Raoult D

References (25)

Title : Draft Genome Sequence of Mycobacterium farcinogenes NCTC 10955 - Croce_2014_Genome.Announc_2_e00523
Author(s) : Croce O , Robert C , Raoult D , Drancourt M
Ref : Genome Announc , 2 : , 2014
Abstract : We report the draft genome sequence of Mycobacterium farcinogenes NCTC 10955 (=DSM 43637(T)), a nontuberculosis species responsible for bovine farcy. The strain described here is composed of 6,139,893 bp, with a G+C content of 65.73%, and contains 5,816 protein-coding genes and 76 RNA genes.
ESTHER : Croce_2014_Genome.Announc_2_e00523
PubMedSearch : Croce_2014_Genome.Announc_2_e00523
PubMedID: 24874688
Gene_locus related to this paper: 9myco-a0a024ly05 , 9myco-a0a024lvn4 , 9myco-a0a024m823 , 9myco-a0a024m0q8 , 9myco-a0a024m4g1 , 9myco-a0a024m133 , 9myco-a0a024m2v2.1 , 9myco-a0a024m2v2.2 , 9myco-a0a024m2v2.3 , 9myco-a0a024m3q2.1 , 9myco-a0a024m3q2.2 , 9myco-a0a024m3q2.3 , 9myco-a0a0j8wms4

Title : Genome Sequence of Bacillus simplex Strain P558, Isolated from a Human Fecal Sample - Croce_2014_Genome.Announc_2_e01241
Author(s) : Croce O , Hugon P , Lagier JC , Bibi F , Robert C , Azhar EI , Raoult D , Fournier PE
Ref : Genome Announc , 2 : , 2014
Abstract : Bacillus simplex strain P558 was isolated from a fecal sample of a 25-year-old Saudi male. We sequenced the 5.98-Mb genome of the strain and compared it to that of B. simplex strain 1NLA3E.
ESTHER : Croce_2014_Genome.Announc_2_e01241
PubMedSearch : Croce_2014_Genome.Announc_2_e01241
PubMedID: 25502663
Gene_locus related to this paper: 9baci-a0a098fhj8 , 9baci-a0a098f6b4 , 9baci-a0a098fiz4 , 9baci-a0a098eta7 , 9baci-a0a098f9v8 , 9baci-a0a098fhu8

Title : Draft Genome Sequence of Mycobacterium triplex DSM 44626 - Sassi_2014_Genome.Announc_2_e00499
Author(s) : Sassi M , Croce O , Robert C , Raoult D , Drancourt M
Ref : Genome Announc , 2 : , 2014
Abstract : We announce the draft genome sequence of Mycobacterium triplex strain DSM 44626, a nontuberculosis species responsible for opportunistic infections. The genome described here is composed of 6,382,840 bp, with a G+C content of 66.57%, and contains 5,988 protein-coding genes and 81 RNA genes.
ESTHER : Sassi_2014_Genome.Announc_2_e00499
PubMedSearch : Sassi_2014_Genome.Announc_2_e00499
PubMedID: 24874681
Gene_locus related to this paper: 9myco-a0a024jwa3 , 9myco-a0a024k0r7

