Dossat C

References (14)

Title : Complete genome sequence of the highly hemolytic strain Bacillus cereus F837\/76 - Auger_2012_J.Bacteriol_194_1630
Author(s) : Auger S , Galleron N , Segurens B , Dossat C , Bolotin A , Wincker P , Sorokin A
Ref : Journal of Bacteriology , 194 :1630 , 2012
Abstract : Highly hemolytic strain Bacillus cereus F837/76 was isolated in 1976 from a contaminated prostate wound. The complete nucleotide sequence of this strain reported here counts nearly 36,500 single-nucleotide differences from the closest sequenced strain, Bacillus thuringiensis Al Hakam. F827/76 also contains a 10-kb plasmid that was not detected in the Al Hakam strain.
ESTHER : Auger_2012_J.Bacteriol_194_1630
PubMedSearch : Auger_2012_J.Bacteriol_194_1630
PubMedID: 22374959
Gene_locus related to this paper: bacan-BA2392 , bacan-BA4324 , bacan-BA5110 , bacce-BC2171

Title : Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82 - Miquel_2010_PLoS.One_5_e12714
Author(s) : Miquel S , Peyretaillade E , Claret L , de Vallee A , Dossat C , Vacherie B , Zineb el H , Segurens B , Barbe V , Sauvanet P , Neut C , Colombel JF , Medigue C , Mojica FJ , Peyret P , Bonnet R , Darfeuille-Michaud A
Ref : PLoS ONE , 5 : , 2010
Abstract : BACKGROUND: Ileal lesions of Crohn's disease (CD) patients are abnormally colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells and macrophages. PRINCIPAL FINDINGS: We report here the complete genome sequence of E. coli LF82, the reference strain of adherent-invasive E. coli associated with ileal Crohn's disease. The LF82 genome of 4,881,487 bp total size contains a circular chromosome with a size of 4,773,108 bp and a plasmid of 108,379 bp. The analysis of predicted coding sequences (CDSs) within the LF82 flexible genome indicated that this genome is close to the avian pathogenic strain APEC_01, meningitis-associated strain S88 and urinary-isolated strain UTI89 with regards to flexible genome and single nucleotide polymorphisms in various virulence factors. Interestingly, we observed that strains LF82 and UTI89 adhered at a similar level to Intestine-407 cells and that like LF82, APEC_01 and UTI89 were highly invasive. However, A1EC strain LF82 had an intermediate killer phenotype compared to APEC-01 and UTI89 and the LF82 genome does not harbour most of specific virulence genes from ExPEC. LF82 genome has evolved from those of ExPEC B2 strains by the acquisition of Salmonella and Yersinia isolated or clustered genes or CDSs located on pLF82 plasmid and at various loci on the chromosome. CONCLUSION: LF82 genome analysis indicated that a number of genes, gene clusters and pathoadaptative mutations which have been acquired may play a role in virulence of AIEC strain LF82.
ESTHER : Miquel_2010_PLoS.One_5_e12714
PubMedSearch : Miquel_2010_PLoS.One_5_e12714
PubMedID: 20862302
Gene_locus related to this paper: ecoli-yeiG , ecoli-yqia

Title : Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains - Pena_2010_ISME.J_4_882
Author(s) : Pena A , Teeling H , Huerta-Cepas J , Santos F , Yarza P , Brito-Echeverria J , Lucio M , Schmitt-Kopplin P , Meseguer I , Schenowitz C , Dossat C , Barbe V , Dopazo J , Rossello-Mora R , Schuler M , Glockner FO , Amann R , Gabaldon T , Anton J
Ref : Isme J , 4 :882 , 2010
Abstract : Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.
ESTHER : Pena_2010_ISME.J_4_882
PubMedSearch : Pena_2010_ISME.J_4_882
PubMedID: 20164864
Gene_locus related to this paper: salrd-q2rzy1 , salrd-q2s0e4 , salrd-q2s1i8

