Accueil
L'unité en quelques chiffres clés :
 Créé en 2022 |
 71 membres |
 5 équipes de recherche |
 181 publications (2015-2022) |
 23 soutenances de thèse (2015-2022) |
Les équipes :
Publications récentes :
Sanejouand, Yves-Henri
On the unknown proteins of eukaryotic proteomes Article de journal À paraître
Dans: arXiv preprint arXiv:2209.11001, À paraître.
@article{sanejouand2022unknown,
title = {On the unknown proteins of eukaryotic proteomes},
author = {Yves-Henri Sanejouand},
url = {https://doi.org/10.48550/arXiv.2209.11001},
doi = {10.48550/arXiv.2209.11001},
year = {2022},
date = {2022-09-22},
urldate = {2022-01-01},
journal = {arXiv preprint arXiv:2209.11001},
abstract = {In order to study unknown proteins on a large scale, a reference system has been set up for the three major eukaryotic lineages, built with 36 proteomes as taxonomically diverse as possible. Proteins from 362 eukaryotic proteomes with no known homologue in this set were then analyzed, focusing noteworthy on singletons, that is, on unknown proteins with no known homologue in their own proteome. Consistently, according to Uniprot, for a given species, no more than 12% of the singletons thus found are known at the protein level. Also, since they rely on the information found in the alignment of homologous sequences, predictions of AlphaFold2 for their tridimensional structure are usually poor. In the case of metazoan species, the number of singletons seems to increase as a function of the evolutionary distance from the reference system. Interestingly, no such trend is found in the cases of viridiplantae and fungi, as if the timescale on which singletons are added to proteomes were different in metazoa and in other eukaryotic kingdoms. In order to confirm this phenomenon, further studies of proteomes closer to those of the reference system are however needed.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
In order to study unknown proteins on a large scale, a reference system has been set up for the three major eukaryotic lineages, built with 36 proteomes as taxonomically diverse as possible. Proteins from 362 eukaryotic proteomes with no known homologue in this set were then analyzed, focusing noteworthy on singletons, that is, on unknown proteins with no known homologue in their own proteome. Consistently, according to Uniprot, for a given species, no more than 12% of the singletons thus found are known at the protein level. Also, since they rely on the information found in the alignment of homologous sequences, predictions of AlphaFold2 for their tridimensional structure are usually poor. In the case of metazoan species, the number of singletons seems to increase as a function of the evolutionary distance from the reference system. Interestingly, no such trend is found in the cases of viridiplantae and fungi, as if the timescale on which singletons are added to proteomes were different in metazoa and in other eukaryotic kingdoms. In order to confirm this phenomenon, further studies of proteomes closer to those of the reference system are however needed.
Chandola, Udita; Trottier, Camille; Gaudin, Marinna; Manirakiza, Erik; Menicot, Samuel; Louvet, Isabelle; Lacour, Thomas; Chaumier, Timothée; Tanaka, Atsuko; Chaffron, Samuel; Tirichine, Leila
Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae Article de journal À paraître
Dans: bioRxiv, À paraître.
@article{Chandola2022.08.25.505241,
title = {Combined in vivo and in situ genome-resolved metagenomics reveals novel symbiotic nitrogen fixing interactions between non-cyanobacterial diazotrophs and microalgae},
author = {Udita Chandola and Camille Trottier and Marinna Gaudin and Erik Manirakiza and Samuel Menicot and Isabelle Louvet and Thomas Lacour and Timothée Chaumier and Atsuko Tanaka and Samuel Chaffron and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2022/08/25/2022.08.25.505241},
doi = {10.1101/2022.08.25.505241},
year = {2022},
date = {2022-08-25},
urldate = {2022-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Non-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatom Phaeodactylum triconrnutum (Pt) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identified PtNCDs using metagenomics sequencing and detected nitrogenase gene in silico and/or by PCR. We demonstrated nitrogen fixation in PtNCDs and their close genetic affiliation with NCDs from the environment. We showed the wide occurrence of this type of symbiosis with the isolation of NCDs from other microalgae and their identification in the environment and in co-occurrence with photosynthetic microalgae. Overall, this study provides evidence for a previously overlooked symbiosis using a multidisciplinary model-based approach which will consequently help understand the different players driving global marine nitrogen fixation.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
Non-cyanobacteria diazotrophs (NCDs) were shown to dominate in surface waters shifting the long-held paradigm of cyanobacteria dominance and raising fundamental questions on how these putative heterotrophic bacteria thrive in sunlit oceans. Here, we report an unprecedented finding in the widely used model diatom Phaeodactylum triconrnutum (Pt) of NCDs sustaining diatom cells in the absence of bioavailable nitrogen. We identified PtNCDs using metagenomics sequencing and detected nitrogenase gene in silico and/or by PCR. We demonstrated nitrogen fixation in PtNCDs and their close genetic affiliation with NCDs from the environment. We showed the wide occurrence of this type of symbiosis with the isolation of NCDs from other microalgae and their identification in the environment and in co-occurrence with photosynthetic microalgae. Overall, this study provides evidence for a previously overlooked symbiosis using a multidisciplinary model-based approach which will consequently help understand the different players driving global marine nitrogen fixation.Competing Interest StatementThe authors have declared no competing interest.
