The Biology and Physics of Prokaryotic Chromosome is an international scientific conference, bringing together experimentalists and theoreticians to discuss discoveries and challenges around building an integrated model of prokaryotic chromosome structure.

The conference focuses on mechanisms of chromosome organisation and structure, chromosome replication, transcription, and segregation, investigated at multiple scale lengths, using both experimental and theoretical approaches. A key goal is to provide a platform for inter-disciplinary work, to foster new collaboration and develop new ideas.

New approaches and technologies have revolutionised the field of prokaryotic chromosome biology in the last fifteen years. For example, super-resolution microscopy is now being used to visualize previously unresolved structure, genomic tools have enabled the capture of new types of proximity information on a genomic-scale, and polymer physics models allow researchers to tackle questions that go far beyond the traditional biological description of chromosome structure. Join us in York for an unforgettable scientific meeting - this is an opportunity you won’t want to miss.

At least half of the oral presentation slots are expected to be selected from submitted abstracts and we will prioritise early career researchers.

Programme Coordinators:
David Grainger, University of Birmingham
Daniela Barillà, University of York
Remus Dame, Leiden University
Virginia Lioy, Institute for Integrative Biology of the Cell

More information: bit.ly/bio-prokaryotic-VII

Contact: Virginia LIOY virginia.lioy@i2bc.paris-saclay.fr

T-DNAs are mobile elements transferred from pathogenic Agrobacterium to plants that reprogram host cells into hairy roots or tumors, and which are used as disarmed forms to deliver transgenes in plants. Here we review the mechanisms that silence the expression of T-DNAs in transgenic plants as well as during pathogenesis.

Mobile elements known as T-DNAs are transferred from pathogenic Agrobacterium to plants and reprogram the host cell to form hairy roots or tumors. Disarmed nononcogenic T-DNAs are extensively used to deliver transgenes in plant genetic engineering. Such T-DNAs were the first known targets of RNA silencing mechanisms, which detect foreign RNA in plant cells and produce small RNAs that induce transcript degradation. These T-DNAs can also be transcriptionally silenced by the deposition of epigenetic marks such as DNA methylation and the dimethylation of lysine 9 (H3K9me2) in plants. Here, we review the targeting and the roles of RNA silencing and DNA methylation on T-DNAs in transgenic plants as well as during pathogenesis. In addition, we discuss the crosstalk between T-DNAs and genome-wide changes in DNA methylation during pathogenesis. We also cover recently discovered regulatory phenomena, such as T-DNA suppression and RNA silencing-independent and epigenetic-independent mechanisms that can silence T-DNAs. Finally, we discuss the implications of findings on T-DNA silencing for the improvement of plant genetic engineering.

More information: https://academic-oup-com.insb.bib.cnrs.fr/plphys/advance-article/doi/10.1093/plphys/kiae583/7876130

Contact: Angélique DELERIS angelique.deleris@i2bc.paris-saclay.fr

We have identified a novel tubulin surface targeted by the Tau protein. From these results, we formulate new hypotheses on the regulation of microtubules by Tau and on Tau oligomerization.

Tau is a protein involved in the regulation of axonal microtubules in neurons. In pathological conditions, it forms filamentous aggregates which are molecular markers of the Alzheimer’s disease and of related neurodegenerative disorders collectively known as tauopathies. Structures of Tau in fibrils or bound to the microtubule have been reported. We have determined the structure of a Tau construct comprising the PHF6 motif, an hexapeptide involved in Tau aggregation, as a complex with tubulin. This Tau fragment binds as a dimer to a new site which, when transposed to the microtubule, would correspond to a pore between protofilaments. These results raise new hypotheses on Tau-induced microtubule assembly and stabilization and on Tau oligomerization. They reconcile apparently contradictory data from the literature, in particular concerning the coexistence of different binding modes of Tau to the microtubule.