Title : Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources - Vuilleumier_2009_PLoS.One_4_e5584
Author(s) : Vuilleumier S , Chistoserdova L , Lee MC , Bringel F , Lajus A , Zhou Y , Gourion B , Barbe V , Chang J , Cruveiller S , Dossat C , Gillett W , Gruffaz C , Haugen E , Hourcade E , Levy R , Mangenot S , Muller E , Nadalig T , Pagni M , Penny C , Peyraud R , Robinson DG , Roche D , Rouy Z , Saenampechek C , Salvignol G , Vallenet D , Wu Z , Marx CJ , Vorholt JA , Olson MV , Kaul R , Weissenbach J , Medigue C , Lidstrom ME
Ref : PLoS ONE , 4 :e5584 , 2009
Abstract : BACKGROUND: Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared. METHODOLOGY/PRINCIPAL FINDINGS: The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm) gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau) gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17) that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid). CONCLUSION/SIGNIFICANCE: These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire methylotrophic lifestyles.
ESTHER : Vuilleumier_2009_PLoS.One_4_e5584
PubMedSearch : Vuilleumier_2009_PLoS.One_4_e5584
PubMedID: 19440302
Gene_locus related to this paper: metc4-b7krz1 , metea-c5asz7 , metea-c5au09 , metea-c5axg7 , metea-c5b1t3 , metea-c5b215 , metea-c5b387 , meted-c7cbs2 , meted-c7ce76 , meted-c7cfe3 , meted-c7cfx5 , meted-c7cg08 , meted-c7cgc9 , meted-c7cge7 , meted-c7chb8 , meted-c7ci36 , meted-c7cln3 , meted-c7cnd9 , metep-a9vxp1 , metep-a9w2b1 , metep-a9w028 , metex-orf5 , metex-Q8RPA1 , metpb-b1zjw5 , metea-c5as87 , metea-c5awv9 , meted-c7cb08 , metea-rutd , meted-rutd

Title : Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths - Touchon_2009_PLoS.Genet_5_e1000344
Author(s) : Touchon M , Hoede C , Tenaillon O , Barbe V , Baeriswyl S , Bidet P , Bingen E , Bonacorsi S , Bouchier C , Bouvet O , Calteau A , Chiapello H , Clermont O , Cruveiller S , Danchin A , Diard M , Dossat C , Karoui ME , Frapy E , Garry L , Ghigo JM , Gilles AM , Johnson J , Le Bouguenec C , Lescat M , Mangenot S , Martinez-Jehanne V , Matic I , Nassif X , Oztas S , Petit MA , Pichon C , Rouy Z , Ruf CS , Schneider D , Tourret J , Vacherie B , Vallenet D , Medigue C , Rocha EP , Denamur E
Ref : PLoS Genet , 5 :e1000344 , 2009
Abstract : The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the approximately 18,000 families of orthologous genes, we found approximately 2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome.
ESTHER : Touchon_2009_PLoS.Genet_5_e1000344
PubMedSearch : Touchon_2009_PLoS.Genet_5_e1000344
PubMedID: 19165319
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C2429 , ecoli-C3633 , ecoli-C3636 , ecoli-C4836 , ecoli-d7xp23 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-IROD , ecoli-IROE , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-Z0347 , ecoli-Z1930 , ecoli-YfhR , ecout-q1r7l6 , escfe-e9z855 , yerpe-YBTT , ecolx-e0qx45

