Researchers from the I2BC, the CNRGH (CEA, National Center of Human Genomics Research), and the University of Edinburgh have revealed how the BAF chromatin remodeler changes the structure and accessibility of genetic material by producing subnucleosomal particles. These findings are published in Nature Structural and Molecular Biology.

Mutations in genes encoding subunits of the BAF complex (BRG1/BRM-associated factors, also known as the SWI/SNF complex) are associated with 20% of human cancers, making this complex the second most frequently mutated factor after the p53 tumor suppressor.
The human genome exists in cells in the form of chromatin, composed of nucleosomes that condense and protect the genetic material. The nucleosomes represent a physical barrier for transcription factors and molecular machinery that regulate gene expression. The BAF complex is known for controlling chromatin opening at gene transcription regulatory elements. Until now, it was believed that the role of the BAF complex was to dissociate the nucleosomes to allow the transcription factors to access DNA.
Using a method that allows them to differentiate histone-free DNA fragments from nucleosomes and histone-containing particles smaller than nucleosomes (subnucleosomes), researchers coordinated by Matthieu Gérard (I2BC) revealed that the BAF complex facilitates the recruitment of the master transcription factor OCT4 using two distinct strategies: i) by generating the well-known histone-free DNA regions, which OCT4 binds if its target DNA motif is present; and ii) by producing a new class of subnucleosomal particles containing 50 to 80 base pairs associated with histones.
They show that the subnucleosomes act as a recruitment platform for OCT4 independently of the presence of its DNA motif. They identify in this publication a molecular mechanism in which the interaction between OCT4 and the subnucleosomes leads to a spectacular expansion of the OCT4 genomic binding interval. This mechanism aims to project OCT4 activity in chromatin opening within a genomic interval up to one order of magnitude larger than the interval bound by OCT4 on histone-free DNA.
This study suggests two main determinants for recruiting transcription factors onto the mammalian genome: the genetic determinant, the transcription factor motif within histone-free DNA, and an epigenetic determinant, which corresponds to the subnucleosomes produced by the BAF complex.

More information: https://www.nature.com/articles/s41594-024-01344-0

Contact: Matthieu GERARD matthieu.gerard@i2bc.paris-saclay.fr

In search of the hidden gene cluster: Synteruptor, a new tool for identifying bacterial genomic islands and exploring their content in the quest for new specialized metabolism gene clusters.

Microbial specialized metabolite biosynthetic gene clusters (SMBGCs) are a formidable source of natural products of pharmaceutical interest. With the multiplication of genomic data available, very efficient bioinformatic tools for automatic SMBGC detection have been developed. Nevertheless, most of these tools identify SMBGCs based on sequence similarity with enzymes typically involved in specialised metabolism and thus may miss SMBGCs coding for undercharacterised enzymes. In this article, we present Synteruptor (https://bioi2.i2bc.paris-saclay.fr/synteruptor), a program that identifies genomic islands, known to be enriched in SMBGCs, in the genomes of closely related species. With this tool, we identified a SMBGC in the genome of Streptomyces ambofaciens ATCC23877, undetected by antiSMASH, the well-known and most used tool for SMBGC identification, prior to antiSMASH 5. We experimentally demonstrated that this SMBGC directs the biosynthesis of two metabolites, one of which was identified as sphydrofuran. Synteruptor is also a valuable resource for the delineation of individual SMBGCs within antiSMASH regions that may encompass multiple clusters, and for refining the boundaries of these SMBGCs.

More information: https://doi.org/10.1093/nargab/lqae069

Contact: Sylvie LAUTRU <sylvie.lautru@i2bc.paris-saclay.fr> & Olivier LESPINET <olivier.lespinet@i2bc.paris-saclay.fr>

The UPR sensors show high plasticity in sensing physiological alterations by closely reporting the variations in ER Ca2+ levels. Through this mechanisms cells could rapidly adapt stress response signaling pathways to variations in ER homeostasis.

