Céline Brochier-Armanet

French National Centre for Scientific Research, Lutetia Parisorum, Île-de-France, France

Are you Céline Brochier-Armanet?

Claim your profile

Publications (68)390.9 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: During the first meiotic prophase, chromosome synapsis is mediated by the synaptonemal complex (SC), an evolutionarily conserved meiosis-specific structure. In mammals, 7 SC protein components have been identified so far. Despite some controversy in the past, we have shown that SC proteins are ancient in metazoans and very likely formed an ancestral SC structure in the ancestor of metazoans. Protein components SYCP1, SYCP3, SYCE2, and TEX12 were identified in basal-branching metazoans, while other components (SYCE1 and SYCE3) are more recent elements. However, the evolutionary history of mammalian SYCP2 is not known. Here, we investigated this aspect with the aid of bioinformatic tools as well as with RNA and protein expression analysis. We conclude that SYCP2 belongs to the group of ancient SC proteins that was already present in the common ancestor of metazoans more than 500 million years ago. © 2015 S. Karger AG, Basel.
    Cytogenetic and Genome Research 03/2015; DOI:10.1159/000381080 · 1.91 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Pseudomonas xanthomarina S11 is an arsenite-oxidizing bacterium isolated from an arsenic-contaminated former gold mine in Salsigne, France. This bacterium showed high resistance to arsenite and was able to oxidize arsenite to arsenate at concentrations up to 42.72 mM As[III]. The genome of this strain was sequenced and revealed the presence of three ars clusters. One of them is located on a plasmid and is organized as an "arsenic island" harboring an aio operon and genes involved in phosphorous metabolism, in addition to the ars genes. Neither the aioXRS genes nor a specific sigma-54-dependent promoter located upstream of aioBA genes, both involved in regulation of arsenite oxidase expression in other arsenite-oxidizing bacteria, could be identified in the genome. This observation is in accordance with the fact that no difference was observed in expression of arsenite oxidase in Pseudomonas xanthomarina S11, whether or not the strain was grown in the presence of As[III]. Copyright © 2015. Published by Elsevier Masson SAS.
    Research in Microbiology 03/2015; 166(3). DOI:10.1016/j.resmic.2015.02.010 · 2.83 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Initial studies of the archaeal phylogeny relied mainly on the analysis of the RNA component of the small subunit of the ribosome (SSU rRNA). The resulting phylogenies have provided interesting but partial information on the evolutionary history of the third domain of life because SSU rRNA sequences do not contain enough phylogenetic signal to resolve all nodes of the archaeal tree. Thus, many relationships, and especially the most ancient ones, remained elusive. Moreover, SSU rRNA phylogenies can be heavily biased by tree reconstruction artifacts. The sequencing of complete genomes allows using a variety of protein markers as an alternative to SSU rRNA. Taking advantage of the recent burst of archaeal complete genome sequences, we have carried out an in-depth phylogenomic analysis of this domain. We have identified 200 new protein families that, in addition to the ribosomal proteins and the subunits of the RNA polymerase, form a conserved phylogenetic core of archaeal genes. The accurate analysis of these markers combined with desaturation approaches shed new light on the evolutionary history of Archaea and reveals that several relationships recovered in recent analyses are likely the consequence of tree reconstruction artifacts. Among others, we resolve a number of important relationships, such as those among methanogens Class I, and we propose the definition of two new super-classes within the Euryarchaeota: 'Methanomada' and 'Diaforarchaea'. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
    Molecular Biology and Evolution 02/2015; 32(5). DOI:10.1093/molbev/msv015 · 14.31 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In human pathogenic bacteria, nickel is required for the activation of two enzymes, urease and [NiFe]-hydrogenase, necessary for host infection. Acquisition of Ni(II) is mediated by either permeases or ABC-importers, the latter including a subclass that involves an extracytoplasmic nickel-binding protein, Ni-BP. This study reports on the structure of three Ni-BPs from a diversity of human pathogens and on the existence of three new nickel-binding motifs. These are different from that previously described for Escherichia coli Ni-BP NikA, known to bind nickel via a nickelophore, and indicate a variegated ligand selectivity for Ni-BPs. The structures are consistent with ligand affinities measured in solution by calorimetry and challenge the hypothesis of a general requirement of nickelophores for nickel uptake by canonical ABC importers. Phylogenetic analyses showed that Ni-BPs have different evolutionary origins and emerged independently from peptide-binding proteins, possibly explaining the promiscuous behavior of this class of Ni(II) carriers.