Title : Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus - Ripoll_2009_PLoS.One_4_e5660
Author(s) : Ripoll F , Pasek S , Schenowitz C , Dossat C , Barbe V , Rottman M , Macheras E , Heym B , Herrmann JL , Daffe M , Brosch R , Risler JL , Gaillard JL
Ref : PLoS ONE , 4 :e5660 , 2009
Abstract : Mycobacterium abscessus is an emerging rapidly growing mycobacterium (RGM) causing a pseudotuberculous lung disease to which patients with cystic fibrosis (CF) are particularly susceptible. We report here its complete genome sequence. The genome of M. abscessus (CIP 104536T) consists of a 5,067,172-bp circular chromosome including 4920 predicted coding sequences (CDS), an 81-kb full-length prophage and 5 IS elements, and a 23-kb mercury resistance plasmid almost identical to pMM23 from Mycobacterium marinum. The chromosome encodes many virulence proteins and virulence protein families absent or present in only small numbers in the model RGM species Mycobacterium smegmatis. Many of these proteins are encoded by genes belonging to a "mycobacterial" gene pool (e.g. PE and PPE proteins, MCE and YrbE proteins, lipoprotein LpqH precursors). However, many others (e.g. phospholipase C, MgtC, MsrA, ABC Fe(3+) transporter) appear to have been horizontally acquired from distantly related environmental bacteria with a high G+C content, mostly actinobacteria (e.g. Rhodococcus sp., Streptomyces sp.) and pseudomonads. We also identified several metabolic regions acquired from actinobacteria and pseudomonads (relating to phenazine biosynthesis, homogentisate catabolism, phenylacetic acid degradation, DNA degradation) not present in the M. smegmatis genome. Many of the "non mycobacterial" factors detected in M. abscessus are also present in two of the pathogens most frequently isolated from CF patients, Pseudomonas aeruginosa and Burkholderia cepacia. This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicity shared by unrelated organisms in CF patients.
ESTHER : Ripoll_2009_PLoS.One_4_e5660
PubMedSearch : Ripoll_2009_PLoS.One_4_e5660
PubMedID: 19543527

Title : Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti - de Groot_2009_PLoS.Genet_5_e1000434
Author(s) : de Groot A , Dulermo R , Ortet P , Blanchard L , Guerin P , Fernandez B , Vacherie B , Dossat C , Jolivet E , Siguier P , Chandler M , Barakat M , Dedieu A , Barbe V , Heulin T , Sommer S , Achouak W , Armengaud J
Ref : PLoS Genet , 5 :e1000434 , 2009
Abstract : To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb. Accurate primary genome annotation of its 3,455 genes was guided by extensive proteome shotgun analysis. From the large corpus of MS/MS spectra recorded, 1,348 proteins were uncovered and semiquantified by spectral counting. Among the highly detected proteins are several orphans and Deinococcus-specific proteins of unknown function. The alliance of proteomics and genomics high-throughput techniques allowed identification of 15 unpredicted genes and, surprisingly, reversal of incorrectly predicted orientation of 11 genes. Reversal of orientation of two Deinococcus-specific radiation-induced genes, ddrC and ddrH, and identification in D. deserti of supplementary genes involved in manganese import extend our knowledge of the radiotolerance toolbox of Deinococcaceae. Additional genes involved in nutrient import and in DNA repair (i.e., two extra recA, three translesion DNA polymerases, a photolyase) were also identified and found to be expressed under standard growth conditions, and, for these DNA repair genes, after exposure of the cells to UV. The supplementary nutrient import and DNA repair genes are likely important for survival and adaptation of D. deserti to its nutrient-poor, dry, and UV-exposed extreme environment.
ESTHER : de Groot_2009_PLoS.Genet_5_e1000434
PubMedSearch : de Groot_2009_PLoS.Genet_5_e1000434
PubMedID: 19370165
Gene_locus related to this paper: deidv-c1cva5 , deidv-c1cvi6 , deidv-c1cwe6 , deidv-c1cwk6 , deidv-c1cxm7 , deidv-c1cy72 , deidv-c1d002 , deidv-c1d2d8 , deidv-c1d3d8 , deidv-c1d3p0 , deidv-c1cxw0 , deidv-c1d2x1 , deidv-c1cvt7

