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A small RNA linking light absorption and photoprotection

A small RNA linking light absorption and photoprotection | I2BC Paris-Saclay | Scoop.it

A posttranscriptional regulatory mechanism links the expression of the cyanobacterial Orange Carotenoid Protein related to photoprotection, directly and in an inverse fashion, to the synthesis of the phycobilisome, the cyanobacterial antenna via a 3’ end-derived sRNA.

The modular photoactive Orange Carotenoid Protein (OCP), which has a crucial role in cyanobacterial photoprotection, has gained a great interest in the recent years due to its ability to act as a molecular photoswitch and to its suppressive 12 Å translocation of the carotenoid upon photoactivation. Upon blue light absorption, the inactive orange form (OCPO) converts to the active red state (OCPR) which is able to interact with the phycobilisome, the cyanobacterial antenna, and to decrease the energy arriving at the photochemical centers. Due to its function in thermal dissipation of excess energy, the expression of OCP must be tightly controlled to avoid a loss of energy under non-stressing conditions and to increase this dissipation under stressing ones. A research group of the I2BC in collaboration of a group of the University of Freiburg discovered the first molecular factor involved in the regulation of OCP expression. Moreover, they show for the first time that a sRNA appended to a long operon mRNA functions in the regulatory network of cyanobacteria.

This factor is the first example in cyanobacteria of a sRNA derived from a polycistronic mRNA regulating at least one other mRNA in trans. The researchers demonstrated that ApcZ, a sRNA originating from the 3’end of the apcABC operon encoding the core phycobilisome proteins, is responsible for the repression of ocp translation under non-stress conditions.  The transcription of the apcABC operon decreases under most stress conditions and as a consequence ApcZ (free and as part of the entire operon transcript) concentration decreases leading to a de-repression of ocp mRNA translation. Thus, light harvesting and photoprotection are connected directly and in an inverse fashion by a single regulatory sRNA. If, under stress conditions, less energy must arrive at the photochemical centers, the transcription of phycobilisome genes decreases and synthesis of OCP increases. Hence, the OCP concentration is controlled in a simple and elegant way.

“Inverse Regulation of Light Harvesting and Photoprotection Is Mediated by a 3’ End-Derived sRNA in Cyanobacteria” Plant Cell (2021) 33, 358-380. Jiao Zhan, Claudia Steglich, Ingeborg Scholz, Wolfgang R. Hess and Diana Kirilovsky

Contact: diana.kirlovsky@cea.fr

 

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November 25th "Host-Microbe Interactions" and "Molecular Tools for Biology"

November 25th "Host-Microbe Interactions" and "Molecular Tools for Biology" | I2BC Paris-Saclay | Scoop.it

The “Drug and Technology for Health” Department is part of the CEA’s Joliot Institute, as is the I2BC. The aim of the DMTS-I2BC day is to get to know each other and to encourage potential collaborations.

Two themes were chosen for this first edition:
“Host-Microbe Interactions” and “Molecular Tools for Biology”.
More information and program: here
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MICROBIOLOGY DEPARTMENT DAY - TRIBUTE TO MICKAEL DUBOW: 30 SEPTEMBER 2022

MICROBIOLOGY DEPARTMENT DAY - TRIBUTE TO MICKAEL DUBOW: 30 SEPTEMBER 2022 | I2BC Paris-Saclay | Scoop.it

The morning was devoted to personal and scientific testimonies which highlighted Mike's imagination, insatiable curiosity and innovative ideas as well as his great popularity with students in France and abroad.

The afternoon was devoted to scientific presentations, around 3 themes that Mike was passionate about: biofilms, extremophilic bacteria and environmental phages.

These presentations were given by researchers from the department and by two guest researchers, Adrienne Kish (MNHN, Paris) and Romain Briandet (Institut Micalis, Jouy-en-Josas).

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6th FRISBI users meeting

6th FRISBI users meeting | I2BC Paris-Saclay | Scoop.it

The 6th users meeting of the The French Infrastructure for Integrated Structural Biology (FRISBI) will be held on December 9th 2022 in Gif-sur-Yvette.

Preliminary program and registration: https://frisbi.eu/network/user-community/

More information: here

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

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Artificials proteins, αReps, targeting the SARS-CoV-2 spike as antivirals

Artificials proteins, αReps, targeting the SARS-CoV-2 spike as antivirals | I2BC Paris-Saclay | Scoop.it

Specific binders targeting the SARS-CoV-2 spike protein were selected from the αRep library. Two combined αRep nanoligands neutralize SARS-CoV-2 variants and reduce infection severity in hamster.

