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1. A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Author: Aouad, Monique, Flandrois, Jean-Pierre, Jauffrit, Frédéric, Gouy, Manolo, Gribaldo, Simonetta, Brochier-Armanet, Celine, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université Catholique de Lyon (UCLy) (UCLy), Bio-Mérieux [Marcy l'Etoile], BIOMERIEUX, Biologie Évolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This work has been funded by the French National Agency for Research, Grant ArchEvol (Grant No. ANR-16-CE02-0005-01). M.A. has been funded by a doctoral fellowship from the Région Rhône-Alpes-ARC 1 Santé., We thank the PRABI (Pôle Rhône-Alpes de Bioinformatique) and the Institut Pasteur for providing computing facilities., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), Innovat Unit, BioMerieux SA, BioMerieux SA, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Asgard, Ecology, Evolution, Stygia, Research, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Eukaryota, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Archaea, Root, QH359-425, Altiarchaea, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, DPANN, Phylogeny, QH540-549.5, Diaforarchaea
Abstract: Background The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal. Results We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study. Conclusions We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01952-0.
Published: 2022

2. Mitochondrial respiration restricts Listeria monocytogenes infection by slowing down host cell receptor recycling

Author: Spier, Anna, Connor, Michael, Steiner, Thomas, Carvalho, Filipe, Cossart, Pascale, Eisenreich, Wolfgang, Wai, Timothy, Stavru, Fabrizia, Biologie Évolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Interactions Bactéries-Cellules, Institut Pasteur [Paris] (IP), Chromatine et Infection - Chromatin and Infection, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Université Paris Cité (UPCité), Biologie mitochondriale – Mitochondrial biology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This study was supported by the European Research Council ( H2020-ERC-2014-ADG 670823-BacCellEpi to P.C.), the DFG ( Project-ID EI 384/16-1 to W.E.), Institut Pasteur , and the Centre National de la Recherche Scientifique (CNRS). A.S. was supported by a BioSPC doctoral fellowship from the Université de Paris . M.G.C. is funded by a Pasteur Foundation Fellowship and his work was funded by ANR JCJC grant 'Epibactin.', We dedicate this work to the memory of Fabrizia Stavru. We thank Frédéric Bouillaud, Anne Lombès, and Nathalie Sauvonnet for useful advice, discussions, and support with Seahorse and endocytosis assays, Nam Tham for technical support, Werner Goebel for insightful discussions, Pierre-Henri Commere and members of the Cytometry & Biomarkers facility (CB_UTechS) at Institut Pasteur for training and help with flow cytometry and the Seahorse analyzer, and Alessandro Pagliuso and Simonetta Gribaldo for critical reading of the manuscript. Other bacterial species were GFP-expressing Salmonella enterica serovar Typhimurium strain 12023 (BUG2562) (a gift from Stéphane Méresse, Centre d’Immunologie de Marseille-Luminy, France) and Shigella flexneri M09T (BUG 2505) (a gift from Phillipe Sansonetti,Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris). We thank Dr. Matthew Lawrenz at the University of Louisville for sharing the Rab11bCA construct generated by M.G.C. while in his laboratory., ANR-17-CE12-0007,EpiBactIn,Modifications epigenomiques induites par l'interaction hote-bacteries(2017), European Project: 670823,H2020,ERC-2014-ADG,BacCellEpi(2015), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)
Subjects: [SDV]Life Sciences [q-bio], Respiration, Membrane Proteins, Proto-Oncogene Proteins c-met, HCT116 Cells, Listeria monocytogenes, infection, Mitochondria, endocytic recycling, Mitochondrial Proteins, mitochondrial disease, 13C isotopologue profiling, Report, Rab11, Colonic Neoplasms, Humans, Listeriosis, Energy Metabolism, metabolism, ComputingMilieux_MISCELLANEOUS
Abstract: Summary Mutations in mitochondrial genes impairing energy production cause mitochondrial diseases (MDs), and clinical studies have shown that MD patients are prone to bacterial infections. However, the relationship between mitochondrial (dys)function and infection remains largely unexplored, especially in epithelial cells, the first barrier to many pathogens. Here, we generate an epithelial cell model for one of the most common mitochondrial diseases, Leigh syndrome, by deleting surfeit locus protein 1 (SURF1), an assembly factor for respiratory chain complex IV. We use this genetic model and a complementary, nutrient-based approach to modulate mitochondrial respiration rates and show that impaired mitochondrial respiration favors entry of the human pathogen Listeria monocytogenes, a well-established bacterial infection model. Reversely, enhanced mitochondrial energy metabolism decreases infection efficiency. We further demonstrate that endocytic recycling is reduced in mitochondrial respiration-dependent cells, dampening L. monocytogenes infection by slowing the recycling of its host cell receptor c-Met, highlighting a previously undescribed role of mitochondrial respiration during infection., Graphical abstract, Highlights • Enhanced mitochondrial respiration decreases L. monocytogenes infection • Bacterial entry is affected by the host cell metabolism • Mitochondrial respiration restricts host cell receptor recycling and thus infection, Spier et al. show that the cellular energy metabolism affects infection of epithelial cells by L. monocytogenes. Mitochondrial respiration modulates L. monocytogenes entry by limiting endocytic recycling of receptors such as c-Met back to the plasma membrane, leading to decreased bacterial load in cells with high respiratory activity.
Published: 2021

3. A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes

Author: Simonetta Gribaldo, Christophe Grangeasse, Pierre Simon Garcia, Jean-Pierre Flandrois, Wandrille Duchemin, Céline Brochier-Armanet, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), This work has been supported by the Centre National de laRechercheScientifique(CNRS),TheUniversitedeLyon,theRegion Rhoˆne-Alpes ARC1 (financial support for P.S.G.), theAgence National de la Recherche (15-CE32-0001-01 and 19-CE15-0011-01), the Bettencourt-Schueller Foundation, andthe Investissement d’Avenir ‘Ancestrome’ (ANR-10-BINF-01-01). Calculations were performed using the computingfacilities of the CC LBBE/PRABI., ANR-15-CE32-0001,Map-CellDiv,MapZ: caractérisation d'un nouveau mécanisme de régulation de la division cellulaire bactérienne(2015), ANR-19-CE15-0011,LookingForPegase,A la recherche de protéines régulant des enzymes responsables de la synthèse du peptidoglycane(2019), ANR-10-BINF-0001,ANCESTROME,Approche de phylogénie intégrative pour la reconstruction de génomes ancestraux(2010), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: cell division, Cell division, Firmicutes, Computational biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, AcademicSubjects/SCI01180, phylogeny, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Synteny, 03 medical and health sciences, Phylogenetics, Phylogenomics, Gene cluster, evolution, Genetics, Computer Simulation, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, Discoveries, 030304 developmental biology, 0303 health sciences, Phylogenetic tree, Bacteria, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], AcademicSubjects/SCI01130, phylogenomics, functional link, Cell cycle, biology.organism_classification, Biological Evolution, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Multigene Family, cell cycle, evolutionary scenario
Abstract: The cell cycle is a fundamental process that has been extensively studied in bacteria. However, many of its components and their interactions with machineries involved in other cellular processes are poorly understood. Furthermore, most knowledge relies on the study of a few models, but the real diversity of the cell division apparatus and its evolution are largely unknown. Here, we present a massive in-silico analysis of cell division and associated processes in around 1,000 genomes of the Firmicutes, a major bacterial phylum encompassing models (i.e. Bacillus subtilis, Streptococcus pneumoniae, and Staphylococcus aureus), as well as many important pathogens. We analyzed over 160 proteins by using an original approach combining phylogenetic reconciliation, phylogenetic profiles, and gene cluster survey. Our results reveal the presence of substantial differences among clades and pinpoints a number of evolutionary hotspots. In particular, the emergence of Bacilli coincides with an expansion of the gene repertoires involved in cell wall synthesis and remodeling. We also highlight major genomic rearrangements at the emergence of Streptococcaceae. We establish a functional network in Firmicutes that allows identifying new functional links inside one same process such as between FtsW (peptidoglycan polymerase) and a previously undescribed Penicilin-Binding Protein or between different processes, such as replication and cell wall synthesis. Finally, we identify new candidates involved in sporulation and cell wall synthesis. Our results provide a previously undescribed view on the diversity of the bacterial cell cycle, testable hypotheses for further experimental studies, and a methodological framework for the analysis of any other biological system.
Published: 2021

