Medigue C

References (42)

Title : Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis - Bastard_2017_Nat.Chem.Biol_13_858
Author(s) : Bastard K , Perret A , Mariage A , Bessonnet T , Pinet-Turpault A , Petit JL , Darii E , Bazire P , Vergne-Vaxelaire C , Brewee C , Debard A , Pellouin V , Besnard-Gonnet M , Artiguenave F , Medigue C , Vallenet D , Danchin A , Zaparucha A , Weissenbach J , Salanoubat M , de Berardinis V
Ref : Nat Chemical Biology , 13 :858 , 2017
Abstract : Experimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases.
ESTHER : Bastard_2017_Nat.Chem.Biol_13_858
PubMedSearch : Bastard_2017_Nat.Chem.Biol_13_858
PubMedID: 28581482
Gene_locus related to this paper: neima-metx , strmk-metx , defds-metxa , desmr-metxa , halvd-metxa , metfp-metxa , sulao-metxa , hallt-metxa , metez-metxa , halaf-metxs , metms-metxa , fraad-sst , halaf-sst , naupa-metxa , metzd-metxa , cycms-metxa , comtk-metxs , metpe-metxa , metrm-metxa , halnc-metxs , breda-metxs

Title : Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms - Ramos_2014_BMC.Genomics_15_54
Author(s) : Ramos PI , Picao RC , Almeida LG , Lima NC , Girardello R , Vivan AC , Xavier DE , Barcellos FG , Pelisson M , Vespero EC , Medigue C , Vasconcelos AT , Gales AC , Nicolas MF
Ref : BMC Genomics , 15 :54 , 2014
Abstract : BACKGROUND: Klebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial and community-acquired infections. A wide repertoire of virulence and antimicrobial resistance genes is present in K. pneumoniae genomes, which can constitute extra challenges in the treatment of infections caused by some strains. K. pneumoniae Kp13 is a multidrug-resistant strain responsible for causing a large nosocomial outbreak in a teaching hospital located in Southern Brazil. Kp13 produces K. pneumoniae carbapenemase (KPC-2) but is unrelated to isolates belonging to ST 258 and ST 11, the main clusters associated with the worldwide dissemination of KPC-producing K. pneumoniae. In this report, we perform a genomic comparison between Kp13 and each of the following three K. pneumoniae genomes: MGH 78578, NTUH-K2044 and 342.
RESULTS: We have completely determined the genome of K. pneumoniae Kp13, which comprises one chromosome (5.3 Mbp) and six plasmids (0.43 Mbp). Several virulence and resistance determinants were identified in strain Kp13. Specifically, we detected genes coding for six beta-lactamases (SHV-12, OXA-9, TEM-1, CTX-M-2, SHV-110 and KPC-2), eight adhesin-related gene clusters, including regions coding for types 1 (fim) and 3 (mrk) fimbrial adhesins. The rmtG plasmidial 16S rRNA methyltransferase gene was also detected, as well as efflux pumps belonging to five different families. Mutations upstream the OmpK35 porin-encoding gene were evidenced, possibly affecting its expression. SNPs analysis relative to the compared strains revealed 141 mutations falling within CDSs related to drug resistance which could also influence the Kp13 lifestyle. Finally, the genetic apparatus for synthesis of the yersiniabactin siderophore was identified within a plasticity region. Chromosomal architectural analysis allowed for the detection of 13 regions of difference in Kp13 relative to the compared strains.
CONCLUSIONS: Our results indicate that the plasticity occurring at many hierarchical levels (from whole genomic segments to individual nucleotide bases) may play a role on the lifestyle of K. pneumoniae Kp13 and underlie the importance of whole-genome sequencing to study bacterial pathogens. The general chromosomal structure was somewhat conserved among the compared bacteria, and recombination events with consequent gain/loss of genomic segments appears to be driving the evolution of these strains.
ESTHER : Ramos_2014_BMC.Genomics_15_54
PubMedSearch : Ramos_2014_BMC.Genomics_15_54
PubMedID: 24450656
Gene_locus related to this paper: klep7-y1077 , klepn-w8uta0

Title : Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain - Ji_2014_Environ.Microbiol_16_525
Author(s) : Ji B , Zhang SD , Arnoux P , Rouy Z , Alberto F , Philippe N , Murat D , Zhang WJ , Rioux JB , Ginet N , Sabaty M , Mangenot S , Pradel N , Tian J , Yang J , Zhang L , Zhang W , Pan H , Henrissat B , Coutinho PM , Li Y , Xiao T , Medigue C , Barbe V , Pignol D , Talla E , Wu LF
Ref : Environ Microbiol , 16 :525 , 2014
Abstract : Magnetotactic bacteria (MTB) are capable of synthesizing intracellular organelles, the magnetosomes, that are membrane-bounded magnetite or greigite crystals arranged in chains. Although MTB are widely spread in various ecosystems, few axenic cultures are available, and only freshwater Magnetospirillum spp. have been genetically analysed. Here, we present the complete genome sequence of a marine magnetotactic spirillum, Magnetospira sp. QH-2. The high number of repeats and transposable elements account for the differences in QH-2 genome structure compared with other relatives. Gene cluster synteny and gene correlation analyses indicate that the insertion of the magnetosome island in the QH-2 genome occurred after divergence between freshwater and marine magnetospirilla. The presence of a sodium-quinone reductase, sodium transporters and other functional genes are evidence of the adaptive evolution of Magnetospira sp. QH-2 to the marine ecosystem. Genes well conserved among freshwater magnetospirilla for nitrogen fixation and assimilatory nitrate respiration are absent from the QH-2 genome. Unlike freshwater Magnetospirillum spp., marine Magnetospira sp. QH-2 neither has TonB and TonB-dependent receptors nor does it grow on trace amounts of iron. Taken together, our results show a distinct, adaptive evolution of Magnetospira sp. QH-2 to marine sediments in comparison with its closely related freshwater counterparts.
ESTHER : Ji_2014_Environ.Microbiol_16_525
PubMedSearch : Ji_2014_Environ.Microbiol_16_525
PubMedID: 23841906
Gene_locus related to this paper: 9prot-w6k5m7 , 9prot-w6khf2 , 9prot-w6kbu9

