Cruveiller S

References (14)

Title : Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis - Supply_2013_Nat.Genet_45_172
Author(s) : Supply P , Marceau M , Mangenot S , Roche D , Rouanet C , Khanna V , Majlessi L , Criscuolo A , Tap J , Pawlik A , Fiette L , Orgeur M , Fabre M , Parmentier C , Frigui W , Simeone R , Boritsch EC , Debrie AS , Willery E , Walker D , Quail MA , Ma L , Bouchier C , Salvignol G , Sayes F , Cascioferro A , Seemann T , Barbe V , Locht C , Gutierrez MC , Leclerc C , Bentley SD , Stinear TP , Brisse S , Medigue C , Parkhill J , Cruveiller S , Brosch R
Ref : Nat Genet , 45 :172 , 2013
Abstract : Global spread and limited genetic variation are hallmarks of M. tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology are restricted to East Africa. Here, we sequenced and analyzed the whole genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5x coverage), 454/Roche (13-18x coverage) and/or Illumina DNA sequencing (45-105x coverage). We show that STB isolates are highly recombinogenic and evolutionarily early branching, with larger genome sizes, higher rates of genetic variation, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse infection experiments showed that STB strains are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral STB-like pool of mycobacteria by gain of persistence and virulence mechanisms, and we provide insights into the molecular events involved.
ESTHER : Supply_2013_Nat.Genet_45_172
PubMedSearch : Supply_2013_Nat.Genet_45_172
PubMedID: 23291586
Gene_locus related to this paper: mycmm-b2ht49 , myctu-cut3 , myctu-cutas1 , myctu-cutas2 , myctu-Rv1069c , myctu-RV1215C , myctu-RV1758 , myctu-Rv2045c , myctu-RV3452 , myctu-RV3724 , myctu-Rv3802c

Title : Genome sequence of the marine bacterium Marinobacter hydrocarbonoclasticus SP17, which forms biofilms on hydrophobic organic compounds - Grimaud_2012_J.Bacteriol_194_3539
Author(s) : Grimaud R , Ghiglione JF , Cagnon C , Lauga B , Vaysse PJ , Rodriguez-Blanco A , Mangenot S , Cruveiller S , Barbe V , Duran R , Wu LF , Talla E , Bonin P , Michotey V
Ref : Journal of Bacteriology , 194 :3539 , 2012
Abstract : Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.
ESTHER : Grimaud_2012_J.Bacteriol_194_3539
PubMedSearch : Grimaud_2012_J.Bacteriol_194_3539
PubMedID: 22689231
Gene_locus related to this paper: marav-a1u338 , marhy-h8w622 , marhy-h8w685 , marav-a1u1j6

Title : Structure, function, and evolution of the Thiomonas spp. genome - Arsene-Ploetze_2010_PLoS.Genet_6_e1000859
Author(s) : Arsene-Ploetze F , Koechler S , Marchal M , Coppee JY , Chandler M , Bonnefoy V , Brochier-Armanet C , Barakat M , Barbe V , Battaglia-Brunet F , Bruneel O , Bryan CG , Cleiss-Arnold J , Cruveiller S , Erhardt M , Heinrich-Salmeron A , Hommais F , Joulian C , Krin E , Lieutaud A , Lievremont D , Michel C , Muller D , Ortet P , Proux C , Siguier P , Roche D , Rouy Z , Salvignol G , Slyemi D , Talla E , Weiss S , Weissenbach J , Medigue C , Bertin PN
Ref : PLoS Genet , 6 :e1000859 , 2010
Abstract : Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.
ESTHER : Arsene-Ploetze_2010_PLoS.Genet_6_e1000859
PubMedSearch : Arsene-Ploetze_2010_PLoS.Genet_6_e1000859
PubMedID: 20195515
Gene_locus related to this paper: thik1-d5x539 , thia3-d6cv72 , thia3-d6clv8