Title : Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity - Lapidus_2008_Chem.Biol.Interact_171_236
Author(s) : Lapidus A , Goltsman E , Auger S , Galleron N , Segurens B , Dossat C , Land ML , Broussolle V , Brillard J , Guinebretiere MH , Sanchis V , Nguen-The C , Lereclus D , Richardson P , Wincker P , Weissenbach J , Ehrlich SD , Sorokin A
Ref : Chemico-Biological Interactions , 171 :236 , 2008
Abstract : The Bacillus cereus group represents sporulating soil bacteria containing pathogenic strains which may cause diarrheic or emetic food poisoning outbreaks. Multiple locus sequence typing revealed a presence in natural samples of these bacteria of about 30 clonal complexes. Application of genomic methods to this group was however biased due to the major interest for representatives closely related to Bacillus anthracis. Albeit the most important food-borne pathogens were not yet defined, existing data indicate that they are scattered all over the phylogenetic tree. The preliminary analysis of the sequences of three genomes discussed in this paper narrows down the gaps in our knowledge of the B. cereus group. The strain NVH391-98 is a rare but particularly severe food-borne pathogen. Sequencing revealed that the strain should be a representative of a novel bacterial species, for which the name Bacillus cytotoxis or Bacillus cytotoxicus is proposed. This strain has a reduced genome size compared to other B. cereus group strains. Genome analysis revealed absence of sigma B factor and the presence of genes encoding diarrheic Nhe toxin, not detected earlier. The strain B. cereus F837/76 represents a clonal complex close to that of B. anthracis. Including F837/76, three such B. cereus strains had been sequenced. Alignment of genomes suggests that B. anthracis is their common ancestor. Since such strains often emerge from clinical cases, they merit a special attention. The third strain, KBAB4, is a typical facultative psychrophile generally found in soil. Phylogenic studies show that in nature it is the most active group in terms of gene exchange. Genomic sequence revealed high presence of extra-chromosomal genetic material (about 530kb) that may account for this phenomenon. Genes coding Nhe-like toxin were found on a big plasmid in this strain. This may indicate a potential mechanism of toxicity spread from the psychrophile strain community. The results of this genomic work and ecological compartments of different strains incite to consider a necessity of creating prophylactic vaccines against bacteria closely related to NVH391-98 and F837/76. Presumably developing of such vaccines can be based on the properties of non-pathogenic strains such as KBAB4 or ATCC14579 reported here or earlier. By comparing the protein coding genes of strains being sequenced in this project to others we estimate the shared proteome, or core genome, in the B. cereus group to be 3000+/-200 genes and the total proteome, or pan-genome, to be 20-25,000 genes.
ESTHER : Lapidus_2008_Chem.Biol.Interact_171_236
PubMedSearch : Lapidus_2008_Chem.Biol.Interact_171_236
PubMedID: 17434157
Gene_locus related to this paper: bacwk-A9VF42 , bacan-BA0954 , bacan-BA5009 , bacan-DHBF , bacce-BC0192 , bacce-BC2141 , bacce-BC2171 , bacce-BC2458 , bacce-BC3133 , bacce-BC4862 , bacce-BC5130 , bacce-c2zq05 , bacce-c2zsv2 , bacce-lipP , bacce-PHAC , bacce-q2edm4 , bacce-q72yu1 , baccn-a7gmc0 , baccn-a7gmj8 , baccn-a7gnr6 , baccn-a7gpf9 , baccn-a7gpl4 , baccn-a7gpr3 , baccn-a7gqf9 , baccn-a7gr85 , baccn-a7gsc6 , baccn-a7gse0 , baccn-a7gt87 , baccn-a7gu34 , baccn-a7gu90 , baccn-a7guq6 , baccr-pepx , bacmy-c3aae7 , bactu-c3ice0 , bacwk-a9vg55 , bacwk-a9vgr5 , bacwk-a9vju9 , bacwk-a9vkh7 , bacwk-a9vm76 , bacwk-a9vql0 , bacwk-a9vqm8 , bacwk-a9vtw7 , bacwk-a9vv54 , baccn-a7gp74

