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Scooped by
I2BC Paris-Saclay
April 15, 2022 8:49 AM
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Limited solvation of an electron donating tryptophan stabilizes a photoinduced charge-separated state in plant (6-4) photolyase.
Photoactivation of DNA repair enzyme 6-4 photolyase from A. thaliana found to be astonishingly efficient - due to limited ultrafast charge recombination and prevention of solvent access to the terminal tryptophan residue of its electron-transferring chain. (6–4) Photolyases ((6–4) PLs) are ubiquitous photoenzymes that use the energy of sunlight to catalyze the repair of carcinogenic UV-induced DNA lesions, pyrimidine(6–4)pyrimidone photoproducts. To repair DNA, (6–4) PLs must first undergo so-called photoactivation, in which their excited flavin adenine dinucleotide (FAD) cofactor is reduced in one or two steps to catalytically active FADH− via a chain of three or four conserved tryptophan residues, transiently forming FAD•−/FADH− ⋯ TrpH•+ pairs separated by distances of 15 to 20 Å. Photolyases and related photoreceptors cryptochromes use a plethora of tricks to prevent charge recombination of photoinduced donor–acceptor pairs, such as chain branching and elongation, rapid deprotonation of TrpH•+ or protonation of FAD•−. Here, we address Arabidopsis thaliana (6–4) PL (At64) photoactivation by combining molecular biology, in vivo survival assays, static and time-resolved spectroscopy and computational methods. We conclude that At64 photoactivation is astonishingly efficient compared to related proteins—due to two factors: exceptionally low losses of photoinduced radical pairs through ultrafast recombination and prevention of solvent access to the terminal Trp3H•+, which significantly extends its lifetime. We propose that a highly conserved histidine residue adjacent to the 3rd Trp plays a key role in Trp3H•+ stabilization. More information: https://www.nature.com/articles/s41598-022-08928-0 Contact: Pavel MULLER <pavel.muller@i2bc.paris-saclay.fr >
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Scooped by
I2BC Paris-Saclay
April 15, 2022 8:16 AM
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Micronutrient homeostasis in plants for more sustainable agriculture and healthier human nutrition
In this prospective review, the authors call for awareness of the importance of micronutrients in crop production and highlight the need for further research on this topic to meet the challenges of developing more sustainable and nutritious crops. Plants need a range of essential micronutrients. Micronutrient deficiencies affect crop yield and quality in many countries. Mild or hidden micronutrient deficiency likely limits crop yields in much wider areas than those where obvious symptoms occur. Animals, including humans, also require micronutrients to be in good health. Insufficient amount and bioavailability of micronutrients in plant-based diets represent a major reason for the high prevalence of micronutrient deficiencies in human populations. In Europe, these deficiencies are a growing concern among pregnant women, children and elderly people, and are prone to become more severe with European diet transition towards vegetarianism. With this review, the authors call for awareness of the importance of micronutrients in crop production. They stress the need for better micronutrient nutrition in human populations, not only in developing but also in developed nations, and describe strategies to identify and characterize new varieties with high micronutrient content. Furthermore, they highlight how adequate nutrition of plants with micronutrients may improve metabolic functions and the capacity of plants to cope with abiotic and biotic constraints. Research in this area is expected to foster the development of sustainable and healthy food crops for human consumption. This review reports part of a prospective on the need for plant improvement in the EU project CropBooster-P (https://www.cropbooster-p.eu/). Its publication received the support of the COST action PLANTMETALS (https://plantmetals.eu/plantmetals-home.html). more information: https://doi.org/10.1093/jxb/erac014 contact: Sébastien THOMINE <sebastien.thomine@i2bc.paris-saclay.fr>
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I2BC Paris-Saclay
April 5, 2022 10:41 AM
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Alex von Appen seminar on April the 14th at 11.am: "Nuclear self-assembly following vertebrate mitosis” in I2BC Gif-sur-Yvette