Wu, Yue; Timothée, Chaumier; Manirakiza, Eric; Veluchamy, Alaguraj; Tirichine, Leila
PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum Article de journal À paraître
Dans: bioRxiv, À paraître.
@article{Wu2022.07.29.502047,
title = {PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum},
author = {Yue Wu and Chaumier Timothée and Eric Manirakiza and Alaguraj Veluchamy and Leila Tirichine},
url = {https://www.biorxiv.org/content/early/2022/08/01/2022.07.29.502047},
doi = {10.1101/2022.07.29.502047},
year = {2022},
date = {2022-08-01},
urldate = {2022-01-01},
journal = {bioRxiv},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Motivation Recent advances in DNA sequencing technologies in particular of long reads type greatly improved genomes assembly leading to discrepancies between both published annotations and epigenome tracks which did not keep pace with new assemblies. This comprises the availability of accurate resources which penalizes the progress in research.Results Here, we used the latest improved telomere to telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genome annotation including genes and transposable elements to map the epigenome landscape, namely DNA methylation and post translational modifications of histones providing the community with PhaeoEpiView, a browser that allows the visualization of epigenome data as well as transcripts on an updated reference genome to better understand the biological significance of the mapped data on contiguous genome rather than a fragmented one. We updated previously published histone marks with a more accurate mapping using monoclonal antibodies instead of polyclonal and deeper sequencing. PhaeoEpiView will be continuously updated with the newly published epigenomic data making it the largest and richest epigenome browser of any stramenopile. We expect that PhaeoEpiView will be a standard tool for the coming era of molecular environmental studies where epigenetics holds a place of choice.Availability PhaeoEpiView is available at: https://PhaeoEpiView.univ-nantes.frCompeting Interest StatementThe authors have declared no competing interest.},
keywords = {},
pubstate = {forthcoming},
tppubtype = {article}
}
Motivation Recent advances in DNA sequencing technologies in particular of long reads type greatly improved genomes assembly leading to discrepancies between both published annotations and epigenome tracks which did not keep pace with new assemblies. This comprises the availability of accurate resources which penalizes the progress in research.Results Here, we used the latest improved telomere to telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genome annotation including genes and transposable elements to map the epigenome landscape, namely DNA methylation and post translational modifications of histones providing the community with PhaeoEpiView, a browser that allows the visualization of epigenome data as well as transcripts on an updated reference genome to better understand the biological significance of the mapped data on contiguous genome rather than a fragmented one. We updated previously published histone marks with a more accurate mapping using monoclonal antibodies instead of polyclonal and deeper sequencing. PhaeoEpiView will be continuously updated with the newly published epigenomic data making it the largest and richest epigenome browser of any stramenopile. We expect that PhaeoEpiView will be a standard tool for the coming era of molecular environmental studies where epigenetics holds a place of choice.Availability PhaeoEpiView is available at: https://PhaeoEpiView.univ-nantes.frCompeting Interest StatementThe authors have declared no competing interest.
Lapaillerie, Delphine; Charlier, Cathy; Guyonnet-Dupérat, Véronique; Murigneux, Emilie; Fernandes, Henrique S.; Martins, Fábio G.; Magalhães, Rita P.; Vieira, Tatiana F.; Richetta, Clémence; Subra, Frédéric; Lebourgeois, Samuel; Charpentier, Charlotte; Descamps, Diane; Visseaux, Benoît; Weigel, Pierre; Favereaux, Alexandre; Beauvineau, Claire; Buron, Frédéric; Teulade-Fichou, Marie-Paule; Routier, Sylvain; Gallois-Montbrun, Sarah; Meertens, Laurent; Delelis, Olivier; Sousa, Sérgio F.; Parissi, Vincent
Selection of Bis-Indolyl Pyridines and Triphenylamines as New Inhibitors of SARS-CoV-2 Cellular Entry by Modulating the Spike Protein/ACE2 Interfaces Article de journal
Dans: Antimicrobial Agents and Chemotherapy, vol. 0, no. 0, p. e00083-22, 2022.