Title : Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia - Amadou_2008_Genome.Res_18_1472
Author(s) : Amadou C , Pascal G , Mangenot S , Glew M , Bontemps C , Capela D , Carrere S , Cruveiller S , Dossat C , Lajus A , Marchetti M , Poinsot V , Rouy Z , Servin B , Saad M , Schenowitz C , Barbe V , Batut J , Medigue C , Masson-Boivin C
Ref : Genome Res , 18 :1472 , 2008
Abstract : We report the first complete genome sequence of a beta-proteobacterial nitrogen-fixing symbiont of legumes, Cupriavidus taiwanensis LMG19424. The genome consists of two chromosomes of size 3.42 Mb and 2.50 Mb, and a large symbiotic plasmid of 0.56 Mb. The C. taiwanensis genome displays an unexpected high similarity with the genome of the saprophytic bacterium C. eutrophus H16, despite being 0.94 Mb smaller. Both organisms harbor two chromosomes with large regions of synteny interspersed by specific regions. In contrast, the two species host highly divergent plasmids, with the consequence that C. taiwanensis is symbiotically proficient and less metabolically versatile. Altogether, specific regions in C. taiwanensis compared with C. eutrophus cover 1.02 Mb and are enriched in genes associated with symbiosis or virulence in other bacteria. C. taiwanensis reveals characteristics of a minimal rhizobium, including the most compact (35-kb) symbiotic island (nod and nif) identified so far in any rhizobium. The atypical phylogenetic position of C. taiwanensis allowed insightful comparative genomics of all available rhizobium genomes. We did not find any gene that was both common and specific to all rhizobia, thus suggesting that a unique shared genetic strategy does not support symbiosis of rhizobia with legumes. Instead, phylodistribution analysis of more than 200 Sinorhizobium meliloti known symbiotic genes indicated large and complex variations of their occurrence in rhizobia and non-rhizobia. This led us to devise an in silico method to extract genes preferentially associated with rhizobia. We discuss how the novel genes we have identified may contribute to symbiotic adaptation.
ESTHER : Amadou_2008_Genome.Res_18_1472
PubMedSearch : Amadou_2008_Genome.Res_18_1472
PubMedID: 18490699
Gene_locus related to this paper: cuppj-metx , cuppj-q46nh7 , cuptr-b2agb4 , cuptr-b2ahd0 , cuptr-b2ahw1 , cuptr-b2ai18 , cuptr-b2ai31 , cuptr-b2aii9 , cuptr-b2aik0 , cuptr-b2aiq3 , cuptr-b3r2j1 , cuptr-b3r3y6 , cuptr-b3r4w6 , cuptr-b3r7p4 , cuptr-b3r8d6 , cuptr-b3r8f5 , cuptr-b3r9z0 , cuptr-b3r255 , cuptr-b3r457 , cuptr-b3r543 , cuptr-b3ras4 , cuptr-b3rau3 , cuptr-b3rb04 , cuptr-b3rbm8 , cuptr-b3rd43 , cuptr-b3r6t6 , cuptr-b3r3f3 , cuptr-b3r2m0

Title : Comparative analysis of Acinetobacters: three genomes for three lifestyles - Vallenet_2008_PLoS.One_3_e1805
Author(s) : Vallenet D , Nordmann P , Barbe V , Poirel L , Mangenot S , Bataille E , Dossat C , Gas S , Kreimeyer A , Lenoble P , Oztas S , Poulain J , Segurens B , Robert C , Abergel C , Claverie JM , Raoult D , Medigue C , Weissenbach J , Cruveiller S
Ref : PLoS ONE , 3 :e1805 , 2008
Abstract : Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.
ESTHER : Vallenet_2008_PLoS.One_3_e1805
PubMedSearch : Vallenet_2008_PLoS.One_3_e1805
PubMedID: 18350144
Gene_locus related to this paper: acib1-e8pgf8 , acib3-b7guy6 , acib3-b7h156 , acib3-metx , aciba-d0c992 , aciba-k1epl1 , aciba-k6lkl9 , acibc-b2huf4 , acibc-b2i0a2 , acibc-b2i0w9 , acibc-b2i2b0 , acibs-b0vt32 , acibt-a3m1g6 , acibt-a3m5r6 , acibt-a3m5t3 , acibt-a3m5x2 , acibt-a3m627 , acibt-a3m707 , aciby-b0v723 , acica-d0s0a7 , aciju-d0sj67 , aciba-f5iht4 , aciba-a0a009wzt4