"Nuclear self-assembly following vertebrate mitosis” is Alex von Appen seminar on April the 14th at 11 am in the auditorium of building 21 at I2BC in CNRS Gif-sur-Yvette. Abstract: During cell division, remodelling of the nuclear envelope enables chromosome segregation by the mitotic spindle1. The reformation of sealed nuclei requires ESCRTs (endosomal sorting complexes required for transport) and LEM2, a transmembrane ESCRT adaptor2-4. Here we show how the ability of LEM2 to condense on microtubules governs the activation of ESCRTs and coordinated spindle disassembly. The LEM motif of LEM2 binds BAF, conferring on LEM2 an affinity for chromatin5,6, while an adjacent low-complexity domain (LCD) promotes LEM2 phase separation. A proline-arginine-rich sequence within the LCD binds to microtubules and targets condensation of LEM2 to spindle microtubules that traverse the nascent nuclear envelope. Furthermore, the winged-helix domain of LEM2 activates the ESCRT-II/ESCRT-III hybrid protein CHMP7 to form co-oligomeric rings. Disruption of these events in human cells prevented the recruitment of downstream ESCRTs, compromised spindle disassembly, and led to defects in nuclear integrity and DNA damage. We propose that during nuclear reassembly LEM2 condenses into a liquid-like phase and coassembles with CHMP7 to form a macromolecular O-ring seal at the confluence between membranes, chromatin and the spindle. The properties of LEM2 described here, and the homologous architectures of related inner nuclear membrane proteins7,8, suggest that phase separation may contribute to other critical envelope functions, including interphase repair8-13 and chromatin organization14-17. In reference to: LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation. von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A.Nature. 2020 Jun;582(7810):115-118. doi: 10.1038/s41586-020-2232-x. Epub 2020 Apr 29.PMID: 32494070 Contact: Sophie Zinn-Justin <sophie.zinn@i2bc.paris-saclay.fr>
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I2BC Paris-Saclay
March 29, 2022 4:21 AM
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Save the date! - I2BC PhD students' symposium - 16-17th June
Today, we announce an exciting event organized on the CNRS campus of Gif-sur-Yvette, by the young scientists of I2BC and for I2BC doctoral students: the I2BC doctoral students' symposium. Save the date : 16 & 17th June. Essentially build around the scientific work of I2BC doctoral students, speakers will also be invited to these two days of seminars and posters. Participating in doctoral students' symposium gives you the opportunity to have an overview of the new projects of I2BC groups.
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I2BC Paris-Saclay
March 21, 2022 5:11 AM
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Insights into the photocatalytic cycle highlighted at I2BC
An iron–porphyrin bearing urea groups exhibits exceptional high performance for CO2-to-CO photocatalytic reduction. A remarkable lesson from the functioning of the natural photosynthetic apparatus concerns the coupling of light-triggered single electron transfer events to the multi-electron catalysis.
In the present quest to use solar energy to convert H2O and CO2 to an energy vector, bioinspired synthetic models that can be activated by light are highly interesting to understand, and optimize, the photocatalytic process. Although terrific progress has been made in the field of electrocatalytic reduction of CO2 using molecular catalysts, powering these catalysts with the help of photosensitizers comes along with the challenge of minimizing deleterious photochemical events leading to poor quantum yields and/or catalyst deactivation.
Iron porphyrins are among the best molecular catalysts for the electrocatalytic CO2 reduction process. In this work the unprecedented photocatalytic activity of an iron porphyrin decorated with urea groups is reported. The photocatalytic system containing the catalyst, a photosensitizer and a sacrificial electron donor (SED) was investigated employing visible and infrared spectroscopy to gain insights into the catalytic mechanism (figure). The entry of UrFeII species in the cycle occurs by the reduction in the dark by the SED. The first photophysical event concerns the reductive quenching of the excited state of the photosensitizer that triggers an electron transfer to yield UrFeI intermediate. At this stage, CO2 binding, identified as the rate determining step, occurs prior to the formation of the catalytic-competent redox UrFe0 state. The input of two protons to release CO and a water molecule close the cycle regenerating the UrFeII state. DFT calculations were performed to bring support to these experimental findings.