4. Resolving phylogenetic and biochemical barriers to functional expression of heterologous iron-sulphur cluster enzymes

Author: Béatrice Py, Fernández-Fueyo E, van den Broek N, Gregory Bokinsky, Manuel Rr, Duraffourg N, Frédéric Barras, D’Angelo F, Martin Pabst, de Choudens So, Ferhat Büke, Martin Pelosse, Simonetta Gribaldo, Shomar H, de Ram C, Pierre Simon Garcia, Liu S, Kavli Institute of Nanosciences [Delft] (KI-NANO), Delft University of Technology (TU Delft), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Adaptation au stress et Métabolisme chez les entérobactéries - Stress adaptation and metabolism in enterobacteria (SAMe), Biocatalyse (BIOCAT), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Catalyse Bioinorganique et Environnement (BioCE ), This project (IRONPLUGNPLAY) has received funding from the European Union’s Horizon 2020 research and innovation programme under grant 722361 and was supported by grants from AgenceNationale Recherche (ANR) ERA-Institut Pasteur and the ANR-10-LABX-62-IBEID. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. SL was supported by the China Scholarship Council., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 722361,ERA CoBioTech, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: chemistry.chemical_classification, 0303 health sciences, Phylogenetic tree, Heterologous, Computational biology, Biology, 010402 general chemistry, medicine.disease_cause, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 01 natural sciences, 0104 chemical sciences, 03 medical and health sciences, Synthetic biology, Enzyme, chemistry, Protein-fragment complementation assay, medicine, Heterologous expression, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Escherichia coli, Biogenesis, 030304 developmental biology
Abstract: Many of the most promising applications of synthetic biology, including engineering of microbes for renewable chemical production, relies upon the ability of genetically-tractable hosts to express heterologous enzymes from foreign species. While countless methods for facilitating heterologous enzyme expression have been developed, comparable tools for facilitating heterologous enzyme activity are generally lacking. Such tools are needed to fully exploit the biosynthetic potential of the natural world. Here, using the model bacterium Escherichia coli, we investigate why iron-sulphur (Fe-S) enzymes are often inactive when heterologously expressed. By applying a simple growth complementation assay with collections of Fe-S enzyme orthologs from a wide range of prokaryotic diversity, we uncover a striking correlation between phylogenetic distance and probability of functional expression. Moreover, co-expression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be functionally expressed. On the other hand, we find that heterologous Fe-S enzymes that require specific electron carrier proteins within their natural host are rarely functionally expressed unless their specific reducing partners are identified and co-expressed. We demonstrate in vitro that such selectivity in part derives from a need for low-potential electron donors. Our results clarify how phylogenetic distance and electron transfer biochemistry each separately impact functional heterologous expression and provide insight into how these barriers can be overcome for successful microbial engineering involving Fe-S enzymes.
Published: 2021

5. New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Author: Erwan Roussel, Amandine Sanvoisin, Laurent Toffin, Guillaume Borrel, Karine Alain, Maxime Allioux, Yann Moalic, Marc Cozannet, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), The study was supported by grants from the French Ministry of Higher Education and Research, the Région Bretagne and the LabexMer (ANR-10-LABX-1) for MC. This work was supported by the program MERLIN Abyss, the 'Laboratoire d’Excellence' LabexMER Axis 3 programs ENDIV and CULTIVENT (ANR-10-LABX-1), and the Sino-French IRP 1211 MicrobSea. Samples from the Mozambic Channel were provided in the frame of the PAMELA collaborative project (Ifremer/TOTAL SA)., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), Methanogenesis, Zoology, Microbiology, Genome, 03 medical and health sciences, environmental cluster, Virology, 14. Life underwater, Clade, Relative species abundance, lcsh:QH301-705.5, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Host (biology), Aquatic ecosystem, Methanomassiliicoccales, methyl-compounds, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, lcsh:Biology (General), cultivation, networks, Candidatus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacteria
Abstract: Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the reconstruction of a high-quality metagenome-assembled genome (MAG) corresponding to a new candidate species, for which we propose the name of Candidatus &lsquo, Methanomassiliicoccus armoricus MXMAG1&rsquo, Comparison of the annotated genome of MXMAG1 with the published genomes and MAGs from Methanomassiliicoccales belonging to the 2 known clades (&lsquo, free-living&rsquo, /non-host-associated environmental clade and &lsquo, host-associated&rsquo, /digestive clade) allowed us to explore the putative physiological traits of Candidatus &lsquo, M. armoricus MXMAG1&rsquo, As expected, Ca. &lsquo, had the genetic potential to produce methane by reduction of methyl compounds and dihydrogen oxidation. This MAG encodes for several putative physiological and stress response adaptations, including biosynthesis of trehalose (osmotic and temperature regulations), agmatine production (pH regulation), and arsenic detoxication, by reduction and excretion of arsenite, a mechanism that was only present in the &lsquo, clade. An analysis of co-occurrence networks carried out on environmental samples and slurries also showed that Methanomassiliicoccales detected in terrestrial and aquatic ecosystems were strongly associated with acetate and dihydrogen producing bacteria commonly found in digestive habitats and which have been reported to form syntrophic relationships with methanogens.
Published: 2020
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6. Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition

