Institute for Integrative Biology of the Cell

  2022 News

Summary

Starting the engine of the powerhouse: mitochondrial transcription and beyond

Mitochondria are the powerhouses of cells thanks to the oxidative phosphorylation system partially encoded by a small mitochondrial genome (mtDNA). Miranda et al review our current knowledge on mtDNA expression, associated disease phenotypes, and how mtDNA and nuclear gene expression are coordinated.

Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.

More information: https://www.degruyter.com/document/doi/10.1515/hsz-2021-0416/html

Contact: Inge Kuhl  <inge.kuhl@i2bc.paris-saclay.fr>

Structural convergence between inhibitors and a regulator of microtubule dynamics

A region of CPAP, a protein regulating the length of the centrioles, is found to have a tubulin binding mode similar to that of bacterial and fungal peptide-like metabolites which inhibit cell division.

Microtubules are dynamic assemblies of αβ-tubulin that are involved in critical cellular functions in Eukaryotes, including cell division, ciliogenesis and intracellular transport. To fulfill these different functions, microtubules rearrange to form different types of networks, like the microtubule aster of interphasic cells or the mitotic spindle of dividing cells. They also form the architecture of well-defined structures like the centrioles. Relatedly, microtubule dynamics is regulated in the cell by different families of proteins. It is also inhibited by small molecules, some of which being used in oncology. The extent to which these compounds target the binding sites of cellular partners of tubulin remains poorly characterized. We have determined the structure of tubulin bound to the PN2-3 domain of CPAP, a protein controlling the length of the centrioles. Our results show in particular that the PN2-3 N-terminal region lies in a β-tubulin binding site known as the vinca domain. This site is also targeted by fungal and bacterial peptide-like inhibitors of tubulin, which share a very similar binding mode with CPAP. Therefore, our work identifies a structural convergence for tubulin binding between inhibitors and a regulator of microtubule dynamics.

More information: https://www.pnas.org/doi/10.1073/pnas.2120098119

Contact: Benoit GIGANT  <benoit.gigant@i2bc.paris-saclay.fr>

Essential role of hyperacetylated microtubules in innate immunity escape
orchestrated by the EBV-encoded BHRF1 protein

BHRF1, a multifunctional viral protein expressed during Epstein-Barr virus reactivation, modulates mitochondrial dynamics and induces MT hyperacetylation to escape innate immunity. Moreover, the loss of MT hyperacetylation impedes BHRF1 to initiate mitophagy, which is essential to inhibit the signaling pathway.

Innate immunity constitutes the first line of defense against viruses, in which mitochondria play an important role in the induction of the interferon (IFN) response. BHRF1, a multifunctional viral protein expressed during Epstein-Barr virus reactivation, modulates mitochondrial dynamics and disrupts the IFN signaling pathway. Mitochondria are mobile organelles that move through the cytoplasm thanks to the cytoskeleton and in particular the microtubule (MT) network. MTs undergo various post-translational modifications, among them tubulin acetylation. In this study, we demonstrated that BHRF1 induces MT hyperacetylation to escape innate immunity. Indeed, the expression of BHRF1 induces the clustering of shortened mitochondria next to the nucleus. This “mito-aggresome” is organized around the centrosome and its formation is MT-dependent. We also observed that the α-tubulin acetyltransferase ATAT1 interacts with BHRF1. Using ATAT1 knockdown or a non-acetylatable α-tubulin mutant, we demonstrated that this hyperacetylation is necessary for the mito-aggresome formation. Similar results were observed during EBV reactivation. We investigated the mechanism leading to the clustering of mitochondria, and we identified dyneins as motors that are required for mitochondrial clustering. Finally, we demonstrated that BHRF1 needs MT hyperacetylation to block the induction of the IFN response. Moreover, the loss of MT hyperacetylation blocks the localization of autophagosomes close to the mito-aggresome, impeding BHRF1 to initiate mitophagy, which is essential to inhibiting the signaling pathway. Therefore, our results reveal the role of the MT network, and its acetylation level, in the induction of a pro-viral mitophagy.

More information: https://journals.plos.org/plospathogens/article/authors?id=10.1371/journal.ppat.1010371

Contact: Audrey ESCLATINE <audrey.esclatine@i2bc.paris-saclay.fr>

ComFC mediates transport and handling of single-stranded DNA during natural transformation

ComFC, a protein essential for natural transformation, is a membrane-associated protein with affinity for ssDNA. This dual-specificity allows us to propose that it provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.