    Structure 09/2014; 22(10). DOI:10.1016/j.str.2014.07.012 · 6.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The seminal work of Carl Woese and co-workers has contributed to promote the RNA component of the small subunit of the ribosome (SSU rRNA) as a "gold standard" of modern prokaryotic taxonomy and systematics, and an essential tool to explore microbial diversity. Yet, this marker has a limited resolving power, especially at deep phylogenetic depth and can lead to strongly biased trees. The ever-larger number of available complete genomes now calls for a novel standard dataset of robust protein markers that may complement SSU rRNA. In this respect, concatenation of ribosomal proteins (r-proteins) is being growingly used to reconstruct large-scale prokaryotic phylogenies, but their suitability for systematic and/or taxonomic purposes has not been specifically addressed. Using Proteobacteria as a case study, we show that amino acid and nucleic acid r-protein sequences contain a reliable phylogenetic signal at a wide range of taxonomic depths, which has not been totally blurred by mutational saturation or horizontal gene transfer. The use of accurate evolutionary models and reconstruction methods allows overcoming most tree reconstruction artefacts resulting from compositional biases and/or fast evolutionary rates. The inferred phylogenies allow clarifying the relationships among most proteobacterial orders and families, along with the position of several unclassified lineages, suggesting some possible revisions of the current classification. In addition, we investigate the root of the Proteobacteria by considering the time-variation of nucleic acid composition of r-protein sequences and the information carried by horizontal gene transfers, two approaches that do not require the use of an outgroup and limit tree reconstruction artefacts. Altogether, our analyses indicate that r-proteins may represent a promising standard for prokaryotic taxonomy and systematics.
    Molecular Phylogenetics and Evolution 06/2014; 75. DOI:10.1016/j.ympev.2014.02.013 · 4.02 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The thermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain VC-16 (DSM 4304), which is known to oxidize fatty acids and n-alkenes, was shown to oxidize saturated hydrocarbons (n-alkanes in the range C10-C21) with thiosulfate or sulfate as a terminal electron acceptor. The amount of n-hexadecane degradation observed was in stoichiometric agreement with the theoretically expected amount of thiosulfate reduction. One of the pathways used by anaerobic microorganisms to activate alkanes is addition to fumarate that involves alkylsuccinate synthase as a key enzyme. A search for genes encoding homologous enzymes in A. fulgidus identified the pflD gene (locus-tag AF1449) that was previously annotated as a pyruvate formate lyase. A phylogenetic analysis revealed that this gene is of bacterial origin and was likely acquired by A. fulgidus from a bacterial donor through a horizontal gene transfer. Based on three-dimensional modeling of the corresponding protein and molecular dynamic simulations, we hypothesize an alkylsuccinate synthase activity for this gene product. The pflD gene expression was upregulated during the growth of A. fulgidus on an n-alkane (C16) compared with growth on a fatty acid. Our results suggest that anaerobic alkane degradation in A. fulgidus may involve the gene pflD in alkane activation through addition to fumarate. These findings highlight the possible importance of hydrocarbon oxidation at high temperatures by A. fulgidus in hydrothermal vents and the deep biosphere.The ISME Journal advance online publication, 24 April 2014; doi:10.1038/ismej.2014.58.
    The ISME Journal 04/2014; 8(11). DOI:10.1038/ismej.2014.58 · 9.27 Impact Factor
  • Source
    Nicolas C Rochette, Céline Brochier-Armanet, Manolo Gouy
    [Show abstract] [Hide abstract]
    ABSTRACT: The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes covering the three domains of life makes it possible to contrast these predictions with empirical data. We performed a systematic analysis of the phylogenetic relationships of ancestral eukaryotic genes with archaeal and bacterial genes. In contrast with previous studies, we emphasize the critical importance of methods accounting for statistical support, horizontal gene transfer and gene loss, and we disentangle the processes underlying the phylogenomic pattern we observe. We first recover a clear signal indicating that a fraction of the bacteria-like eukaryotic genes are of alphaproteobacterial origin. Then, we show that the majority of bacteria-related eukaryotic genes actually do not point to a relationship with a specific bacterial taxonomic group. We also provide evidence that eukaryotes branch close to the last archaeal common ancestor. Our results demonstrate that there is no phylogenetic support for hypotheses involving a fusion with a bacterium other than the ancestor of mitochondria. Overall, they leave only two possible interpretations, based respectively on the early-mitochondria hypotheses, which suppose an early endosymbiosis of an alphaproteobacterium in an archaeal host, and on the slow-drip autogenous hypothesis, in which early eukaryotic ancestors were particularly prone to horizontal gene transfers.
