2Go” leaps over the “three red lights” of premature stop codons to re-express critical protein and correct genetic diseases.

The project, recently funded by an ERC Synergy Grant 2025, aims to target premature termination codon (PTC)mutations, which prematurely halt protein translation and are involved in about 11% of human genetic diseases.
By combining expertise in protist biology, RNA biology, and gene therapy, the consortium of four researchers (Leoš Valášek (Institute of Microbiology, Czech Academy of Sciences, Czech Republic), Julius Lukeš (Biology Centre, Czech Academy of Sciences, Czech Republic), Olivier Namy (Université Paris-Saclay, CEA, CNRS, France / I2BC, France), and Mark Osborn (University of Minnesota, USA)) aims to harness natural stop-codon bypass mechanisms to develop therapeutic tools (engineered tRNAs and readthrough inducers), test them in patient-derived cells and animal models, and ultimately pave the way toward clinical applications.

More information: https://erc.europa.eu/news-events/news/synergy-grants-2025-examples-projects

Contact: Olivier Namy olivier.namy@i2bc.paris-saclay.fr>

Cécile Courret, CNRS Researcher and recipient of an ATIP-Avenir grant, has joined the Department of Genome Biology to establish her team ‘Intragenomic Conflict and Evolution’.

Cécile's research focus on genetic conflicts and their impact on genome evolution. The basic principles of Mendelian inheritance state that in heterozygous individuals, two alleles have equal chances of being transmitted to the next generation. However, some genetic elements do not follow these rules. These so-called selfish genetic elements, such as transposons or meiotic drivers, bias inheritance in their own favor, often at the expense of the organism.

Because they disrupt essential processes like meiosis, heterochromatin regulation, and cell division, selfish elements create a persistent conflict with the host genome. This conflict triggers an evolutionary “arms race,” in which genomes evolve defense mechanisms to counterbalance the harmful effects of these elements. Far from being rare exceptions, such conflicts are now recognized as a major force shaping genome structure and function.

My research relies on the Drosophila model and combines genomic, molecular, and cytological approaches to investigate both how selfish elements perturb fundamental biological processes and how organisms respond to mitigate these disruptions. By studying systems where these conflicts are still active in natural populations, as well as the genomic signatures left by past events, Cécile's team aims to better understand how conflicts drive evolutionary innovation and shed light on the molecular basis of essential biological mechanisms.

Contact: Cécile Courret, cecile.courret@i2bc.paris-saclay.fr

The microtubule depolymerase KIF2C forms membrane-less organelles at the kinetochore through its N-terminal phospho-peptide binding domain that interacts with BRCA2 and other phosphorylated targets in mitosis.

During mitosis, the microtubule depolymerase KIF2C, the tumor suppressor BRCA2, and the kinase PLK1 contribute to the control of kinetochore-microtubule attachments. Both KIF2C and BRCA2 are phosphorylated by PLK1, and BRCA2 phosphorylated at T207 (BRCA2-pT207) serves as a docking site for PLK1. Reducing this interaction results in unstable microtubule-kinetochore attachments. Here we identified that KIF2C also directly interacts with BRCA2-pT207. Indeed, the N-terminal domain of KIF2C adopts a Tudor/PWWP/MBT fold that unexpectedly binds to phosphorylated motifs. Using an optogenetic platform, we found that KIF2C forms membrane-less organelles that assemble through interactions mediated by this phospho-binding domain. KIF2C condensation does not depend on BRCA2-pT207 but requires active Aurora B and PLK1 kinases. Moreover, it concentrates PLK1 and BRCA2-pT207 in an Aurora B-dependent manner. Finally, KIF2C depolymerase activity promotes the formation of KIF2C condensates, but strikingly, KIF2C condensates exclude tubulin: they are located on microtubules, especially at their extremities. Altogether, our results suggest that, during the attachment of kinetochores to microtubules, the assembly of KIF2C condensates amplifies PLK1 and KIF2C catalytic activities and spatially concentrates BRCA2-pT207 at the extremities of microtubules. We propose that this novel and highly regulated mechanism contributes to the control of microtubule-kinetochore attachments, chromosome alignment, and stability.

More Information : https://academic.oup.com/nar/article/53/11/gkaf476/8160319

Contact: Sophie Zinn sophie.zinn@i2bc.paris-saclay.fr

The expansion of PolX DNA polymerases in the ciliate Paramecium tetraurelia has favored the functional diversification of a subset of these enzymes, with enhanced nuclear localization in DNA repair foci during programmed DNA elimination.