Title : Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia - Giraud_2007_Science_316_1307
Author(s) : Giraud E , Moulin L , Vallenet D , Barbe V , Cytryn E , Avarre JC , Jaubert M , Simon D , Cartieaux F , Prin Y , Bena G , Hannibal L , Fardoux J , Kojadinovic M , Vuillet L , Lajus A , Cruveiller S , Rouy Z , Mangenot S , Segurens B , Dossat C , Franck WL , Chang WS , Saunders E , Bruce D , Richardson P , Normand P , Dreyfus B , Pignol D , Stacey G , Emerich D , Vermeglio A , Medigue C , Sadowsky M
Ref : Science , 316 :1307 , 2007
Abstract : Leguminous plants (such as peas and soybeans) and rhizobial soil bacteria are symbiotic partners that communicate through molecular signaling pathways, resulting in the formation of nodules on legume roots and occasionally stems that house nitrogen-fixing bacteria. Nodule formation has been assumed to be exclusively initiated by the binding of bacterial, host-specific lipochito-oligosaccharidic Nod factors, encoded by the nodABC genes, to kinase-like receptors of the plant. Here we show by complete genome sequencing of two symbiotic, photosynthetic, Bradyrhizobium strains, BTAi1 and ORS278, that canonical nodABC genes and typical lipochito-oligosaccharidic Nod factors are not required for symbiosis in some legumes. Mutational analyses indicated that these unique rhizobia use an alternative pathway to initiate symbioses, where a purine derivative may play a key role in triggering nodule formation.
ESTHER : Giraud_2007_Science_316_1307
PubMedSearch : Giraud_2007_Science_316_1307
PubMedID: 17540897
Gene_locus related to this paper: brasb-a5e8s7 , brasb-a5e9h9 , brasb-a5e9x2 , brasb-a5eac3 , brasb-a5eb24 , brasb-a5ech6 , brasb-a5eck9 , brasb-a5ed44 , brasb-a5edz7 , brasb-a5ee62 , brasb-a5ees1 , brasb-a5ef53 , brasb-a5efp3 , brasb-a5efp4 , brasb-a5eg29 , brasb-a5eh09 , brasb-a5ei81 , brasb-a5eiy7 , brasb-a5ej26 , brasb-a5ek41 , brasb-a5elh0 , brasb-a5ema7 , brasb-a5emc8 , brasb-a5eml7 , brasb-a5ene5 , brasb-a5ent6 , brasb-a5eny8 , brasb-a5ep81 , brasb-a5eph8 , brasb-a5epv4 , brasb-a5epx9 , brasb-a5eqb3 , brasb-a5erc8 , brasb-a5esb1 , brasb-a5ese9 , brasb-a5esl7 , brasb-a5esv5 , brasb-a5esw6 , brasb-a5etk7 , brasb-a5eul1 , braso-a4yk16 , braso-a4yl66 , braso-a4ylm4 , braso-a4ylr9 , braso-a4ylx7 , braso-a4ymj8 , braso-a4ynl1 , braso-a4ypd9 , braso-a4yqh3 , braso-a4yr10 , braso-a4yri0 , braso-a4yt56 , braso-a4yul4 , braso-a4yw76 , braso-a4ywb6 , braso-a4yxg2 , braso-a4yy49 , braso-a4yyj6 , braso-a4yzd7 , braso-a4yzh0 , braso-a4z0q9 , braso-a4z0v7 , braso-a4z1h1 , braso-a4z1p1 , braso-a4z1p8 , braso-a4z1v6 , braso-a4z2a5 , braso-a4z152 , braso-a4yl32 , brasb-a5et63 , brasb-a5emr8 , braso-a4ynl2 , brasb-a5eqb2 , braso-a4yr63