The coronavirus SARS-CoV-2 emerged as a human pathogen in China's Hubei province, causing severe respiratory diseases and pneumonia. Since the beginning of 2020, more than 600 million people have been infected with SARS-CoV-2 and more than 6.5 million have died during the COVID-19 crisis. Vaccines, although very effective in limiting severe forms, do not block the spread of the virus. Thus, reducing the multiplication of the virus in the nasal cavity is a promising approach to limit its spread.
In a new study published in the journal PLOS Pathogens, αRep artificial proteins were selected and used to prevent the virus from binding to its target cells and thus limit its multiplication. These proteins are able to recognize the SPIKE protein of the virus. More precisely, two αReps proteins, named F9 and C2 bind to the spike RBD domain with affinities in the nM range, and exhibit virus neutralization activity in vitro by recognizing two distinct sites. The combination of these αReps through covalent (F9-C2) or non-covalent (C2-foldon) linkages blocked the entry of the virus with a higher efficiency displaying affinity in the 0.1 nM range and EC50 of 8–18 nM for neutralization of SARS-CoV-2. These combination of αReps neutralize a broad spectrum of SARS-CoV-2 β, γ, δ and Omicron virus variants. Instillation of an αRep F9-C2 nanoligand in the nasal cavity of hamster effectively reduced virus replication and pathogenicity of SARS-CoV-2.
In addition to their strong antiviral capacity, these αReps can be very efficiently produced, at low cost, by recombinant protein expression technologies in bacteria. They are particularly robust, highly thermostable, and can be stored at room temperature. Taken together, the antiviral capacity associated with the attractive properties of these proteins are highly promising for the development of molecules able to reduce the pathology and spread of SARS-CoV-2 variants.

More information: here

Contact: Philippe Minard, <philippe.minard@i2bc.paris-saclay.fr>, Agathe Urvoas <agathe.urvoas@i2bc.paris-saclay.fr>, Marielle Valerio <marielle.valerio@i2bc.paris-saclay.fr>

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A functional protein complex, associated to ciliopathies, dictates the future position of distal appendages

A functional protein complex, associated to ciliopathies, dictates the future position of distal appendages | I2BC Paris-Saclay | Scoop.it

Using BioID and expansion microscopy, the study uncover a conserved functional complex required for determining the future position of centriolar distal appendages and their assembly, allowing the basal body anchoring process during ciliogenesis.

Cilia/flagella play fundamental and diverse biological functions in a wide variety of eukaryotes. The cilia assembly process, also called ciliogenesis, is a multistep process involving 4 major events: basal body (BB) duplication, migration to the cell surface, membrane anchoring of the BB via the distal appendages, and ciliary growth. The conservation of this sequence of events in most phyla is paralleled by an important conservation of the proteins involved. The BB anchoring step requires the tethering of the distal appendages to a membrane. The interaction of the BB with the membrane leads to the formation of the transition zone (TZ), recognized to act as a diffusion barrier between the intracellular space and the cilium. Mutations in numerous genes involved in BB docking and TZ assembly are associated with the most severe ciliopathies highlighting the importance of these events in ciliogenesis.
To discover novel molecular actors involved in the BB anchoring process, the Tassin’s team used BioID technology in human cells. They focused their attention on a protein, CEP90, together with its bait (FOPNL) and another protein (OFD1) involved in ciliopathies and known to interact with FOPNL. These 3 proteins are conserved from Protist to mammals despite absent from some phyla. They unveiled using ultrastructure expansion microscopy that the 3 proteins localize at the distal end of both centrioles/BB in Paramecium and mammalian cells. Functional analysis performed both in Paramecium and mammalian cells demonstrate that the 3 proteins form a functional complex required for distal appendage assembly and BB docking. Intriguingly, these proteins are recruited early during centriole duplication on the external surface of the procentriole. This early recruitment on procentriole led us to propose that this functional complex dictates the future distal appendage location in mammalian cells one or two cell cycle before their assembly.

 

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Contact: Anne-Marie Tassin  <anne-marie.tassin@i2bc.paris-saclay.fr>

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A quantitative modelling approach for DNA repair on a population scale

A quantitative modelling approach for DNA repair on a population scale | I2BC Paris-Saclay | Scoop.it

A new analysis pipeline for NGS data based on a population of individual cells reveals unknown links between genomic features and DNA repair.

As DNA encodes our very identity, it has been subject to a plethora of studies over the last century. The advent of new technologies that permit rapid sequencing of large DNA and RNA samples opened doors to before unknown mechanisms and interactions on a genomic scale. This led to an in-depth analysis of several nuclear processes, including transcription of genes and DNA lesion repair. However, the applied protocols do not allow a high temporal resolution. Quite the contrary, the experiments yield often only some few data signals over several hours. The details of the dynamics between time points are chiefly ignored, implicitly assuming that they straightforwardly transition from one to another. Here, we show that such an understanding can be flawed. We use the repair process of UV-induced DNA damage as an example to present a quantitative analysis framework that permits the representation of the entire temporal process. We subsequently describe how they can be linked to other heterogeneous data sets. Consequently, we evaluate a correlation to the whole kinetic process rather than to a single time point. Although the approach is exemplified using DNA repair, it can be readily applied to any other mechanism and sequencing data that represent a transition between two states, such as damaged and repaired.