During its sexual cycle, Paramecium massively rearranges its genome by removing tens of thousands of internal eliminated sequences (IESs) from its developing somatic nucleus. This process involves the introduction of programmed DNA double-strand breaks (DSBs), followed by efficient DSB repair using the non-homologous end joining (NHEJ) pathway. In this system, DSB repair requires not only the core NHEJ factors Ku70/80 and Xrcc4/Lig4, but also additional enzymes that accurately process the 4-base 5′-overhangs of the broken DNA ends created at IES excision sites.

In this study, we identify four orthologs of human DNA polymerase lambda in P. tetraurelia —PolXa, PolXb, PolXc, and PolXd— as key players in repairing IES excision junctions. Cells lacking these PolX enzymes accumulate genome-wide DNA damage, including unrepaired double-strand breaks, small deletions, and retained IESs. All four PolX proteins can process DNA ends, but PolXa and PolXb are specifically produced during programmed genome rearrangement and possess a unique internal linker region that enhances their nuclear localization.

In contrast to PolXc, we show that PolXa concentrates in nuclear foci along with core NHEJ factors and a Dicer-like enzyme involved in producing IES-specific small RNAs that regulate IES excision. We propose that these foci are the sites where excised IESs are ligated into concatemers, which serve as templates for small RNA production, linking DNA repair to RNA-mediated regulation of genome dynamics.

More information: https://academic.oup.com/nar/article/53/7/gkaf286/8113560

Contact: Mireille Bétermier mireille.betermier@i2bc-paris-saclay.fr, Julien Bischerour julien.bischerour@i2bc.paris-saclay.fr 

The unicellular cyanobacterium Gloeomargarita lithophora is able to stably sequester and withstand 90Sr and efficiently remove this hazardous anthropogenic radionuclide from aqueous solutions, including a synthetic nuclear effluent.

Strontium (Sr) is an alkaline earth metal commonly occurring in nature. In aqueous environments, it prevails as Sr2+ ions form chemically similar to Ca2+. In most organisms, the non-selective Sr intake primarily comes from water and food. In human, it is mainly localized in bones and dental enamel and is involved in the control of bone formation. Radioactive isotopes such as 90Sr are artificially produced by nuclear fission. 90Sr, a b-emitter with a half-life of 28.8 years, is one of the most hazardous anthropogenic radionuclides. It has been massively released into the environment during nuclear weapons testing and nuclear reactor accidents, such as those at Chernobyl and Fukushima. It is also found in radioactive water effluents produced by nuclear power plants, requiring specific treatment before being discharged. In humans, its accumulation in bone tissues increases the risk of cancers. Current physico-chemical techniques for remediating 90Sr traces from effluents are costly and can exhibit a low selectivity for Sr over Ca. Therefore, there is an incentive to develop an alternative method of remediation. In this study, we demonstrate that the cyanobacterium Gloeomargarita lithophora can remove more than 90% of the 90Sr activity that could be found in a nuclear plant effluent within 24 hours. This process occurs through two steps: a first rapid and passive phase of 90Sr sorbtion to the cell surface, followed by an active phase of 90Sr accumulation within the cells, partially driven by photosynthesis. We also showed that this cyanobacterium is able to stably sequester and withstand 90Sr and to efficiently remove this hazardous radionuclide from aqueous solutions, including a synthetic nuclear effluent. These results highlight Gloeomargarita lithophora as a promising solution for effective bioremediation of water contaminated with 90Sr thereby safeguarding the well-being of our ecosystems.

More information : https://doi.org/10.1016/j.jhazmat.2025.138155

Contact : Corinne CASSIER-CHAUVAT  Corinne.CASSIER-CHAUVAT@cea.fr

This study uncovers a fission yeast small nucleolar RNA (snoRNA) that guides ribosomal RNA 2’- O-methylation and modulates the activities of RNA-binding proteins involved in gametogenesis, expanding our vision of the non-canonical functions exerted by snoRNAs.