    Molecular Biology and Evolution 01/2014; DOI:10.1093/molbev/mst272 · 14.31 Impact Factor
  • Source
    Kasie Raymann, Patrick Forterre, Céline Brochier-Armanet, Simonetta Gribaldo
    [Show abstract] [Hide abstract]
    ABSTRACT: The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential 'core' of replication components that were mainly vertically inherited, or to a variable and highly divergent 'shell' of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extra-chromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.
    Genome Biology and Evolution 01/2014; DOI:10.1093/gbe/evu004 · 4.53 Impact Factor
  • Source
  • [Show abstract] [Hide abstract]
    ABSTRACT: A moderately halophilic, Gram negative, non-sporulating bacterium designed as strain TYRC17T was isolated from olive-processing effluents. The organism is a straight rod, motile by peritrichous flagella, able to respire both oxygen and nitrate. Growth occurred with 0-25 % (w/v) NaCl (optimum, 7 %), at pH 5-11 (optimum, pH 7.0) and at 4-50 °C (optimally at 35 °C). It accumulates poly-β-hydroxyalkanoate granules and produces exopolysaccharides. The predominant fatty acids are C18:1w7c (42.2 %), C16:1w7c (15.6 %), C16:0 (14.2 %). Ubiquinone 9 (Q-9) is the only respiratory quinone. The DNA G+C content of TYRC17T is 53.9 mol%. Phylogenetic analyses of 16S rRNA gene sequences revealed that the strain falls within the genus Halomonas, and more precisely within the subgroup containing Halomonas sulfidaeris, H. titanicae, H. variabilis, H. zhanjiangensis, H. alkaliantarctica, H. boliviensis and H. neptunia. TYRC17T showed high 16S-rRNA sequence identities in particular with the three last species (99.4-99.5 %). However, a Multilocus Sequence Analysis (MLSA) using the 23S rRNA, gyrB, rpoD and secA genes allowed clarifying the phylogenetic position of TYRC17T. This, combined to the level of DNA-DNA hybridization between TYRC17T and its closest relatives ranging only from 21.6 % to 48.4 %, indicated that TYRC17T does not belong to any of these species. On the basis of phenotypic and genotypic characteristics, and also genomic and phylogenetic evidences, strain TYRC17T represents a novel species of the genus Halomonas. The name Halomonas olivaria sp. nov. is proposed with TYRC17T (= DSM 19074T = CCUG 53850BT) as the type strain.
    International Journal of Systematic and Evolutionary Microbiology 09/2013; DOI:10.1099/ijs.0.049007-0 · 2.80 Impact Factor
  • Johanna Fraune, Céline Brochier-Armanet, Manfred Alsheimer, Ricardo Benavente
    [Show abstract] [Hide abstract]
    ABSTRACT: During meiosis, the stable pairing of the homologous chromosomes is mediated by the assembly of the synaptonemal complex (SC). Its tripartite structure is well conserved in Metazoa and consists of two lateral elements (LEs) and a central region (CR) that in turn is formed by several transverse filaments (TFs) and a central element (CE). In a previous paper we have shown that not only the structure, but also the major structural proteins SYCP1 (TFs) and SYCP3 (LEs) of the mammalian SC are conserved in metazoan evolution. In continuation of this work, we now investigated the evolution of the mammalian CE-specific proteins using phylogenetic and biochemical/cytological approaches. In analogy to the observations made for SYCP1 and SYCP3, we did not detect homologues of the mammalian CE proteins in insects or nematodes, but in several other metazoan clades. We were able to identify homologues of three mammalian CE proteins in several vertebrate and invertebrate species, for two of these proteins down to the basal-branching phylum of Cnidaria. Our approaches indicate that the SC arose only once, but evolved dynamically during diversification of Metazoa. Certain proteins appear to be ancient in animals, but successive addition of further components as well as protein loss and/or replacements have also taken place in some lineages.
    Genetics 09/2013; DOI:10.1534/genetics.113.156679 · 4.87 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolise the compound. Here we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonising capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes which enable it to metabolise arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.