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Scooped by
I2BC Paris-Saclay
March 21, 2022 5:04 AM
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A new family of genes coding for the biomineralization of carbonates in cyanobacteria
Cyanobacteria contribute to biomineralization of Calcium carbonates over the geological history. By combining genomics and biochemistry, I2BC researchers and their collaborators discovered a new family of genes coding an enzyme (calcyanin) involved in the biomeneralization of cacium carbonates in cynobacteria. Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria-forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineral ization. Proteins of the calcyanin family are composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating four major types among the 35 known calcyanin homologs.
Calcyanin lacks detectable full-length homologs with known function. The overexpression of ccyA in iACC-lacking cyanobacteria resulted in an increased intracellular Ca content. Moreover, ccyA presence was correlated and/or colocalized with genes involved in Ca or HCO 3 transport and homeostasis, supporting the hypothesis of a functional role of calcyanin in iACC biomineralization.
Whatever its function, ccyA appears as diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC, as confirmed by microscopy. This extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Moreover, ccyA was probably present in ancient cyanobacteria, with independent losses in various lineages that resulted in a broad but patchy distribution across modern cyanobacteria.
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I2BC Paris-Saclay
March 21, 2022 4:56 AM
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Call for new group leaders in Microbiology
The Institute for Integrative Biology of the Cell (I2BC) is seeking to recruit junior and mid-career group leaders
to develop independent research programs in the field of Microbiology.
Dead line for application: May 10, 2022 All information: here
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Scooped by
I2BC Paris-Saclay
March 1, 2022 5:29 AM
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The contribution of uncharted RNA sequences to tumor identity in lung cancer
Uncharted, unannotated RNAs contribute to cancer patient stratification and constitute novel theraputic targets. Cancer alters our RNAs in many ways, producing a wide diversity of aberrant RNAs of which many are specific to tumor types. Computational RNA sequence analysis in oncology typically focuses on specific RNA families such as mRNAs. Here we undertook to capture at once all RNAs found in lung cancer. To this aim we selected two lung cancer cohorts with 737 RNA sequence sets from lung biopsies, and we applied a technique called k-mer differential analysis, where we identify all RNA fragments that are either over or under-expressed in tumors. We then focused on fragments that were not previously known (uncharted RNAs) and reproducibly observed in both cohorts. Here is what we found:
– Uncharted RNAs come from many different locations (introns, intergenic regions, repeats) and in many forms (spliced, polyadenylated, chimeric etc.)
– A limited set of hypervariable genes such as immunoglobulins contribute a large amount of uncharted RNAs
– Uncharted RNAs from human retroelements define patient subclasses with distinct clinical and genomic features, a well documented phenomenon in cancer
– several uncharted RNAs, including one from a lung bacterium, correlate with the presence of specific immune cells.
– A number of uncharted can be translated and produce tumor-specific antigens that could be targeted by anti-cancer drugs
We hope to convince readers that large amounts of non-reference RNAs of functional significance remain hidden in bulk RNA-seq data. More information: https://academic.oup.com/narcancer/article/4/1/zcac001/6519484?searchresult=1 Contact: Daniel Gautheret <daniel.gautheret@i2bc.paris-saclay.fr>
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Scooped by
I2BC Paris-Saclay
March 1, 2022 5:06 AM
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HubP-dependent cell pole organization in Vibrio cholerae
By comparative proteomics we identified several novel proteins localize to the cell pole in Vibrio cholerae. Characterization of these proteins revealed an ever more versatile role for the landmark cell pole organizer HubP and identify novel mechanisms of motility regulation. Cell polarity is the result of controlled asymmetric distribution of protein macrocomplexes, genetic material, membrane lipids and cellular metabolites, and can play crucial physiological roles not only in multicellular organisms but also in unicellular bacteria. In the opportunistic cholera pathogen Vibrio cholerae, the polar landmark protein HubP tethers key actors in chromosome segregation, chemotaxis and flagellar biosynthesis and thus converts the cell pole into an important functional microdomain for cell proliferation, environmental sensing and adaptation