Small nucleolar RNAs are non-coding transcripts that guide chemical modifications of RNA substrates and modulate gene expression at the epigenetic and post-transcriptional levels. However, the extent of their regulatory potential and the underlying molecular mechanisms remain poorly understood. In a collaborative work with the I2BC B3S department and NGS facility, the epiRNA-Seq facility in Nancy and the Palancade lab at the Institut Jacques Monod, we have identified a conserved, previously unannotated intronic C/D-box snoRNA, termed snR107, hosted in the fission yeast long non-coding RNA mamRNA and carrying two independent cellular functions. On the one hand, snR107 guides site-specific 25S rRNA 2’-O-methylation and promotes pre-rRNA processing and 60S subunit biogenesis. On the other hand, snR107 associates with the gametogenic RNA-binding proteins Mmi1 and Mei2, mediating their reciprocal inhibition and restricting meiotic gene expression during sexual differentiation. Both functions require distinct cis-motifs within snR107, including a conserved 2’-O-methylation guiding sequence. Together, our results position snR107 as a dual regulator of rRNA modification and gametogenesis effectors, expanding our vision on the non-canonical functions exerted by snoRNAs in cell fate decisions.

More Information: https://www.nature.com/articles/s41467-025-58664-y

Contact: Mathieu Rougemaille mathieu.rougemaille@i2bc.paris-saclay.fr

Novel regulation of adenosine kinase activity in plants

Adenosine undergoes ATP-dependent phosphorylation catalyzed by adenosine kinase (ADK). In plants, ADK also phosphorylates cytokinin ribosides, transport forms of the hormone. Here, we investigated the substrate preferences, oligomeric states, and structures of ADKs from moss (Physcomitrella patens) and maize (Zea mays) alongside metabolomic and phenotypic analyses. We showed that dexamethasone-inducible ZmADK overexpressor lines in Arabidopsis can benefit from a higher number of lateral roots and larger root areas under nitrogen starvation. We discovered that maize and moss enzymes can form dimers upon increasing protein concentration, setting them apart from the monomeric human and protozoal ADKs. Structural and kinetic analyses revealed a catalytically inactive unique dimer. Within the dimer, both active sites are mutually blocked. The activity of moss ADKs, exhibiting a higher propensity to dimerize, was 10-fold lower compared with maize ADKs. Two monomeric structures in a ternary complex highlight the characteristic transition from an open to a closed state upon substrate binding. This suggests that the oligomeric state switch can modulate the activity of moss ADKs and probably other plant ADKs. Moreover, dimer association represents a novel negative feedback mechanism, helping to maintain steady levels of adenosine and AMP.

More information: https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/eraf094/8068880

Contact: Solange Morera solange.morera@i2bc.paris-saclay.fr

The N-STORM (Nikon) microscope of the Imagerie-Gif platform has been upgraded to allow wide-field and TIRF imaging.

In addition, a new 100x objective for phase contrast has been added.

These enhancements enable very sensitive imaging and allows automatic object detection through the use of AI based tools.

For further information and training opportunities:

Contact: phot@i2bc.paris-saclay.fr

Web site: https://www.i2bc.paris-saclay.fr/bioimaging/light-microscopy-facility/

Researchers at the I2BC and the Ecole Normale Supérieure found that the borders that create separation between functional domains in our chromosomes have an unexpectedly large influence on those domains themselves.

Chromosomes in humans and other mammals are subdivided into “functional neighborhoods” that guide the fidelity of biological processes, including gene regulation and DNA repair. Perturbations of these neighborhoods, resulting in the fusion of adjacent domains, can lead to a variety of diseases, including cancer and developmental disorders.
In a study published in PNAS (Proceedings of the National Academy of Sciences of the USA), scientists from the Noordermeer group at the I2BC, together with their colleagues at the Ecole Normale Supérieure in Paris, report how chromosomal border elements influence the organization of the adjacent functional neighborhoods. By combining genomics-based analysis and biophysical simulations of chromosome structure, they find that the size of these borders is highly diverse, from simple “points” on the chromosome to highly extended zones of transition between neighborhoods. Computer simulations of chromosome behavior of different types of borders in-between revealed an unexpected and far-reaching impact of the borders on their neighboring domains. Rather than creating a static separation, the borders will actively influence the degree of neighborhood mixing due to a previously unrecognized mechanism whereby the borders reel-in the adjacent neighborhoods. At narrow borders, this actively promotes mixing and may cause interference between biological activity on both side of the border. Extended borders buffer against this mechanism by adding additional separation. Border structure can thus constitute a new regulatory layer in the genome to fine-tune biological processes.

More information: https://www.pnas.org/doi/10.1073/pnas.2413112122

Contact: Daan Noordermeer daan.noordermeer@i2bc.paris-saclay.fr

Despite having low homology with BRCA2 proteins from other organisms and no folded domain, the newly discovered BRCA2 protein from Physcomitrium patens (the green yeast) promotes homologous recombination by binding to recombinases and DNA.