Title : From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later - Barbe_2009_Microbiology_155_1758
Author(s) : Barbe V , Cruveiller S , Kunst F , Lenoble P , Meurice G , Sekowska A , Vallenet D , Wang T , Moszer I , Medigue C , Danchin A
Ref : Microbiology , 155 :1758 , 2009
Abstract : Comparative genomics is the cornerstone of identification of gene functions. The immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. The bacterial domain is split into large branches, among which the Firmicutes occupy a considerable space. Bacillus subtilis has been the model of Firmicutes for decades and its genome has been a reference for more than 10 years. Sequencing the genome involved more than 30 laboratories, with different expertises, in a attempt to make the most of the experimental information that could be associated with the sequence. This had the expected drawback that the sequencing expertise was quite varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The recent development of very efficient, fast and accurate sequencing techniques, in parallel with the development of high-level annotation platforms, motivated the present resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that B. subtilis is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.
ESTHER : Barbe_2009_Microbiology_155_1758
PubMedSearch : Barbe_2009_Microbiology_155_1758
PubMedID: 19383706

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 : 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 : 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 : 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 characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography - Normand_2007_Genome.Res_17_7
Author(s) : Normand P , Lapierre P , Tisa LS , Gogarten JP , Alloisio N , Bagnarol E , Bassi CA , Berry AM , Bickhart DM , Choisne N , Couloux A , Cournoyer B , Cruveiller S , Daubin V , Demange N , Francino MP , Goltsman E , Huang Y , Kopp OR , Labarre L , Lapidus A , Lavire C , Marechal J , Martinez M , Mastronunzio JE , Mullin BC , Niemann J , Pujic P , Rawnsley T , Rouy Z , Schenowitz C , Sellstedt A , Tavares F , Tomkins JP , Vallenet D , Valverde C , Wall LG , Wang Y , Medigue C , Benson DR
Ref : Genome Res , 17 :7 , 2007
Abstract : Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%-98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
ESTHER : Normand_2007_Genome.Res_17_7
PubMedSearch : Normand_2007_Genome.Res_17_7
PubMedID: 17151343
Gene_locus related to this paper: frasn-a8leg3 , fraaa-q0rau9 , fraaa-q0rbj9 , fraaa-q0rc03 , fraaa-q0rc89 , fraaa-q0rci1 , fraaa-q0rdx4 , fraaa-q0ref4 , fraaa-q0rel4 , fraaa-q0req5 , fraaa-q0rev2 , fraaa-q0rfl4 , fraaa-q0rfz5 , fraaa-q0rhz6 , fraaa-q0rjm3 , fraaa-q0rjt2 , fraaa-q0rkm8 , fraaa-q0rkv5 , fraaa-q0rl43 , fraaa-q0rlp9 , fraaa-q0rm04 , fraaa-q0rmn2 , fraaa-q0rmz5 , fraaa-q0rqg7 , fraaa-q0rr69 , fraaa-q0rrm7 , fraaa-q0rs07 , fraaa-q0rt07 , fraaa-q0rt55 , fraaa-q0rt70 , fraaa-q0rt91 , fraaa-q0rtc4 , fraaa-q0rte4 , fraaa-q0rtv2 , fraaa-q0rum6 , frasc-q2j5v5 , frasc-q2j8e6 , frasc-q2jct6 , frasn-a8kx42 , frasn-a8kyp2 , frasn-A8L0F8 , frasn-a8l0g7 , frasn-a8l1j7 , frasn-a8l1t9 , frasn-a8l4h8 , frasn-a8l7f8 , frasn-a8l8i4 , frasn-a8l8k8 , frasn-a8l9e9 , frasn-a8l051 , frasn-a8l115 , frasn-a8l161 , frasn-a8l265 , frasn-a8l268 , frasn-a8l720 , frasn-a8l745 , frasn-a8l755 , frasn-a8l875 , frasn-a8lab3 , frasn-a8lag3 , frasn-a8lb99 , frasn-a8lbd8 , frasn-a8lbj7 , frasn-a8lbj8 , frasn-a8lby7 , frasn-a8ldb7 , frasn-a8ldd0 , frasn-a8le91 , frasn-a8leg6 , frasn-a8leq6 , frasn-a8let0 , frasn-a8lf43 , frasn-a8lfg3 , frasn-a8lfl1 , frasn-a8lgw1 , frasn-a8lgy1 , frasc-q2j553 , frasn-a8l2m3 , fraaa-q0rd38 , frasc-q2j6h2 , frasn-a8lfl3 , frasn-a8leg7 , frasn-a8l5b8 , fraaa-q0rgz4 , fraaa-q0rtv3 , frasn-a8le98 , frasn-a8leb4