The unfolded protein response (UPR) is a widespread signal transduction pathway triggered by endoplasmic reticulum (ER) stress. Because calcium (Ca2+) is a key factor in the maintenance of ER homeostasis, massive Ca2+ depletion of the ER is a potent inducer of ER stress. Although moderate changes in ER Ca2+ drive the ubiquitous Ca2+ signaling pathways, a possible incremental relationship between UPR activation and Ca2+ changes has yet to be described. Here, we determine the sensitivity and time-dependency of activation of the three ER stress sensors, IRE1α, PERK and ATF6α in response to controlled changes in the concentration of ER Ca2+ in human cultured cells. Combining Ca2+ imaging, FRAP experiments, biochemical analyses and mathematical modeling, we uncover a non-linear rate of activation of the IRE1α branch of UPR, as compared to the PERK and ATF6α branches that become activated gradually with time and are sensitive to more important ER Ca2+ depletions. However, the three arms are all activated within a 1h timescale. The model predicted the deactivation of PERK and IRE1α upon refilling the ER with Ca2+. Accordingly, we showed that ER Ca2+ replenishment leads to the complete reversion of IRE1α and PERK phosphorylation in less than 15 min, thus revealing the highly plastic character of the activation of the upstream UPR sensors. In conclusion, our results reveal a dynamic and dose-sensitive Ca2+-dependent activation/deactivation cycle of UPR induction, which could tightly control cell fate upon acute and/or chronic stress.

More information: https://doi.org/10.1093/pnasnexus/pgae229

Contact: Ilaria Pontisso (ilaria.pontisso@i2bc.paris-saclay.fr)

We are seeking one highly motivated PhD candidate to join our research team at the Institute for Integrative Biology of the Cell (I2BC).

The project entitled “Selective autophagy receptors in viral antigen presentation” is an exciting opportunity to explore the intersection
of immunology and virology.

More information: https://www.i2bc.paris-saclay.fr/equipe-autophagy-and-antiviral-immunity/

Contact: Arnaud Moris (arnaud.moris@i2bc.paris-saclay.fr)

Researchers from the AMIG team (I2BC department), in collaboration with the IRB (Switzerland), have modeled the interaction between HROB and the helicases MCM8-MCM9, some mutations of which predispose individuals to infertility or cancer. They demonstrate that HROB promotes the catalytic activity of the MCM8-MCM9 complex but does not play a role in its recruitment or stability.

The proteins MCM8 and MCM9 have recently been discovered as involved in multiple processes, normal and pathological, related to DNA replication, meiosis, homologous recombination, and mismatch repair. These proteins are helicases that have the ability to move along DNA and separate the two DNA strands. Variants of these proteins may predispose carriers to disorders such as infertility and cancer. In 2019, a third partner, HROB, was identified as associated with these two helicases without its mechanisms of action being understood. Since HROB is capable of interacting with DNA, three functional hypotheses can be considered:
1) HROB participates in the recruitment of helicases on DNA,
2) HROB stabilizes the assembly of MCM8 and MCM9 on DNA,
3) HROB promotes the catalytic activity of pre-assembled helicases.

In a study published in the journal Nature Communications, researchers from the AMIG team at the Institute of Integrative Biology of the Cell (I2BC) collaborated with a team from the Institute of Research in Biomedicine (IRB) in Switzerland to establish different structural models of the MCM8-MCM9-HROB complex. Guided by these models, a set of simple and compensatory mutations allowed the dissection of the functional role of HROB. The teams showed that only the third hypothesis was correct and that HROB is an essential factor for activating the MCM8-MCM9 helicase but not for its recruitment or stability. The structural model suggests that by transiently altering the conformation of a MCM9 subunit, HROB stimulates the translocation of the helicase along the DNA. Based on this model, it was even possible to design mutations that increase the efficiency of the helicase in the presence of HROB.