BRCA2 is crucial for mediating homology-directed DNA repair (HDR) through its binding to single-stranded DNA (ssDNA) and the recombinases RAD51 and DMC1. Most BRCA2 orthologs have a canonical DNA-binding domain (DBD) with the exception of Drosophila melanogaster. It remains unclear whether such a noncanonical BRCA2 variant without DBD possesses a DNA-binding activity. Here, we identify a new noncanonical BRCA2 in the model plant Physcomitrium patens (PpBRCA2). We establish that PpBRCA2 is essential for genome integrity maintenance, somatic DNA double-strand break (DSB) repair, HDR-mediated gene targeting, and RAD51 foci recruitment at DNA break sites. PpBRCA2 is also critical for DSB repair during meiosis. Interestingly, PpBRCA2 interacts strongly with RAD51 but weakly with DMC1, suggesting a distinct meiotic function compared to other BRCA2 homologs. Despite lacking the canonical DBD, PpBRCA2 binds ssDNA through its disordered N-terminal region and efficiently promotes HDR. Our work highlights that the ssDNA binding capacity of BRCA2 homologs is conserved regardless of the presence of a canonical DBD and provides a deeper understanding of BRCA2’s functional diversity across species.

More information:

https://pmc.ncbi.nlm.nih.gov/articles/PMC12412785/

Contact: Sophie Zinn sophie.zinn@i2bc.paris-saclay.fr

How Ku inward translocation can be restricted to protect telomere ends from NHEJ without altering other important functions.

The Electron Microscopy facility at the I2BC is organising a training session on TEM in cell biology in October this year. Registration deadline: 23rd of September 2025

The programme and pre-registration form can be accessed at the address below:
https://cnrsformation.cnrs.fr/stage-25445-Microscopie-volumique-FIB-SEM-pour-la-biologie-et-les-applications-3D-a-temperature-ambiante.html

For further information, please contact:
CNRS Formation Entreprise: CFE.contact@cnrs.fr
The organising committee: claire.boulogne@i2bc.paris-saclay.fr

Imagerie-Gif Electron Microscopy facility: https://www.i2bc.paris-saclay.fr/bioimaging/electron-microscopy/

A new training session dedicated to FIB-SEM applications in biology at ambient temperature is being launched this year by the I2BC's Electron Microscopy facility in collaboration with the CEA@Grenoble. This course will be held every year, alternating between Grenoble and Gif-sur-Yvette.

The next session will take place in Grenoble from the 17th to the 20th of June 2025. Registration deadline: 27th of May 2025

The programme and pre-registration form can be accessed at the address below:
https://cnrsformation.cnrs.fr/stage-25445-Microscopie-volumique-FIB-SEM-pour-la-biologie-et-les-applications-3D-a-temperature-ambiante.html

For further information, please contact:
CNRS Formation Entreprise: CFE.contact@cnrs.fr
The organising committee: claire.boulogne@i2bc.paris-saclay.fr

Imagerie-Gif Electron Microscopy facility: https://www.i2bc.paris-saclay.fr/bioimaging/electron-microscopy/

In this study, a new essential player of cell cycle regulation has been characterized in the nitrogen fixing symbiont Sinorhizobium meliloti.

During the nitrogen-fixing symbiosis between the alphaproteobacterium Sinorhizobium meliloti and the plant Medicago sativa (alfalfa), the interplay of molecular mechanisms governing cell cycle and bacteroid differentiation is a remarkable system that has still many details to be discovered. Here, we describe a bacterial cell cycle regulator, named FcrX, that controls two of the main essential players of cell cycle and bacteroid differentiation: the master regulator CtrA and the tubulin-like Z-ring component FtsZ. This essential factor is potentially participating with the degradosome complex driving the proteolysis of those two important regulators. Constitutive expression of FcrX during nodule development shows an increase of plant biomass, opening interesting paths in the amelioration of biological nitrogen fixation for a sustainable agriculture.

More information : https://doi.org/10.1073/pnas.2412367122

Contact : Emanuele Biondi - emanuele.biondi@i2bc.paris-saclay.fr

The Ribosome Quality Complex protein 2 is a major player in peptide release from stalled ribosomes.