Title : Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8 - Kits_2013_Genome.Announc_1_e0017013
Author(s) : Kits KD , Kalyuzhnaya MG , Klotz MG , Jetten MS , Op den Camp HJ , Vuilleumier S , Bringel F , DiSpirito AA , Murrell JC , Bruce D , Cheng JF , Copeland A , Goodwin L , Hauser L , Lajus A , Land ML , Lapidus A , Lucas S , Medigue C , Pitluck S , Woyke T , Zeytun A , Stein LY
Ref : Genome Announc , 1 :e0017013 , 2013
Abstract : The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N fixation.
ESTHER : Kits_2013_Genome.Announc_1_e0017013
PubMedSearch : Kits_2013_Genome.Announc_1_e0017013
PubMedID: 23580712

Title : Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits - Goudenege_2013_ISME.J_7_1985
Author(s) : Goudenege D , Labreuche Y , Krin E , Ansquer D , Mangenot S , Calteau A , Medigue C , Mazel D , Polz MF , Le Roux F
Ref : Isme J , 7 :1985 , 2013
Abstract : Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed 'nigritoxin', is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.
ESTHER : Goudenege_2013_ISME.J_7_1985
PubMedSearch : Goudenege_2013_ISME.J_7_1985
PubMedID: 23739050
Gene_locus related to this paper: 9vibr-f9tu24 , 9vibr-u4ij97 , 9vibr-u4g9i9 , 9vibr-f9tk00

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 : Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26 - Andres_2013_Genome.Biol.Evol_5_934
Author(s) : Andres J , Arsene-Ploetze F , Barbe V , Brochier-Armanet C , Cleiss-Arnold J , Coppee JY , Dillies MA , Geist L , Joublin A , Koechler S , Lassalle F , Marchal M , Medigue C , Muller D , Nesme X , Plewniak F , Proux C , Ramirez-Bahena MH , Schenowitz C , Sismeiro O , Vallenet D , Santini JM , Bertin PN
Ref : Genome Biol Evol , 5 :934 , 2013
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 metabolize 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 colonizing 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 metabolize 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.
ESTHER : Andres_2013_Genome.Biol.Evol_5_934
PubMedSearch : Andres_2013_Genome.Biol.Evol_5_934
PubMedID: 23589360
Gene_locus related to this paper: rhisp-l0nkx2 , 9rhiz-l0net0

Title : Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z - Vuilleumier_2012_J.Bacteriol_194_551
Author(s) : Vuilleumier S , Khmelenina VN , Bringel F , Reshetnikov AS , Lajus A , Mangenot S , Rouy Z , Op den Camp HJ , Jetten MS , DiSpirito AA , Dunfield P , Klotz MG , Semrau JD , Stein LY , Barbe V , Medigue C , Trotsenko YA , Kalyuzhnaya MG
Ref : Journal of Bacteriology , 194 :551 , 2012
Abstract : Methylomicrobium strains are widespread in saline environments. Here, we report the complete genome sequence of Methylomicrobium alcaliphilum 20Z, a haloalkaliphilic methanotrophic bacterium, which will provide the basis for detailed characterization of the core pathways of both single-carbon metabolism and responses to osmotic and high-pH stresses. Final assembly of the genome sequence revealed that this bacterium contains a 128-kb plasmid, making M. alcaliphilum 20Z the first methanotrophic bacterium of known genome sequence for which a plasmid has been reported.
ESTHER : Vuilleumier_2012_J.Bacteriol_194_551
PubMedSearch : Vuilleumier_2012_J.Bacteriol_194_551
PubMedID: 22207753

Title : Draft genome sequence of the purple photosynthetic bacterium Phaeospirillum molischianum DSM120, a particularly versatile bacterium - Duquesne_2012_J.Bacteriol_194_3559
Author(s) : Duquesne K , Prima V , Ji B , Rouy Z , Medigue C , Talla E , Sturgis JN
Ref : Journal of Bacteriology , 194 :3559 , 2012
Abstract : Here we present the draft genome sequence of the versatile and adaptable purple photosynthetic bacterium Phaeospirillum molischianum DSM120. This study advances the understanding of the adaptability of this bacterium, as well as the differences between the Phaeospirillum and Rhodospirillum genera.
ESTHER : Duquesne_2012_J.Bacteriol_194_3559
PubMedSearch : Duquesne_2012_J.Bacteriol_194_3559
PubMedID: 22689244
Gene_locus related to this paper: phamo-h8fpa5 , phamo-h8fpu9 , phamo-h8fqh7

Title : Genome sequence of radiation-resistant Modestobacter marinus strain BC501, a representative actinobacterium that thrives on calcareous stone surfaces - Normand_2012_J.Bacteriol_194_4773
Author(s) : Normand P , Gury J , Pujic P , Chouaia B , Crotti E , Brusetti L , Daffonchio D , Vacherie B , Barbe V , Medigue C , Calteau A , Ghodhbane-Gtari F , Essoussi I , Nouioui I , Abbassi-Ghozzi I , Gtari M
Ref : Journal of Bacteriology , 194 :4773 , 2012
Abstract : Here we report the full genome sequence of Modestobacter marinus strain BC501, an actinobacterial isolate that thrives on stone surfaces. The generated chromosome is circular, with a length of 5.57 Mb and a G+C content of 74.13%, containing 5,445 protein-coding genes, 48 tRNAs, and 3 ribosomal operons.
ESTHER : Normand_2012_J.Bacteriol_194_4773
PubMedSearch : Normand_2012_J.Bacteriol_194_4773
PubMedID: 22887672
Gene_locus related to this paper: modmb-i4eyb4 , modmb-i4f114 , modmb-i4f525 , modmb-i4f4c1