between free-living and pathogenic life-styles. Using a comparative proteomics approach, we here-in present a comprehensive analysis of HubP-dependent cell pole protein sorting and identify novel HubP partners including ones likely involved in cell wall remodeling (DacB), chemotaxis (HlyB) and motility regulation (MotV and MotW). Unlike previous studies which have identified early roles for HubP in flagellar assembly, functional, genetic and phylogenetic analyses of its MotV and MotW partners suggest a direct role in flagellar rotary mechanics and provide new insights into the coevolution and functional interdependence of chemotactic signaling, bacterial motility and biofilm formation. This work was done in collaboration of Petya Krasteva team, former in B3S Dept of I2BC currently in IECB Bordeaux. More information: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009991 Contact: Yoshi Yamaichi <yoshiharu.yamaichi@i2bc.paris-saclay.fr>
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Scooped by
I2BC Paris-Saclay
March 1, 2022 4:58 AM
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Kinetics of electron returns in the two-photon DNA repair by (6-4) photolyase
DNA repairing enzymes photolyases are ubiquitous natural catalysts using sunlight to revert cancerogenic chemical changes in DNA caused by UV light. The 3P Team Photobiology, Photosynthesis, Photocatalysis from the Institute of Integrative Biology of the Cell (I2BC) explores the molecular mechanism by which these essential photoenzymes have been repairing DNA since the beginnings of life evolution on Earth. In their latest work published in the journal ACS Catalysis, the researchers have shown that the repair of the UV-induced lesions called ‘(6-4) photoproducts’ occurs in two successive photoreactions (requiring absorption of two separate photons), each beginning with electron transfer from the excited flavin to the lesion. Transient absorption spectroscopy (https://www.pluginlabs-universiteparissaclay.fr/fr/entity/a5ad9e5d-53a4-4194-8653-3d8feebfafc8/i2bc-plateforme-de-spectroscopies-electroniques) was used to follow the return of electrons to the flavin after chemical transformations of the lesion. The team was able to dissect the electron return kinetics finalizing the first and the second photoreactions (in ~40 μs and ~200 ns, respectively), corroborating and detailing the two-photon reaction model. More information: https://doi.org/10.1021/acscatal.2c00492 Authors: Klaus Brettel, Pavel Müller (I2BC) and Junpei Yamamoto (Osaka University). The project was funded by the French National Research Agency (ANR). Contact: Pavel Müller <pavel.muller@i2bc.paris-saclay.fr.>
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I2BC Paris-Saclay
February 21, 2022 8:59 AM
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dnaJ: a New Approach to Identify Species within the Genus Enterobacter.
We propose a new approach for Enterobacter species identification based on the diversity of the gene encoding the heat shock protein DnaJ. This new tool can be easily implemented in clinical laboratories in addition to identification by MALDI-TOF. The taxonomy of the genus Enterobacter can be confusing and has been considerably revised in recent years. We propose a PCR and amplicon sequencing technique based on a partial sequence of the dnaJ gene for species assignment consistent with DNA-DNA digital hybridization (dDDH) and pairwise average nucleotide identity (ANI).We performed a validation of the method by comparing the type strains of each species, sequences obtained from the GenBank database, and clinical specimens. Our results show that the polymorphism of the target sequence of dnaJ allows the identification of species. Using this gene, we assigned the species to 100 strains deposited in the GenBank database that were consistent with the species assignment by dDDH and ANI. The analysis showed that using the partial dnaJ sequence is congruent with WGS as far as correct identification of Enterobacter species is concerned. Finally, we applied our dnaJ method on a national collection of 68 strains identified as Enterobacter isolated from the blood cultures of premature babies using an algorithm based on a type strain library and the SeqScape® software. For the first time, we identified Enterobacter quasihormaechei in blood cultures from four neonatal sepsis cases. We also noticed a higher prevalence of E. bugandensis (36.3%; 32/88) and E. xiangfangensis (46.5%; 41/88). E. bugandensis is a novel species recently described specifically in instances of neonatal sepsis. In conclusion, sequencing a part of the dnaJ gene could be a quick, more economical, and highly discriminating method of identifying Enterobacter species in clinical practice and research. More information here. Contact person: Nadege Bourgeois-Nicolaos
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I2BC Paris-Saclay
February 21, 2022 8:45 AM
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The strange case of Drp1 in autophagy: Jekyll and Hyde?