More information here 

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

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The BAF A12T mutation, associated to the Nestor–Guillermo progeria syndrome, disrupts lamin A/C interaction, impairing robust repair of nuclear envelope ruptures

The BAF A12T mutation, associated to the Nestor–Guillermo progeria syndrome, disrupts lamin A/C interaction, impairing robust repair of nuclear envelope ruptures | I2BC Paris-Saclay | Scoop.it

The A12T mutation in BAF destabilizes the interaction with the nucleoskeletal lamin A/C and prevents robust repair of nuclear envelope ruptures in cells from patients with Nestor-Guillermo progeria.

Nestor-Guillermo progeria syndrome (NGPS) is caused by a homozygous alanine-to-threonine mutation at position 12 (A12T) in barrier-to-autointegration factor (BAF). It is characterized by accelerated aging with severe skeletal abnormalities. BAF is an essential protein binding to DNA and nuclear envelope (NE) proteins, involved in NE rupture repair. The team of Dr Delphine Larrieu at the Cambridge Institute for Medical Research (UK), together with the team of Dr Sophie Zinn-Justin at I2BC and Dr Pierre Legrand at Synchrotron SOLEIL, assessed the impact of BAF A12T on NE integrity using NGPS-derived patient fibroblasts. The team of Dr Delphine Larrieu engineered the first NGPS isogenic cell lines by correcting the homozygous BAF A12T mutation in NGPS patient cells using CRISPR-Cas9 mediated genome editing. They observed a strong defect in lamin A/C accumulation to NE ruptures in NGPS cells, restored upon homozygous reversion of the pathogenic BAF A12T mutation. The team of Dr Sophie Zinn-Justin at I2BC, together with Dr Pierre Legrand at Synchrotron SOLEIL, demonstrated that, while the A12T mutation does not affect BAF 3D structure and phosphorylation by VRK1, it specifically decreases the interaction between BAF and lamin A/C. The team of Dr Delphine Larrieu revealed that the disrupted interaction does not prevent repair of NE ruptures but instead generates weak points in the NE that lead to a higher frequency of NE re-rupturing in NGPS cells. Altogether, we propose that this NE fragility could directly contribute to the premature aging phenotype in patients.

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

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BSI@Paris-Saclay - nov 29, 2022

BSI@Paris-Saclay - nov 29, 2022 | I2BC Paris-Saclay | Scoop.it

The Structural Integrative Biology (BSI) community is organising its first Scientific Day on Tuesday 29 November 2022 from 9:00 am to 5:00 pm at the I2BC (Auditorium of Bât21, CNRS campus, Gif-sur-Yvette) with the participation of the national infrastructures Soleil, Infranalytics and FRISBI and the European infrastructure Instruct-Eric. The objective of this day is to bring together the local BSI community of Paris-Saclay in order to foster new interactions.

Speakers:
Harald SCHWALBE (Director of INSTRICT-ERIC)
Carine VAN HEIJENOORT (Director of Infranalytics)
Andy THOMPSON (Resp. scientist Synchrotron Soleil)
Stéphane BRESSANELLI (Resp. PF CryoEM, I2BC, FRISBI)

And 5 oral presentations selected on abstract

– Free but mandatory registration on the conference website
– Submission of abstracts (Posters and Oral Presentations) on the congress website.
The deadline for submission of abstracts for oral presentations is 21 October 2022. The selection will be made by the organising committee.

We are looking forward to seeing many of you.

Contacts:
julie.menetrey@i2bc.paris-saclay.fr and ewen.lescop@cnrs.fr

Sponsors :
I2BC, ICSN, FRISBI, Infranalytics, Soleil, LM@W

More information: here

Contact: Julie Ménétrey  <julie.menetrey@i2bc.paris-saclay.fr>

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c-di-AMP signaling is required for bile salt resistance, osmotolerance, and long-term host colonization by Clostridioides difficile

c-di-AMP signaling is required for bile salt resistance, osmotolerance, and long-term host colonization by Clostridioides difficile | I2BC Paris-Saclay | Scoop.it

The cyclic dinucleotide c-di-AMP is a mediator of osmotic stress and bile salt resistance with a role in host colonization in the opportunistic pathogen Clostridioides difficile.