More information: https://www.nature.com/articles/s41467-024-47936-8

Contact: Raphaël Guerois raphael.guerois@i2bc.paris-saclay.fr 

“Ménage à trois”: coordination of lipid transfer, metabolism and storage at the new mitochondria-ER-lipid droplet junction.

Over the past two decades, we have witnessed a growing appreciation for the importance of membrane contact sites (CS) in facilitating direct communication between organelles. CS are tiny regions where the membranes of two organelles meet but do not fuse and allow the transfer of metabolites between organelles, playing crucial roles in the coordination of cellular metabolic activities. The significant advancements in imaging techniques, and molecular and cell biology research has revealed that CS are more complex than what originally thought, as they are extremely dynamics, they can remodel their shape, composition and functions in accord to metabolic and environmental changes, and can occur between more than two organelles. In this review, for the Special Issue “Lipid droplets, metabolic hubs in health and disease“ in FEBS Letters, Vera F. Monteiro-Cardoso and Francesca Giordano describe how recent studies led to the identification of a three-way mitochondria-ER-lipid droplet CS and discuss the emerging functions of these contacts in maintaining lipid storage, homeostasis and balance. They also summarize properties and functions of key protein components localized at the mitochondria-ER-lipid droplet interface, with a special focus on lipid transfer proteins. Understanding tripartite CS is essential for unraveling the complexities of inter-organelle communication and cooperation within cells.

more information: https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14893

contact: Francesca GIORDANO <francesca.giordano@i2bc.paris-saclay.fr>

The Dlk1-Meg3-Dio3 domain is imprinted. Scientists at the IGMM and the I2BC have determined that Meg3 long non-coding RNA, as well as DNA methylation levels at an essential CTCF binding site in the domain, control Dlk1 imprinting in cis.

The imprinted Dlk1-Dio3 domain comprises the Dlk1 and Rtl1 developmental genes that are solely expressed from the paternal chromosome, and a maternally-expressed polycistron that is further processed into the Meg3 long non-coding RNA (lncRNA) and many other small non-coding RNAs.

In collaborative work between scientists at the IGMM (R. Feil’s group; Montpellier) and at the I2BC (D. Noordermeer’s group; Gif-sur-Yvette), researchers studied the precise role of Meg3 lncRNA and of its promoter for the control of Dlk1 and Rtl1 imprinted gene expression. Using mutant cells with either premature termination of transcription or deletion of part of the polycistron, they found that Meg3 lncRNA, but not other non-coding RNAs produced by the polycistron, controls Dlk1 imprinting in cis.

The maternal expression of this polycistron is driven by the Meg3 differentially methylated region (Meg3-DMR) which is unmethylated on the maternal allele and acts there as an active promoter. Besides, the Meg3-DMR includes a known binding site for the architectural CTCF protein, that binds to the unmethylated maternal allele only. In this study, the researcher showed that the maternal Dlk1-Dio3 locus is organized into sub-Topologically Associating domains (sub-TADs) that are hinged by the allelic binding of CTCF to the maternal Meg3-DMR. They further found that the methylation levels at the Meg3-DMR are instructive for CTCF binding and thereby dictate distinctive sub-TAD organization at the two parental alleles which, in turns, facilitates Dlk1 repression on the maternal allele.

Altogether, this collaborative work revealed that, the maternally-expressed Meg3 lncRNA controls Dlk1 silencing in cis, and that the low methylation levels at the maternal Meg3-DMR allows for specific sub-TADs structuration that concurrently contributes to Dlk1 silencing.

