Mangenot S

References (27)

Title : Structural and functional partitioning of bread wheat chromosome 3B - Choulet_2014_Science_345_1249721
Author(s) : Choulet F , Alberti A , Theil S , Glover N , Barbe V , Daron J , Pingault L , Sourdille P , Couloux A , Paux E , Leroy P , Mangenot S , Guilhot N , Le Gouis J , Balfourier F , Alaux M , Jamilloux V , Poulain J , Durand C , Bellec A , Gaspin C , Safar J , Dolezel J , Rogers J , Vandepoele K , Aury JM , Mayer K , Berges H , Quesneville H , Wincker P , Feuillet C
Ref : Science , 345 :1249721 , 2014
Abstract : We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
ESTHER : Choulet_2014_Science_345_1249721
PubMedSearch : Choulet_2014_Science_345_1249721
PubMedID: 25035497
Gene_locus related to this paper: wheat-a0a080yuw6 , wheat-w5d1z6 , wheat-a0a077rex4 , wheat-a0a077s1q2

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 : 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 : 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 : Genome sequence of the human- and animal-pathogenic strain Nocardia cyriacigeorgica GUH-2 - Zoropogui_2012_J.Bacteriol_194_2098
Author(s) : Zoropogui A , Pujic P , Normand P , Barbe V , Beaman B , Beaman L , Boiron P , Colinon C , Deredjian A , Graindorge A , Mangenot S , Nazaret S , Neto M , Petit S , Roche D , Vallenet D , Rodriguez-Nava V , Richard Y , Cournoyer B , Blaha D
Ref : Journal of Bacteriology , 194 :2098 , 2012
Abstract : The pathogenic strain Nocardia cyriacigeorgica GUH-2 was isolated from a fatal human nocardiosis case, and its genome was sequenced. The complete genomic sequence of this strain contains 6,194,645 bp, an average G+C content of 68.37%, and no plasmids. We also identified several protein-coding genes to which N. cyriacigeorgica's virulence can potentially be attributed.
ESTHER : Zoropogui_2012_J.Bacteriol_194_2098
PubMedSearch : Zoropogui_2012_J.Bacteriol_194_2098
PubMedID: 22461543
Gene_locus related to this paper: noccg-h6r1f5 , noccg-h6r6y9 , noccg-h6r479 , noccg-h6rch6 , noccg-h6r8b1 , noccg-h6r6b6 , noccg-h6r249 , noccg-h6r9n3 , noccg-h6r4q8 , noccg-h6rbg1 , noccg-h6r7g5 , noccg-h6r481 , noccg-h6r0w3 , noccg-h6r3f1

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 : 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 : 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 : Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments - Wisniewski-Dye_2011_PLoS.Genet_7_e1002430
Author(s) : Wisniewski-Dye F , Borziak K , Khalsa-Moyers G , Alexandre G , Sukharnikov LO , Wuichet K , Hurst GB , McDonald WH , Robertson JS , Barbe V , Calteau A , Rouy Z , Mangenot S , Prigent-Combaret C , Normand P , Boyer M , Siguier P , Dessaux Y , Elmerich C , Condemine G , Krishnen G , Kennedy I , Paterson AH , Gonzalez V , Mavingui P , Zhulin IB
Ref : PLoS Genet , 7 :e1002430 , 2011
Abstract : Fossil records indicate that life appeared in marine environments approximately 3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land.
ESTHER : Wisniewski-Dye_2011_PLoS.Genet_7_e1002430
PubMedSearch : Wisniewski-Dye_2011_PLoS.Genet_7_e1002430
PubMedID: 22216014
Gene_locus related to this paper: azobr-g8al65 , azol4-g7zc95 , azol4-g7zc98 , azol4-g7zfp9 , azol4-g7zcr5 , azobr-g8b0i6

Title : Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites - Barbe_2011_J.Bacteriol_193_5055
Author(s) : Barbe V , Bouzon M , Mangenot S , Badet B , Poulain J , Segurens B , Vallenet D , Marliere P , Weissenbach J
Ref : Journal of Bacteriology , 193 :5055 , 2011
Abstract : Streptomyces cattleya, a producer of the antibiotics thienamycin and cephamycin C, is one of the rare bacteria known to synthesize fluorinated metabolites. The genome consists of two linear replicons. The genes involved in fluorine metabolism and in the biosynthesis of the antibiotic thienamycin were mapped on both replicons.
ESTHER : Barbe_2011_J.Bacteriol_193_5055
PubMedSearch : Barbe_2011_J.Bacteriol_193_5055
PubMedID: 21868806
Gene_locus related to this paper: stren-f8jjf8 , stren-f8jk65 , stren-f8jly2 , stren-f8jm04 , stren-f8juv4 , stren-f8k466 , stren-f8jvj2 , stren-f8k4s8