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 : Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila - Vodovar_2006_Nat.Biotechnol_24_673
Author(s) : Vodovar N , Vallenet D , Cruveiller S , Rouy Z , Barbe V , Acosta C , Cattolico L , Jubin C , Lajus A , Segurens B , Vacherie B , Wincker P , Weissenbach J , Lemaitre B , Medigue C , Boccard F
Ref : Nat Biotechnol , 24 :673 , 2006
Abstract : Pseudomonas entomophila is an entomopathogenic bacterium that, upon ingestion, kills Drosophila melanogaster as well as insects from different orders. The complete sequence of the 5.9-Mb genome was determined and compared to the sequenced genomes of four Pseudomonas species. P. entomophila possesses most of the catabolic genes of the closely related strain P. putida KT2440, revealing its metabolically versatile properties and its soil lifestyle. Several features that probably contribute to its entomopathogenic properties were disclosed. Unexpectedly for an animal pathogen, P. entomophila is devoid of a type III secretion system and associated toxins but rather relies on a number of potential virulence factors such as insecticidal toxins, proteases, putative hemolysins, hydrogen cyanide and novel secondary metabolites to infect and kill insects. Genome-wide random mutagenesis revealed the major role of the two-component system GacS/GacA that regulates most of the potential virulence factors identified.
ESTHER : Vodovar_2006_Nat.Biotechnol_24_673
PubMedSearch : Vodovar_2006_Nat.Biotechnol_24_673
PubMedID: 16699499
Gene_locus related to this paper: pseae-PA1622 , psee4-q1i2k0 , psee4-q1i3a7 , psee4-q1i3n8 , psee4-q1i4y6 , psee4-q1i4z6 , psee4-q1i5s3 , psee4-q1i5s9 , psee4-q1i6r6 , psee4-q1i9a0 , psee4-q1i9c3 , psee4-q1i9h5 , psee4-q1i9t2 , psee4-q1iaa7 , psee4-q1ibu9 , psee4-q1icm5 , psee4-q1idp8 , psee4-q1idv7 , psee4-q1ie27 , psee4-q1ie44 , psee4-q1ifj6 , psee4-q1ifn8 , psee4-q1ig13 , psee4-q1ige4 , psep1-a5wax1 , psepg-b0kir7 , psepk-q88nk6 , psepu-METX , psepu-PHAZ , psepu-PIP , psepu-PP1617 , psepu-PP4178 , psepu-PP4551 , psee4-q1icg3

Title : Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125 - Medigue_2005_Genome.Res_15_1325
Author(s) : Medigue C , Krin E , Pascal G , Barbe V , Bernsel A , Bertin PN , Cheung F , Cruveiller S , D'Amico S , Duilio A , Fang G , Feller G , Ho C , Mangenot S , Marino G , Nilsson J , Parrilli E , Rocha EP , Rouy Z , Sekowska A , Tutino ML , Vallenet D , von Heijne G , Danchin A
Ref : Genome Res , 15 :1325 , 2005
Abstract : A considerable fraction of life develops in the sea at temperatures lower than 15 degrees C. Little is known about the adaptive features selected under those conditions. We present the analysis of the genome sequence of the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. We find that it copes with the increased solubility of oxygen at low temperature by multiplying dioxygen scavenging while deleting whole pathways producing reactive oxygen species. Dioxygen-consuming lipid desaturases achieve both protection against oxygen and synthesis of lipids making the membrane fluid. A remarkable strategy for avoidance of reactive oxygen species generation is developed by P. haloplanktis, with elimination of the ubiquitous molybdopterin-dependent metabolism. The P. haloplanktis proteome reveals a concerted amino acid usage bias specific to psychrophiles, consistently appearing apt to accommodate asparagine, a residue prone to make proteins age. Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome.
ESTHER : Medigue_2005_Genome.Res_15_1325
PubMedSearch : Medigue_2005_Genome.Res_15_1325
PubMedID: 16169927
Gene_locus related to this paper: pseht-q3icg6 , pseht-q3icm3 , pseht-q3icu1 , pseht-q3id97 , pseht-q3ida0 , pseht-q3idf4 , pseht-q3ie89 , pseht-q3ieu0 , pseht-q3iev9 , pseht-q3if93 , pseht-q3ifd8 , pseht-q3ife2 , pseht-q3ig70 , pseht-q3igp2 , pseht-q3igv0 , pseht-q3ihr6 , pseht-q3ii38 , pseht-q3iid7 , pseht-q3iip2 , pseht-q3iir1 , pseht-q3iis4 , pseht-q3ijn3 , pseht-q3ijt3 , pseht-q3ijy1 , pseht-q3ijy8 , pseht-q3ik03 , pseht-q3ikv5 , pseht-q3il66 , pseht-q3ik88