More information: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae247/7645245?searchresult=1

Contact: Benoit Moindrot benoit.moindrot@i2bc.paris-saclay.fr 

Plants can benefit from fast nucleoside breakdown

Cells save their energy during nitrogen starvation by selective autophagy of ribosomes and degradation of RNA to ribonucleotides and nucleosides. Nucleosides are hydrolyzed by nucleoside N-ribohydrolases (nucleosidases, NRHs). Subclass I of NRHs preferentially hydrolyzes the purine ribosides while subclass II is more active towards uridine and xanthosine. Here, we performed a crystallographic and kinetic study to shed light on nucleoside preferences among plant NRHs followed by in vivo metabolomic and phenotyping analyses to reveal the consequences of enhanced nucleoside break-down. We report the crystal structure of Zea mays NRH2b (subclass II) and NRH3 (subclass I) in complexes with the substrate analog forodesine. Purine and pyrimidine catabolism are inseparable because nucleobase binding in the active site of ZmNRH is mediated via a water network and is thus unspecific. Dexamethasone-inducible ZmNRH overexpressor lines of Arabidopsis thaliana, as well as double nrh knockout lines of moss Physcomitrium patents, reveal a fine control of adenosine in contrast to other ribosides. ZmNRH overexpressor lines display an accelerated early vegetative phase including faster root and rosette growth upon nitrogen starvation or osmotic stress. Moreover, the lines enter the bolting and flowering phase much earlier. We observe changes in the pathways related to nitrogen-containing compounds such as β-alanine and several polyamines, which allow plants to reprogram their metabolism to escape stress. Taken together, crop plant breeding targetting enhanced NRH-mediated nitrogen recycling could therefore be a strategy to enhance plant growth tolerance and productivity under adverse growth conditions.

more information: https://onlinelibrary.wiley.com/doi/10.1111/tpj.16572

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

Phanie is a phi-29 like phage that protects its genome inside non-infectious podovirus-like particles, requiring acquisition of the tail from a myovirus helper for production of infectious chimeras.

Viruses of bacteria (bacteriophages or phages) display a remarkable genomic diversity reflecting the complex interaction they have built with their host during evolution. In addition to fully infectious viral particles, different types of genetic elements were described to require a helper phage for production of infectious virions. The genome of these satellite parasite sequences may share sequences with phages or be more closely related to non-viral chromosome islands. We describe a new mode of satellite phage dependence on a helper phage. Phanie, like the genetically related Bacillus subtilis phage phi29, replicates its linear dsDNA by a protein primed-mechanism and protects it inside podovirus-like particles. However, these particles are defective, requiring acquisition of the tail from a myovirus helper for production of infectious virions. Formation of chimeras between a phi29-like podovirus and a helper contractile tail reveals an unexpected association between very different bacterial viruses.

More information: https://journals-asm-org.insb.bib.cnrs.fr/doi/10.1128/jvi.00667-24

Contact: Christine Pourcel christine.pourcel@i2bc.paris-saclay.fr

October 14th -16th

Site Henri Moissan Université Paris-Saclay Orsay

More information: https://www.universite-paris-saclay.fr/evenements/physchemcell2024

Researchers at I2BC and their collaborators have conducted an extensive functional analysis of a highly conserved Tail Completion Protein (TCP) in the assembly and infectivity of tailed bacteriophages.

Their investigation highlights the role of bacteriophage SPP1 TCP gp16.1 as a structural element of the tail, serving two distinct purposes. Firstly, gp16.1 assists assembly of the tail interface that binds to the phage capsid. Secondly, it ensures proper delivery of phage DNA to the bacterial cytoplasm.
In the absence of gp16.1, assembled viral particles are undistinguishable from wild-type virions and eject DNA efficiently in vitro. However, upon interaction with the host bacteria, they release their DNA into the extracellular space. Transfer of DNA from the viral particle to the bacterial cytoplasm requires prior localized digestion of the bacterial cell wall, likely facilitated by the tail tip, and the formation of a lipophilic channel in the bacterial membrane for DNA passage. Successful infection depends on precise timing, involving phage binding to the receptor, creating a pathway for DNA passage through the cell envelope, and DNA exit from the particle into the bacterial cytoplasm.
The authors propose that the gp16.1 critical function is achieved by its positioning at the tail end proximal to the capsid to form a complex with the Tape Measure Protein (TMP) and the Tail Tube Protein (TTP). These interactions conceivably regulate the timing of TMP and DNA release. This could result of narrowing the internal diameter of the tail tube to retain the TMP, slowing down release of the TMP and DNA until a continuous hydrophilic channel forms between the tail and the bacterial cytoplasm. Their study unravels the dual role of gp16.1 in tail assembly and in delivery of viral DNA into bacteria. Both functions are most likely exerted by the large superfamily of TCPs that are essential components of phages with long tails.