    Genome Biology and Evolution 04/2013; DOI:10.1093/gbe/evt061 · 4.53 Impact Factor
  • Source
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Based on phylogenetic analyses and gene distribution patterns of a few complete genomes, a new distinct phylum within the Archaea, the Thaumarchaeota, has recently been proposed. Here we present analyses of six archaeal fosmid sequences derived from a microbial hot spring community in Kamchatka. The phylogenetic analysis of informational components (ribosomal RNAs and proteins) reveals two major (hyper-)thermophilic clades ("Hot Thaumarchaeota-related Clade" 1 and 2, HTC1 and HTC2) related to Thaumarchaeota, representing either deep branches of this phylum or a new archaeal phylum and provides information regarding the ancient evolution of Archaea and their evolutionary links with Eukaryotes.
    Research in Microbiology 03/2013; DOI:10.1016/j.resmic.2013.02.006 · 2.83 Impact Factor
  • Source
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Strain VNs100T, a novel mesophilic anaerobic rod-cocoid-shaped bacterium, having a sheath-like outer structure (toga) was isolated from a water sample collected in the area of underground gas storage. It was non-motile with cells appearing singly (2-4 μm long x 1-2 μm wide), in pairs, or as long chains and stained Gram-negative. Strain VNs100T was heterotrophic, able to use arabinose, cellobiose, fructose, galactose, glucose, lactose, lactate, mannose, maltose, raffinose, ribose, sucrose and xylose as energy sources only in the presence of elemental sulfur as terminal electron acceptor. Acetate, CO2 and sulfide were the end-products of sugar metabolism. Hydrogen was not detected. Elemental sulfur, but not thiosulfate, sulfate and sulfite, were reduced into sulfide. It grew at temperatures between 30°C and 50°C (optimum 45°C), at pH between 6.2 and 7.9 (optimum 7.3-7.5) and at NaCl concentrations between 0 and 15 g.L-1 (optimum 2 g.L-1). The DNA G+C content was 47.5 mol%. The main cellular fatty acid was C16:0. Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain VNs100T had as its closest relatives 'Mesotoga sulfurireducens' (97.1 % similarity) and Mesotoga prima (similarity of 97.1 % and 97.7 % with each of its two genes respectively) within the order Thermotogales. Hybridization between strain VNS100T and 'Mesotoga sulfurireducens' and between strain VNS100T and Mesotoga prima is 12.9% and 20.6 %, respectively. Based on phenotypic, phylogenetic and taxonomic characteristics, strain VNs100T is proposed as a novel species of genus Mesotoga within the family Thermotogaceae, order Thermotogales. The name Mesotoga infera, sp. nov. is proposed. The type strain is VNs100T (= DSM 25546 = JCM 18154).
    International Journal of Systematic and Evolutionary Microbiology 02/2013; 63. DOI:10.1099/ijs.0.047993-0 · 2.80 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: BACKGROUND: In 2004, we discovered an atypical protein in metagenomic data from marine thaumarchaeotal species. This protein, referred as DnaJ-Fer, is composed of a J domain fused to a Ferredoxin (Fer) domain. Surprisingly, the same protein was also found in Viridiplantae (green algae and land plants). Because J domain-containing proteins are known to interact with the major chaperone DnaK/Hsp70, this suggested that a DnaK protein was present in Thaumarchaeota. DnaK/Hsp70, its co-chaperone DnaJ and the nucleotide exchange factor GrpE are involved, among others, in heat shocks and heavy metal cellular stress responses. RESULTS: Using phylogenomic approaches we have investigated the evolutionary history of the DnaJ-Fer protein and of interacting proteins DnaK, DnaJ and GrpE in Thaumarchaeota. These proteins have very complex histories, involving several inter-domain horizontal gene transfers (HGTs) to explain the contemporary distribution of these proteins in archaea. These transfers include one from Cyanobacteria to Viridiplantae and one from Viridiplantae to Thaumarchaeota for the DnaJ-Fer protein, as well as independent HGTs from Bacteria to mesophilic archaea for the DnaK/DnaJ/GrpE system, followed by HGTs among mesophilic and thermophilic archaea. CONCLUSIONS: We highlight the chimerical origin of the set of proteins DnaK, DnaJ, GrpE and DnaJ-Fer in Thaumarchaeota and suggest that the HGT of these proteins has played an important role in the adaptation of several archaeal groups to mesophilic and thermophilic environments from hyperthermophilic ancestors. Finally, the evolutionary history of DnaJ-Fer provides information useful for the relative dating of the diversification of Archaeplastida and Thaumarchaeota.