Title : Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium - Barbe_2004_Nucleic.Acids.Res_32_5766
Author(s) : Barbe V , Vallenet D , Fonknechten N , Kreimeyer A , Oztas S , Labarre L , Cruveiller S , Robert C , Duprat S , Wincker P , Ornston LN , Weissenbach J , Marliere P , Cohen GN , Medigue C
Ref : Nucleic Acids Research , 32 :5766 , 2004
Abstract : Acinetobacter sp. strain ADP1 is a nutritionally versatile soil bacterium closely related to representatives of the well-characterized Pseudomonas aeruginosa and Pseudomonas putida. Unlike these bacteria, the Acinetobacter ADP1 is highly competent for natural transformation which affords extraordinary convenience for genetic manipulation. The circular chromosome of the Acinetobacter ADP1, presented here, encodes 3325 predicted coding sequences, of which 60% have been classified based on sequence similarity to other documented proteins. The close evolutionary proximity of Acinetobacter and Pseudomonas species, as judged by the sequences of their 16S RNA genes and by the highest level of bidirectional best hits, contrasts with the extensive divergence in the GC content of their DNA (40 versus 62%). The chromosomes also differ significantly in size, with the Acinetobacter ADP1 chromosome <60% of the length of the Pseudomonas counterparts. Genome analysis of the Acinetobacter ADP1 revealed genes for metabolic pathways involved in utilization of a large variety of compounds. Almost all of these genes, with orthologs that are scattered in other species, are located in five major 'islands of catabolic diversity', now an apparent 'archipelago of catabolic diversity', within one-quarter of the overall genome. Acinetobacter ADP1 displays many features of other aerobic soil bacteria with metabolism oriented toward the degradation of organic compounds found in their natural habitat. A distinguishing feature of this genome is the absence of a gene corresponding to pyruvate kinase, the enzyme that generally catalyzes the terminal step in conversion of carbohydrates to pyruvate for respiration by the citric acid cycle. This finding supports the view that the cycle itself is centrally geared to the catabolic capabilities of this exceptionally versatile organism.
ESTHER : Barbe_2004_Nucleic.Acids.Res_32_5766
PubMedSearch : Barbe_2004_Nucleic.Acids.Res_32_5766
PubMedID: 15514110
Gene_locus related to this paper: aciad-q6f6s6 , aciad-q6f6x6 , aciad-q6f6x7 , aciad-q6f6z2 , aciad-q6f7m0 , aciad-q6f7y3 , aciad-q6f8t1 , aciad-q6f8v6 , aciad-q6f8x2 , aciad-q6f9b1 , aciad-q6f9f4 , aciad-q6f933 , aciad-q6f951 , aciad-q6fa15 , aciad-q6fa93 , aciad-q6fag8 , aciad-q6fak6 , aciad-q6fal1 , aciad-q6fas4 , aciad-q6faz3 , aciad-q6fbp9 , aciad-q6fbr2 , aciad-q6fbr5 , aciad-q6fc40 , aciad-q6fd43 , aciad-q6fd56 , aciad-q6fdd3 , aciad-q6fdh2 , aciad-q6fe39 , aciad-q6feb1 , aciad-q6fen4 , aciad-q6feq3 , aciad-q6ff86 , aciad-q6ffz9 , aciad-q8rlz8 , acica-elh1 , acica-elh2 , acica-estB , acica-este2 , acica-este3