Cells employ many quality control mechanisms during protein biosynthesis. Defects impairing messenger RNA decoding can cause ribosomes to stall, thereby distorting gene expression. Ribosome stalling results in ribosomes being sequestered in an inactive state on mRNA and represents a challenge for both ribosome homeostasis and cell survival. Eukaryotic cells prevent the accumulation of potentially toxic aberrant polypeptides and maintain ribosome availability by employing surveillance and clearance mechanisms, including the evolutionarily conserved ribosome-associated quality control complex (RQC). The rescue pathways dissociate the stalled ribosome, leading to the release of a 40S subunit attached to the mRNA and a 60S subunit still attached to a tRNA with the elongating peptide. RQC mediates the ubiquitination, extraction, and rapid degradation of the aberrant nascent peptide. In particular, Rqc2p recruits charged alanyl- and threonyl-tRNAs at the same position as an A-site tRNA, resulting in C-terminal extensions composed of alanine and threonine residues (CAT tails). These CAT tails may expose potential tunnel-embedded lysine residues for ubiquitination by the E3 ligase Ltn1. Using a genetic screen, we identified a mutant allele of RQC2 as involved in peptide release from stalled ribosomes. We characterized the mutant protein both biochemically and structurally, in collaboration with Reynald Gillet’s team (IGDR, Rennes University). We determining how the underlying point mutation reduced tRNA recruitment to the A site, thereby limiting CAT tail formation. These findings provide further mechanistic insight into the role of Rqc2p in ribosome rescue and the maintenance of ribosome homeostasis.

More Information:https://pubmed.ncbi.nlm.nih.gov/40187343/

Contact: Céline Fabret celine.fabret@i2bc.paris-saclay.fr

DNA duplication of the genetic material is a crucial step of cell proliferation. The study reveals that this step comprises two opposed strategies, coordinated by the enzyme Plk1.

In vertebrates, DNA replication involves the activation of thousands of starting points for DNA copying, known as “origins of replication”. These points are irregularly scattered across the genome. However, the precise mechanisms controlling the coordinated activation of these starting points and the regulation of the rate at which DNA is copied remain poorly understood. Any dysfunction can lead to genetic abnormalities and promote the development of cancers.
The scientists studied DNA replication using cell-free extracts from the eggs of the amphibian Xenopus laevis. This model is quite similar to replication in human cells, and has made it possible to develop a new method for analyzing the distribution of replication starting points (initiations) and the speed of replication in individualized DNA molecules. Combining this analysis with kinetic models, the scientists discovered that DNA replication relies on two dynamic and opposing strategies:
A fast strategy: high replication speed, but with fewer starting points.
A slow strategy: a slower replication speed compensated by the activation of numerous starting points.
In this context, the scientists determined that the enzyme Polo-like kinase 1 (Plk1) played a key role in coordinating these two strategies. Plk1, frequently mutated in many cancers, regulates this balance, opening up new perspectives on the control of replication and its implications in oncology. (published by Paris-Saclay and CNRS Biologie Actu (https://www.insb.cnrs.fr/fr/cnrsinfo/yin-yang-dans-la-duplication-des-chromosomes )

More Information: https://doi.org/10.1093/nar/gkaf007

Contact: Arach Goldar arach.goldar@i2bc.paris-saclay.fr Kathrin Marheineke kathrin.marheineke@ijm.fr

The crystallization platform has evolved into a crystallography platform and now offers new services (including protein structure determination and/or analysis) as well as scientific support for clients in structural biology projects.

Protein crystallography is the main approach for characterizing the 3D structure of proteins associated with drug candidates and for determining the molecular basis of complexes between soluble or membrane proteins and their partners (DNA, RNA, other proteins, peptides, lipids, cofactors, various ligands including metals). Initially, the crystallization platform was dedicated to automated screening, analysis, and optimization of crystallization conditions for soluble and membrane macromolecules.

Now, the crystallography platform provides extended services, including protein structure determination and/or analysis. The successive steps, starting from a purified protein sample of interest, include crystal formation, diffraction image collection at the Synchrotron Soleil, electron density map calculation, atomic model refinement of the protein or complex of interest, and structural analysis. Emphasis is placed on obtaining the most accurate models for the most successful structural analysis. Additionally, an AlphaFold service, including predicted model analysis, is available, relying on services established at I2BC by the BIOI2 integrative bioinformatics platform. Routine upstream steps before obtaining a protein crystal include obtaining an optimized synthetic gene for expression in prokaryotic hosts, expression, and purification of the recombinant protein of interest. The platform can advise clients on these various steps, and collaboration or service provision can be considered depending on project complexity. The crystallography platform is open to all scientists, from beginners to experienced crystallographers. It is important to note that the quality of the protein sample is a crucial criterion. The sample must be pure and verified on a denaturing acrylamide gel before crystallization. Do not hesitate to contact us.

Contact: cristallographie@i2bc.paris-saclay.fr
More information: https://www.i2bc.paris-saclay.fr/structural-biology/crystallography/