Chen et al. review the roles of Drp1, a GTPase essential for mitochondria fission but whose functions during autophagy are controversial. They speculate on its non-canonical functions and the prerequisite of the reduction of mitochondria size during mitophagy. There is a debate regarding the function of Drp1, a GTPase involved in mitochondrial fission, during the elimination of mitochondria by autophagy. A number of experiments indicate that Drp1 is needed to eliminate mitochondria during mitophagy, either by reducing the mitochondrial size or by providing a non-canonical mitophagy function. Yet, other convincing experimental results support the conclusion that Drp1 is not necessary. Chen et al. review herethe possible functions for Drp1 in mitophagy and autophagy, depending on tissues, organisms and stresses, and discuss these apparent discrepancies. In this regard, it appears that the reduction of mitochondria size is often required for mitophagy but not always in a Drp1-dependent manner. Finally, we speculate on Drp1-independent mitochondrial fission mechanism that may take place during mitophagy and on non-canonical roles, which Drp1 may play such as modulating organelle contact sites dynamic during the autophagosome formation. More information here. Contact person: Renaud LEGOUIS
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I2BC Paris-Saclay
February 21, 2022 8:28 AM
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Rectifying function of electron relays finally unravelled in a photo-synthetic model
Nature’s trick in conversion of light into chemical energy is revealed when an artificial photo-synthetic model showed evidence of intermediate state pertaining to functionality of electron relay in controlling unidirectional flow and accumulation of charges. In photosynthesis, Photosystem II is the enzyme that captures sunlight to drive the four-electron, four-proton oxidation of water. It contains a series of co-factors in a defined setup to convoy electrons in a vectorial fashion from the initial locus of light excitation to accumulate charges at the catalytic unit. A pair of Tyr and His amino acids plays a decisive role as relay between the P680 chlorophyll, the primary photooxidant, and the Mn4Ca water oxidizing catalyst (WOC) as it couples the one-photon, one-electron photochemistry of the light absorber to multi-electronic catalysis. A “rocking proton” mechanism operating between these two residues has been identified as a crucial feature of this electron relay. Implementing such functionalities in chemical modular assemblies may help chemists to gain control over the directionality of electron transfer when developing molecular systems for artificial photosynthesis.
Gotico et al. have investigated a set of molecular triads holding a photosensitizer, an imidazole as redox relay, and a monometallic manganese complex as a proxy for a WOC. Time-resolved spectroscopy coupled with the electrochemical properties has permitted to track the formation of an imdazolyl radical, initiated from the photooxidized chromophore, and its subsequent decay connected to oxidation of the Mn(II) site. Comprehensive analysis of the thermodynamic and kinetic parameters reveal the importance of the acid-base properties of this electron relay and highlight the crucial role of reversible proton transfer to allow the system to display a light-induced two-step electron hopping process. This study sets the path for further optimization in the directional electron transfer and charge accumulation for using photons to drive the oxidation of water. More information here. Contact person: Winfried LEIBL
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Scooped by
I2BC Paris-Saclay
April 15, 2022 8:30 AM
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Metabiodivex summer school
METABIODIVEX, in which the I2BC is participating, and the IRN i-NPChem are organising the first thematic school entitled "Molecular Exploration of Biodiversity: New Challenges, New Strategies". It will take place from June 26 to July 1st 2022 in Aussois. The themes will be : - Chemodiversity in the era of "Big Data"
- Drug Discovery: Challenges and Strategies
- Evolution and diversity of plant metabolism
- Chemical ecology of marine organisms
- Discovery and production of microbial metabolites: from the gene to the molecule
- Digital chemistry and quantum computing Registrations until May 15th 2022: https://www.azur-colloque.fr/DR04/inscription More information: https://metabiodivex.sciencesconf.org/ Contact: Sylvie LAUTRU <sylvie.lautru@i2bc.paris-saclay.fr>