Author: Jerzy Witwinowski, Simonetta Gribaldo, Guillaume Borrel, Panagiotis S. Adam, Daniela Megrian, Najwa Taib, Christophe Beloin, Daniel Poppleton, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Génétique des Biofilms - Genetics of Biofilms, S.G., C.B. and J.W. acknowledge funding from the French National Research Agency (ANR), project Fir-OM (grant no. ANR-16-CE12-0010) and from the Institut Pasteur Programmes Transversaux de Recherche (grant no. PTR 39–16). D.M. and D.P. were supported by the Pasteur-Paris University (PPU) International PhD Program. This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris., ANR-16-CE12-0010,Fir-OM,Firmicutes avec une membrane externe: vers des nouveaux modeles d'étude de la transition monodermes/didermes(2016), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Collège Doctoral
Subjects: Firmicutes, Chemie, Gram-Positive Bacteria, Genome, MESH: Gram-Positive Bacteria, 03 medical and health sciences, Gram-Negative Bacteria, MESH: Gram-Negative Bacteria, Humans, Clade, MESH: Phylogeny, MESH: Firmicutes, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, 0303 health sciences, Halanaerobiales, Negativicutes, MESH: Humans, Ecology, Phylogenetic tree, biology, Bacteria, 030306 microbiology, Phylum, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Bacteria, Evolutionary biology, Bacterial outer membrane
Abstract: Phylogenomic analysis supports a diderm ancestor of the Firmicutes and points to an early origin of two-membraned cells in Bacteria and the derived nature of the Gram-positive envelope following multiple outer membrane losses. The transition between cell envelopes with one membrane (Gram-positive or monoderm) and those with two membranes (Gram-negative or diderm) is a fundamental open question in the evolution of Bacteria. Evidence of the presence of two independent diderm lineages, the Halanaerobiales and the Negativicutes, within the classically monoderm Firmicutes has blurred the monoderm/diderm divide and specifically anticipated that other members with an outer membrane (OM) might exist in this phylum. Here, by screening 1,639 genomes of uncultured Firmicutes for signatures of an OM, we highlight a third and deep branching diderm clade, the Limnochordia, strengthening the hypothesis of a diderm ancestor and the occurrence of independent transitions leading to the monoderm phenotype. Phyletic patterns of over 176,000 protein families constituting the Firmicutes pan-proteome identify those that strongly correlate with the diderm phenotype and suggest the existence of new potential players in OM biogenesis. In contrast, we find practically no largely conserved core of monoderms, a fact possibly linked to different ways of adapting to repeated OM losses. Phylogenetic analysis of a concatenation of main OM components totalling nearly 2,000 amino acid positions illustrates the common origin and vertical evolution of most diderm bacterial envelopes. Finally, mapping the presence/absence of OM markers onto the tree of Bacteria shows the overwhelming presence of diderm phyla and the non-monophyly of monoderm ones, pointing to an early origin of two-membraned cells and the derived nature of the Gram-positive envelope following multiple OM losses.
Published: 2020

7. A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes

Author: Ahmed Haouz, Simonetta Gribaldo, Pierre Simon Garcia, Najwa Taib, Pascal Röthlisberger, Pierre Alexandre Kaminski, Marion Lagune, Philippe Marliere, Jérôme Loc’h, Dona Sleiman, Biologie des Bactéries pathogènes à Gram-positif - Biology of Gram-Positive Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Adaptation au stress et Métabolisme chez les entérobactéries - Stress adaptation and metabolism in enterobacteria (SAMe), Dynamique structurale des Macromolécules / Structural Dynamics of Macromolecules, Cristallographie (Plateforme) - Crystallography (Platform), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Chimie bioorganique des acides nucléiques - Bioorganic chemistry of nucleic acids, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), D.S. and P.S.G. were supported by an ERASynBio 'TNA episome' and by an ERACoBioTech 'Iron Plug’n Play' fellowship, respectively. S.G. acknowledges funding from the French National Agency for research grant Archaevol (ANR-16-CE02-0005-01). This study was funded from the French government’s Investissement d’Avenir program, Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (grant no. ANR-10-LABX-62-IBEID)., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: Purine, DNA polymerase, Guanine, Genome, Viral, Viral Nonstructural Proteins, Crystallography, X-Ray, Genome, 03 medical and health sciences, chemistry.chemical_compound, Adenylosuccinate Synthase, MESH: 2-Aminopurine, A-DNA, MESH: Adenylosuccinate Synthase, Bacteriophages, MESH: Bacteriophages, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], MESH: Phylogeny, 2-Aminopurine, Phylogeny, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Multidisciplinary, biology, ATP synthase, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030302 biochemistry & molecular biology, MESH: Crystallography, X-Ray, MESH: DNA, Viral, Biosynthetic Pathways, Enzyme, chemistry, Biochemistry, DNA, Viral, biology.protein, MESH: Viral Nonstructural Proteins, MESH: Biosynthetic Pathways, MESH: Genome, Viral, DNA
Abstract: Biosynthesis and replication, from A to Z Four nucleobases. adenine (A), cytosine (C), guanine (G), and thymine (T), are usually thought to be invariable in DNA. In bacterial viruses, however, each of the DNA bases have variations that help them to escape degradation by bacterial restriction enzymes. In the genome of cyanophage S-2L, A is completely replaced by diaminopurine (Z), which forms three hydrogen bonds with T and thus creates non–Watson-Crick base pairing in the DNA of this virus (see the Perspective by Grome and Isaacs). Zhou et al. and Sleiman et al. determined the biochemical pathway that produces Z, which revealed more Z genomes in viruses hosted in bacteria distributed widely in the environment and phylogeny. Pezo et al. identified a DNA polymerase that incorporates Z into DNA while rejecting A. These findings enrich our understanding of biodiversity and expand the genetic palette for synthetic biology. Science , this issue p. 512 , 516 , 520 ; see also p. 460
Published: 2020

8. Autotransporters Drive Biofilm Formation and Autoaggregation in the Diderm Firmicute Veillonella parvula

Author: Jean-Marc Ghigo, Nathalie Béchon, Emilie Bierque, Najwa Taib, Christophe Beloin, Jerzy Witwinowski, Laurence Ma, Simonetta Gribaldo, Thomas Cokelaer, Alicia Jiménez-Fernández, Génétique des Biofilms - Genetics of Biofilms, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (USPC), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Biomics (plateforme technologique), Institut Pasteur [Paris], French National Research Agency (ANR) (Fir-OM ANR-16-CE12-0010), from the Institut Pasteur 'Programmes Transversaux de Recherche' (PTR 39-16), from the French government's Investissement d'Avenir Program, Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant n°ANR-10-LABX-62-IBEID) and from the Fondation pour la Recherche Médicale (grant DEQ20180339185). N.B. was supported by a MENESR (Ministère Français de l’Education Nationale, de l’Enseignement Supérieur et de la Recherche) fellowship. A.J.F. was supported by a PRESTIGE program from Campus France., ANR-16-CE12-0010,Fir-OM,Firmicutes avec une membrane externe: vers des nouveaux modeles d'étude de la transition monodermes/didermes(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, and Institut Pasteur [Paris] (IP)
Subjects: Type V Secretion Systems, Firmicutes, Veillonella, Microbiology, Bacterial Adhesion, Veillonella parvula, Clostridia, 03 medical and health sciences, stomatognathic system, Spotlight, Adhesins, Bacterial, Molecular Biology, 030304 developmental biology, 0303 health sciences, Negativicutes, biology, diderm firmicutes, 030306 microbiology, autotransporter proteins, Biofilm, adhesins, biology.organism_classification, Bacterial adhesin, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biofilms, Proteobacteria, Bacterial outer membrane, Bacteria, Research Article, Autotransporters
Abstract: Veillonella parvula is an anaerobic commensal and opportunistic pathogen whose ability to adhere to surfaces or other bacteria and form biofilms is critical for it to inhabit complex human microbial communities such as the gut and oral microbiota. Although the adhesive capacity of V. parvula has been previously described, very little is known about the underlying molecular mechanisms due to a lack of genetically amenable Veillonella strains. In this study, we took advantage of a naturally transformable V. parvula isolate and newly adapted genetic tools to identify surface-exposed adhesins called autotransporters as the main molecular determinants of adhesion in this bacterium. This work therefore provides new insights on an important aspect of the V. parvula lifestyle, opening new possibilities for mechanistic studies of the contribution of biofilm formation to the biology of this major commensal of the oral-digestive tract., The Negativicutes are a clade of the Firmicutes that have retained the ancestral diderm character and possess an outer membrane. One of the best studied Negativicutes, Veillonella parvula, is an anaerobic commensal and opportunistic pathogen inhabiting complex human microbial communities, including the gut and the dental plaque microbiota. Whereas the adhesion and biofilm capacities of V. parvula are expected to be crucial for its maintenance and development in these environments, studies of V. parvula adhesion have been hindered by the lack of efficient genetic tools to perform functional analyses in this bacterium. Here, we took advantage of a recently described naturally transformable V. parvula isolate, SKV38, and adapted tools developed for the closely related Clostridia spp. to perform random transposon and targeted mutagenesis to identify V. parvula genes involved in biofilm formation. We show that type V secreted autotransporters, typically found in diderm bacteria, are the main determinants of V. parvula autoaggregation and biofilm formation and compete with each other for binding either to cells or to surfaces, with strong consequences for V. parvula biofilm formation capacity. The identified trimeric autotransporters have an original structure compared to classical autotransporters identified in Proteobacteria, with an additional C-terminal domain. We also show that inactivation of the gene coding for a poorly characterized metal-dependent phosphohydrolase HD domain protein conserved in the Firmicutes and their closely related diderm phyla inhibits autotransporter-mediated biofilm formation. This study paves the way for further molecular characterization of V. parvula interactions with other bacteria and the host within complex microbiota environments. IMPORTANCE Veillonella parvula is an anaerobic commensal and opportunistic pathogen whose ability to adhere to surfaces or other bacteria and form biofilms is critical for it to inhabit complex human microbial communities such as the gut and oral microbiota. Although the adhesive capacity of V. parvula has been previously described, very little is known about the underlying molecular mechanisms due to a lack of genetically amenable Veillonella strains. In this study, we took advantage of a naturally transformable V. parvula isolate and newly adapted genetic tools to identify surface-exposed adhesins called autotransporters as the main molecular determinants of adhesion in this bacterium. This work therefore provides new insights on an important aspect of the V. parvula lifestyle, opening new possibilities for mechanistic studies of the contribution of biofilm formation to the biology of this major commensal of the oral-digestive tract.
Published: 2020