More information : https://academic.oup.com/pnasnexus/article/3/11/pgae487/7850850

Contact : Benoît GIGANT benoit.gigant@i2bc.paris-saclay.fr

Ultrafast formation of triplet statates by singlet fission in water solution.

We provide evidence that singlet fission—a process where one excited state splits into two—can occur in water-soluble compounds. Specifically, we studied perylene-3,4,9,10-tetracarboxylate, a molecule that forms transient disordered dimers. Using a combination of advanced techniques like time-resolved absorption and fluorescence spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and theoretical modeling, we were able to detect the key features of singlet fission and map out the behavior of the molecular assemblies. Our results show that the constant structural changes within these dimers play a crucial role in steering the process toward either singlet fission or charge separation. The quantum efficiency of producing triplet states is over 100%, with these states lasting for nanoseconds—highlighting how disordered systems can drive highly efficient photophysical processes.

More information: https://pubs.rsc.org/en/content/articlehtml/2024/sc/d4sc04732j

Contact: Manuel LLANSOLA <manuel.llansola@I2bc.paris-saclay.fr>

We explored the ribosome profiling landscape of yeast and showed that noncoding regions are associated with a wide diversity of translation signals among which some led to detectable protein products.

Pervasive translation is a widespread phenomenon that plays a critical
role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear. Based on 54 ribosome profiling (Ribo-Seq) datasets, we investigated the yeast Ribo-Seq landscape using a representation framework that allows the comprehensive inventory and classification of the entire diversity of Ribo-Seq signals, including non-canonical ones. We show that if coding regions occupy specific areas of the Ribo-Seq landscape, noncoding regions encompass a wide diversity of Ribo-Seq signals and, conversely, populate the entire landscape. Our results show that pervasive translation can, nevertheless, be associated with high specificity, with 1055 noncoding ORFs exhibiting canonical Ribo-Seq signals. Using mass spectrometry under standard conditions or proteasome inhibition with an in-house analysis protocol, we report 239 microproteins originating from noncoding ORFs that display canonical but also non-canonical Ribo-Seq signals. Each condition yields dozens of additional microprotein candidates with comparable translation properties, suggesting a larger population of volatile microproteins that are challenging to detect. Our findings suggest that non-canonical translation signals may harbor valuable information and underscore the significance of considering them in proteogenomic studies. Finally, we show that the translation outcome of a noncoding ORF is primarily determined by the initiating codon and the codon distribution in its two alternative frames, rather than features indicative of functionality. Our results enable us to propose a topology of a species’ Ribo-Seq landscape, opening the way to comparative analyses of this translation landscape under different conditions.

More information: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03403-7

Contact: Anne Lopes  anne.lopes@i2bc.paris-saclay.fr

Bioinformaticians finds new ways to analyze cancer RNA in very large datasets

Cancer cells produce an immense diversity of RNA molecules. Using deep sequencing technologies, scientists explore these RNAs to uncover key insights into cancer onset and progression. However, cancer RNA datasets are becoming so large that directly searching them for a given sequence is impossible. Currently, scientists must rely on simplified representations, such as gene expression tables. Yet, many cancer-causing RNAs are absent from standard gene expression tables. The Transipedia consortium, bringing together bioinformaticians from I2BC/University Paris-Saclay, University of Lille, and University of Montpellier, introduces a new approach to mining RNA-seq databases using k-mer indexes. In their latest paper, they demonstrate that an index of 1,019 cancer cell lines can be queried in real time while providing accurate quantification of cancer mutations, fusions, or splicing variants. In future work, the consortium plans to expand this technology to offer access to an even larger database of cancer and normal tissues, aiming to accelerate cancer genomics research.

More information: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03413-5

Contact:  Daniel Gautheret daniel.gautheret@i2bc.paris-saclay.fr

Peptides fitting the optimal human NMT Gly-myristoylation recognition pattern act as potent inhibitors. Lys-myristoylation-based inhibitors from these peptides were designed. Each series’ inhibitory properties are unique, relying on distinct interactions.