To colonize the host and cause disease, the human enteropathogen Clostridioides difficile must sense, respond,
and adapt to the harsh environment of the gastrointestinal tract. We showed that the production and
degradation of cyclic diadenosine monophosphate (c-di-AMP) were necessary during different phases of
C. difficile growth, environmental adaptation, and infection. The production of this nucleotide second messenger
was essential for growth because it controlled the uptake of potassium and also contributed to biofilm
formation and cell wall homeostasis, whereas its degradation was required for osmotolerance and resistance
to detergents and bile salts. The c-di-AMP binding transcription factor BusR repressed the expression of genes
encoding the compatible solute transporter BusAA-AB. Compared with the parental strain, a mutant lacking
BusR was more resistant to hyperosmotic and bile salt stresses, whereas a mutant lacking BusAA was more
susceptible. A short exposure of C. difficile cells to bile salts decreased intracellular c-di-AMP concentrations,
suggesting that changes in membrane properties induce alterations in the intracellular c-di-AMP concentration.
A C. difficile strain that could not degrade c-di-AMP failed to persist in a mouse gut colonization model as
long as the wild-type strain did. Thus, the production and degradation of c-di-AMP in C. difficile have pleiotropic
effects, including the control of osmolyte uptake to confer osmotolerance and bile salt resistance, and
its degradation is important for host colonization.

More information here

Contact: Johann Peltier <johann.peltier@i2bc.paris-saclay.fr>

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Expanded dataset reveals the emergence and evolution of DNA gyrase in Archaea

Expanded dataset reveals the emergence and evolution of DNA gyrase in Archaea | I2BC Paris-Saclay | Scoop.it

Single horizonal gene transfer explains the emergence of DNA gyrase in Archaea.

DNA gyrase is a type II topoisomerase with the unique capacity to introduce negative supercoiling in DNA. In bacteria, DNA gyrase has an essential role in the homeostatic regulation of supercoiling. While ubiquitous in Bacteria, DNA gyrase was previously reported to have a patchy distribution in Archaea but its emergent function and evolutionary history in this domain of life remains elusive. In this study, we used phylogenomic approaches and an up-to date sequence dataset to establish global and archaeaspecific phylogenies of DNA gyrases. The most parsimonious evolutionary scenario infers that DNA gyrase was introduced into the lineage leading to Euryarchaeal group II via a single horizontal gene transfer from a bacterial donor which we identified as an ancestor of Gracilicutes and/or Terrabacteria. The archaea-focused trees indicate that DNA gyrase spread from Euryarchaeal group II to some DPANN and Asgard lineages via rare horizontal gene transfers. The analysis of successful recent transfers suggests a requirement for syntropic or symbiotic/parasitic relationship between donor and recipient organisms. We further show that the ubiquitous archaeal Topoisomerase VI may have co-evolved with DNA gyrase to allow the division of labour in the management of topological constraints. Collectively, our study reveals the evolutionary history of DNA gyrase in Archaea and provides testable hypotheses to understand the prerequisites for successful establishment of DNA gyrase in a naïve archaeon and the associated adaptations in the management of topological constraints.

More information here

Contact: Tamara Basta <tamara.basta@i2bc.paris-saclay.fr>

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Looking for an intership ?

Looking for an intership ? | I2BC Paris-Saclay | Scoop.it

You are looking for an internship, come and meet us on October 15 at I2BC, 1 avenue de la terrasse in Gif sur Yvette.

More information: here

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Transmission Electron Microscopy Explore the architecture of a virus in all its forms

Transmission Electron Microscopy Explore the architecture of a virus in all its forms | I2BC Paris-Saclay | Scoop.it

From October the 3rd to October the 10th

Registration before September the 28th.

More information here

Contact: Claire Boulogne <claire.boulogne@i2bc.paris-saclay.fr>

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E-cadherin acts as a positive regulator of the JAK-STAT signaling pathway during Drosophila oogenesis

E-cadherin acts as a positive regulator of the JAK-STAT signaling pathway during Drosophila oogenesis | I2BC Paris-Saclay | Scoop.it

What is Drosophila teaching us? Usually famous for being part of epithelial adherens junctions, the E-Cadherin conserved protein is identified in this work as a new regulator of the famous JAK-STAT signaling pathway.