Title : Comparative genomics analysis of Lactobacillus species associated with weight gain or weight protection - Drissi_2014_Nutr.Diabetes_4_e109
Author(s) : Drissi F , Merhej V , Angelakis E , El Kaoutari A , Carriere F , Henrissat B , Raoult D
Ref : Nutr Diabetes , 4 :e109 , 2014
Abstract : BACKGROUND: Some Lactobacillus species are associated with obesity and weight gain while others are associated with weight loss. Lactobacillus spp. and bifidobacteria represent a major bacterial population of the small intestine where lipids and simple carbohydrates are absorbed, particularly in the duodenum and jejunum. The objective of this study was to identify Lactobacillus spp. proteins involved in carbohydrate and lipid metabolism associated with weight modifications.
METHODS: We examined a total of 13 complete genomes belonging to seven different Lactobacillus spp. previously associated with weight gain or weight protection. We combined the data obtained from the Rapid Annotation using Subsystem Technology, Batch CD-Search and Gene Ontology to classify gene function in each genome.
RESULTS: We observed major differences between the two groups of genomes. Weight gain-associated Lactobacillus spp. appear to lack enzymes involved in the catabolism of fructose, defense against oxidative stress and the synthesis of dextrin, L-rhamnose and acetate. Weight protection-associated Lactobacillus spp. encoded a significant gene amount of glucose permease. Regarding lipid metabolism, thiolases were only encoded in the genome of weight gain-associated Lactobacillus spp. In addition, we identified 18 different types of bacteriocins in the studied genomes, and weight gain-associated Lactobacillus spp. encoded more bacteriocins than weight protection-associated Lactobacillus spp.
CONCLUSIONS: The results of this study revealed that weight protection-associated Lactobacillus spp. have developed defense mechanisms for enhanced glycolysis and defense against oxidative stress. Weight gain-associated Lactobacillus spp. possess a limited ability to breakdown fructose or glucose and might reduce ileal brake effects.
ESTHER : Drissi_2014_Nutr.Diabetes_4_e109
PubMedSearch : Drissi_2014_Nutr.Diabetes_4_e109
PubMedID: 24567124

Title : Genome Sequence of Legionella anisa, Isolated from a Respiratory Sample, Using an Amoebal Coculture Procedure - Pagnier_2014_Genome.Announc_2_
Author(s) : Pagnier I , Croce O , Robert C , Raoult D , La Scola B
Ref : Genome Announc , 2 : , 2014
Abstract : Legionella anisa is a gammaproteobacterium from the class Legionellaceae, which is responsible for nosocomial pneumonia. We sequenced the genome from the L. anisa strain Linanisette, which was recovered from a clinical sample using an amoebal coculture procedure but not with standard culture methods.
ESTHER : Pagnier_2014_Genome.Announc_2_
PubMedSearch : Pagnier_2014_Genome.Announc_2_
PubMedID: 24503989

Title : Draft Genome Sequence of Mycobacterium vulneris DSM 45247T - Croce_2014_Genome.Announc_2_e00370
Author(s) : Croce O , Robert C , Raoult D , Drancourt M
Ref : Genome Announc , 2 : , 2014
Abstract : We report the draft genome sequence of Mycobacterium vulneris DSM 45247(T) strain, an emerging, opportunistic pathogen of the Mycobacterium avium complex. The genome described here is composed of 6,981,439 bp (with a G+C content of 67.14%) and has 6,653 protein-coding genes and 84 predicted RNA genes.
ESTHER : Croce_2014_Genome.Announc_2_e00370
PubMedSearch : Croce_2014_Genome.Announc_2_e00370
PubMedID: 24812218
Gene_locus related to this paper: 9myco-x5ldy7 , 9myco-x5lja3 , 9myco-x5lj65 , 9myco-x5lb13 , 9myco-x5ldh4 , 9myco-x5ltp5 , 9myco-x5lqd9 , 9myco-x5l9l5

Title : Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling - Clarke_2013_Genome.Biol_14_R11
Author(s) : Clarke M , Lohan AJ , Liu B , Lagkouvardos I , Roy S , Zafar N , Bertelli C , Schilde C , Kianianmomeni A , Burglin TR , Frech C , Turcotte B , Kopec KO , Synnott JM , Choo C , Paponov I , Finkler A , Heng Tan CS , Hutchins AP , Weinmeier T , Rattei T , Chu JS , Gimenez G , Irimia M , Rigden DJ , Fitzpatrick DA , Lorenzo-Morales J , Bateman A , Chiu CH , Tang P , Hegemann P , Fromm H , Raoult D , Greub G , Miranda-Saavedra D , Chen N , Nash P , Ginger ML , Horn M , Schaap P , Caler L , Loftus BJ
Ref : Genome Biol , 14 :R11 , 2013
Abstract : BACKGROUND: The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii (Ac) the first representative from a solitary free-living amoebozoan.
RESULTS: Ac encodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms.
CONCLUSIONS: Our analysis highlights the important role of LGT in the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Ac genome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.
ESTHER : Clarke_2013_Genome.Biol_14_R11
PubMedSearch : Clarke_2013_Genome.Biol_14_R11
PubMedID: 23375108
Gene_locus related to this paper: acaca-l8gel0 , acaca-l8gri8 , acaca-l8h8h3 , acaca-l8gtb6 , acaca-l8gr27 , acaca-l8h9l6 , acaca-l8hhi6 , acaca-l8grd3 , acaca-l8gju3 , acaca-l8h8t7 , acaca-l8h0a7