Title : Nitrite-driven anaerobic methane oxidation by oxygenic bacteria - Ettwig_2010_Nature_464_543
Author(s) : Ettwig KF , Butler MK , Le Paslier D , Pelletier E , Mangenot S , Kuypers MM , Schreiber F , Dutilh BE , Zedelius J , de Beer D , Gloerich J , Wessels HJ , van Alen T , Luesken F , Wu ML , van de Pas-Schoonen KT , Op den Camp HJ , Janssen-Megens EM , Francoijs KJ , Stunnenberg H , Weissenbach J , Jetten MS , Strous M
Ref : Nature , 464 :543 , 2010
Abstract : Only three biological pathways are known to produce oxygen: photosynthesis, chlorate respiration and the detoxification of reactive oxygen species. Here we present evidence for a fourth pathway, possibly of considerable geochemical and evolutionary importance. The pathway was discovered after metagenomic sequencing of an enrichment culture that couples anaerobic oxidation of methane with the reduction of nitrite to dinitrogen. The complete genome of the dominant bacterium, named 'Candidatus Methylomirabilis oxyfera', was assembled. This apparently anaerobic, denitrifying bacterium encoded, transcribed and expressed the well-established aerobic pathway for methane oxidation, whereas it lacked known genes for dinitrogen production. Subsequent isotopic labelling indicated that 'M. oxyfera' bypassed the denitrification intermediate nitrous oxide by the conversion of two nitric oxide molecules to dinitrogen and oxygen, which was used to oxidize methane. These results extend our understanding of hydrocarbon degradation under anoxic conditions and explain the biochemical mechanism of a poorly understood freshwater methane sink. Because nitrogen oxides were already present on early Earth, our finding opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis.
ESTHER : Ettwig_2010_Nature_464_543
PubMedSearch : Ettwig_2010_Nature_464_543
PubMedID: 20336137
Gene_locus related to this paper: 9bact-d5mm47

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 : Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity - Nouvel_2010_BMC.Genomics_11_86
Author(s) : Nouvel LX , Sirand-Pugnet P , Marenda MS , Sagne E , Barbe V , Mangenot S , Schenowitz C , Jacob D , Barre A , Claverol S , Blanchard A , Citti C
Ref : BMC Genomics , 11 :86 , 2010
Abstract : BACKGROUND: While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study.
RESULTS: The two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms. CONCLUSION: Overall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.
ESTHER : Nouvel_2010_BMC.Genomics_11_86
PubMedSearch : Nouvel_2010_BMC.Genomics_11_86
PubMedID: 20122262
Gene_locus related to this paper: myca6-d3vqz4 , mycap-a5ixe1 , mycap-a5ixe2 , mycap-a5ixk0 , mycap-a5ixt9 , mycap-a5iy19 , mycap-a5iza3 , mycap-a5ixl0

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 : The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae - Pieretti_2009_BMC.Genomics_10_616
Author(s) : Pieretti I , Royer M , Barbe V , Carrere S , Koebnik R , Cociancich S , Couloux A , Darrasse A , Gouzy J , Jacques MA , Lauber E , Manceau C , Mangenot S , Poussier S , Segurens B , Szurek B , Verdier V , Arlat M , Rott P
Ref : BMC Genomics , 10 :616 , 2009
Abstract : BACKGROUND: The Xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, Xanthomonas albilineans and Xylella fastidiosa. X. fastidiosa was the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possess hrp genes which encode a Type III secretion system found in most plant pathogenic bacteria. X. fastidiosa was excluded from the Xanthomonas group based on phylogenetic analyses with rRNA sequences.
RESULTS: The complete genome of X. albilineans was sequenced and annotated. X. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possess hrp genes. Phylogenetic analysis using X. albilineans genomic sequences showed that X. fastidiosa belongs to the Xanthomonas group. Order of divergence of the Xanthomonadaceae revealed that X. albilineans and X. fastidiosa experienced a convergent reductive genome evolution during their descent from the progenitor of the Xanthomonas genus. Reductive genome evolutions of the two xylem-limited Xanthomonadaceae were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens. CONCLUSION: The two xylem-limited Xanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. Adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. However, genome characteristics of X. albilineans differ from those of X. fastidiosa and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. The possible role in genome reduction of the unique toxin albicidin, produced by X. albilineans, is discussed.
ESTHER : Pieretti_2009_BMC.Genomics_10_616
PubMedSearch : Pieretti_2009_BMC.Genomics_10_616
PubMedID: 20017926
Gene_locus related to this paper: xanal-q53b17 , xanap-d2u924 , xanap-d2uar7 , xanap-d2ub15 , xanap-d2ucz4 , xanap-d2ue41 , xanap-d2ue72 , xanap-d2ueb5 , xanap-d2uf40 , xanap-d2ugg6 , xanap-d2ugj3 , xanap-d2ugr3 , xanap-d2ugv1 , xanap-d2ubh2 , xanap-d2ud71 , xanap-d2u9n1 , xanap-d2uci9