The JAK-STAT pathway is evolutionary conserved. The simplicity of this signaling in Drosophila, due to the limited redundancy between pathway components, makes it an ideal model for investigation. In the Drosophila follicular epithelium, highly stereotyped functions of JAK-STAT signaling have been well characterized, but how signaling activity is regulated precisely to allow the different outcomes is not well understood. In this tissue, the ligand is secreted by the polar cells positioned at each follicle extremity, thus generating a gradient of JAK-STAT activity in adjacent cells. One way to control the delivered quantity of ligand is by regulating the number of polar cells, which is reduced by apoptosis to exactly two at each pole by mid-oogenesis. Hence, JAK-STAT activity is described as symmetrical between follicle anterior and posterior regions. Here, we show that JAK-STAT signaling activity is actually highly dynamic, resulting in asymmetry between poles by mid-oogenesis. Interestingly, we found similar temporal dynamics at follicle poles in the accumulation of the adherens junction E-cadherin protein. Remarkably, E-cadherin and JAK-STAT signaling not only display patterning overlaps but also share functions during oogenesis. In particular, we show that E-cadherin, like JAK-STAT signaling, regulates polar cell apoptosis non-cell-autonomously from follicle cells. Finally, our work reveals that E-cadherin is required for optimal JAK-STAT activity throughout oogenesis and that E-cadherin and Stat92E, the transcription factor of the pathway, form part of a physical complex in follicle cells. Taken together, our study establishes E-cadherin as a new positive regulator of JAK-STAT signaling during oogenesis. Fig legend: A Drosophila ovarian follicle stained for the adherens junction marker E-Cadherin showing the honeycomb-like structure of the epithelium.

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Contact: Marianne Malartre et Anne-Marie Pret  <marianne.malartre@i2bc.paris-saclay.fr> et<anne-marie.pret@i2bc.paris-saclay.fr>

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The Genome Biology Department has its own logo!

The Genome Biology Department has its own logo! | I2BC Paris-Saclay | Scoop.it

The Genome Biology department of the I2BC created its own logo!

During the last months, Pierre Grognet launched a contest inviting all the Genome Biology (GB) researchers to create an official logo for the department. Fourteen great creations (Figure A) were submitted for voting, all of them representing the spirit of the department. With a participation of more than 50%, and after a second round of votes to break the tie, the new logo was selected (Figure B). Thank to all the researchers that participated and congratulations to Stéphanie Bury-Moné, the creative mind behind the new logo. Stéphanie explained to us that she created a logo in the I2BC style, with the GBD colors, represented in the triangle. According to Stéphanie, the logo also represents the science carried out in the department: “in the center, a DNA double helix with a perspective effect seems to open a way to future research or applications; the circle could represent a RNA chain, and the triangle a protein bound to it. These are the multiple facets of our research activities within our department". The new logo will used in the webpage of the GB department and also in all the official documents. You can find the GB logo on the intranet of the I2BC (Documents and administrative tools/Logos)

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Holy coli: a mouse in the odour of sanctity

Holy coli: a mouse in the odour of sanctity | I2BC Paris-Saclay | Scoop.it

An art project to pay tribute to the laboratory mouse, often sacrificed on the altar of science.

More information: here

Contact: Sylvie Lautru <sylvie.lautru@i2bc.paris-saclay.fr>

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Autophagy Receptors in antigen presentation and antiviral T cell immunity

Autophagy Receptors in antigen presentation and antiviral T cell immunity | I2BC Paris-Saclay | Scoop.it

Autophagy receptor T6BP (TAX1BP1) stabilizes the invariant chain (CD74) and regulates MHC-II molecule (MHC-II) trafficking, thereby favouring the presentation of high affinity peptides to virus-specific CD4+ T cells.

CD4+ T cells play a major role in establishing and maintaining antiviral immunity. They determine, in particular, the quality of antibody responses to viruses. CD4+ T cells are activated by antigenic peptides derived from extracellular or newly synthesized (endogenous) viral proteins presented by MHC-II molecules on the cell surface. The pathways leading to the processing and presentation of endogenous antigens remain poorly characterized.
Here, we hypothesize that the so-called autophagy receptors (AR) may contribute at various, so far unknown, levels to MHC II-restricted viral antigen presentation. We demonstrate that the AR, TAX1BP1, promotes endogenous presentation of HIV- and HCMV-derived peptides. In fact, the role of TAX1BP1 is not limited to viral antigens since the global repertoire of peptides presented by MHC-II molecules is dramatically changed upon TAX1BP1 silencing. We show that TAX1BP1 silencing induces a relocalization of MHC-II peptide-loading compartments, the generation of unstable MHC-II-peptide complexes and a rapid degradation of the invariant chain CD74, which might directly influence the quality of the MHC-II peptide repertoire.
To get a hint on possible mechanisms, we defined the interactome of TAX1BP1 and identified novel protein partners that potentially participate in the TAX1BP1-mediated regulation of MHC-II peptide loading complexes, amongst them the ER chaperone calnexin (CANX). We show that TAX1BP1 binds the cytoplasmic tail of CANX, which regulates its ER functions. Finally, we provide the direct demonstration that silencing CANX also induces CD74 degradation and decreases the ability of cells to activate antiviral CD4+ T cells.
Altogether, this study identifies TAX1BP1 as a key player in MHC-II-restricted antigen presentation and CD4+ T cell immunity. We are currently asking whether viruses might target TAX1BP1 to escape immune responses.