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Scooped by
I2BC Paris-Saclay
April 15, 2022 7:56 AM
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Ecole thématique Ecoclim2022 - Orsay - 7 au 10 juin 2022
L'école thématique Ecoclim2022 aura lieu à Orsay du 7 au 10 juin 2022. Cette école a pour objectif d'offrir une formation de base sur les enjeux environnementaux aux chercheuses et chercheurs de toutes disciplines. Les renseignements et le formulaire d'inscription sont disponibles sur la page https://indico.ijclab.in2p3.fr/event/7951 Notez qu'un suivi en distanciel sera possible, de préférence pour les personnes en province, mais sans interaction possible. Les organisateurs : Guillaume Blanc et Guillaume Roux Au programme Cours introductif sur le climat Jean-Yves Grandpeix (LMD) Dérèglement climatique et impacts Amaëlle Landais (LSCE)
Didier Paillard (LSCE)
Jeanne Gherardi (LSCE)
Mélanie Becker (LIENSs) Cycles biogéochimiques, sols et agriculture Bertrand Guenet (LG-ENS)
Julia Le Noé (ENS)
Petros Chatzimpiros (LIED) Trajectoires de décarbonation Henri Waisman (IDDRI)
Gilles Billen (METIS) ( à confirmer)
Aurélien Bigo ()
Emmanuelle Frenoux (LISN)
Tamara Ben Ari (iEES, Labo1point5) Scénarios et modèles de sociétés Luc Semal (CESCO)
Timothée Parrique (Lund University)
Emmanuel Combet / Valérie Quiniou / David Marchal (Ademe)
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I2BC Paris-Saclay
March 30, 2022 5:55 AM
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Scientific day in memory of Agnès Delahodde
Throughout the day, there will be scientific presentations by colleagues and collaborators and personal tributes to Agnès Delahodde. Josette Banroques - IBPC, Paris & Bruno Sargueil - Faculty of Pharmacy, Paris DNA endonuclease and RNA maturase activities of two intron-encoded proteins from yeast mitochondria Teresa Rinaldi - Universita la Sapienza, Rome Mitochondrial function and lipids in S. cerevisiae Monique Bolotin - GQE-Le Moulon, Gif-sur-Yvette Vincent Procaccio - CHU, Angers Disease modeling and drug screening of mitochondrial complex I disorders: from Podospora anserina to Human Agnès Rötig - Institut Imagine, Paris & Véronique Paquis - CHU, Nice Yeast does not lose the north or the south in the field of mitochondrial diseases: in the North Agnès Rötig in the South Véronique Paquis Laras Pitayu - IJM, Paris (Mitochondrial) Genome Stability Testimony Renaud Legouis - I2BC, Gif-sur-Yvette Mitochondrial rebuilding after acute heat stress relies on autophagy Free but required registration before 22 April 2022 https://evento.renater.fr/survey/inscriptionjournee-d-hommage-agnes-delahodde-ideapch1 Capacity 200 people + Video broadcast more information: here Contact: day4agnes@i2bc.paris-saclay.fr
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I2BC Paris-Saclay
March 21, 2022 5:18 AM
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23rd National Congress on Transposable elements (CNET) July 4th-6th
We are pleased to announce the 23rd annual meeting organized by the French research community working on transposable elements (CNET). This event gathers researchers interested in transposable elements, including population and comparative genomics, molecular and cellular mechanisms, ecology and evolution. This year the meeting will take place July 4–6 in Gif-sur-Yvette, near Paris. We invite contributions including molecular, genetics and cellular studies, as well as bioinformatics and mathematical modeling approaches, applied to a wide range of model organisms (prokaryotes, plants, yeast, insects, ciliates, vertebrates, ...). The program will include invited talks, selected talks and ample time for poster presentation and discussions. Junior researchers are particularly encouraged to apply for oral presentations. More information: here
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I2BC Paris-Saclay
March 21, 2022 5:08 AM
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French Days of Photosynthesis: June 9th-10th
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Scooped by
I2BC Paris-Saclay
March 21, 2022 5:01 AM
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Distribution of Vibrionales' chromosome 2 in the gammaproteobacteria
Plesiomonas shigelloides, an atypical Enterobacterales with a Vibrio-related secondary chromosome