Title : Large-scale identification of human genes implicated in epidermal barrier function - Toulza_2007_Genome.Biol_8_R107
Author(s) : Toulza E , Mattiuzzo NR , Galliano MF , Jonca N , Dossat C , Jacob D , de Daruvar A , Wincker P , Serre G , Guerrin M
Ref : Genome Biol , 8 :R107 , 2007
Abstract : BACKGROUND: During epidermal differentiation, keratinocytes progressing through the suprabasal layers undergo complex and tightly regulated biochemical modifications leading to cornification and desquamation. The last living cells, the granular keratinocytes (GKs), produce almost all of the proteins and lipids required for the protective barrier function before their programmed cell death gives rise to corneocytes. We present here the first analysis of the transcriptome of human GKs, purified from healthy epidermis by an original approach. RESULTS: Using the ORESTES method, 22,585 expressed sequence tags (ESTs) were produced that matched 3,387 genes. Despite normalization provided by this method (mean 4.6 ORESTES per gene), some highly transcribed genes, including that encoding dermokine, were overrepresented. About 330 expressed genes displayed less than 100 ESTs in UniGene clusters and are most likely to be specific for GKs and potentially involved in barrier function. This hypothesis was tested by comparing the relative expression of 73 genes in the basal and granular layers of epidermis by quantitative RT-PCR. Among these, 33 were identified as new, highly specific markers of GKs, including those encoding a protease, protease inhibitors and proteins involved in lipid metabolism and transport. We identified filaggrin 2 (also called ifapsoriasin), a poorly characterized member of the epidermal differentiation complex, as well as three new lipase genes clustered with paralogous genes on chromosome 10q23.31. A new gene of unknown function, C1orf81, is specifically disrupted in the human genome by a frameshift mutation. CONCLUSION: These data increase the present knowledge of genes responsible for the formation of the skin barrier and suggest new candidates for genodermatoses of unknown origin.
ESTHER : Toulza_2007_Genome.Biol_8_R107
PubMedSearch : Toulza_2007_Genome.Biol_8_R107
PubMedID: 17562024

Title : A tale of two oxidation states: bacterial colonization of arsenic-rich environments - Muller_2007_PLoS.Genet_3_e53
Author(s) : Muller D , Medigue C , Koechler S , Barbe V , Barakat M , Talla E , Bonnefoy V , Krin E , Arsene-Ploetze F , Carapito C , Chandler M , Cournoyer B , Cruveiller S , Dossat C , Duval S , Heymann M , Leize E , Lieutaud A , Lievremont D , Makita Y , Mangenot S , Nitschke W , Ortet P , Perdrial N , Schoepp B , Siguier P , Simeonova DD , Rouy Z , Segurens B , Turlin E , Vallenet D , Van Dorsselaer A , Weiss S , Weissenbach J , Lett MC , Danchin A , Bertin PN
Ref : PLoS Genet , 3 :e53 , 2007
Abstract : Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the beta-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.
ESTHER : Muller_2007_PLoS.Genet_3_e53
PubMedSearch : Muller_2007_PLoS.Genet_3_e53
PubMedID: 17432936
Gene_locus related to this paper: herar-a4g4w8 , herar-a4g5p0 , herar-a4g6p3 , herar-a4g378 , herar-a4g411 , herar-a4g622 , herar-a4g818 , herar-a4g899 , herar-a4gac3 , herar-metx , herar-a4g8n7