More information: here

Contact: Arnaud Moris <arnaud.moris@i2bc.paris-saclay.fr>

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Crystal structures of free and ligand-bound forms of the TetR/AcrR-like regulator SCO3201 from Streptomyces coelicolor suggest a novel allosteric mechanism.

Crystal structures of free and ligand-bound forms of the TetR/AcrR-like regulator SCO3201 from Streptomyces coelicolor suggest a novel allosteric mechanism. | I2BC Paris-Saclay | Scoop.it

The over-expression of an atypical TetR regulator totally abolishes the production of antibiotics of the strong antibiotic producer, S. coelicolor.

Conditions of phosphate and nitrogen proficiency are known to strongly repress antibiotic biosynthesis in Streptomyces species. Consistently, S. coelicolor, a strain characterized by a poor ability to assimilate nitrogen and phosphate, produces abundantly antibiotics. The group MES characterized an atypical regulator of TetR family (SCO3201) that in condition of over-expression, strongly represses the strong antibiotic production and sporulation of S. coelicolor. Crystal structures of dimers of ligand-free SCO3201 obtained by scientists of the Universities of Greifswald (Germany) and Innsbruck (Austria) revealed that the DNA-binding domains of the dimer are held together in an unusually compact conformation and as a result, cannot span the distance between the two half-of its operator sites. Interestingly, the interaction of SCO3201 with its putative ligand, spermidine, coincides with a major structural rearrangement leading to an increased distance between the DNA-binding domains of the dimer that is predicted to allow its interaction with its operator sites. Consequently and in sharp contrast to what was observed for most TetR-like regulators, the binding of the ligand might facilitate, rather than abrogate, interaction of the regulator with its operator sites. Such ‘reverse’ induction mechanism, triggered by a nitrogen rich molecule, may explain the dramatic negative impact that over-expression of SCO3201 has on the ability of S. coelicolor to produce antibiotics and sporulate. The group MES characterized numerous potential targets of SCO3201 and the high promiscuity of this regulator was attributed to its long N terminal extension containing four positively charged residues (Arg28, 29, 34 and Lys30) that seem to be ideally positioned to stabilize SCO3201’s weak interaction with poorly related operator sites conferring to SCO3201 its relaxed specificity.

More information: here

Contact: Marie-Joëlle Virolle <marie-joelle.virolle@i2bc.paris-saclay.fr>

 

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First in vivo analysis of the regulatory protein CP12 of the model cyanobacterium Synechocystis PCC 6803: Biotechnological implications

First in vivo analysis of the regulatory protein CP12 of the model cyanobacterium Synechocystis PCC 6803: Biotechnological implications | I2BC Paris-Saclay | Scoop.it

First in vivo analysis of CP12, the intrinsically-disordered protein that regulates CO2 assimilation in micro-algae : implication for the production of terpenes the volatile chemicals of interest for the cosmectic and biofuel industries.

We report the first in vivo analysis of a canonical CP12 regulatory protein, namely the unique CP12 of the model cyanobacterium Synechocystis PCC 6803, which has the advantage of being able to grow photoautotrophically, photomixotrophically, and photoheterotrophically. The data showed that CP12 is dispensable to cell growth under standard (continuous) light and light/dark cycle, whereas it is essential for the catabolism of exogenously added glucose that normally sustains cell growth in absence of photosynthesis. Furthermore, to be active in glucose catabolism, CP12 requires its three conserved features: its AWD_VEEL motif and its two pairs of cysteine residues. Also interestingly, CP12 was found to regulate the redox equilibrium of NADPH, an activity involving its AWD_VEEL motif and its C-ter cysteine residues, but not its N-ter cysteine residues. This finding is important because NADPH powers up the methylerythritol 4-phosphate (MEP) pathway that synthesizes the geranyl-diphosphate (GPP) and farnesyl-diphosphate (FPP) metabolites, which can be transformed into high-value terpenes by recombinant cyanobacteria producing plant terpene synthase.

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Contact: Corinne Cassier-Chauvat

  <corinne.cassier-chauvat@i2bc.paris-saclay.fr>

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ORP5 AND ORP8 ORCHESTRATE LIPID DROPLET BIOGENESIS AT ENDOPLASMIC RETICULUM-MITOCHONDRIA CONTACT SITES

ORP5 AND ORP8 ORCHESTRATE LIPID DROPLET BIOGENESIS AT ENDOPLASMIC RETICULUM-MITOCHONDRIA CONTACT SITES | I2BC Paris-Saclay | Scoop.it

It takes two to birth a lipid droplet in the cell: the encounter of endoplasmic reticulum with mitochondria membranes regulates lipid droplet biogenesis in ORP5/8-dependent way.