Title : Ralstonia syzygii, the Blood Disease Bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles - Remenant_2011_PLoS.One_6_e24356
Author(s) : Remenant B , de Cambiaire JC , Cellier G , Jacobs JM , Mangenot S , Barbe V , Lajus A , Vallenet D , Medigue C , Fegan M , Allen C , Prior P
Ref : PLoS ONE , 6 :e24356 , 2011
Abstract : The Ralstonia solanacearum species complex includes R. solanacearum, R. syzygii, and the Blood Disease Bacterium (BDB). All colonize plant xylem vessels and cause wilt diseases, but with significant biological differences. R. solanacearum is a soilborne bacterium that infects the roots of a broad range of plants. R. syzygii causes Sumatra disease of clove trees and is actively transmitted by cercopoid insects. BDB is also pathogenic to a single host, banana, and is transmitted by pollinating insects. Sequencing and DNA-DNA hybridization studies indicated that despite their phenotypic differences, these three plant pathogens are actually very closely related, falling into the Phylotype IV subgroup of the R. solanacearum species complex. To better understand the relationships among these bacteria, we sequenced and annotated the genomes of R. syzygii strain R24 and BDB strain R229. These genomes were compared to strain PSI07, a closely related Phylotype IV tomato isolate of R. solanacearum, and to five additional R. solanacearum genomes. Whole-genome comparisons confirmed previous phylogenetic results: the three phylotype IV strains share more and larger syntenic regions with each other than with other R. solanacearum strains. Furthermore, the genetic distances between strains, assessed by an in-silico equivalent of DNA-DNA hybridization, unambiguously showed that phylotype IV strains of BDB, R. syzygii and R. solanacearum form one genomic species. Based on these comprehensive data we propose a revision of the taxonomy of the R. solanacearum species complex. The BDB and R. syzygii genomes encoded no obvious unique metabolic capacities and contained no evidence of horizontal gene transfer from bacteria occupying similar niches. Genes specific to R. syzygii and BDB were almost all of unknown function or extrachromosomal origin. Thus, the pathogenic life-styles of these organisms are more probably due to ecological adaptation and genomic convergence during vertical evolution than to the acquisition of DNA by horizontal transfer.
ESTHER : Remenant_2011_PLoS.One_6_e24356
PubMedSearch : Remenant_2011_PLoS.One_6_e24356
PubMedID: 21931687
Gene_locus related to this paper: 9rals-g2zrs4 , 9rals-g3a1g4 , ralsl-a0a072zy50 , 9rals-g3a7g7

Title : Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia - Mornico_2011_Genes.(Basel)_3_35
Author(s) : Mornico D , Miche L , Bena G , Nouwen N , Vermeglio A , Vallenet D , Smith AA , Giraud E , Medigue C , Moulin L
Ref : Genes (Basel) , 3 :35 , 2011
Abstract : Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing different phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses.
ESTHER : Mornico_2011_Genes.(Basel)_3_35
PubMedSearch : Mornico_2011_Genes.(Basel)_3_35
PubMedID: 24704842
Gene_locus related to this paper: 9brad-h0sq52 , 9brad-h0rwm8 , 9brad-h0sa48 , 9brad-h0t9f2 , 9brad-h0tzi3 , 9brad-h0t2z1 , 9brad-h0trw8 , 9brad-h0tue9 , 9brad-h0t676 , 9brad-h0sxc0 , 9brad-h0tmw5 , 9brad-h0s7i3 , 9brad-h0sie9 , 9brad-h0swe3 , 9brad-h0stz0

Title : Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales - Kittichotirat_2011_J.Bacteriol_193_4541
Author(s) : Kittichotirat W , Good NM , Hall R , Bringel F , Lajus A , Medigue C , Smalley NE , Beck D , Bumgarner R , Vuilleumier S , Kalyuzhnaya MG
Ref : Journal of Bacteriology , 193 :4541 , 2011
Abstract : Rhodocyclales are representative of versatile bacteria that are able to utilize a wide variety of organic compounds for growth, but only a few strains have been isolated in pure culture thus far. Here we present the genome sequence of Methyloversatilis universalis FAM5(T), the first cultivable methylotrophic member of the order.
ESTHER : Kittichotirat_2011_J.Bacteriol_193_4541
PubMedSearch : Kittichotirat_2011_J.Bacteriol_193_4541
PubMedID: 21725020
Gene_locus related to this paper: 9rhoo-f5rf80 , metuf-f5rhz8

Title : The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes - Chaston_2011_PLoS.One_6_e27909
Author(s) : Chaston JM , Suen G , Tucker SL , Andersen AW , Bhasin A , Bode E , Bode HB , Brachmann AO , Cowles CE , Cowles KN , Darby C , de Leon L , Drace K , Du Z , Givaudan A , Herbert Tran EE , Jewell KA , Knack JJ , Krasomil-Osterfeld KC , Kukor R , Lanois A , Latreille P , Leimgruber NK , Lipke CM , Liu R , Lu X , Martens EC , Marri PR , Medigue C , Menard ML , Miller NM , Morales-Soto N , Norton S , Ogier JC , Orchard SS , Park D , Park Y , Qurollo BA , Sugar DR , Richards GR , Rouy Z , Slominski B , Slominski K , Snyder H , Tjaden BC , van der Hoeven R , Welch RD , Wheeler C , Xiang B , Barbazuk B , Gaudriault S , Goodner B , Slater SC , Forst S , Goldman BS , Goodrich-Blair H
Ref : PLoS ONE , 6 :e27909 , 2011
Abstract : Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.
ESTHER : Chaston_2011_PLoS.One_6_e27909
PubMedSearch : Chaston_2011_PLoS.One_6_e27909
PubMedID: 22125637
Gene_locus related to this paper: xenna-d3vdr8 , xenne-n1nl20 , xenbs-d3v2h2