N-myristoyltransferases (NMTs) catalyze essential acylations of N-terminal alpha or epsilon amino groups of glycines or lysines. Here, we reveal that peptides tightly fitting the optimal glycine recognition pattern of human NMTs are potent prodrugs relying on a single-turnover mechanism. Sequence scanning of the inhibitory potency of the series closely reflects NMT glycine substrate specificity rules, with the lead inhibitor blocking myristoylation by NMTs of various species. We further redesigned the series based on the recently recognized lysine-myristoylation mechanism by taking advantage of (i) the optimal peptide chassis and (ii) lysine side chain mimicry with unnatural enantiomers. Unlike the lead series, the inhibitory properties of the new compounds rely on the protonated state of the side chain amine, which stabilizes a salt bridge with the catalytic base at the active site. Our study provides the basis for designing first-in-class NMT inhibitors tailored for infectious diseases and alternative active site targeting.

More information: https://www-cell-com.insb.bib.cnrs.fr/structure/abstract/S0969-2126(24)00318-6?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0969212624003186%3Fshowall%3Dtrue

Contact: Thierry Meinnel thierry.meinnel@i2bc.paris-saclay.fr

Learn with great scientists about cell mechanotransduction and microbial invasion processes

Morning session: Cell Mechanotransduction 9H00-9H30 : Christophe Leclainche, I2BC, Gif-sur-Yvette.
Understanding mechanotransduction through in vitro reconstitution of actomyosin-dependent protein machineries
9H30-10H00 : Benoit Ladoux, MPZPM, Erlangen, Germany.
Mechanical imprints of cell extrusion from epithelial tissues.
10H00-10H30 : Patricia Bassereau, Institut Curie, Paris.
Cell spreading on fluid membranes requires strong integrin ligands and microtubules
10H30-10H50 : Coffee break
10H50-11H20: Gregory Giannone, Université de Bordeaux.
Unraveling the nanoscale spatial and mechanical regulation of actin binding proteins.
11H20-12H00 : Keynote lecture - Michael Sheetz, UTMB, Texas, USA.
Mechanical Oscillations Kill Cancer Cells and Reverse Aging
 
Afternoon session « Microbial Invasion»

14H00-14H30 : Sven Hammerschmidt, Greifswald university, Germany
TBA
14H30-15H00 :  Sandrine Bourdoulous, Institut Cochin, Paris.
Angptl4 prevents endothelial dysfunction during bacterial sepsis
15H00-15H40 : Keynote lecture - Linda Kenney, UTMB, Texas, USA.
Imaging Salmonella Lifestyles: From Virulence to Biofilms to Tumors
15H40-16H00 : Coffee break
16H00-16H30 : Jost Enninga, Institut Pasteur, Paris.
Endomembrane breakage by enteroinvasive bacterial pathogens- new insights by in cellulo structural biology
16H30-17H00 : Marc Prudhomme, Université Paul Sabatier, Toulouse
Bacterial communication and antibiotic tolerance in Pneumooccus
17H00-17H30 : Guy Tran Van Nhieu, I2BC, Gif-sur-Yvette.
Characterization of pneumococcal secreted factors associated with bacterial meningitis

more information: https://archaea2024.sciencesconf.org/

Contact: tamara.basta@i2bc.paris-saclay.fr

Acetylation of some proteins plays a positive role in the regulation of the production of specialized metabolites and in the morphological differentiation of Streptomyces.