9. Roadmap for naming uncultivated Archaea and Bacteria

Author: William P. Inskeep, Iain C. Sutcliffe, Roland Hatzenpichler, Takuro Nunoura, William B. Whitman, Paul Carini, Alison E. Murray, Kristen M. DeAngelis, Carlos Pedrós-Alió, Daniel R. Colman, Stephanus N. Venter, Rudolf Amann, Karen G. Lloyd, David R. Emerson, Donovan H. Parks, Simonetta Gribaldo, Roman A. Barco, Jonathan A. Eisen, Duane P. Moser, Andrew D. Steen, Elena P. Ivanova, Damien Eveillard, Laura A. Hug, Konstantinos T. Konstantinidis, Hans-Peter Klenk, J. Cameron Thrash, Alexander J. Probst, Brett J. Baker, Anja Spang, Fengping Wang, Paulina Estrada-de los Santos, Peter R. Girguis, Ramon Rosselló-Móra, Anna-Louise Reysenbach, Maria Asuncion de los Rios, Jean Armengaud, R. Thane Papke, Emma Theodora Steenkamp, Theo H. M. Smits, Ute Hentschel, John V. Freudenstein, Frank E. Löffler, Victor Parro, Peter Kämpfer, Wen-Jun Li, Frank J. Stewart, Christopher A. Dunlap, Karthik Anantharaman, Thulani P. Makhalanyane, Christopher E. Lane, Helge B. Bode, Philip Hugenholtz, Eric S. Boyd, Carrie Brady, Marike Palmer, Matthew B. Stott, Michael Wagner, Thisjs J. G. Ettema, James M. Tiedje, Brian P. Hedlund, Patrick S. G. Chain, Pablo Yarza, James T. Hollibaugh, Silvia G. Acinas, Peter Vandamme, Desert Research Institute (DRI), Ecology and Organismal Biology, Ohio State University [Columbus] (OSU), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Montana State University (MSU), University of Queensland [Brisbane], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Botanical and Environmental Consultant, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire Environnement Profond (LEP), Etudes des Ecosystèmes Profonds (EEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Texas at Austin [Austin], Buchmann Institute for Molecular Life Sciences [Frankfurt am Main] (BMLS), Goethe-Universität Frankfurt am Main, Istituto delle Scienze dell' Atmosfera e dell'Oceano [Bologna] (ISAO), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Bigelow Laboratory for Ocean Sciences, Uppsala University, Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Department of Theoretical Mechanics, St. Petersburg State Polytechnical University, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Sun Yat-Sen University [Guangzhou] (SYSU), Physikalisch-Technische Bundesanstalt [Braunschweig] (PTB), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Earth and Planetary Science [UC Berkeley] (EPS), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), The Center for Microbial Ecology, Department of Microbiology and Molecular Genetics, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Universiteit Gent = Ghent University (UGENT), SANOFI (Research and Development), Research and Development, Support for this effort was provided by the National Science Foundation (grant no. DEB-1841658), We extend deep appreciation to all who attended the Microbial Taxonomy 2018 seminars, the Microbial Systematics for the Next Decade workshop held in Hood River, Oregon, USA, in October 2018, and those that participated in subsequent discussions and provided comments to mature the concept communicated here., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Justus-Liebig-Universität Gießen (JLU), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Consiglio Nazionale delle Ricerche (CNR), Universidad Nacional Autónoma de México (UNAM), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), University of California [Berkeley], University of California-University of California, Universiteit Gent = Ghent University [Belgium] (UGENT), Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737, Murray, A. E. [0000-0001-5790-7584], Gribaldo, S. [0000-0002-7662-021X], Hatzenpichler, R. [0000-0002-5489-3444], Hugenholtz, P. [0000-0001-5386-7925], Lane, C. [0000-0003-2558-2767], Parks, D. H. [0000-0001-6662-9010], Stott, M. B. [0000-0002-2082-9460], Thrash, J. C. [0000-0003-0896-9986], Anantharaman, K. [0000-0002-9584-2491], Armegaud, J. [0000-0003-1589-445X], Bode, H. B. [0000-0001-6048-5909], De Angelis, K. M. [0000-0002-5585-4551], De los Santos, P. E. [0000-0003-2407-0284], Eisen, J. A. [0000-0002-0159-2197], Ettema, T. J. G. [0000-0002-6898-6377], Eveillard, D. [0000-0002-8162-7360], Hentschel, U. [0000-0003-0596-790X], Inskeep, W. P. [0000-0002-5203-817X], Klenk, H. P. [0000-0001-6758-8150], Palmer, M. [0000-0001-8395-8465], Probst, A. [0000-0002-9392-6544], Smits, T. H. M. [0000-0002-1237-235X], Steen, A. D. [0000-0003-4297-4332], Spang, A. [0000-0002-6518-8556], Wang, F. [0000-0002-3429-8410], Hedlund, B. [0000-0001-8530-0448], Reysenbach, A. L. [0000-0001-9130-7750], Amann, R. [0000-0002-0846-7372], National Science Foundation (NSF), National Science Foundation, DEB-1841658, National Science Foundation (US), and Agencia Estatal de Investigación (España)
Subjects: [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Applied Microbiology and Biotechnology, Genome, Microbiologie, Nomenclature, Phylogeny, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Environmental microbiology, Bacterial, C500, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Microbes, Medical Microbiology, Taxonomy (biology), Biologie, Sequence Analysis, Microbiology (medical), DNA, Bacterial, Immunology, Chemie, Computational biology, Biology, Microbiology, DNA sequencing, 03 medical and health sciences, Type (biology), Microbial ecology, Terminology as Topic, Genetics, Life Science, Author Correction, 030304 developmental biology, Taxonomy, WIMEK, Bacteria, 030306 microbiology, Consensus Statement, Biology and Life Sciences, NEED, Cell Biology, DNA, Sequence Analysis, DNA, 570: Biologie, Archaea, Mikrobiologi, Taxon, Prokaryotic Cells, Metagenomics, AD-HOC COMMITTEE, Metagenome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 8 pages, 2 figures, 1 table, 2 boxes, supplementary information https://doi.org/10.1038/s41564-020-0733-x.-- Author Correction: Roadmap for naming uncultivated Archaea and Bacteria: n the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online, The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity, Support for this effort was provided by the National Science Foundation (grant no. DEB-1841658). We extend deep appreciation to all who attended the Microbial Taxonomy 2018 seminars, the Microbial Systematics for the Next Decade workshop held in Hood River, Oregon, USA, in October 2018, and those that participated in subsequent, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2020