Title : Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella - Engel_2011_PLoS.Genet_7_e1001296
Author(s) : Engel P , Salzburger W , Liesch M , Chang CC , Maruyama S , Lanz C , Calteau A , Lajus A , Medigue C , Schuster SC , Dehio C
Ref : PLoS Genet , 7 :e1001296 , 2011
Abstract : Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the alpha-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens. Furthermore, our study highlights the remarkable evolvability of T4SSs and their effector proteins, explaining their broad application in bacterial interactions with the environment.
ESTHER : Engel_2011_PLoS.Genet_7_e1001296
PubMedSearch : Engel_2011_PLoS.Genet_7_e1001296
PubMedID: 21347280
Gene_locus related to this paper: 9rhiz-e6ylz4 , 9rhiz-e6yvr1 , barsr-e6yyv8 , brume-BMEI1594 , 9rhiz-e6ylv9 , 9rhiz-e6yr44

Title : Genome sequence of the methanotrophic alphaproteobacterium Methylocystis sp. strain Rockwell (ATCC 49242) - Stein_2011_J.Bacteriol_193_2668
Author(s) : Stein LY , Bringel F , DiSpirito AA , Han S , Jetten MS , Kalyuzhnaya MG , Kits KD , Klotz MG , Op den Camp HJ , Semrau JD , Vuilleumier S , Bruce DC , Cheng JF , Davenport KW , Goodwin L , Hauser L , Lajus A , Land ML , Lapidus A , Lucas S , Medigue C , Pitluck S , Woyke T
Ref : Journal of Bacteriology , 193 :2668 , 2011
Abstract : Methylocystis sp. strain Rockwell (ATCC 49242) is an aerobic methane-oxidizing alphaproteobacterium isolated from an aquifer in southern California. Unlike most methanotrophs in the Methylocystaceae family, this strain has a single pmo operon encoding particulate methane monooxygenase but no evidence of the genes encoding soluble methane monooxygenase. This is the first reported genome sequence of a member of the Methylocystis species of the Methylocystaceae family in the order Rhizobiales.
ESTHER : Stein_2011_J.Bacteriol_193_2668
PubMedSearch : Stein_2011_J.Bacteriol_193_2668
PubMedID: 21441518
Gene_locus related to this paper: 9rhiz-e8ky64 , 9rhiz-e8l0f5 , 9rhiz-e8l1r9 , 9rhiz-e8l2p9 , 9rhiz-e8l5j3 , 9rhiz-e8l733

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 : From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma - Thiberge_2010_BMC.Genomics_11_368
Author(s) : Thiberge JM , Boursaux-Eude C , Lehours P , Dillies MA , Creno S , Coppee JY , Rouy Z , Lajus A , Ma L , Burucoa C , Ruskone-Foumestraux A , Courillon-Mallet A , De Reuse H , Boneca IG , Lamarque D , Megraud F , Delchier JC , Medigue C , Bouchier C , Labigne A , Raymond J
Ref : BMC Genomics , 11 :368 , 2010
Abstract : BACKGROUND: Helicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach. RESULTS: A set of 254 H. pylori genes was used to perform array-based comparative genomic hybridization among 120 French H. pylori strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with cagPAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released H. pylori genomes (i.e. J99, 26695, HPAG1, P12, G27 and Shi470). B38 has the smallest H. pylori genome described thus far (1,576,758 base pairs containing 1,528 CDSs); it contains the vacAs2m2 allele and lacks the genes encoding the major virulence factors (absence of cagPAI, babB, babC, sabB, and homB). Comparative genomics led to the identification of very few sequences that are unique to the B38 strain (9 intact CDSs and 7 pseudogenes). Pair-wise genomic synteny comparisons between B38 and the 6 H. pylori sequenced genomes revealed an almost complete co-linearity, never seen before between the genomes of strain Shi470 (a Peruvian isolate) and B38. CONCLUSION: These isolates are deprived of the main H. pylori virulence factors characterized previously, but are nonetheless associated with gastric neoplasia.
ESTHER : Thiberge_2010_BMC.Genomics_11_368
PubMedSearch : Thiberge_2010_BMC.Genomics_11_368
PubMedID: 20537153

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 : Genome sequence of the obligate methanotroph Methylosinus trichosporium strain OB3b - Stein_2010_J.Bacteriol_192_6497
Author(s) : Stein LY , Yoon S , Semrau JD , DiSpirito AA , Crombie A , Murrell JC , Vuilleumier S , Kalyuzhnaya MG , Op den Camp HJ , Bringel F , Bruce D , Cheng JF , Copeland A , Goodwin L , Han S , Hauser L , Jetten MS , Lajus A , Land ML , Lapidus A , Lucas S , Medigue C , Pitluck S , Woyke T , Zeytun A , Klotz MG
Ref : Journal of Bacteriology , 192 :6497 , 2010
Abstract : Methylosinus trichosporium OB3b (for "oddball" strain 3b) is an obligate aerobic methane-oxidizing alphaproteobacterium that was originally isolated in 1970 by Roger Whittenbury and colleagues. This strain has since been used extensively to elucidate the structure and function of several key enzymes of methane oxidation, including both particulate and soluble methane monooxygenase (sMMO) and the extracellular copper chelator methanobactin. In particular, the catalytic properties of soluble methane monooxygenase from M. trichosporium OB3b have been well characterized in context with biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of the M. trichosporium OB3b genome is the first reported from a member of the Methylocystaceae family in the order Rhizobiales.
ESTHER : Stein_2010_J.Bacteriol_192_6497
PubMedSearch : Stein_2010_J.Bacteriol_192_6497
PubMedID: 20952571
Gene_locus related to this paper: mettr-d5qk82 , mettr-d5qqb3 , mettr-d5qrl9