Title : The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new killer bugs are created because of a sympatric lifestyle - Diene_2013_Mol.Biol.Evol_30_369
Author(s) : Diene SM , Merhej V , Henry M , El Filali A , Roux V , Robert C , Azza S , Gavory F , Barbe V , La Scola B , Raoult D , Rolain JM
Ref : Molecular Biology Evolution , 30 :369 , 2013
Abstract : Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepancies of this bacterium and show that its core genome originates from another genus, Klebsiella. Atypical characteristics of this bacterium (i.e., motility, presence of ornithine decarboxylase, and lack of urease activity) are attributed to genomic mosaicism, by acquisition of additional genes, such as the complete 60,582 bp flagellar assembly operon acquired "en bloc" from the genus Serratia. The genealogic tree of the 162,202 bp multidrug-resistant conjugative plasmid shows that it is a chimera of transposons and integrative conjugative elements from various bacterial origins, resembling a rhizome. Moreover, we demonstrate biologically that a G53S mutation in the pmrA gene results in colistin resistance. E. aerogenes has a large RNA population comprising 8 rRNA operons and 87 cognate tRNAs that have the ability to translate transferred genes that use different codons, as exemplified by the significantly different codon usage between genes from the core genome and the "mobilome." On the basis of our findings, the evolution of this bacterium to become a "killer bug" with new genomic repertoires was from three criteria that are "opportunity, power, and usage" to indicate a sympatric lifestyle: "opportunity" to meet other bacteria and exchange foreign sequences since this bacteria was similar to sympatric bacteria; "power" to integrate these foreign sequences such as the acquisition of several mobile genetic elements (plasmids, integrative conjugative element, prophages, transposons, flagellar assembly system, etc.) found in his genome; and "usage" to have the ability to translate these sequences including those from rare codons to serve as a translator of foreign languages.
ESTHER : Diene_2013_Mol.Biol.Evol_30_369
PubMedSearch : Diene_2013_Mol.Biol.Evol_30_369
PubMedID: 23071100
Gene_locus related to this paper: entak-g0ea28 , entae-l8bq29 , entae-y1gc81 , entae-y1evy4

Title : Provirophages and transpovirons as the diverse mobilome of giant viruses - Desnues_2012_Proc.Natl.Acad.Sci.U.S.A_109_18078
Author(s) : Desnues C , La Scola B , Yutin N , Fournous G , Robert C , Azza S , Jardot P , Monteil S , Campocasso A , Koonin EV , Raoult D
Ref : Proc Natl Acad Sci U S A , 109 :18078 , 2012
Abstract : A distinct class of infectious agents, the virophages that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements, the transpovirons. The transpovirons are linear DNA elements of ~7 kb that encompass six to eight protein-coding genes, two of which are homologous to virophage genes. Fluorescence in situ hybridization showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns and inteins constitute the complex, interconnected mobilome of the giant viruses and are likely to substantially contribute to interviral gene transfer.
ESTHER : Desnues_2012_Proc.Natl.Acad.Sci.U.S.A_109_18078
PubMedSearch : Desnues_2012_Proc.Natl.Acad.Sci.U.S.A_109_18078
PubMedID: 23071316
Gene_locus related to this paper: mimvi-cxes