Streptomyces species possess in their genomes numerous silent biosynthetic pathways likely to direct the biosynthesis of novel bioactive specialized metabolites. Enhancing the expression of these cryptic pathways might lead to the discovery of most needed novel antibiotics to limit the spreading of pathogenic bacteria resistant to most antibiotics in current use.
We characterized, an acetyl transferase (SCO0988) whose over-expression led to enhanced antibiotic production and accelerated sporulation of a low antibiotic producing strain, Streptomyces lividans, while the deletion of this gene had opposite effects in a strong antibiotic producer, Streptomyces coelicolor. Comparative analysis of the acetylome of the S. lividans strain overexpressing SCO0988 with that of the original strain revealed that 92 peptides, belonging to various proteins involved in different cellular processes, were exclusively acetylated in the strain over-expressing SCO0988. This led to the definition of a consensus SCO0988 acetylation site (v/q-P-l/g-D-p/e-KR-v/l-h/f-y/a-t/m). Among the acetylated proteins, BldKB was found to be over-acetylated on four lysine residues including Lys425 in the strain overexpressing SCO0988. BldKB is the solute binding protein of an ABC transporter involved in the up-take of an oligopeptide that plays a role in the triggering of a quorum sensing regulatory cascade controlling positively specialized metabolism, aerial mycelium formation and sporulation in S. coelicolor. A bldKB mutant has a reduced antibiotic production and does not develop aerial mycelium. The bldKB mutant phenotypes can be complemented by the native bldKB gene but not by a variant of this gene encoding a protein in which Lys425 was replaced by Arg (that cannot be acetylated) or by Glu (a putative structural analogue of acetylated lysine). Our study thus demonstrated that Lys425 is critical for BldKB function but could not clearly establish the impact of Lys425 acetylation on BldKB function.

More information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303876/

Contact: Marie-Joëlle VIROLLE marie-joelle.virolle@i2bc.paris-saclay.fr

The Apicomplexa-specific ACDC domain adopts a never before seen protein fold.

In collaboration with the Nessler team at the I2BC and the Llinás lab at PSU, US, we reveal that the ACDC domain, only found in DNA-binding proteins of the Apicomplexa phylum, grouping several important human pathogens including malaria, has a never before seen protein fold. We also identify potential ligands that may be optimized in the future as protein inhibitors.

More information:https://journals.iucr.org/paper?S2059798324012518

Conatct: Joana SANTOS joana.santos@i2bc.paris-saclay.fr

This study shows that DciA, the bacterial replicative helicase loader, promotes condensates in the presence of DNA. This opens the way to the possibility of non-membrane compartments in bacteria. The goal could be to concentrate the players involved in replication and thus facilitate it.

The loading of the bacterial replicative helicase DnaB is an essential step for genome replication and depends on the assistance of accessory proteins. Several of these proteins have been identified across the bacterial phyla. DciA is the most common loading protein in bacteria, yet the one whose mechanism is the least understood. We have previously shown that DciA from Vibrio cholerae is composed of a globular domain followed by an unfolded extension and demonstrated its strong affinity for DNA. Here, drawing on the skills of two I2BC facilities, Light microscopy (Imagerie-Gif) and PIM (Structural biology), we characterize the condensates formed by VcDciA upon interaction with a short single-stranded DNA substrate. We demonstrate the fluidity of these condensates using light microscopy and address their network organization through electron microscopy, thereby bridging events to conclude on a liquid-liquid phase separation behavior. Additionally, we observe the recruitment of DnaB in the droplets, concomitant with the release of DciA. We show that the well-known helicase loader DnaC from Escherichia coli is also competent to form these phase-separated condensates in the presence of ssDNA. Our phenomenological data are still preliminary as regards the existence of these condensates in vivo, but open the way for exploring the potential involvement of DciA in the formation of non-membrane compartments within the bacterium to facilitate the assembly of replication players on chromosomal DNA.

More information : https://pubmed.ncbi.nlm.nih.gov/39603490/

Contact : Sophie CHERUEL sophie.quevillon-cheruel@i2bc.paris-saclay.fr  and Stéphanie MARSIN stephanie.marsin@i2bc.paris-saclay.fr

Ribosome remodeling drives cancer cell transformation: A single protein, RPL36A, triggers EMT.