 

Natural transformation plays a major role in the spreading of antibiotic resistance genes and virulence factors. Whilst bacterial species display specificities in the molecular machineries allowing transforming DNA capture and integration into their genome, the ComFC protein is essential for natural transformation in all Gram- positive and -negative species studied. Despite this, its role remains largely unknown. Here, we show that Helicobacter pylori ComFC is not only involved in DNA transport through the cell membrane, but is required for the handling of the ssDNA once it is delivered into the cytoplasm. ComFC crystal structure revealed the presence of a zinc-finger motif and a putative phosphoribosyl transferase domain, both necessary for the protein’s in vivo activity. ComFC is a membrane-associated protein with affinity for single-stranded DNA. Collectively, our results suggest that ComFC provides the link between the transport of the transforming DNA into the cytoplasm and its handling by the recombination machinery.

More information: https://doi.org/10.1038/s41467-022-29494-z

Contact: Sophie CHERUEL <sophie.cheruel@i2bc.paris-saclay.fr >

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.

N(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 >

Throughout the day, there will be scientific presentations by colleagues and collaborators and personal tributes to Agnès Delahodde..

Programme

9:00-9:30 Accueil

9:30-9:45 Direction I2BC 

9:45-10:15 Josette Banroques – IBPC, Paris & Bruno Sargueil – Faculté de Pharmacie, Paris

DNA endonuclease and RNA maturase activities of two intron-encoded proteins from yeast mitochondria

10:15-11:00 Teresa Rinaldi – Universita la Sapienza, Rome

Mitochondrial function and lipids in S. cerevisiae

11:00-11:30 Pause Café

11:30-11:45 Monique Bolotin – GQE-Le Moulon, Gif-sur-Yvette

Témoignages

11:45-12:30 Vincent Procaccio – CHU, Angers

Disease modeling and drug screening of mitochondrial complex I disorders: from Podospora anserina to Human

12:30-14:15 Buffet

14:15-15:45 Agnès Rötig – Institut Imagine, Paris & Véronique Paquis – CHU, Nice

La levure ne perd ni le nord ni le sud dans le domaine des maladies mitochondriales :
               au Nord Agnès Rötig
               au Sud Véronique Paquis

15:45-16:15 Pause Café

16:15-16:30 Line Hofmann – BioVersys AG
         Témoignages

16:30-17:15 Laras Pitayu – IJM, Paris

(Mitochondrial) Genome Stability 

17:15-18:30 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

Contact: day4agnes@i2bc.paris-saclay.fr

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.

More information: https://onlinelibrary.wiley.com/doi/10.1002/anie.202117530

Contact: Annamaria Quaranta <annamaria.quaranta@i2bc.paris-saclay.fr>

French Days of Photosynthesis: June 9th-10th

More information: click on the ad

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.

More information: https://academic.oup.com/gbe/advance-article-abstract/doi/10.1093/gbe/evac026/6526398

Contact: Corinne Cassier-Chauvat <corinne.cassier-chauvat@i2bc.paris-saclay.f>

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>

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

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.>

Multiplexed Biosensing and Bioimaging Using Lanthanide
-Based Time-Gated Förster Resonance Energy Transfer

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>

HubP-dependent cell pole organization in Vibrio cholerae

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>

Precipitation of greigite and pyrite induced by Thermococcales:
an advantage to live in Fe- and S-rich environments?

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>

The contribution of uncharted RNA sequences to tumor identity in lung cancer

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>

First ICNS/I2BC Morning-Meeting February 8th at 9.30 a.m

The ICSN and the I2BC are the two major units of the CNRS campus of Gif sur Yvette.

The “institut de Chimie des substances naturelles” (ICSN), with a staff of nearly 150 people, is the chemistry pole of the CNRS campus in Gif sur Yvette. This unit develops activities at the chemistry-biology interface, with natural substances as the object of study and main source of inspiration. Equipped with numerous platforms, including two NMR platforms, the ICSN will host an NMR apparatus from an I2BC team when it moves from the CEA-Saclay to the Gif-sur-Yvette campus. However, the links between our two institutes are not limited to NMR; the purpose of this first morning is to introduce you to ICSN in the hope of encouraging new collaborations.

This first Morning-Meeting, which will be the first of a series, will be oriented towards the platforms of the two units and duos of researchers to illustrate the fruitful collaborations already in place.

Please come in large numbers to meet your chemical colleagues.

Due to health conditions, the meeting will be held in hybrid mode, both in the auditorium of Building 21 on the Gif-sur-Yvette campus and on Zoom.