Title : Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes - Colson_2011_Genome.Biol.Evol_3_737
Author(s) : Colson P , Yutin N , Shabalina SA , Robert C , Fournous G , La Scola B , Raoult D , Koonin EV
Ref : Genome Biol Evol , 3 :737 , 2011
Abstract : The genome sequence of the Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, is reported. With 1,191,693 nt in length and 1,023 predicted protein-coding genes, the Mamavirus has the largest genome among the known viruses. The genomes of the Mamavirus and the previously described Mimivirus are highly similar in both the protein-coding genes and the intergenic regions. However, the Mamavirus contains an extra 5'-terminal segment that encompasses primarily disrupted duplicates of genes present elsewhere in the genome. The Mamavirus also has several unique genes including a small regulatory polyA polymerase subunit that is shared with poxviruses. Detailed analysis of the protein sequences of the two Mimiviruses led to a substantial amendment of the functional annotation of the viral genomes.
ESTHER : Colson_2011_Genome.Biol.Evol_3_737
PubMedSearch : Colson_2011_Genome.Biol.Evol_3_737
PubMedID: 21705471
Gene_locus related to this paper: mimvi-cxes

Title : Insight into cross-talk between intra-amoebal pathogens - Gimenez_2011_BMC.Genomics_12_542
Author(s) : Gimenez G , Bertelli C , Moliner C , Robert C , Raoult D , Fournier PE , Greub G
Ref : BMC Genomics , 12 :542 , 2011
Abstract : BACKGROUND: Amoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to different bacterial phyla and often show a larger genome size than human-infecting pathogens. This characteristic is proposed to be the result of frequent gene exchanges with other bacteria that share a sympatric lifestyle and contrasts with the genome reduction observed among strict human pathogens.
RESULTS: We sequenced the genome of a new amoebal pathogen, Legionella drancourtii, and compared its gene content to that of a Chlamydia-related bacterium, Parachlamydia acanthamoebae. Phylogenetic reconstructions identified seven potential horizontal gene transfers (HGTs) between the two amoeba-resistant bacteria, including a complete operon of four genes that encodes an ABC-type transporter. These comparisons pinpointed potential cases of gene exchange between P. acanthamoebae and Legionella pneumophila, as well as gene exchanges between other members of the Legionellales and Chlamydiales orders. Moreover, nine cases represent possible HGTs between representatives from the Legionellales or Chlamydiales and members of the Rickettsiales order.
CONCLUSIONS: This study identifies numerous gene exchanges between intracellular Legionellales and Chlamydiales bacteria, which could preferentially occur within common inclusions in their amoebal hosts. Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle.
ESTHER : Gimenez_2011_BMC.Genomics_12_542
PubMedSearch : Gimenez_2011_BMC.Genomics_12_542
PubMedID: 22047552
Gene_locus related to this paper: 9gamm-g9eqk0 , legpn-i7i328 , 9gamm-g9etp4

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 : Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle - Kirkness_2010_Proc.Natl.Acad.Sci.U.S.A_107_12168
Author(s) : Kirkness EF , Haas BJ , Sun W , Braig HR , Perotti MA , Clark JM , Lee SH , Robertson HM , Kennedy RC , Elhaik E , Gerlach D , Kriventseva EV , Elsik CG , Graur D , Hill CA , Veenstra JA , Walenz B , Tubio JM , Ribeiro JM , Rozas J , Johnston JS , Reese JT , Popadic A , Tojo M , Raoult D , Reed DL , Tomoyasu Y , Kraus E , Mittapalli O , Margam VM , Li HM , Meyer JM , Johnson RM , Romero-Severson J , Vanzee JP , Alvarez-Ponce D , Vieira FG , Aguade M , Guirao-Rico S , Anzola JM , Yoon KS , Strycharz JP , Unger MF , Christley S , Lobo NF , Seufferheld MJ , Wang N , Dasch GA , Struchiner CJ , Madey G , Hannick LI , Bidwell S , Joardar V , Caler E , Shao R , Barker SC , Cameron S , Bruggner RV , Regier A , Johnson J , Viswanathan L , Utterback TR , Sutton GG , Lawson D , Waterhouse RM , Venter JC , Strausberg RL , Berenbaum MR , Collins FH , Zdobnov EM , Pittendrigh BR
Ref : Proc Natl Acad Sci U S A , 107 :12168 , 2010
Abstract : As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.
ESTHER : Kirkness_2010_Proc.Natl.Acad.Sci.U.S.A_107_12168
PubMedSearch : Kirkness_2010_Proc.Natl.Acad.Sci.U.S.A_107_12168
PubMedID: 20566863
Gene_locus related to this paper: pedhb-ACHE1 , pedhb-ACHE2 , pedhc-e0v9b5 , pedhc-e0v9b6 , pedhc-e0v9b7 , pedhc-e0vbv5 , pedhc-e0vcd0 , pedhc-e0vcl7 , pedhc-e0vd69 , pedhc-e0ve50 , pedhc-e0vel6 , pedhc-e0vel7 , pedhc-e0vf98 , pedhc-e0vfs8 , pedhc-e0vfv0 , pedhc-e0vg01 , pedhc-e0vha2 , pedhc-e0vha4 , pedhc-e0vi52 , pedhc-e0vp42 , pedhc-e0vqu6 , pedhc-e0vuj9 , pedhc-e0vup6 , pedhc-e0vv55 , pedhc-e0vwv3 , pedhc-e0vxf7 , pedhc-e0vxg1 , pedhc-e0w4a6 , pedhc-e0w4c8 , pedhc-e0w271 , pedhc-e0w444 , pedhc-e0vym0 , pedhc-e0vdk9 , pedhc-e0vk10 , pedhc-e0vgw4 , pedhc-e0vgw7 , pedhc-e0vga1 , pedhc-e0w3s1 , pedhc-e0vzt2