Epithelial-mesenchymal transition (EMT) is a biological process whereby a cell loses its usual characteristics to acquire properties allowing it to move. EMT is involved in embryo formation and tissue repair in adults. However, when altered, EMT contributes to the formation of fibrosis or, in the case of a tumor cell, to the formation of metastases. In cancers, this change is comparable to a cellular metamorphosis that allows cancer cells to become more aggressive and resistant to treatments. EMT is therefore a key player in tumor progression.
EMT is extensively studied at the molecular and cellular levels because a better understanding of this process will enable the development of new therapeutic approaches. However, the translational changes that occur during EMT have so far been very poorly studied.
In this work, we have identified that the overexpression of a single ribosomal protein, called RPL36A, is sufficient to induce EMT. We have also highlighted the various translational changes that occur during EMT.
Our work reveals the importance of ribosome remodeling itself in finely modulating translation during the change in cellular identity that occurs during EMT.

More information : https://www.pnas.org/doi/10.1073/pnas.2408114121 ; In French: https://www.insb.cnrs.fr/fr/cnrsinfo/des-modifications-de-la-composition-du-ribosome-accompagnent-les-changements.

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

Discovering the mycoloylome of Corynebacterium glutamicum : a new type of lipidated-modified proteins.

Protein mycoloylation is a lipidation pathway exclusively observed in Mycobacteriales, an order of bacteria that includes several human pathogens. These bacteria possess a distinctive outer membrane, known as the mycomembrane, composed of very long-chain fatty acids called mycolic acids. It has been demonstrated that a few mycomembrane proteins undergo covalent modification with mycolic acids in the model organism Corynebacterium glutamicum, through the action of mycoloyltransferase MytC. This PTM represents the first example of protein O-acylation in prokaryotes and also the first example of protein modification by mycolic acid. Here, we have developed a unique bioorthogonal mycolate donor featuring the natural mycolic acid pattern, enabling direct unambiguous transfer of the lipid moiety to its acceptors and efficient metabolic labeling and enrichment of MytC protein substrates. Mass spectrometry analysis of the labeled proteins and comparative proteomic analysis of the cell envelope proteome between wild-type and ∆mytC strains identified an unbiased list of 21 proteins likely mycoloylated in the cell. The robustness of our approach is demonstrated by the successful biological validation of mycoloylation in 6 random candidate proteins within wild-type cells, revealing the characteristic profile of proteins modified with natural mycolates. These findings provide interesting insights into the significance of this new lipidation pathway and pave the way for understanding their function, especially concerning the mycoloyltransferase family that includes the essential Antigen85 enzymes in Mycobacteria.

More information: https://doi.org/10.1021/acschembio.4c00502.

Contact: Cécile LABARRE <cecile.labarre@i2bc.paris-saclay.fr>

The study of Vibrio cholerae MatP reveals the degree of integration of the plasmid-derived chromosome carried by the bacterium, and suggests that the ancestral role of MatP is to promote cell division at the end of the chromosome replication and segregation cycle.

V. cholerae harbours a primary chromosome derived from the monochromosomal ancestor of the Vibrionales (ChrI) and a secondary chromosome derived from a megaplasmid (ChrII). The coordinated segregation of the replication terminus of both chromosomes (TerI and TerII) determines when and where cell division occurs. ChrI encodes a homolog of Escherichia coli MatP, a protein that binds to a DNA motif (matS) that is overrepresented in replication termini. Here, we use a combination of deep sequencing and fluorescence microscopy techniques to show that V. cholerae MatP structures TerI and TerII into macrodomains, targets them to mid-cell during replication, and delays their segregation, thus supporting that ChrII behaves as a bona fide chromosome. We further show that the extent of the segregation delay mediated by MatP depends on the number and local density of matS sites, and is independent of its assembly into tetramers and any interaction with the divisome, in contrast to what has been previously observed in E. coli.

More information: https://www.nature.com/articles/s41467-024-54195-0

Contact: E. Galli elisa.galli@i2bc.paris-saclay.fr

& FX Barre francois-xavier.barre@i2bc.paris-saclay.fr

The Graduate School Life Sciences & Health of the Université Paris-Saclay organizes a scientific day about Single-cell & Spatial-omics.