More information: https://www.nature.com/articles/s42003-024-06221-6

Contact: Isabelle Auzat isabelle.auzat@i2bc.paris-saclay.fr 

The production of unhealthy eggs leads to improved maternal stress resilience and proteostasis in C. elegans. This study identifies the nuclear hormone receptor NHR-49 as a critical regulator that is activated by elevated fat stores and acts by potentiating the heat shock response.

The ability to sense and respond to proteotoxic insults declines with age, leaving cells vulnerable to chronic and acute stressors. Reproductive cues modulate this decline in cellular proteostasis to influence organismal stress resilience in Caenorhabditis elegans We previously uncovered a pathway that links the integrity of developing embryos to somatic health in reproductive adults. Here, we show that the nuclear receptor NHR-49, an ortholog of mammalian peroxisome proliferator-activated receptor α (PPARα), regulates stress resilience and proteostasis downstream from embryo integrity and other pathways that influence lipid homeostasis and upstream of HSF-1. Disruption of the vitelline layer of the embryo envelope, which activates a proteostasis-enhancing intertissue pathway in somatic cells, triggers changes in lipid catabolism gene expression that are accompanied by an increase in fat stores. NHR-49, together with its coactivator, MDT-15, contributes to this remodeling of lipid metabolism and is also important for the elevated stress resilience mediated by inhibition of the embryonic vitelline layer. Our findings indicate that NHR-49 also contributes to stress resilience in other pathways known to change lipid homeostasis, including reduced insulin-like signaling and fasting, and that increased NHR-49 activity is sufficient to improve proteostasis and stress resilience in an HSF-1-dependent manner. Together, our results establish NHR-49 as a key regulator that links lipid homeostasis and cellular resilience to proteotoxic stress.

More information: https://genesdev.cshlp.org/content/early/2024/05/30/gad.351829.124

Contact: Ambre Sala  ambre.sala@i2bc.paris-saaclay.fr

In this work, we reviewed the latest Hi-C findings and discuss the principles of bacterial chromosome folding that can be inferred from them.

The use of Hi-C not only revealed the diversity of 3D-genome architectures in multiple bacterial species across the phylogenetic tree, but also the different scales of genome organization and the mechanisms of action of key structural factors and processes. Here, we revisited the work performed on these bacteria and discussed the rules of genome folding that can be deduced from it.

more information: https://onlinelibrary.wiley.com/doi/10.1111/mmi.15290

contact: Virginia LIOY <virginia.lioy@i2bc.paris-saclay.fr>

Mark your calendars for Jun. 26-28, 2024! Join us at Ecole Polytechnique in Palaiseau for the 7th International Conference on Physics and Biological Systems, where top-notch scientists converge to explore the dynamic interplay between physics and life sciences.

The 7th International Conference on Physics and Biological Systems will be held on Jun. 26-28 2024 at Ecole Polytechnique in Palaiseau, in the south of Paris. It aims to bring together a broad range of physical and life scientists working at the interface between the two disciplines around in-depth talks by first-rate international speakers. Attendance will be limited to 200 participants. We look forward to welcoming you in Palaiseau!

more information: https://www.lptms.universite-paris-saclay.fr/physbio2024/

contact: Pavel MULLER <pavel.muller@i2bc.paris-saclay.fr>