Title : Analysis of the Rickettsia africae genome reveals that virulence acquisition in Rickettsia species may be explained by genome reduction - Fournier_2009_BMC.Genomics_10_166
Author(s) : Fournier PE , El Karkouri K , Leroy Q , Robert C , Giumelli B , Renesto P , Socolovschi C , Parola P , Audic S , Raoult D
Ref : BMC Genomics , 10 :166 , 2009
Abstract : BACKGROUND: The Rickettsia genus includes 25 validated species, 17 of which are proven human pathogens. Among these, the pathogenicity varies greatly, from the highly virulent R. prowazekii, which causes epidemic typhus and kills its arthropod host, to the mild pathogen R. africae, the agent of African tick-bite fever, which does not affect the fitness of its tick vector. RESULTS: We evaluated the clonality of R. africae in 70 patients and 155 ticks, and determined its genome sequence, which comprises a circular chromosome of 1,278,540 bp including a tra operon and an unstable 12,377-bp plasmid. To study the genetic characteristics associated with virulence, we compared this species to R. prowazekii, R. rickettsii and R. conorii. R. africae and R. prowazekii have, respectively, the less and most decayed genomes. Eighteen genes are present only in R. africae including one with a putative protease domain upregulated at 37 degrees C. CONCLUSION: Based on these data, we speculate that a loss of regulatory genes causes an increase of virulence of rickettsial species in ticks and mammals. We also speculate that in Rickettsia species virulence is mostly associated with gene loss.The genome sequence was deposited in GenBank under accession number [GenBank: NZ_AAUY01000001].
ESTHER : Fournier_2009_BMC.Genomics_10_166
PubMedSearch : Fournier_2009_BMC.Genomics_10_166
PubMedID: 19379498
Gene_locus related to this paper: ricco-PTRB , ricco-RC0603 , ricco-RC1147

Title : High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach - Greub_2009_PLoS.One_4_e8423
Author(s) : Greub G , Kebbi-Beghdadi C , Bertelli C , Collyn F , Riederer BM , Yersin C , Croxatto A , Raoult D
Ref : PLoS ONE , 4 :e8423 , 2009
Abstract : BACKGROUND: With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. METHODS/PRINCIPAL FINDINGS: We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. CONCLUSIONS/SIGNIFICANCE: This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.
ESTHER : Greub_2009_PLoS.One_4_e8423
PubMedSearch : Greub_2009_PLoS.One_4_e8423
PubMedID: 20037647
Gene_locus related to this paper: 9chla-d1rad2 , 9chla-d1rb34