10. The host-associated archaeome

Author: Simonetta Gribaldo, Christine Moissl-Eichinger, Jean-François Brugère, Ruth A. Schmitz, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Christian-Albrechts University of Kiel, Medical University Graz, Funding given by the Austrian Science Fund (FWF) to C.M.-E. (Project IDs P 30796 and P 32697) is highly appreciated, as is the funding from the German Science Foundation (DFG) given to R.A.S. (SCHM1052/11-1/2). The French National Agency for Research is gratefully acknowledged for funding to G.B. and S.G. (Grants ArchEvol ANR-16-CE02-0005-01 and Methevol ANR-19-CE02-0005-01), and we acknowledge a grant to J.-F.B. from Hub Innovergne (‘Investissements d’Avenir’ 16-IDEX-0001 CAP 20–25)., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), ANR-19-CE02-0005,METHEVOL,Caractérisation de nouveaux acteurs et des transitions évolutives dans le métabolisme du méthane, un métabolisme clef dans l'évolution du domaine Archaea(2019), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Thaumarchaeota, Disease, Microbiology, 03 medical and health sciences, Phylogenetics, Animals, Humans, Microbiome, Phylogeny, 0303 health sciences, General Immunology and Microbiology, biology, 030306 microbiology, Host (biology), Microbiota, Gastrointestinal Microbiome, 15. Life on land, Plants, biology.organism_classification, Archaea, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolutionary biology, Euryarchaeota
Abstract: Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host–archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease. The archaeal community, the archaeome, is now increasingly recognized as an important component of host-associated microbiomes. In this Review, Moissl-Eichinger and colleagues discuss the diversity and potential roles of the archaea associated with protists, plants and animals, highlighting the potential roles of archaea in human health and disease.
Published: 2020

11. When bacteria meet mitochondria: The strange case of the tick symbiont Midichloria mitochondrii †

Author: Jan Riemer, Fabrizia Stavru, Aaron R. Jex, Davide Sassera, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Cologne, The Walter and Eliza Hall Institute of Medical Research (WEHI), University of Melbourne, University of Pavia, Human Frontier Science Program for funding (Grant RGY0075/2017). A.J. also acknowledges funding the Australian National Health and Medical Research Council (APP1126345) and infrastructure support funding through the Victorian state government. D.S. acknowledges the Italian Ministry of Education, University and Research (MIUR): Dipartimenti di Eccellenza Programme (2018–2022)—Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia. F.S. acknowledges the support of Institut Pasteur., Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Università degli Studi di Pavia = University of Pavia (UNIPV)
Subjects: Midichloria mitochondrii, Mitochondrial intermembrane space, Immunology, Ixodes ricinus, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Mitochondrion, Microbiology, 03 medical and health sciences, Virology, Organelle, Animals, Phylogeny, Tropism, Alphaproteobacteria, 030304 developmental biology, 0303 health sciences, Innate immune system, Ixodes, biology, 030306 microbiology, Host (biology), intracellular bacteria, Intracellular parasite, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, symbiosis, Cell biology, mitochondria, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Viral Tropism, Bacteria, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Mitochondria are key eukaryotic organelles that perform several essential functions. Not surprisingly, many intracellular bacteria directly or indirectly target mitochondria, interfering with innate immunity, energy production or apoptosis, to make the host cell a more hospitable niche for bacterial replication. The alphaproteobacterium Midichloria mitochondrii has taken mitochondrial targeting to another level by physically colonising mitochondria, as shown by transmission electron micrographs of bacteria residing in the mitochondrial intermembrane space. This unique localization provokes a number of questions around the mechanisms allowing, and reasons driving intramitochondrial tropism. We suggest possible scenarios that could lead to this peculiar localization and hypothesize potential costs and benefits of mitochondrial colonisation for the bacterium and its host.
Published: 2020

12. Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem

Author: Céline Leroy, Guillaume Borrel, Mélanie Gerphagnon, Jean-François Carrias, Héctor Rodríguez-Pérez, Camille Loiseau, Isabelle Mary, Bruno Corbara, Régis Céréghino, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris], Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was supported by the Agence Nationale de la Recherche throughout the Rainwebs project (grant number ANR-12-BSV7- 0022–01) and an ‘Investissement d'Avenir’ (Labex CEBA, grant number ANR- 10-LABX-25–01)., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-12-BSV7-0022,RAINWEBS,Que se passera-t-il si les forêts tropicales s'assèchent ? Changement climatique et réseaux trophiques le long d'un gradient latitudinal(2012), Institut Pasteur [Paris] (IP), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)
Subjects: 0106 biological sciences, Niche, Ecological succession, ecological succession, Biology, Environment, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Ecosystem, Community ecology, Primary succession, 030304 developmental biology, Amplicon sequencing, 0303 health sciences, Decomposition, decomposition, Ecology, Community, Bacteria, amplicon sequencing, Community structure, bacterial diversity, 15. Life on land, Plant litter, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Plant Leaves, Bacterial diversity, 16S rRNA gene, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microcosm, community ecology
Abstract: Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.
Published: 2020

13. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide

Author: Najwa Taib, Jerzy Witwinowski, Simonetta Gribaldo, Christophe Beloin, Daniela Megrian, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Collège Doctoral, Sorbonne Université (SU), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Génétique des Biofilms, Funding from the French National Research Agency (ANR), project Fir-OM (ANR-16-CE12-0010) and from the Institut Pasteur Programmes Transversaux de Recherche (PTR 39-16). D.M. was supported by the Pasteur-Paris University (PPU) International PhD Program., ANR-16-CE12-0010,Fir-OM,Firmicutes avec une membrane externe: vers des nouveaux modeles d'étude de la transition monodermes/didermes(2016), Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Sorbonne Universités
Subjects: Lipopolysaccharides, Firmicutes, Gram-Positive Bacteria, Microbiology, Bacterial cell structure, Evolution, Molecular, 03 medical and health sciences, Cell Wall, Gram-Negative Bacteria, Molecular Biology, Phylogeny, 030304 developmental biology, 0303 health sciences, Negativicutes, Bacteria, biology, 030306 microbiology, Phylum, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Cell Membrane, Human microbiome, biology.organism_classification, Biological Evolution, Phenotype, Evolutionary biology, Cell envelope, Bacterial outer membrane
Abstract: How, when and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.
Published: 2020