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 : Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome - Sirand-Pugnet_2007_PLoS.Genet_3_e75
Author(s) : Sirand-Pugnet P , Lartigue C , Marenda M , Jacob D , Barre A , Barbe V , Schenowitz C , Mangenot S , Couloux A , Segurens B , de Daruvar A , Blanchard A , Citti C
Ref : PLoS Genet , 3 :e75 , 2007
Abstract : Mycoplasmas are commonly described as the simplest self-replicating organisms, whose evolution was mainly characterized by genome downsizing with a proposed evolutionary scenario similar to that of obligate intracellular bacteria such as insect endosymbionts. Thus far, analysis of mycoplasma genomes indicates a low level of horizontal gene transfer (HGT) implying that DNA acquisition is strongly limited in these minimal bacteria. In this study, the genome of the ruminant pathogen Mycoplasma agalactiae was sequenced. Comparative genomic data and phylogenetic tree reconstruction revealed that approximately 18% of its small genome (877,438 bp) has undergone HGT with the phylogenetically distinct mycoides cluster, which is composed of significant ruminant pathogens. HGT involves genes often found as clusters, several of which encode lipoproteins that usually play an important role in mycoplasma-host interaction. A decayed form of a conjugative element also described in a member of the mycoides cluster was found in the M. agalactiae genome, suggesting that HGT may have occurred by mobilizing a related genetic element. The possibility of HGT events among other mycoplasmas was evaluated with the available sequenced genomes. Our data indicate marginal levels of HGT among Mycoplasma species except for those described above and, to a lesser extent, for those observed in between the two bird pathogens, M. gallisepticum and M. synoviae. This first description of large-scale HGT among mycoplasmas sharing the same ecological niche challenges the generally accepted evolutionary scenario in which gene loss is the main driving force of mycoplasma evolution. The latter clearly differs from that of other bacteria with small genomes, particularly obligate intracellular bacteria that are isolated within host cells. Consequently, mycoplasmas are not only able to subvert complex hosts but presumably have retained sexual competence, a trait that may prevent them from genome stasis and contribute to adaptation to new hosts.
ESTHER : Sirand-Pugnet_2007_PLoS.Genet_3_e75
PubMedSearch : Sirand-Pugnet_2007_PLoS.Genet_3_e75
PubMedID: 17511520
Gene_locus related to this paper: mycap-a5ixe1 , mycap-a5ixe2 , mycap-a5ixk0 , mycap-a5ixt9 , mycap-a5iy19 , mycap-a5iza3 , mycap-a5ixl0

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 : Evolution of the terminal regions of the Streptomyces linear chromosome - Choulet_2006_Mol.Biol.Evol_23_2361
Author(s) : Choulet F , Aigle B , Gallois A , Mangenot S , Gerbaud C , Truong C , Francou FX , Fourrier C , Guerineau M , Decaris B , Barbe V , Pernodet JL , Leblond P
Ref : Molecular Biology Evolution , 23 :2361 , 2006
Abstract : Comparative analysis of the Streptomyces chromosome sequences, between Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces ambofaciens ATCC23877 (whose partial sequence is released in this study), revealed a highly compartmentalized genetic organization of their genome. Indeed, despite the presence of specific genomic islands, the central part of the chromosome appears highly syntenic. In contrast, the chromosome of each species exhibits large species-specific terminal regions (from 753 to 1,393 kb), even when considering closely related species (S. ambofaciens and S. coelicolor). Interestingly, the size of the central conserved region between species decreases as the phylogenetic distance between them increases, whereas the specific terminal fraction reciprocally increases in size. Between highly syntenic central regions and species-specific chromosomal parts, there is a notable degeneration of synteny due to frequent insertions/deletions. This reveals a massive and constant genomic flux (from lateral gene transfer and DNA rearrangements) affecting the terminal contingency regions. We speculate that a gradient of recombination rate (i.e., insertion/deletion events) toward the extremities is the force driving the exclusion of essential genes from the terminal regions (i.e., chromosome compartmentalization) and generating a fast gene turnover for strong adaptation capabilities.
ESTHER : Choulet_2006_Mol.Biol.Evol_23_2361
PubMedSearch : Choulet_2006_Mol.Biol.Evol_23_2361
PubMedID: 16956972
Gene_locus related to this paper: stram-a0abw5 , stram-a0ac15 , stram-a0ac26 , stram-a0ac27 , stram-a0acp3 , stram-a0acq4 , stram-a0acx2.1 , stram-a0acx2.2 , stram-a0adx4 , stram-a0aeb0 , stram-a3ki49 , stram-a3ki77 , stram-a3ki84 , stram-a3ki91 , stram-a3kik7 , stram-a3kj27 , stram-a3kkf9 , stram-a3kkk4 , stram-a3kkk5 , stram-q1rrf2 , strco-SCF11.06 , strco-SCO7057 , stram-a0acr7