Lipid droplets (LDs) are intracellular organelles that play a central role in lipid metabolism and regulate cellular energy balance. In their hydrophobic core, surrounded by a phospholipid monolayer, LDs store energy in the form of neutral lipids and prevent their toxic accumulation in the cell. LDs are formed from the endoplasmic reticulum (ER) membrane and alterations in their biogenesis are associated with many metabolic diseases such as diabetes and heart disease or viral infections. However, the molecular mechanisms that spatially and temporally regulate LD biogenesis in the cell remain largely unknown.
The teams of Francesca Giordano at the I2BC (https://www.i2bc.paris-saclay.fr/lipid-trafficking-and-membrane-contact-sites/) and Abdou Rachid Thiam at the ENS (https://arthiam.com), and their close collaborators such as the ImagerieGif platform at I2BC, have addressed this question using complementary cell biology and imaging approaches. Their study, recently published in Journal of Cell Biology (https://doi.org/10.1083/jcb.202112107) reveals a key role of the lipid transfer proteins ORP5 and ORP8 in the regulation of LD biogenesis at the mitochondria-associated membrane subdomains of the ER (MAM). ORP5/ORP8 control the recruitment to MAM of seipin, an ER protein critical for early steps of LD biogenesis, and their loss or inhibition impairs LD biogenesis at ER-mitochondria contact sites.
This study highlights a key role of ORP5/ORP8 proteins in orchestrating LD biogenesis at MAM and provides new mechanistic insights into the metabolic crosstalk between mitochondria, ER and LDs at membrane contact sites.

More information: https://doi.org/10.1083/jcb.202112107

Contact: Francesca Giordano  <francesca.giordano@i2bc.paris-saclay.fr>

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ORP5/8 and MIB/MICOS link ER-mitochondria and intra-mitochondrial contacts for non-vesicular transport of phosphatidylserine

ORP5/8 and MIB/MICOS link ER-mitochondria and intra-mitochondrial contacts for non-vesicular transport of phosphatidylserine | I2BC Paris-Saclay | Scoop.it

The ER lipid transfer proteins ORP5 and ORP8 interact and cooperate with the mitochondrial MIB/MICOS complexes to mediate non-vesicular transport of phosphatidylserine from the ER to the mitochondria.

Mitochondria are dynamic organelles essential for cell survival whose structural and functional integrity rely on selective and regulated transport of lipids from/to the endoplasmic reticulum (ER) and across the mitochondrial intermembrane space. As they are not connected by vesicular transport, the exchange of lipids between ER and mitochondria occurs at membrane contact sites. However, the mechanisms and proteins involved in these processes are only beginning to emerge.
In an article recently published in Cell Reports, the team of Francesca Giordano at the I2BC (Cell Biology Department) and their close collaborators, including the ImagerieGif platform at I2BC, have shown that the lipid transfer proteins ORP5 and ORP8 localize at mitochondria-associated ER membrane (MAM) subdomains physically linked to the MIB/ MICOS complexes that bridge the two mitochondrial membranes. Their study also reveals that ORP5 and ORP8 mediate non-vesicular transport of phosphatidylserine (PS) lipids from the ER to mitochondria by cooperating with the MIB/MICOS complexes. Overall this work uncovers a physical and functional link between ER-mitochondria contacts involved in lipid transfer and intra-mitochondrial membrane contacts maintained by the MIB/MICOS complexes.
On the cover of Cell Reports (September 20, 2022): 3D reconstructions of mitochondrial network and ORP5-ORP8 interactions (proximity ligation assay) in a HeLa cell. Illustration by Vera F. Monteiro-Cardoso.

More information: here

Contact: Francesca Giordano  <francesca.giordano@i2bc.paris-saclay.fr>

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Making sense from nonsense mutations

Making sense from nonsense mutations | I2BC Paris-Saclay | Scoop.it

Personalized medicine: how to repair a defective gene without modifying the genome?

Premature termination codons (PTCs) account for 10 to 20% of genetic diseases in humans. The gene inactivation resulting from PTCs can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a reporter cell line and performed high-throughput screening (HTS) to identify potential readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy (DMD). We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of normal stop codons (TC).

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

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A non-coding RNA in Staphylococcus aureus spares iron and contributes to virulence

A non-coding RNA in Staphylococcus aureus spares iron and contributes to virulence | I2BC Paris-Saclay | Scoop.it

Post-transcriptional control by a small regulatory RNA allows the opportunistic pathogen Staphylococcus aureus to spare iron under iron-starved conditions and increase its pathogenicity.