On Tuesday the 19th of November, the Graduate School Life Sciences and Health (GS LSH) of the Université Paris-Saclay is organizing its 8th scientific day, which is dedicated to “Single-cell and spatial-omics”. During the symposium, speakers from Université Paris-Saclay institutes and elsewhere will present their work involving single-cell and spatial -omics technologies. As part of the day, I2BC team leaders Kasia Siudeja and Joana Santos will present their work on the aging process in Drosophila and the infection cycle of the Malaria parasite. The day will take place in the Henri Moissan building on the Université Paris-Saclay campus. Participation is free, but registration is mandatory.

Registration: https://forms.office.com/e/6T3rVgPAYE

More information: https://openagenda.com/fr/universite-paris-saclay/events/journee-scientifique-gs-lsh-single-cell-and-spatial-omics

By comparing the collection of Next-Generation Sequencing data to the superimposition of several chess games, we demonstrate the limits of current temporal analysis approaches.

The development of next-generation sequencing (NGS) technologies paved the way for studying the spatiotemporal coordination of cellular processes along the genome. However, data sets are commonly limited to a few time points, and missing information needs to be interpolated. Most models assume that the studied dynamics are similar between individual cells, so that a homogeneous cell culture can be represented by a population-wide average. Here, we demonstrate that this understanding can be inappropriate. We developed a thought experiment—which we call the NGS chess problem—in which we compare the temporal sequencing data analysis to observing a superimposed picture of many independent games of chess at a time. The analysis of the spatiotemporal kinetics advocates for a new methodology that considers DNA-particle interactions in each cell independently even for a homogeneous cell population.

More information: https://academic.oup.com/nargab/article/6/4/lqae144/7833696

Contact: Julie Soutourina julie.soutourina@i2bc.paris-saclay.fr

Following the French MOOC 'Voyage au cœur du vivant avec des rayons X : la cristallographie', available on FUN-MOOC from 2017 to 2022, and the book in French 'Introduction à la cristallographie biologique', we now present an English version.

Following the French MOOC 'Voyage au cœur du vivant avec des rayons X : la cristallographie', available on FUN-MOOC from 2017 to 2022, and the book in French 'Introduction à la cristallographie biologique', we now present an English version.
This book is primarily designed for beginners in biological crystallography.
It provides an introduction to the different steps of biological crystallography, from the crystallisation to the three-dimensional structure of a macromolecule. The QR codes at the end of each chapter give you access to the videos in French, that are part of the MOOC. English subtitles are available for all the videos. In the early stages of learning biological crystallography, the digital version of this book can therefore be a particularly useful companion.

 - Marie-Hélène Le Du, Pierre Legrand, Serena Sirigu, Sylvain Ravy - EDP Sciences & Science Press Introduction to biological crystallography

link: https://bit.ly/3zBC6p5

Gif-sur-Yvette B22 N001

DciA secures bidirectional replication initiation in Vibrio cholerae.

Replication is initiated bidirectionally in the three domains of life by the assembly of two replication forks at an origin of replication. This is made possible by the recruitment of two replicative helicases to a nucleoprotein platform built at the origin of replication with the initiator protein. The reason why replication is initiated bidirectionally has never been experimentally addressed due to the lack of a suitable biological system. Using genetic and genomic approaches, we show that upon depletion of DciA, replication is no longer initiated bidirectionally at the origin of replication of Vibrio cholerae chromosome 1. We show that following unidirectional replication on the left replichore, nascent DNA strands at ori1 anneal to each other to form a double-stranded DNA end. While this DNA end can be efficiently resected in recB+ cells, only a few cells use it to trigger replication on the right replichore. In most DciA-depleted cells, chromosome 1 is degraded leading to cell death. Our results suggest that DciA is essential to ensuring bidirectional initiation of replication in bacteria, preventing a cascade of deleterious events following unidirectional replication initiation.

More information: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae795/7759985

Contact: Amelie BESOMBES amelie.besombes@i2bc.paris-saclay.fr