Title : Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens - Choulet_2006_J.Bacteriol_188_6599
Author(s) : Choulet F , Gallois A , Aigle B , Mangenot S , Gerbaud C , Truong C , Francou FX , Borges F , Fourrier C , Guerineau M , Decaris B , Barbe V , Pernodet JL , Leblond P
Ref : Journal of Bacteriology , 188 :6599 , 2006
Abstract : The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.
ESTHER : Choulet_2006_J.Bacteriol_188_6599
PubMedSearch : Choulet_2006_J.Bacteriol_188_6599
PubMedID: 16952952
Gene_locus related to this paper: stram-q0jwm8 , stram-q1rql3 , stram-q1rqp7 , stram-q1rqu8 , stram-q1rqw8 , stram-q1rr14 , stram-q1rr40 , stram-q1rr62 , stram-q1rrc9 , stram-q1rrf2 , stram-Q9KWX3

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 : The complete genome sequence of Lactobacillus bulgaricus reveals extensive and ongoing reductive evolution - van de Guchte_2006_Proc.Natl.Acad.Sci.U.S.A_103_9274
Author(s) : van de Guchte M , Penaud S , Grimaldi C , Barbe V , Bryson K , Nicolas P , Robert C , Oztas S , Mangenot S , Couloux A , Loux V , Dervyn R , Bossy R , Bolotin A , Batto JM , Walunas T , Gibrat JF , Bessieres P , Weissenbach J , Ehrlich SD , Maguin E
Ref : Proc Natl Acad Sci U S A , 103 :9274 , 2006
Abstract : Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.
ESTHER : van de Guchte_2006_Proc.Natl.Acad.Sci.U.S.A_103_9274
PubMedSearch : van de Guchte_2006_Proc.Natl.Acad.Sci.U.S.A_103_9274
PubMedID: 16754859
Gene_locus related to this paper: lacda-q1g8l1 , lacdb-q04ci8 , lacdb-q04cw3 , lacdl-pepx , lacdl-pip

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 : Genome sequence of the plant pathogen Ralstonia solanacearum - Salanoubat_2002_Nature_415_497
Author(s) : Salanoubat M , Genin S , Artiguenave F , Gouzy J , Mangenot S , Arlat M , Billault A , Brottier P , Camus JC , Cattolico L , Chandler M , Choisne N , Claudel-Renard C , Cunnac S , Demange N , Gaspin C , Lavie M , Moisan A , Robert C , Saurin W , Schiex T , Siguier P , Thebault P , Whalen M , Wincker P , Levy M , Weissenbach J , Boucher CA
Ref : Nature , 415 :497 , 2002
Abstract : Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.
ESTHER : Salanoubat_2002_Nature_415_497
PubMedSearch : Salanoubat_2002_Nature_415_497
PubMedID: 11823852
Gene_locus related to this paper: ralso-DEHH , ralso-METX , ralso-PCAD , ralso-PCAD2 , ralso-PHAZ , ralso-PHBC , ralso-q8xsf9 , ralso-q8xta6 , ralso-q8xtf1 , ralso-RSC0055 , ralso-RSC0206 , ralso-RSC0268 , ralso-RSC0328 , ralso-RSC0439 , ralso-RSC0563 , ralso-RSC0604 , ralso-RSC0827 , ralso-RSC1003 , ralso-RSC1125 , ralso-RSC1135 , ralso-RSC1344 , ralso-RSC1396 , ralso-RSC1561 , ralso-RSC1573 , ralso-RSC1770 , ralso-RSC1772 , ralso-RSC1804 , ralso-RSC1811 , ralso-RSC1841 , ralso-RSC1887 , ralso-RSC2082 , ralso-RSC2149 , ralso-RSC2228 , ralso-RSC2317 , ralso-RSC2319 , ralso-RSC2328 , ralso-RSC2593 , ralso-RSC2781 , ralso-RSC3165 , ralso-RSC3312 , ralso-RSC3346 , ralso-RSC3406 , ralso-RSP0196 , ralso-RSP0232 , ralso-RSP0642 , ralso-RSP0769 , ralso-RSP0780 , ralso-RSP0790 , ralso-RSP0795 , ralso-RSP1108 , ralso-RSP1111 , ralso-RSP1148 , ralso-RSP1167 , ralso-RSP1229 , ralso-RSP1248 , ralso-RSP1339 , ralso-RSP1355 , ralso-RSP1418 , ralso-RSP1419 , ralso-RSP1422 , ralso-RSP1429 , ralso-RSP1435 , ralso-RSP1484 , ralso-RSP1521 , ralso-hboh , ralso-q8y0t3