    BMC Evolutionary Biology 11/2012; 12(1):226. DOI:10.1186/1471-2148-12-226 · 3.41 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: BACKGROUND: The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distribution profiles, physical clustering, gene fusion, co-expression profiles, structural information and other genomic or post-genomic derived associations can be now used to make very strong functional hypotheses. Here, we illustrate this shift with the analysis of the DUF71/COG2102 family, a subgroup of the PP-loop ATPase family. RESULTS: The DUF71 family contains at least two subfamilies, one of which was predicted to be the missing diphthine-ammonia ligase (EC 6.3.1.14), Dph6. This enzyme catalyzes the last ATP-dependent step in the synthesis of diphthamide, a complex modification of Elongation Factor 2 that can be ADP-ribosylated by bacterial toxins. Dph6 orthologs are found in nearly all sequenced Archaea and Eucarya, as expected from the distribution of the diphthamide modification. The DUF71 family appears to have originated in the Archaea/Eucarya ancestor and to have been subsequently horizontally transferred to Bacteria. Bacterial DUF71 members likely acquired a different function because the diphthamide modification is absent in this Domain of Life. In-depth investigations suggest that some archaeal and bacterial DUF71 proteins participate in B12 salvage. CONCLUSIONS: This detailed analysis of the DUF71 family members provides an example of the power of integrated data-miming for solving important "missing genes" or "missing function" cases and illustrates the danger of functional annotation of protein families by homology alone.Reviewers' namesThis article was reviewed by Arcady Mushegian, Michael Galperin and L. Aravind.
    Biology Direct 09/2012; 7(1):32. DOI:10.1186/1745-6150-7-32 · 4.04 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Biosynthesis of iron-sulphur (Fe-S) proteins is catalysed by multi-protein systems, ISC and SUF. However, 'non-ISC, non-SUF' Fe-S biosynthesis factors have been described, both in prokaryotes and eukaryotes. Here we report in vitro and in vivo investigations of such a 'non-ISC, non SUF' component, the Nfu proteins. Phylogenomic analysis allowed us to define four subfamilies. Escherichia coli NfuA is within subfamily II. Most members of this subfamily have a Nfu domain fused to a 'degenerate' A-type carrier domain (ATC*) lacking Fe-S cluster co-ordinating Cys ligands. The Nfu domain binds a [4Fe-4S] cluster while the ATC* domain interacts with NuoG (a complex I subunit) and aconitase B (AcnB). In vitro, holo-NfuA promotes maturation of AcnB. In vivo, NfuA is necessary for full activity of complex I under aerobic growth conditions, and of AcnB in the presence of superoxide. NfuA receives Fe-S clusters from IscU/HscBA and SufBCD scaffolds and eventually transfers them to the ATCs IscA and SufA. This study provides significant information on one of the Fe-S biogenesis factors that has been often used as a building block by ISC and/or SUF synthesizing organisms, including bacteria, plants and animals.
    Molecular Microbiology 09/2012; 86(1):155-71. DOI:10.1111/j.1365-2958.2012.08181.x · 5.03 Impact Factor
  • Simonetta Gribaldo, Céline Brochier-Armanet
    Trends in Microbiology 03/2012; 20(5):209-10. DOI:10.1016/j.tim.2012.02.006 · 9.81 Impact Factor

Publication Stats

2k Citations
390.90 Total Impact Points

Institutions

  • 2008–2015
    • French National Centre for Scientific Research
      Lutetia Parisorum, Île-de-France, France
  • 2012–2014
    • Claude Bernard University Lyon 1
      • Laboratoire de biométrie et biologie evolutive (LBBE)
      Villeurbanne, Rhône-Alpes, France
  • 2006–2013
    • Aix-Marseille Université
      • • Laboratoire de Chimie Bactérienne (UMR 7283 LCB)
      • • Institut de Microbiologie de la Méditerranée (FR 3479 IMM)
      Marsiglia, Provence-Alpes-Côte d'Azur, France
  • 2010
    • University of Florida
      • Department of Microbiology and Cell Science
      Gainesville, FL, United States
    • Institute of Microbiology of the Mediterranean
      Marsiglia, Provence-Alpes-Côte d'Azur, France
  • 2007
    • Laboratoire d'Enzymologie et Biochimie Structurales
      Gif, Île-de-France, France