Vibrionales and Enterobacterales are two closely related orders that derive from a common ancestor. While Vibrionales are multi-chromosome species, Enterobacterales are known to be mono-chromosome bacteria. What are the features and factors needed to ensure the sustainability of multiple chromosomes in a cell? We addressed this question by searching and identifying an Enterobacterium with multiple chromosomes, Plesiomonas shigelloides, and by carring out a comparative analysis of its genome and proteome with those of the mono-chromosome Enterobacterales and the multi-chromosome Vibrionales. More information: https://academic.oup.com/gbe/article/14/2/evac011/6515279?login=true Contact: Jean-Luc FERAT <jean-luc.ferat@i2bc.paris-saclay.fr>
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I2BC Paris-Saclay
March 1, 2022 9:36 AM
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LivingMachines@Work opens 3 calls for proposals: Internship, Seeding, Meeting
Apply to the first calls opened by LM@W in March 2022! LivingMachines@Work (LM@W) is an interdisciplinary network of research teams within Paris-Saclay University dedicated to understand the structure and function of cellular machineries to innovate in health and biotechnology. LM@W is supported by 5 Graduate Schools: Life Sciences and Health, Biosphera, Computer Science, Mathematics and Physics.
LM@W opens 3 calls for proposals to support interdisciplinary internships, collaborative projects and the organization of meetings in the Paris-Saclay area More information here. Contact: LM@W or Christophe Le Clainche
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I2BC Paris-Saclay
March 1, 2022 5:25 AM
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Precipitation of greigite and pyrite induced by Thermococcales: an advantage to live in Fe- and S-rich environments?
The diverse metabolic pathways and biologically induced mineralization mechanisms employed by Thermococcales would thus help them to survive in a broad range of extreme environments characterized by the high temperatures and high iron and sulfide contents. Thermococcales, a major order of archaea inhabiting the iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS2 in iron–sulfur-rich fluids at 85°C, suggesting that they may contribute to the formation of ‘low temperature’ FeS2 in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero-valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero-valent sulfur, significant amounts of Fe3S4 greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non-mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron-sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high-temperature hydrothermal environments. More information: https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1462-2920.15915 Contact: Aurore Gorlas <aurore.gorlas@i2bc.paris-saclay.fr>
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I2BC Paris-Saclay
March 1, 2022 5:03 AM
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Multiplexed Biosensing and Bioimaging Using Lanthanide -Based Time-Gated Förster Resonance Energy Transfer
The necessity to scrutinize biological molecules and their interactions in solution and on the cellular level leads to an increasing demand for specific diagnostic analysis. FRET is ideally suited for multiplexed biosensing because it is rapid and sensitive and allows the use of any fluorescent probe. The most frequently used technique to detect multiple parameters from a single sample is color multiplexing with different fluorophores. In conventional biosensing approaches, each fluorophore requires a distinct detection channel and excitation wavelength. This drawback can be overcome by Förster resonance energy transfer (FRET) from lanthanide donors to other fluorophore acceptors. The lanthanide multiple and spectrally narrow emission bands over a broad spectral range can overlap with several different acceptors at once, thereby allowing FRET from one donor to multiple acceptors. Their extremely long lifetimes provide two important features: efficient suppression of background from the biological environment using time-gated (TG) detection and detection of specific biomolecules and/or their conformation using temporal multiplexing. Applications range from fundamental analysis of biomolecular interactions and conformations to high-throughput and point-of-care in vitro diagnostics and DNA sequencing to advanced optical encoding, using both liquid and solid samples and in situ, in vitro, and in vivo detection with high sensitivity and selectivity.