14. Evolutionary relationships between Archaea and eukaryotes

Author: Simonetta Gribaldo, Céline Brochier-Armanet, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]
Subjects: 0303 health sciences, Ecology, 030306 microbiology, Evolution, Tree of life (biology), [SDV]Life Sciences [q-bio], Biology, biology.organism_classification, Microbiology, 03 medical and health sciences, Data sequences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Evolutionary biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Archaea
Abstract: International audience; A phylogenomic re-analysis of sequence data strongly supports the emergence of eukaryotes from within the archaeal radiation and underlines the importance of using the most accurate approaches to reconstruct ancient divergences in the tree of life.
Published: 2020

15. A dynamic, ring-forming MucB / RseB-like protein influences spore shape in Bacillus subtilis

Author: Kearns, Daniel B., Luhur, Johana, Chan, Helena, Kachappilly, Benson, Mohamed, Ahmed, Morlot, Cécile, Awad, Milena, Lyras, Dena, Taib, Najwa, Gribaldo, Simonetta, Rudner, David Z., Rodrigues, Christopher D.A., University of Technology Sydney (UTS), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Department of Microbiology [Monash University, Australia], School of Biomedical Sciences [Monash University, Clayton], Monash University [Clayton]-Monash University [Clayton], Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Harvard Medical School [Boston] (HMS), This work was funded by grant DP190100793 awarded to C.D.A.R from the Australian Research Council (https://www.arc.gov.au), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cancer Research, Mutant, Cell Membranes, Bacillus subtilis, QH426-470, Endospore, MESH: Spores, Bacterial, Cell Wall, Microbial Physiology, Fluorescence microscope, Bacterial Physiology, Cell Cycle and Cell Division, MESH: Bacterial Proteins, Genetics (clinical), Spores, Bacterial, Staining, 0303 health sciences, Bacterial Sporulation, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Cell biology, Membrane Staining, Aspect Ratio, Cell Processes, Physical Sciences, MESH: Protein Domains, Cell envelope, Cellular Structures and Organelles, Research Article, MESH: Mutation, Imaging Techniques, Protein domain, Geometry, Biology, Research and Analysis Methods, Microbiology, 03 medical and health sciences, MESH: Cell Wall, Bacterial Proteins, Protein Domains, Fluorescence Imaging, Genetics, Compartment (development), Bacterial Spores, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 030306 microbiology, QH, fungi, Biology and Life Sciences, Membrane Proteins, Bacteriology, Cell Biology, MESH: Bacillus subtilis, biology.organism_classification, Outer Membrane Proteins, QP, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, QR, Spore, Specimen Preparation and Treatment, Mutation, Mathematics
Abstract: How organisms develop into specific shapes is a central question in biology. The maintenance of bacterial shape is connected to the assembly and remodelling of the cell envelope. In endospore-forming bacteria, the pre-spore compartment (the forespore) undergoes morphological changes that result in a spore of defined shape, with a complex, multi-layered cell envelope. However, the mechanisms that govern spore shape remain poorly understood. Here, using a combination of fluorescence microscopy, quantitative image analysis, molecular genetics and transmission electron microscopy, we show that SsdC (formerly YdcC), a poorly-characterized new member of the MucB / RseB family of proteins that bind lipopolysaccharide in diderm bacteria, influences spore shape in the monoderm Bacillus subtilis. Sporulating cells lacking SsdC fail to adopt the typical oblong shape of wild-type forespores and are instead rounder. 2D and 3D-fluorescence microscopy suggest that SsdC forms a discontinuous, dynamic ring-like structure in the peripheral membrane of the mother cell, near the mother cell proximal pole of the forespore. A synthetic sporulation screen identified genetic relationships between ssdC and genes involved in the assembly of the spore coat. Phenotypic characterization of these mutants revealed that spore shape, and SsdC localization, depend on the coat basement layer proteins SpoVM and SpoIVA, the encasement protein SpoVID and the inner coat protein SafA. Importantly, we found that the ΔssdC mutant produces spores with an abnormal-looking cortex, and abolishing cortex synthesis in the mutant largely suppresses its shape defects. Thus, SsdC appears to play a role in the proper assembly of the spore cortex, through connections to the spore coat. Collectively, our data suggest functional diversification of the MucB / RseB protein domain between diderm and monoderm bacteria and identify SsdC as an important factor in spore shape development., Author summary Cell shape is an important cellular attribute linked to cellular function and environmental adaptation. Bacterial endospores are one of the toughest cell types on Earth, with a defined shape and complex, highly-resistant, multi-layered cell envelope. Although decades of research have focused on defining the composition and assembly of the multi-layered spore envelope, little is known about how these layers contribute to spore shape. Here, we identify SsdC, a poorly-characterized new member of the MucB / RseB family of proteins that bind lipopolysaccharide in diderm bacteria. We show that SsdC is an important factor in spore shape development in the monoderm, model organism Bacillus subtilis. Our data suggest that SsdC influences the assembly of the spore cortex, through connections to the spore coat, by forming an intriguing, dynamic ring-like structure adjacent to the developing spore. Furthermore, our identification of SsdC suggests evolutionary diversification of the MucB /RseB protein domain between diderm and monoderm bacteria.
Published: 2020

16. The rise of diversity in metabolic platforms across the Candidate Phyla Radiation

Author: Simonetta Gribaldo, Jillian F. Banfield, Alexander L. Jaffe, Paula B. Matheus Carnevali, Cindy J. Castelle, University of California [Berkeley] (UC Berkeley), University of California (UC), Chan Zuckerberg BioHub [San Francisco, CA], Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Funding was provided by the Chateaubriand Fellowship to A.L.J. and the France Berkeley Fund to J.F.B. and S.G., University of California [Berkeley], University of California, and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Candidate Phyla Radiation, Physiology, health care facilities, manpower, and services, Gene Transfer, Bacterial carbon metabolism, Plant Science, Genome, Structural Biology, Phylogenomics, Clade, lcsh:QH301-705.5, Phylogeny, health care economics and organizations, 0303 health sciences, Phylogenetic tree, Bacterial, Biological Sciences, Lateral gene transfer, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Horizontal gene transfer, General Agricultural and Biological Sciences, Research Article, Biotechnology, Gene Transfer, Horizontal, Evolution, education, Context (language use), Biology, General Biochemistry, Genetics and Molecular Biology, Horizontal, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, health services administration, Genetics, cardiovascular diseases, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Metabolic evolution, Bacteria, 030306 microbiology, Phylum, Molecular, Cell Biology, 15. Life on land, lcsh:Biology (General), Genes, Genes, Bacterial, Evolutionary biology, NiFe hydrogenase, Genome, Bacterial, Developmental Biology
Abstract: Background A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved. Results Here, we selected ~ 1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution, we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer. Conclusions We infer that patterns of gene gain and loss in CPR, including acquisition of accessory traits in independent transfer events, could have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories.
Published: 2019

17. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling

Author: Alessandro Pagliuso, Bruno Dupuy, Christophe Bécavin, Mikael Koutero, Alice Lebreton, Frédéric Tangy, Andréa Dessen, Marie-Anne Nahori, Valérie Najburg, Fabrizia Stavru, Eric Allemand, To Nam Tham, Pascale Cossart, Anastassia V. Komarova, Christian Muchardt, Stevens Robertin, Sergey Bessonov, Quentin Bertrand, Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Régulation épigénétique - Epigenetic regulation, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Génomique virale et vaccination, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Brazilian National Laboratory for Biosciences (LNBio), Centro Nacional de Pesquisa em Energia e materiais, Centra Nacional de Pesquisa-Centra Nacional de Pesquisa, Institut National de la Recherche Agronomique (INRA), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Platform access was supported by FRISBI (ANR-10-INBS-05-02) and GRAL, a project of the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). The IBS acknowledges integration into the Interdisciplinary Research Institute of Grenoble (IRIG, CEA). We are grateful to R.Y. Sanchez David and R. Viber for technical support. Work in A.L.’s team was supported by Inserm ATIP-Avenir and Mairie de Paris (Programme Émergences—Recherche médicale). This work was supported by grants from the European Research Council (ERC) advanced grant BacCellEpi (670823) and the Fondation Le Roch to P.C., We thank all members of the Cossart laboratory for helpful discussions. We thank Dr. B. Kallipolitis for providing the anti-Listeria Hfq antibody and Dr. E. Hajnsdorf for the anti-E.coli Hfq. We acknowledge the platforms of the Grenoble Instruct-ERIC Center (ISBG, UMS 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB)., ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), European Project: 670823,H2020,ERC-2014-ADG,BacCellEpi(2015), Stavru, Fabrizia, Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, Bacterial, cellular and epigenetic factors that control enteropathogenicity - BacCellEpi - - H20202015-10-01 - 2018-09-30 - 670823 - VALID, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-10-INBS-05-01/10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR: 17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris, Laboratoire d’innovation : vaccins – Innovation lab : vaccines, Institut Pasteur [Paris], Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Génétique des Interactions Macromoléculaires, and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: [SDV]Life Sciences [q-bio], Virulence, RNA-binding protein, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, medicine.disease_cause, Microbiology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Mice, 03 medical and health sciences, 0302 clinical medicine, Bacterial Proteins, Listeria monocytogenes, Virology, Extracellular, medicine, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Animals, Humans, Pathogen, [SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity, 030304 developmental biology, 0303 health sciences, Innate immune system, Host Microbial Interactions, RIG-I, RNA-Binding Proteins, food and beverages, Interferon-beta, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Immunity, Innate, extracellular RNA, 3. Good health, Cell biology, RNA, Bacterial, HEK293 Cells, DEAD Box Protein 58, Parasitology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030217 neurology & neurosurgery, bacteriophage A118, type I IFN, Signal Transduction, Extracellular RNA
Abstract: International audience; RNA-binding proteins (RBPs) perform key cellular activities by controlling the function of bound RNAs. The widely held assumption that RBPs are strictly intracellular has been challenged by the discovery of secreted RBPs. However, extracellular RBPs have been described in eukaryotes, while secreted bacterial RBPs have not been reported. Here, we show that the bacterial pathogen Listeria monocytogenes secretes a small RBP that we named Zea. We show that Zea binds a subset of L. monocytogenes RNAs, causing their accumulation in the extracellular medium. Furthermore, during L. monocytogenes infection, Zea binds RIG-I, the non-self-RNA innate immunity sensor, potentiating interferon-β production. Mouse infection studies reveal that Zea affects L. monocytogenes virulence. Together, our results unveil that bacterial RNAs can be present extracellularly in association with RBPs, acting as “social RNAs” to trigger a host response during infection.
Published: 2019

18. The SUF system: an ABC ATPase-dependent protein complex with a role in Fe–S cluster biogenesis

Author: Simonetta Gribaldo, Frédéric Barras, Béatrice Py, Pierre Simon Garcia, Adaptation au stress et métabolisme chez les entérobactéries - Stress adaptation and metabolism in enterobacteria, Institut Pasteur [Paris], Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Laboratoire de chimie bactérienne (LCB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), This work was supported by Institut Pasteur, CNRS, Aix-Marseille University, and by grants from Agence Nationale de la Recherche Investissement d’Avenir Programme (10-LABX-62-IBEID) and ERACoBioTech « Iron Plug'n Play »., Institut Pasteur [Paris] (IP), and ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010)
Subjects: Iron-Sulfur Proteins, Iron, ATPase, [SDV]Life Sciences [q-bio], Iron–sulfur cluster, P-loop ATPase, Microbiology, Cofactor, 03 medical and health sciences, chemistry.chemical_compound, Suf proteins, SufBCD complex, Escherichia coli, Cluster (physics), Molecular Biology, 030304 developmental biology, Adenosine Triphosphatases, 0303 health sciences, biology, 030306 microbiology, Escherichia coli Proteins, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Iron-sulfur biogenesis, General Medicine, Proton-Translocating ATPases, chemistry, biology.protein, Biophysics, ATP-Binding Cassette Transporters, Carrier Proteins, Iron-sulfur cluster, Sulfur, Biogenesis
Abstract: International audience; Iron-sulfur (Fe–S) clusters are considered one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe–S clusters can act as redox sensors or catalysts and are found to be used by a large number of functional and structurally diverse proteins. Here, we cover current knowledge of the SUF multiprotein machinery that synthesizes and inserts Fe–S clusters into proteins. Specific focus is put on the ABC ATPase SufC, which contributes to building Fe–S clusters, and appeared early on during evolution.
Published: 2019

19. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Author: Panagiotis S. Adam, Guillaume Borrel, Wen-Jun Li, Steven J. Hallam, William P. Inskeep, Luke J. McKay, Gary L. Andersen, Simonetta Gribaldo, Quentin Letourneur, Amine Ghozlane, Isabel N. Sierra-Garcia, Gerard Muyzer, Valéria Maia de Oliveira, Lin-Xing Chen, Jillian F. Banfield, Christian M. K. Sieber, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), Montana State University (MSU), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University [Guangzhou] (SYSU), University of British Columbia (UBC), University of Amsterdam [Amsterdam] (UvA), G.B. acknowledges support from the Institut Pasteur through a Roux-Cantarini fellowship. P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme ‘Frontières du Vivant (FdV)-Programme Bettencourt’. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (No. ANR-16-CE02-0005-01). This work used the computational and storage services (TARS cluster) provided by the IT department at Institut Pasteur, Paris. S.J.H. acknowledges support from the US Department of Energy (DOE) JGI supported by the Office of Science of US DOE Contract No. DE-AC02–05CH11231, the Natural Sciences and Engineering Research Council (NSERC) of Canada, Genome British Columbia, Genome Canada, Canada Foundation for Innovation (CFI) and the Tula Foundation. I.N.S.-G. and V.M.d.O. are grateful to São Paulo Research Foundation—FAPESP (process Nos. 2011/14501-6 and 2013/20436-8) and Petrobras for financial support and to N. Gray and I. Head from the School of Civil Engineering and Geosciences at Newcastle University for lab facilities. W-J.L. was supported by Key Projects of Ministry of Science and Technology (MOST) (Nos. 2013DFA31980 and 2015FY110100). G.M. was supported by the ERC Advanced Grant PARASOL (No. 322551). L.J.M. appreciates funding from the NASA Postdoctoral Programme through the NASA Astrobiology Institute and W.P.I. was supported by the Montana Agricultural Experiment Station (Project No. 911300)., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), European Project: 322551,EC:FP7:ERC,ERC-2012-ADG_20120314,PARASOL(2013), Institut Pasteur [Paris], University of Campinas [Campinas] (UNICAMP), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sun Yat-Sen University (SYSU), and Freshwater and Marine Ecology (IBED, FNWI)
Subjects: Microbiology (medical), Methanogenesis, Immunology, Biodiversity, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Applied Microbiology and Biotechnology, Microbiology, Genome, Article, 03 medical and health sciences, Phylogenetics, Alkanes, Genetics, Gene, Phylogeny, 030304 developmental biology, 0303 health sciences, 030306 microbiology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], DNA, Cell Biology, biology.organism_classification, Archaea, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Archaeal, Medical Microbiology, 13. Climate action, Metagenomics, Evolutionary biology, Candidatus, Metagenome, Methane, Oxidation-Reduction
Abstract: International audience; Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth's climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea. Five of these MAGs represent under-sampled (Verstraetearchaeota, Methanonatronarchaeia, ANME-1 and GoM-Arc1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation substantially expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea ('Candidatus Methanoliparia'). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.
Published: 2019