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 : Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria - Audic_2007_PLoS.Genet_3_e138
Author(s) : Audic S , Robert C , Campagna B , Parinello H , Claverie JM , Raoult D , Drancourt M
Ref : PLoS Genet , 3 :e138 , 2007
Abstract : Filtration usually eliminates water-living bacteria. Here, we report on the complete genome sequence of Minibacterium massiliensis, a beta-proteobacteria that was recovered from 0.22-mum filtered water used for patients in the hospital. The unexpectedly large 4,110,251-nucleotide genome sequence of M. massiliensis was determined using the traditional shotgun sequencing approach. Bioinformatic analyses shows that the M. massiliensis genome sequence illustrates characteristic features of water-living bacteria, including overrepresentation of genes encoding transporters and transcription regulators. Phylogenomic analysis based on the gene content of available bacterial genome sequences displays a congruent evolution of water-living bacteria from various taxonomic origins, principally for genes involved in energy production and conversion, cell division, chromosome partitioning, and lipid metabolism. This phylogenomic clustering partially results from lateral gene transfer, which appears to be more frequent in water than in other environments. The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors.
ESTHER : Audic_2007_PLoS.Genet_3_e138
PubMedSearch : Audic_2007_PLoS.Genet_3_e138
PubMedID: 17722982
Gene_locus related to this paper: janma-a6sug3 , janma-a6sx64 , janma-a6sy27 , janma-a6sz66 , janma-a6szj6 , janma-a6t0i5 , janma-a6t1z4 , janma-a6t2m6 , janma-a6t3c3 , janma-a6t3c4 , janma-a6t422 , janma-metx , janma-a6t2a9

Title : Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome - Blanc_2007_Genome.Res_17_1657
Author(s) : Blanc G , Ogata H , Robert C , Audic S , Claverie JM , Raoult D
Ref : Genome Res , 17 :1657 , 2007
Abstract : Rickettsia massiliae is a tick-borne obligate intracellular alpha-proteobacteria causing spotted fever in humans. Here, we present the sequence of its genome, comprising a 1.3-Mb circular chromosome and a 15.3-kb plasmid. The chromosome exhibits long-range colinearity with the other Spotted Fever Group Rickettsia genomes, except for a large fragment specific to R. massiliae that contains 14 tra genes presumably involved in pilus formation and conjugal DNA transfer. We demonstrate that the tra region was acquired recently by lateral gene transfer (LGT) from a species related to Rickettsia bellii. Further analysis of the genomic sequences identifies additional candidates of LGT between Rickettsia. Our study indicates that recent LGT between obligate intracellular Rickettsia is more common than previously thought.
ESTHER : Blanc_2007_Genome.Res_17_1657
PubMedSearch : Blanc_2007_Genome.Res_17_1657
PubMedID: 17916642
Gene_locus related to this paper: ricco-PTRB , ricco-RC0603 , ricco-RC0617 , ricco-RC1147

Title : Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens - Ogata_2006_PLoS.Genet_2_e76
Author(s) : Ogata H , La Scola B , Audic S , Renesto P , Blanc G , Robert C , Fournier PE , Claverie JM , Raoult D
Ref : PLoS Genet , 2 :e76 , 2006
Abstract : The recently sequenced Rickettsia felis genome revealed an unexpected plasmid carrying several genes usually associated with DNA transfer, suggesting that ancestral rickettsiae might have been endowed with a conjugation apparatus. Here we present the genome sequence of Rickettsia bellii, the earliest diverging species of known rickettsiae. The 1,552,076 base pair-long chromosome does not exhibit the colinearity observed between other rickettsia genomes, and encodes a complete set of putative conjugal DNA transfer genes most similar to homologues found in Protochlamydia amoebophila UWE25, an obligate symbiont of amoebae. The genome exhibits many other genes highly similar to homologues in intracellular bacteria of amoebae. We sought and observed sex pili-like cell surface appendages for R. bellii. We also found that R. bellii very efficiently multiplies in the nucleus of eukaryotic cells and survives in the phagocytic amoeba, Acanthamoeba polyphaga. These results suggest that amoeba-like ancestral protozoa could have served as a genetic "melting pot" where the ancestors of rickettsiae and other bacteria promiscuously exchanged genes, eventually leading to their adaptation to the intracellular lifestyle within eukaryotic cells.
ESTHER : Ogata_2006_PLoS.Genet_2_e76
PubMedSearch : Ogata_2006_PLoS.Genet_2_e76
PubMedID: 16703114
Gene_locus related to this paper: ricbr-q1rh50 , ricbr-q1rie6 , ricbr-q1rin0 , ricbr-q1rj78 , ricbr-q1rjb2 , ricbr-q1rjd9 , ricbr-q1rjx9 , ricbr-q1rk93 , ricbr-Y1307 , ricco-PTRB