In response to microbial aggression, host organisms sequester essential nutrients including iron to limit the growth of pathogens. This defense mechanism is called nutritional immunity. Staphylococcus aureus, a pathogen that causes many diseases worldwide, has developed strategies to cope with many adverse growth conditions including surviving within the host. Using a competition assay that we developed, we identified IsrR as a unique small regulatory RNA (sRNA) required for optimal growth in iron-depleted environments. Unlike most staphylococcal sRNAs, IsrR is conserved throughout the genus Staphylococci. Its expression is induced under iron deficiency conditions and its function is to downregulate non-essential enzymes containing iron. Among them, we show that IsrR down-regulates enzymes catalyzing the anaerobic nitrate respiration by blocking the translation of their corresponding mRNA. The structures of IsrR alone and in interaction with its targets were determined in collaboration with Bruno Sargueil's team from Université Paris Cité. The absence of IsrR which leads to a growth defect in iron-starved media is also responsible for reduced virulence (in collaboration with Brice Felden's team, Université Rennes 1), presumably because IsrR is required for the resistance of S. aureus to nutritional immunity.

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Contact: Philippe Bouloc <philippe.bouloc@i2bc.paris-saclay.fr>

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N-acetylation of secreted of secreted proteins in Apicomplexa is widespread and is indipendent of the ER acetyl-CoA transporter AT1

N-acetylation of secreted of secreted proteins in Apicomplexa is widespread and is indipendent of the ER acetyl-CoA transporter AT1 | I2BC Paris-Saclay | Scoop.it

Apicomplexa N-acetylation independent of AT1.

Acetylation of secreted proteins occurs post-translationally to regulate their function and secretion. This process is believed to take place in the ER and requires acetyl-CoA, a metabolite that is transported into the ER by a membrane acetyl-CoA transporter (AT1). N-acetyltransferases (NATs) transfer acetyl groups from acetyl-CoA to the N-termini of proteins and N-terminal acetylation is known to occur in Apicomplexa parasites, including Toxoplasma gondii, which causes toxoplasmosis and Plasmodium berghei a rodent malaria model. However, the importance of acetyl-CoA and its ER transport has not been assessed in these species. In this study, Carmela Giglione and colleagues (Nyonda et al., 2022) identify homologues of AT1 and NAT8 in these parasites. They report that deletion of AT1 gene impairs erythrocytic proliferation of P. berghei and reduces overall parasite fitness. Additionally, female gametocytogenesis and male gametogenesis, which are required for transmission to the mosquito, are attenuated by AT1 deficiency, despite having no detectable impact on the global levels of N-terminal and lysine acetylation. In T. gondii, AT1deletion causes defective growth in the lytic cycle but invasion of host cells is not impaired. Overall, these findings highlight the importance of AT1 in P. berghei development and malaria transmission. However, the preservation of N-terminal and lysine acetylation in AT1-deficient mutants suggests an uncoupling between AT1 function in development and active acetylation in the secretory pathway and that a bypass alternative route ensures acetyl-CoA import along the secretory pathway in the absence of AT1.”

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Contact: Carmela Giglione  <carmela.giglione@i2bc.paris-saclay.fr>

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Third MéDynA plenary meeting (Assembly mechanisms and dynamics of self-organised protein-based complexes)

Third MéDynA plenary meeting (Assembly mechanisms and dynamics of self-organised protein-based complexes) | I2BC Paris-Saclay | Scoop.it

MéDynA third plenary meeting, 17-21 October, 2022 at Ile d'Oléron.

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Contact: Stéphane Bressanelli <stephane.bressanelli@i2bc.paris-saclay.fr>

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Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction

Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction | I2BC Paris-Saclay | Scoop.it

An unusual asymmetric domain-swapped dimer.

Deinococcus radiodurans is a spherical bacterium well known for its exceptional resistance to DNA damaging agents. One of the DNA damage response genes specifically encoded by this bacterium, named DdrC, is expressed shortly after exposure to γ-radiation and is rapidly recruited to the nucleoid. In vitro, we have previously shown that DdrC compacts circular DNA, circularizes linear DNA, anneals complementary ss-DNA and protects DNA from nucleases. To shed light on the possible functions of DdrC in D. radiodurans, we determined the crystal structure of the domain-swapped DdrC dimer at 2.5 Å resolution and further characterized its DNA binding and compaction properties. In particular, we show that DdrC bears two asymmetric DNA binding sites located on either side of the dimer and can modulate the topology and compaction level of circular DNA. These results suggest that DdrC may be a DNA damage-induced nucleoid-associated protein that enhances nucleoid compaction to limit the dispersion of the fragmented genome and facilitate DNA repair after exposure to severe DNA damage conditions.

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Contact: Fabrice Confalonieri <fabrice.confalonieri@i2bc.paris-saclay.fr>

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