20. Evolutionary placement of Methanonatronarchaeia

Author: Céline Brochier-Armanet, Simonetta Gribaldo, Monique Aouad, Guillaume Borrel, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris], Institut Pasteur [Paris] (IP), and ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016)
Subjects: 0106 biological sciences, Microbiology (medical), 0303 health sciences, Chemoautotrophic Growth, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Immunology, MEDLINE, Cell Biology, Biological evolution, Computational biology, Biology, Euryarchaeota, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Applied Microbiology and Biotechnology, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biological Evolution, 03 medical and health sciences, Genetics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2019

21. Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion

Author: John F. Atkins, Paul W. O'Toole, Jean-François Brugère, Guillaume Borrel, Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University College Cork (UCC), University of Utah, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, archaea, Lineage (evolution), Pyrrolysine, Computational biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, chemistry.chemical_compound, Human gut, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], methanogens, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], chemistry.chemical_classification, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 030102 biochemistry & molecular biology, biology, pyrrolysine Pyl, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, Genetic code, methylamines, Methanomassiliicoccales, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Amino acid, genetic code, 030104 developmental biology, chemistry, Methanosarcinales, Anaerobic bacteria, General Agricultural and Biological Sciences, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Archaea, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The 22nd amino acid discovered to be directly encoded, pyrrolysine, is specified by UAG. Until recently, pyrrolysine was only known to be present in archaea from a methanogenic lineage (Methanosarcinales), where it is important in enzymes catalysing anoxic methyla-mines metabolism, and a few anaerobic bacteria. Relatively new discoveries have revealed wider presence in archaea, deepened functional understanding, shown remarkable carbon source-dependent expression of expanded decoding and extended exploitation of the pyrrolysine machinery for synthetic code expansion. At the same time, other studies have shown the presence of pyrrolysine-containing archaea in the human gut and this has prompted health considerations. The article reviews our knowledge of this fascinating exception to the 'standard' genetic code.
Published: 2018

22. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

Author: Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, Enzyme complex, MESH: Genome, Archaeal, LUCA, [SDV]Life Sciences [q-bio], MESH: Genome, Bacterial, Genome, Corrections, chemistry.chemical_compound, Genome, Archaeal, MESH: Multienzyme Complexes/genetics, methanogens, Phylogeny, MESH: Phylogeny, Genetics, Carbon Monoxide, Multidisciplinary, Last universal ancestor, Carbon fixation, Acetyl-CoA, MESH: Carbon Cycle, Aldehyde Oxidoreductases, Biological Evolution, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, PNAS Plus, MESH: Bacteria/enzymology, Wood–Ljungdahl pathway, Wood-Ljungdahl pathway, MESH: Aldehyde Oxidoreductases/metabolism, Carbon monoxide dehydrogenase, 030106 microbiology, MESH: Bacteria/genetics, Acetate-CoA Ligase, Bacterial genome size, Biology, MESH: Biological Evolution, MESH: Aldehyde Oxidoreductases/genetics, Carbon Cycle, 03 medical and health sciences, MESH: Carbon Monoxide/metabolism, Multienzyme Complexes, MESH: Archaea/genetics, evolution, MESH: Acetate-CoA Ligase/metabolism, MESH: Multienzyme Complexes/metabolism, MESH: Archaea/enzymology, Bacteria, MESH: Acetate-CoA Ligase/genetics, Archaea, acetogens, 030104 developmental biology, chemistry, biology.protein, Genome, Bacterial
Abstract: Erratum in : Correction for Adam et al., Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. [Proc Natl Acad Sci U S A. 2018]; International audience; Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ ACS) is a five-subunit enzyme complex responsible for the carbonyl branch of the Wood-Ljungdahl (WL) pathway, considered one of the most ancient metabolisms for anaerobic carbon fixation, but its origin and evolutionary history have been unclear. While traditionally associated with methanogens and acetogens, the presence of CODH/ACS homologs has been reported in a large number of un-cultured anaerobic lineages. Here, we have carried out an exhaustive phylogenomic study of CODH/ACS in over 6,400 archaeal and bacterial genomes. The identification of complete and likely functional CODH/ACS complexes in these genomes significantly expands its distribution in microbial lineages. The CODH/ACS complex displays astounding conservation and vertical inheritance over geological times. Rare intradomain and interdomain transfer events might tie into important functional transitions, including the acquisition of CODH/ACS in some archaeal methanogens not known to fix carbon, the tinkering of the complex in a clade of model bacterial acetogens, or emergence of archaeal-bacterial hybrid complexes. Once these transfers were clearly identified, our results allowed us to infer the presence of a CODH/ACS complex with at least four subunits in the last universal common ancestor (LUCA). Different scenarios on the possible role of ancestral CODH/ACS are discussed. Despite common assumptions, all are equally compatible with an autotrophic, mixotrophic, or heterotrophic LUCA. Functional characterization of CODH/ACS from a larger spectrum of bacterial and archaeal lineages and detailed evolutionary analysis of the WL methyl branch will help resolve this issue.
Published: 2018

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22 results on '"Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell"'

1. A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

2. Mitochondrial respiration restricts Listeria monocytogenes infection by slowing down host cell receptor recycling

3. A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes

4. Resolving phylogenetic and biochemical barriers to functional expression of heterologous iron-sulphur cluster enzymes

5. New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

6. Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition

7. A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes

8. Autotransporters Drive Biofilm Formation and Autoaggregation in the Diderm Firmicute Veillonella parvula

9. Roadmap for naming uncultivated Archaea and Bacteria

10. The host-associated archaeome

11. When bacteria meet mitochondria: The strange case of the tick symbiont Midichloria mitochondrii †

12. Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem

13. One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide

14. Evolutionary relationships between Archaea and eukaryotes

15. A dynamic, ring-forming MucB / RseB-like protein influences spore shape in Bacillus subtilis

16. The rise of diversity in metabolic platforms across the Candidate Phyla Radiation

17. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling

18. The SUF system: an ABC ATPase-dependent protein complex with a role in Fe–S cluster biogenesis

19. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

20. Evolutionary placement of Methanonatronarchaeia

21. Pyrrolysine in archaea: a 22nd amino acid encoded through a genetic code expansion

22. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes

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22 results on '"Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell"'

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