Title : Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype - Jaillon_2004_Nature_431_946
Author(s) : Jaillon O , Aury JM , Brunet F , Petit JL , Stange-Thomann N , Mauceli E , Bouneau L , Fischer C , Ozouf-Costaz C , Bernot A , Nicaud S , Jaffe D , Fisher S , Lutfalla G , Dossat C , Segurens B , Dasilva C , Salanoubat M , Levy M , Boudet N , Castellano S , Anthouard V , Jubin C , Castelli V , Katinka M , Vacherie B , Biemont C , Skalli Z , Cattolico L , Poulain J , de Berardinis V , Cruaud C , Duprat S , Brottier P , Coutanceau JP , Gouzy J , Parra G , Lardier G , Chapple C , McKernan KJ , McEwan P , Bosak S , Kellis M , Volff JN , Guigo R , Zody MC , Mesirov J , Lindblad-Toh K , Birren B , Nusbaum C , Kahn D , Robinson-Rechavi M , Laudet V , Schachter V , Quetier F , Saurin W , Scarpelli C , Wincker P , Lander ES , Weissenbach J , Roest Crollius H
Ref : Nature , 431 :946 , 2004
Abstract : Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
ESTHER : Jaillon_2004_Nature_431_946
PubMedSearch : Jaillon_2004_Nature_431_946
PubMedID: 15496914
Gene_locus related to this paper: tetng-3neur , tetng-4neur , tetng-ACHE , tetng-BCHE , tetng-h3cfz4 , tetng-h3ci57 , tetng-h3cl30 , tetng-h3cnh2 , tetng-nlgn2b , tetng-h3czr1 , tetng-h3dbr5 , tetng-nlgn2a , tetng-nlgn3b , tetng-q4ref8 , tetng-q4rjp3 , tetng-q4rjy3 , tetng-q4rk53 , tetng-q4rk63 , tetng-q4rk66 , tetng-q4rkk3 , tetng-q4rli3 , tetng-q4rn09 , tetng-q4rqj4 , tetng-q4rqz6 , tetng-q4rr22 , tetng-q4rru9 , tetng-q4rtq6 , tetng-q4rvf8 , tetng-q4rwa0 , tetng-q4rx90 , tetng-q4ryv8 , tetng-q4ryz3 , tetng-q4s0h8 , tetng-q4s5x0 , tetng-q4s6r1 , tetng-q4s6t6 , tetng-q4s7e3 , tetng-q4s7x6 , tetng-q4s8t5 , tetng-q4s9w9 , tetng-q4s050 , tetng-q4s091 , tetng-q4s144 , tetng-q4s309 , tetng-q4s578 , tetng-q4sal4 , tetng-q4sbm6 , tetng-q4sbp0 , tetng-q4sbu0 , tetng-q4sd49 , tetng-q4ser6 , tetng-q4sfm7 , tetng-q4sgm5 , tetng-q4sgv2 , tetng-q4sh74 , tetng-q4shl7 , tetng-q4si60 , tetng-q4sie5 , tetng-q4sku6 , tetng-q4smu0 , tetng-q4smy3 , tetng-q4snp0 , tetng-q4snq3 , tetng-q4spa7 , tetng-q4spq0 , tetng-q4sqr3 , tetng-q4sty0 , tetng-q4suu2 , tetng-q4suz1 , tetng-q4sxh3 , tetng-q4syn6 , tetng-q4szk0 , tetng-q4szy0 , tetng-q4t3m9 , tetng-q4t4a1 , tetng-q4t6m1 , tetng-q4t7r6 , tetng-q4t173 , tetng-q4t826 , tetng-q4t920 , tetng-q4ta33 , tetng-q4tab8 , tetng-q4tb62 , tetng-q4tbe2 , tetng-h3dbw2 , tetng-h3cpc8 , tetng-h3cjy0 , tetng-h3d966 , tetng-h3d3e3 , tetng-h3d961 , tetng-h3ctg6 , tetng-h3dde8 , tetng-h3dde9 , tetng-h3det9 , tetng-h3cre8 , tetng-h3dfb4 , tetng-h3clj8