Title : Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence - Remenant_2010_BMC.Genomics_11_379
Author(s) : Remenant B , Coupat-Goutaland B , Guidot A , Cellier G , Wicker E , Allen C , Fegan M , Pruvost O , Elbaz M , Calteau A , Salvignol G , Mornico D , Mangenot S , Barbe V , Medigue C , Prior P
Ref : BMC Genomics , 11 :379 , 2010
Abstract : BACKGROUND: The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, which have major socio-economic impacts. Pathogenicity is an ancestral trait in R. solanacearum and strains with high genetic variation can be subdivided into four phylotypes, correlating to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB), Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome sequences strains representative of this phylogenetic diversity can help determine which traits allow this bacterium to be such a pathogen of so many different plant species and how the bacteria survive in many different habitats.
RESULTS: The genomes of three tomato bacterial wilt pathogens, CFBP2957 (phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were sequenced and manually annotated. These genomes were compared with those of three previously sequenced R. solanacearum strains: GMI1000 (tomato, phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The major genomic features (size, G+C content, number of genes) were conserved across all of the six sequenced strains. Despite relatively high genetic distances (calculated from average nucleotide identity) and many genomic rearrangements, more than 60% of the genes of the megaplasmid and 70% of those on the chromosome are syntenic. The three new genomic sequences revealed the presence of several previously unknown traits, probably acquired by horizontal transfers, within the genomes of R. solanacearum, including a type IV secretion system, a rhi-type anti-mitotic toxin and two small plasmids. Genes involved in virulence appear to be evolving at a faster rate than the genome as a whole.
CONCLUSIONS: Comparative analysis of genome sequences and gene content confirmed the differentiation of R. solanacearum species complex strains into four phylotypes. Genetic distances between strains, in conjunction with CGH analysis of a larger set of strains, revealed differences great enough to consider reclassification of the R. solanacearum species complex into three species. The data are still too fragmentary to link genomic classification and phenotypes, but these new genome sequences identify a pan-genome more representative of the diversity in the R. solanancearum species complex.
ESTHER : Remenant_2010_BMC.Genomics_11_379
PubMedSearch : Remenant_2010_BMC.Genomics_11_379
PubMedID: 20550686
Gene_locus related to this paper: ralsl-d8p4i2 , ralso-d8njk6 , ralso-PCAD , ralso-PCAD2 , ralso-PHAZ , ralso-PHBC , ralso-RSC0439 , ralso-RSC0563 , ralso-RSC0604 , ralso-RSC1003 , ralso-RSC1344 , ralso-RSC1772 , ralso-RSC1804 , ralso-RSC1811 , ralso-RSC1887 , ralso-RSC2149 , ralso-RSC2228 , ralso-RSC2781 , ralso-RSC3346 , ralso-RSP0196 , ralso-RSP0795 , ralso-RSP1108 , ralso-RSP1248 , ralso-RSP1521 , ralsl-d8ny30 , ralsl-y0kx85 , ralsl-a0a072zy50

Title : The genome sequence of the cyanobacterium Oscillatoria sp. PCC 6506 reveals several gene clusters responsible for the biosynthesis of toxins and secondary metabolites - Mejean_2010_J.Bacteriol_192_5264
Author(s) : Mejean A , Mazmouz R , Mann S , Calteau A , Medigue C , Ploux O
Ref : Journal of Bacteriology , 192 :5264 , 2010
Abstract : We report a draft sequence of the genome of Oscillatoria sp. PCC 6506, a cyanobacterium that produces anatoxin-a and homoanatoxin-a, two neurotoxins, and cylindrospermopsin, a cytotoxin. Beside the clusters of genes responsible for the biosynthesis of these toxins, we have found other clusters of genes likely involved in the biosynthesis of not-yet-identified secondary metabolites.
ESTHER : Mejean_2010_J.Bacteriol_192_5264
PubMedSearch : Mejean_2010_J.Bacteriol_192_5264
PubMedID: 20675499
Gene_locus related to this paper: 9cyan-d8fuq7 , 9cyan-d8g8x6 , 9cyan-d8g419 , 9cyan-d8g600 , 9cyan-d8fxr9

Title : Genomic, proteomic, and transcriptomic analysis of virulent and avirulent Rickettsia prowazekii reveals its adaptive mutation capabilities - Bechah_2010_Genome.Res_20_655
Author(s) : Bechah Y , El Karkouri K , Mediannikov O , Leroy Q , Pelletier N , Robert C , Medigue C , Mege JL , Raoult D
Ref : Genome Res , 20 :655 , 2010
Abstract : Rickettsia prowazekii, the agent of epidemic typhus, is an obligate intracellular bacterium that is transmitted to human beings by the body louse. Several strains that differ considerably in virulence are recognized, but the genetic basis for these variations has remained unknown since the initial description of the avirulent vaccine strain nearly 70 yr ago. We use a recently developed murine model of epidemic typhus and transcriptomic, proteomic, and genetic techniques to identify the factors associated with virulence. We identified four phenotypes of R. prowazekii that differed in virulence, associated with the up-regulation of antiapoptotic genes or the interferon I pathway in the host cells. Transcriptional and proteomic analyses of R. prowazekii surface protein expression and protein methylation varied with virulence. By sequencing a virulent strain and using comparative genomics, we found hotspots of mutations in homopolymeric tracts of poly(A) and poly(T) in eight genes in an avirulent strain that split and inactivated these genes. These included recO, putative methyltransferase, and exported protein. Passage of the avirulent Madrid E strain in cells or in experimental animals was associated with a cascade of gene reactivations, beginning with recO, that restored the virulent phenotype. An area of genomic plasticity appears to determine virulence in R. prowazekii and represents an example of adaptive mutation for this pathogen.
ESTHER : Bechah_2010_Genome.Res_20_655
PubMedSearch : Bechah_2010_Genome.Res_20_655
PubMedID: 20368341
Gene_locus related to this paper: ricpr-RP738