In this Account, we discuss recent advances in lanthanide-based TG-FRET for the development and application of advanced immunoassays, nucleic acid sensing, and fluorescence imaging. We highlight the importance of the careful design and combination of different biological, organic, and inorganic molecules and nanomaterials for an adjustable FRET donor–acceptor distance that determines the ultimate performance of the diagnostic assays and conformational sensors in their physiological environment. We conclude by sharing our vision on how progress in the development of new sensing concepts, material combinations, and instrumentation can further advance TG-FRET multiplexing and accelerate its translation into routine clinical practice and the investigation of challenging biological systems. More information: https://pubs.acs.org/doi/10.1021/acs.accounts.1c00691 Contact: Marcelina Cardoso dos santos <marcelina.cardoso-dos-santos@i2bc.paris-saclay.fr>
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I2BC Paris-Saclay
February 21, 2022 9:09 AM
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New member has joined the Programmed Genome Rearrangement Team in I2BC Genome Biology Department.
My name is Valerio VITALI, I am a new Italian postdoc in the Programmed Genome Rearrangement Team (Bétermier Lab) since Feb 1st. Under the guidance of Mireille—and in close collaboration with the team—I am tasked to design and implement creative strategies to characterize the complex machinery that catalyzes developmentally programmed DNA rearrangements in Paramecium (removal of intervening sequences coupled with DNA repair).
I have received my PhD in Evolutionary Genomics and Bioinformatics from the University of Münster (WWU), Germany. While at the Institute for Evolution and Biodiversity, my research has focused on the highly plastic genome architecture of Paramecium, and its evolutionary potential. During my doctoral and (brief) post-doctoral research, I have gained transferable experience in comparative genomics and trancriptomics, single cell whole-genome sequencing, and the analysis of Structural Variants (SVs) from NGS data.
When not in the Lab, I enjoy running, reading books about evolution and aging, learning new languages (or at least trying!) and cooking traditional meals.
I am excited to have joined the Genome Biology Department at the I2BC and can't wait to greatly expand my knowledge of Genome and Cell Biology, Biochemistry, Biophysics, Structural biology.....and beyond. GitHub Profile: https://github.com/biowalter/senes Full list of Publications: https://scholar.google.com/citations?hl=en&user=BI3IdwwAAAAJ
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Scooped by
I2BC Paris-Saclay
February 21, 2022 8:54 AM
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STÉPHANIE BURY MONÉ: REVEALING THE HIDDEN POTENTIAL OF BACTERIA
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Scooped by
I2BC Paris-Saclay
February 21, 2022 8:41 AM
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A new RNA–DNA interaction required for integration of group II intron retrotransposons into DNA targets
A novel structural device used by bacterial retrotransposons to efficiently invade host genomes was identified. These results will also contribute to the rational design of new RNA-based gene targeting systems for bacterial genome engineering. Mobile group II introns are site-specific retrotransposable elements widespread in bacterial genomes and in organelles (mitochondria and chloroplasts) of plants, algae and fungi. They constitute the most abundant class of retrotransposons in bacteria and play a major role in the diversification and evolution of bacterial genomes. Mobile group II introns are composed of a large and highly structured self-splicing intron and an intron-encoded reverse transcriptase. They colonize genomes by 'Retrohoming', a very efficient and specific pathway that is operated by the combined activities of the self-splicing intron and its reverse transcriptase. During the first stage of mobility, the intron RNA catalyzes its own insertion directly into the DNA target site. Recognition of the proper target rests primarily on multiple base pairing interactions between the intron segments ‘EBS’ and complementary 'IBS' sequences present on the double-stranded DNA target (Figure 1A). Remarkably, the sequence of the EBS sites can be modified, thus allowing to 'reprogram' a group II intron to specifically integrate into a desired DNA target. This feature is at the basis of the powerful 'Targetron' technology, now commonly used for bacterial genome engineering. Using bioinformatics and genetic approaches, Maria Costa and collaborators have identified a novel base pairing interaction between the intron RNA and the DNA target that is essential for intron mobility. This pairing, named 'EBS2a-IBS2a', adopts a Watson–Crick geometry and helps inducing a structural conformation that favors the opening of the DNA double helix and the integration of the retrotransposon into the genome (Figure 1B). The authors also showed that the EBS2a-IBS2a interaction is perfectly 'reprogrammable'. This work has direct biotechnological applications by allowing the development of new 'targetrons' capable of inserting themselves into genomic sites that were previously inaccessible to disruption by these systems. More information here. Contact person: Maria Costa
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