Download the program : here

Contact for link: communication@i2bc.paris-saclay.fr

Cryo-EM allows entering the fabulous nanometric world of peptide assemblies

Peptide assemblies forming hydrogels or fibrils are used for biomedical applications such as drug and vaccine formulation, cell culture and tissue regeneration. To enable the rational design of these self-assembled peptides, a thorough understanding of the chemical and physico-chemical rules guiding the folding and assembly of these molecules is required. With recent developments in cryo-electron microscopy (cryo-EM), the determination of these structures at the atomic scale has become possible. The study presented makes it possible to reveal by cryo-EM the atomic structure of nanotubes of a therapeutic peptide, Lanreotide. This structure is of a complexity that nothing allowed to suspect until now. These results are published in the journal PNAS.

Functional and versatile nano- and micro-assemblies formed by biological molecules are found at all levels of life, from cellular organelles to complete organisms. Understanding the chemical and physico-chemical determinants guiding the formation of these assemblies is crucial not only to understand the biological processes that they implement but also to mimic nature through the rational design of self-assembled objects that can be used in particular biomedical level. These assemblies result from deterministic chemical interactions and are therefore all potentially predictable. But currently we simply lack the tools to predict how peptides assemble and the potentially polymorphic architectures they can form. To acquire predictive tools based on learning, we need to identify and understand a large number of peptide assembly structures.

Among synthetic peptides forming well-defined nanostructures, the octapeptide Lanreotide has been considered one of the best characterized, both in terms of structure and self-assembly process. Lanreotide is a therapeutic peptide used against acromegaly and certain neuroendocrine cancers. This peptide self-assembles spontaneously in water in the form of nanotubes 24 nm in diameter and extremely long (around one mm), explaining the formation of a hydrogel. This hydrogel allows Lanreotide not only to be protected against chemical degradation but also to be released in a controlled manner over time (more than a month after injection) ensuring its continuous circulation in the blood. The detailed understanding of the chemical and physicochemical rules guiding the assembly of peptides would make it possible to design new controlled-release formulations in which, as in the case of Lanreotide, the drug would be its own formulation. Scientists elucidated the atomic structure of Lanreotide nanotubes obtained at a resolution of 2.5 Å by cryo-EM. This structure reveals a complexity that nothing let suspect in the many previous works and that it would have been impossible to predict by the methods we have today.

The recent and phenomenal success of the artificial intelligence software AlphaFold for the prediction of the tertiary structure of proteins has only been possible thanks to the database of experimentally determined protein atomic structures. However, AlphaFold is not at this stage able to predict peptide folding and assembly. The experimental verification of models at a level of resolution close to the atom must therefore become the norm in this field. This will be an essential step towards the development of reliable predictive methods which will pave the way for the de novo design of peptide materials whose controlled properties will thus find applications in many fields of biology, pharmacy and medicine and may inspire developments in the field of nanotechnology.

Figure: Structure of Lanreotide nanotubes. A: Density map of the nanotube obtained after image processing and helical reconstruction; B: zoom on an elementary building block of the helix made up of a peptide octamer organized into 2 tetramers. The 8 molecules all have different conformations. They are however grouped into two families according to the position of the amino-terminal naphthylalanine residue: the “pink” family (molecules a, b, g & h) and the “green” family (molecules c, d e & f). The yellow and orange circles underline the hydrophobic cores of the 2 tetramers of the elementary brick made up of 4 valines in strong interaction. C: Highlighting the different types of structure-maintaining interaction: interaction between tetramers, interaction between aromatic residues, β-sheet between molecules a, d, g & f and β-sheet between molecules c, b, h & e.

Contact person: Maïté Paternostre

Team Interactions and assembly mechanisms of proteins and peptides

Genome methylation dynamics in Sinorhizobium meliloti during symbiotic differentiation

In the rhizobium-legume symbiosis, the symbiotic bacteria are housed inside specific plant cells of root nodules where they fix nitrogen. These endosymbiotic rhizobia, called bacteroids, are metabolically differentiated and adapted to intracellular life. In legumes belonging to the genus Medicago, bacteroid differentiation of the symbiont Sinorhizobium meliloti involves also irreversible cellular modifications, including cell enlargement and genome amplification. By genome-wide DNA methylation analysis with SMRT-seq during the different stages of bacteroid differentiation in wild type plants as well as in a panel of plant mutants whose nodules contain endosymbionts blocked at various stages of differentiation, we obtained in this study evidence of dysregulated GANTC methylation patterns during bacteroid differentiation. We therefore propose that epigenetic control by the DNA methylase CcrM is a driving factor for the endoreduplication of the differentiated bacteroids.

More information: https://doi.org/10.1128/mSystems.01092-21

Contact person: Peter Mergaert 

Team Plant-Bacteria Interactions

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