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 : NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis - Rusniok_2009_Genome.Biol_10_R110
Author(s) : Rusniok C , Vallenet D , Floquet S , Ewles H , Mouze-Soulama C , Brown D , Lajus A , Buchrieser C , Medigue C , Glaser P , Pelicic V
Ref : Genome Biol , 10 :R110 , 2009
Abstract : BACKGROUND: Genome sequences, now available for most pathogens, hold promise for the rational design of new therapies. However, biological resources for genome-scale identification of gene function (notably genes involved in pathogenesis) and/or genes essential for cell viability, which are necessary to achieve this goal, are often sorely lacking. This holds true for Neisseria meningitidis, one of the most feared human bacterial pathogens that causes meningitis and septicemia.
RESULTS: By determining and manually annotating the complete genome sequence of a serogroup C clinical isolate of N. meningitidis (strain 8013) and assembling a library of defined mutants in up to 60% of its non-essential genes, we have created NeMeSys, a biological resource for Neisseria meningitidis systematic functional analysis. To further enhance the versatility of this toolbox, we have manually (re)annotated eight publicly available Neisseria genome sequences and stored all these data in a publicly accessible online database. The potential of NeMeSys for narrowing the gap between sequence and function is illustrated in several ways, notably by performing a functional genomics analysis of the biogenesis of type IV pili, one of the most widespread virulence factors in bacteria, and by identifying through comparative genomics a complete biochemical pathway (for sulfur metabolism) that may potentially be important for nasopharyngeal colonization.
CONCLUSIONS: By improving our capacity to understand gene function in an important human pathogen, NeMeSys is expected to contribute to the ongoing efforts aimed at understanding a prokaryotic cell comprehensively and eventually to the design of new therapies.
ESTHER : Rusniok_2009_Genome.Biol_10_R110
PubMedSearch : Rusniok_2009_Genome.Biol_10_R110
PubMedID: 19818133
Gene_locus related to this paper: neimb-q9k0t9 , neime-ESD , neime-NMA2216 , neime-NMB0276 , neime-NMB1828

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 : Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of leptospirosis - Picardeau_2008_PLoS.One_3_e1607
Author(s) : Picardeau M , Bulach DM , Bouchier C , Zuerner RL , Zidane N , Wilson PJ , Creno S , Kuczek ES , Bommezzadri S , Davis JC , McGrath A , Johnson MJ , Boursaux-Eude C , Seemann T , Rouy Z , Coppel RL , Rood JI , Lajus A , Davies JK , Medigue C , Adler B
Ref : PLoS ONE , 3 :e1607 , 2008
Abstract : Leptospira biflexa is a free-living saprophytic spirochete present in aquatic environments. We determined the genome sequence of L. biflexa, making it the first saprophytic Leptospira to be sequenced. The L. biflexa genome has 3,590 protein-coding genes distributed across three circular replicons: the major 3,604 chromosome, a smaller 278-kb replicon that also carries essential genes, and a third 74-kb replicon. Comparative sequence analysis provides evidence that L. biflexa is an excellent model for the study of Leptospira evolution; we conclude that 2052 genes (61%) represent a progenitor genome that existed before divergence of pathogenic and saprophytic Leptospira species. Comparisons of the L. biflexa genome with two pathogenic Leptospira species reveal several major findings. Nearly one-third of the L. biflexa genes are absent in pathogenic Leptospira. We suggest that once incorporated into the L. biflexa genome, laterally transferred DNA undergoes minimal rearrangement due to physical restrictions imposed by high gene density and limited presence of transposable elements. In contrast, the genomes of pathogenic Leptospira species undergo frequent rearrangements, often involving recombination between insertion sequences. Identification of genes common to the two pathogenic species, L. borgpetersenii and L. interrogans, but absent in L. biflexa, is consistent with a role for these genes in pathogenesis. Differences in environmental sensing capacities of L. biflexa, L. borgpetersenii, and L. interrogans suggest a model which postulates that loss of signal transduction functions in L. borgpetersenii has impaired its survival outside a mammalian host, whereas L. interrogans has retained environmental sensory functions that facilitate disease transmission through water.
ESTHER : Picardeau_2008_PLoS.One_3_e1607
PubMedSearch : Picardeau_2008_PLoS.One_3_e1607
PubMedID: 18270594
Gene_locus related to this paper: lepba-b0s8t1 , lepba-b0s8u7 , lepba-b0s8y3 , lepba-b0s9i9 , lepba-b0sav1 , lepba-b0sbc1 , lepba-b0sc63 , lepba-b0scl1 , lepba-b0sct4 , lepba-b0sgs6 , lepba-b0sif1 , lepba-metx , lepbp-b0sju7 , lepbp-b0slj1 , lepbp-b0smw1 , lepbp-b0spz3 , lepbp-b0sqw9 , lepbp-b0ssy9 , lepbp-b0sui7

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 : 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 : 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 : 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 : Deciphering the evolution and metabolism of an anammox bacterium from a community genome - Strous_2006_Nature_440_790
Author(s) : Strous M , Pelletier E , Mangenot S , Rattei T , Lehner A , Taylor MW , Horn M , Daims H , Bartol-Mavel D , Wincker P , Barbe V , Fonknechten N , Vallenet D , Segurens B , Schenowitz-Truong C , Medigue C , Collingro A , Snel B , Dutilh BE , Op den Camp HJ , van der Drift C , Cirpus I , van de Pas-Schoonen KT , Harhangi HR , van Niftrik L , Schmid M , Keltjens J , van de Vossenberg J , Kartal B , Meier H , Frishman D , Huynen MA , Mewes HW , Weissenbach J , Jetten MS , Wagner M , Le Paslier D
Ref : Nature , 440 :790 , 2006
Abstract : Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.
ESTHER : Strous_2006_Nature_440_790
PubMedSearch : Strous_2006_Nature_440_790
PubMedID: 16598256
Gene_locus related to this paper: 9bact-q1py93 , 9bact-q1q3k9 , 9bact-q1q414