@article{doi:10.1128/aac.00083-22,
title = {Selection of Bis-Indolyl Pyridines and Triphenylamines as New Inhibitors of SARS-CoV-2 Cellular Entry by Modulating the Spike Protein/ACE2 Interfaces},
author = {Delphine Lapaillerie and Cathy Charlier and Véronique Guyonnet-Dupérat and Emilie Murigneux and Henrique S. Fernandes and Fábio G. Martins and Rita P. Magalhães and Tatiana F. Vieira and Clémence Richetta and Frédéric Subra and Samuel Lebourgeois and Charlotte Charpentier and Diane Descamps and Benoît Visseaux and Pierre Weigel and Alexandre Favereaux and Claire Beauvineau and Frédéric Buron and Marie-Paule Teulade-Fichou and Sylvain Routier and Sarah Gallois-Montbrun and Laurent Meertens and Olivier Delelis and Sérgio F. Sousa and Vincent Parissi},
url = {https://journals.asm.org/doi/abs/10.1128/aac.00083-22},
doi = {10.1128/aac.00083-22},
year = {2022},
date = {2022-07-05},
urldate = {2022-07-05},
journal = {Antimicrobial Agents and Chemotherapy},
volume = {0},
number = {0},
pages = {e00083-22},
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Disrupting this interaction would lead to early blockage of viral replication. To identify chemical tools to further study these functional interfaces, 139,146 compounds from different chemical libraries were screened through an S/ACE2 in silico virtual molecular model. The best compounds were selected for further characterization using both cellular and biochemical approaches, reiterating SARS-CoV-2 entry and the S/ACE2 interaction. We report here two selected hits, bis-indolyl pyridine AB-00011778 and triphenylamine AB-00047476. Both of these compounds can block the infectivity of lentiviral vectors pseudotyped with the SARS-CoV-2 S protein as well as wild-type and circulating variant SARS-CoV-2 strains in various human cell lines, including pulmonary cells naturally susceptible to infection. AlphaLISA and biolayer interferometry confirmed a direct inhibitory effect of these drugs on the S/ACE2 association. A specific study of the AB-00011778 inhibitory properties showed that this drug inhibits viral replication with a 50% effective concentration (EC50) between 0.1 and 0.5 μM depending on the cell lines. Molecular docking calculations of the interaction parameters of the molecules within the S/ACE2 complex from both wild-type and circulating variants of the virus showed that the molecules may target multiple sites within the S/ACE2 interface. Our work indicates that AB-00011778 constitutes a good tool for modulating this interface and a strong lead compound for further therapeutic purposes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Disrupting this interaction would lead to early blockage of viral replication. To identify chemical tools to further study these functional interfaces, 139,146 compounds from different chemical libraries were screened through an S/ACE2 in silico virtual molecular model. The best compounds were selected for further characterization using both cellular and biochemical approaches, reiterating SARS-CoV-2 entry and the S/ACE2 interaction. We report here two selected hits, bis-indolyl pyridine AB-00011778 and triphenylamine AB-00047476. Both of these compounds can block the infectivity of lentiviral vectors pseudotyped with the SARS-CoV-2 S protein as well as wild-type and circulating variant SARS-CoV-2 strains in various human cell lines, including pulmonary cells naturally susceptible to infection. AlphaLISA and biolayer interferometry confirmed a direct inhibitory effect of these drugs on the S/ACE2 association. A specific study of the AB-00011778 inhibitory properties showed that this drug inhibits viral replication with a 50% effective concentration (EC50) between 0.1 and 0.5 μM depending on the cell lines. Molecular docking calculations of the interaction parameters of the molecules within the S/ACE2 complex from both wild-type and circulating variants of the virus showed that the molecules may target multiple sites within the S/ACE2 interface. Our work indicates that AB-00011778 constitutes a good tool for modulating this interface and a strong lead compound for further therapeutic purposes.
Sulser, Sandra; Vucicevic, Andrea; Bellini, Veronica; Moritz, Roxane; Delavat, François; Sentchilo, Vladimir; Carraro, Nicolas; van der Meer, Jan Roelof
A bistable prokaryotic differentiation system underlying development of conjugative transfer competence Article de journal
Dans: Plos Genetics, vol. 18, iss. 6, p. e1010286, 2022.
@article{doi.org/10.1371/journal.pgen.1010286,
title = {A bistable prokaryotic differentiation system underlying development of conjugative transfer competence},
author = {Sandra Sulser and Andrea Vucicevic and Veronica Bellini and Roxane Moritz and François Delavat and Vladimir Sentchilo and Nicolas Carraro and Jan Roelof van der Meer},
doi = {10.1371/journal.pgen.1010286},
year = {2022},
date = {2022-06-28},
urldate = {2022-06-28},
journal = {Plos Genetics},
volume = {18},
issue = {6},
pages = {e1010286},
abstract = {The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7-4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7-4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.