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

Title : Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis - Chain_2004_Proc.Natl.Acad.Sci.U.S.A_101_13826
Author(s) : Chain PS , Carniel E , Larimer FW , Lamerdin J , Stoutland PO , Regala WM , Georgescu AM , Vergez LM , Land ML , Motin VL , Brubaker RR , Fowler J , Hinnebusch J , Marceau M , Medigue C , Simonet M , Chenal-Francisque V , Souza B , Dacheux D , Elliott JM , Derbise A , Hauser LJ , Garcia E
Ref : Proc Natl Acad Sci U S A , 101 :13826 , 2004
Abstract : Yersinia pestis, the causative agent of plague, is a highly uniform clone that diverged recently from the enteric pathogen Yersinia pseudotuberculosis. Despite their close genetic relationship, they differ radically in their pathogenicity and transmission. Here, we report the complete genomic sequence of Y. pseudotuberculosis IP32953 and its use for detailed genome comparisons with available Y. pestis sequences. Analyses of identified differences across a panel of Yersinia isolates from around the world reveal 32 Y. pestis chromosomal genes that, together with the two Y. pestis-specific plasmids, to our knowledge, represent the only new genetic material in Y. pestis acquired since the the divergence from Y. pseudotuberculosis. In contrast, 149 other pseudogenes (doubling the previous estimate) and 317 genes absent from Y. pestis were detected, indicating that as many as 13% of Y. pseudotuberculosis genes no longer function in Y. pestis. Extensive insertion sequence-mediated genome rearrangements and reductive evolution through massive gene loss, resulting in elimination and modification of preexisting gene expression pathways, appear to be more important than acquisition of genes in the evolution of Y. pestis. These results provide a sobering example of how a highly virulent epidemic clone can suddenly emerge from a less virulent, closely related progenitor.
ESTHER : Chain_2004_Proc.Natl.Acad.Sci.U.S.A_101_13826
PubMedSearch : Chain_2004_Proc.Natl.Acad.Sci.U.S.A_101_13826
PubMedID: 15358858
Gene_locus related to this paper: yerpe-BIOH , yerpe-dlhh , yerpe-IRP1 , yerpe-PIP , yerpe-PLDB , yerpe-PTRB , yerpe-Y0507 , yerpe-Y0644 , yerpe-y1616 , yerpe-y3224 , yerpe-YBTT , yerpe-YPLA , yerpe-YPO0180 , yerpe-YPO0667 , yerpe-YPO0773 , yerpe-YPO0776 , yerpe-YPO0986 , yerpe-YPO1501 , yerpe-YPO1997 , yerpe-YPO2002 , yerpe-YPO2336 , yerpe-YPO2526 , yerpe-YPO2638 , yerpe-YPO2814

Title : The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens - Duchaud_2003_Nat.Biotechnol_21_1307
Author(s) : Duchaud E , Rusniok C , Frangeul L , Buchrieser C , Givaudan A , Taourit S , Bocs S , Boursaux-Eude C , Chandler M , Charles JF , Dassa E , Derose R , Derzelle S , Freyssinet G , Gaudriault S , Medigue C , Lanois A , Powell K , Siguier P , Vincent R , Wingate V , Zouine M , Glaser P , Boemare N , Danchin A , Kunst F
Ref : Nat Biotechnol , 21 :1307 , 2003
Abstract : Photorhabdus luminescens is a symbiont of nematodes and a broad-spectrum insect pathogen. The complete genome sequence of strain TT01 is 5,688,987 base pairs (bp) long and contains 4,839 predicted protein-coding genes. Strikingly, it encodes a large number of adhesins, toxins, hemolysins, proteases and lipases, and contains a wide array of antibiotic synthesizing genes. These proteins are likely to play a role in the elimination of competitors, host colonization, invasion and bioconversion of the insect cadaver, making P. luminescens a promising model for the study of symbiosis and host-pathogen interactions. Comparison with the genomes of related bacteria reveals the acquisition of virulence factors by extensive horizontal transfer and provides clues about the evolution of an insect pathogen. Moreover, newly identified insecticidal proteins may be effective alternatives for the control of insect pests.
ESTHER : Duchaud_2003_Nat.Biotechnol_21_1307
PubMedSearch : Duchaud_2003_Nat.Biotechnol_21_1307
PubMedID: 14528314
Gene_locus related to this paper: pholl-q7maz3 , pholl-q7mb82 , pholl-q7mza3 , pholl-q7mzf6 , pholl-q7n0d9 , pholl-q7n2c6 , pholl-q7n2f0 , pholl-q7n2f7 , pholl-q7n2k4 , pholl-q7n3k0 , pholl-q7n3p5 , pholl-q7n3s1 , pholl-q7n4k8 , pholl-q7n4l0 , pholl-q7n4l7 , pholl-q7n4q6 , pholl-q7n4x6 , pholl-q7n5r3 , pholl-q7n6m7 , pholl-q7n6m8 , pholl-q7n6m9 , pholl-q7n6n0 , pholl-q7n7d3 , pholl-q7n8a5 , pholl-q7n132 , pholl-q7n239 , pholl-q7n246 , pholl-q7n258 , pholl-y1242 , pholu-BIOH , pholu-LUXD2 , pholu-PIP , pholu-PLDB , pholu-PLU0113 , pholu-PLU0399 , pholu-PLU1261 , pholu-PLU1531 , pholu-PLU1532 , pholu-PLU2160 , pholu-PLU2202 , pholu-PLU2437 , pholu-PLU3206

Title : Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv - Camus_2002_Microbiology_148_2967
Author(s) : Camus JC , Pryor MJ , Medigue C , Cole ST
Ref : Microbiology , 148 :2967 , 2002
Abstract : Original genome annotations need to be regularly updated if the information they contain is to remain accurate and relevant. Here the complete re-annotation of the genome sequence of Mycobacterium tuberculosis strain H37Rv is presented almost 4 years after the first submission. Eighty-two new protein-coding sequences (CDS) have been included and 22 of these have a predicted function. The majority were identified by manual or automated re-analysis of the genome and most of them were shorter than the 100 codon cut-off used in the initial genome analysis. The functional classification of 643 CDS has been changed based principally on recent sequence comparisons and new experimental data from the literature. More than 300 gene names and over 1000 targeted citations have been added and the lengths of 60 genes have been modified. Presently, it is possible to assign a function to 2058 proteins (52% of the 3995 proteins predicted) and only 376 putative proteins share no homology with known proteins and thus could be unique to M. tuberculosis.
ESTHER : Camus_2002_Microbiology_148_2967
PubMedSearch : Camus_2002_Microbiology_148_2967
PubMedID: 12368430
Gene_locus related to this paper: myctu-d5yk66 , myctu-ephA , myctu-ephB , myctu-LPQP , myctu-p71654 , myctu-Rv0160c , myctu-RV0774C , myctu-Rv2485c , myctu-RV2672 , myctu-RV2695 , myctu-RV2765 , myctu-RV2800 , myctu-Rv2970c , myctu-Rv3084 , myctu-Rv3097c , myctu-RV3452

Title : Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence - Medigue_1999_Genome.Res_9_1116
Author(s) : Medigue C , Rose M , Viari A , Danchin A
Ref : Genome Res , 9 :1116 , 1999
Abstract : During the determination of a DNA sequence, the introduction of artifactual frameshifts and/or in-frame stop codons in putative genes can lead to misprediction of gene products. Detection of such errors with a method based on protein similarity matching is only possible when related sequences are available in databases. Here, we present a method to detect frameshift errors in DNA sequences that is based on the intrinsic properties of the coding sequences. It combines the results of two analyses, the search for translational initiation/termination sites and the prediction of coding regions. This method was used to screen the complete Bacillus subtilis genome sequence and the regions flanking putative errors were resequenced for verification. This procedure allowed us to correct the sequence and to analyze in detail the nature of the errors. Interestingly, in several cases in-frame termination codons or frameshifts were not sequencing errors but confirmed to be present in the chromosome, indicating that the genes are either nonfunctional (pseudogenes) or subject to regulatory processes such as programmed translational frameshifts. The method can be used for checking the quality of the sequences produced by any prokaryotic genome sequencing project.
ESTHER : Medigue_1999_Genome.Res_9_1116
PubMedSearch : Medigue_1999_Genome.Res_9_1116
PubMedID: 10568751
Gene_locus related to this paper: bacsu-YUKL

Title : The complete genome sequence of the gram-positive bacterium Bacillus subtilis - Kunst_1997_Nature_390_249
Author(s) : Kunst F , Ogasawara N , Moszer I , Albertini AM , Alloni G , Azevedo V , Bertero MG , Bessieres P , Bolotin A , Borchert S , Borriss R , Boursier L , Brans A , Braun M , Brignell SC , Bron S , Brouillet S , Bruschi CV , Caldwell B , Capuano V , Carter NM , Choi SK , Cordani JJ , Connerton IF , Cummings NJ , Daniel RA , Denziot F , Devine KM , Dusterhoft A , Ehrlich SD , Emmerson PT , Entian KD , Errington J , Fabret C , Ferrari E , Foulger D , Fritz C , Fujita M , Fujita Y , Fuma S , Galizzi A , Galleron N , Ghim SY , Glaser P , Goffeau A , Golightly EJ , Grandi G , Guiseppi G , Guy BJ , Haga K , Haiech J , Harwood CR , Henaut A , Hilbert H , Holsappel S , Hosono S , Hullo MF , Itaya M , Jones L , Joris B , Karamata D , Kasahara Y , Klaerr-Blanchard M , Klein C , Kobayashi Y , Koetter P , Koningstein G , Krogh S , Kumano M , Kurita K , Lapidus A , Lardinois S , Lauber J , Lazarevic V , Lee SM , Levine A , Liu H , Masuda S , Mauel C , Medigue C , Medina N , Mellado RP , Mizuno M , Moestl D , Nakai S , Noback M , Noone D , O'Reilly M , Ogawa K , Ogiwara A , Oudega B , Park SH , Parro V , Pohl TM , Portelle D , Porwollik S , Prescott AM , Presecan E , Pujic P , Purnelle B , Rapoport G , Rey M , Reynolds S , Rieger M , Rivolta C , Rocha E , Roche B , Rose M , Sadaie Y , Sato T , Scanlan E , Schleich S , Schroeter R , Scoffone F , Sekiguchi J , Sekowska A , Seror SJ , Serror P , Shin BS , Soldo B , Sorokin A , Tacconi E , Takagi T , Takahashi H , Takemaru K , Takeuchi M , Tamakoshi A , Tanaka T , Terpstra P , Togoni A , Tosato V , Uchiyama S , Vandebol M , Vannier F , Vassarotti A , Viari A , Wambutt R , Wedler H , Weitzenegger T , Winters P , Wipat A , Yamamoto H , Yamane K , Yasumoto K , Yata K , Yoshida K , Yoshikawa HF , Zumstein E , Yoshikawa H , Danchin A
Ref : Nature , 390 :249 , 1997
Abstract : Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.
ESTHER : Kunst_1997_Nature_390_249
PubMedSearch : Kunst_1997_Nature_390_249
PubMedID: 9384377
Gene_locus related to this paper: bacsu-CAH , bacsu-cbxnp , bacsu-lip , bacsu-LIPB , bacsu-PKSR , bacsu-pnbae , bacsu-PPSE , bacsu-srf4 , bacsu-srfac , bacsu-YBAC , bacsu-YBDG , bacsu-ybfk , bacsu-ycgS , bacsu-yczh , bacsu-YDEN , bacsu-ydjp , bacsu-yfhM , bacsu-yisY , bacsu-YITV , bacsu-yjau , bacsu-YJCH , bacsu-MHQD , bacsu-yqjl , bacsu-yqkd , bacsu-YRAK , bacsu-YTAP , bacsu-YTMA , bacsu-YTPA , bacsu-ytxm , bacsu-yugF , bacsu-YUII , bacsu-YUKL , bacsu-YVAK , bacsu-YvaM , bacsu-RsbQ