Title : The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite - Ogata_2005_PLoS.Biol_3_e248
Author(s) : Ogata H , Renesto P , Audic S , Robert C , Blanc G , Fournier PE , Parinello H , Claverie JM , Raoult D
Ref : PLoS Biol , 3 :e248 , 2005
Abstract : We sequenced the genome of Rickettsia felis, a flea-associated obligate intracellular alpha-proteobacterium causing spotted fever in humans. Besides a circular chromosome of 1,485,148 bp, R. felis exhibits the first putative conjugative plasmid identified among obligate intracellular bacteria. This plasmid is found in a short (39,263 bp) and a long (62,829 bp) form. R. felis contrasts with previously sequenced Rickettsia in terms of many other features, including a number of transposases, several chromosomal toxin-antitoxin genes, many more spoT genes, and a very large number of ankyrin- and tetratricopeptide-motif-containing genes. Host-invasion-related genes for patatin and RickA were found. Several phenotypes predicted from genome analysis were experimentally tested: conjugative pili and mating were observed, as well as beta-lactamase activity, actin-polymerization-driven mobility, and hemolytic properties. Our study demonstrates that complete genome sequencing is the fastest approach to reveal phenotypic characters of recently cultured obligate intracellular bacteria.
ESTHER : Ogata_2005_PLoS.Biol_3_e248
PubMedSearch : Ogata_2005_PLoS.Biol_3_e248
PubMedID: 15984913
Gene_locus related to this paper: ricco-PTRB , ricfe-q4ujz0 , ricfe-q4uk95 , ricfe-q4ul94 , ricfe-q4ulp2 , ricfe-q4ulq5 , ricfe-q4um26 , ricfe-q4umw9 , ricfe-q4un45

Title : The 1.2-megabase genome sequence of Mimivirus - Raoult_2004_Science_306_1344
Author(s) : Raoult D , Audic S , Robert C , Abergel C , Renesto P , Ogata H , La Scola B , Suzan M , Claverie JM
Ref : Science , 306 :1344 , 2004
Abstract : We recently reported the discovery and preliminary characterization of Mimivirus, the largest known virus, with a 400-nanometer particle size comparable to mycoplasma. Mimivirus is a double-stranded DNA virus growing in amoebae. We now present its 1,181,404-base pair genome sequence, consisting of 1262 putative open reading frames, 10% of which exhibit a similarity to proteins of known functions. In addition to exceptional genome size, Mimivirus exhibits many features that distinguish it from other nucleocytoplasmic large DNA viruses. The most unexpected is the presence of numerous genes encoding central protein-translation components, including four amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. The size and complexity of the Mimivirus genome challenge the established frontier between viruses and parasitic cellular organisms. This new sequence data might help shed a new light on the origin of DNA viruses and their role in the early evolution of eukaryotes.
ESTHER : Raoult_2004_Science_306_1344
PubMedSearch : Raoult_2004_Science_306_1344
PubMedID: 15486256
Gene_locus related to this paper: mimiv-q5uq83 , mimiv-q5uqk4 , mimiv-q5urb6 , mimiv-yr595 , mimvi-cxes

Title : Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains - Fournier_2004_J.Clin.Microbiol_42_5757
Author(s) : Fournier PE , Zhu Y , Ogata H , Raoult D
Ref : J Clin Microbiol , 42 :5757 , 2004
Abstract : By use of the nearly perfectly colinear genomes of Rickettsia conorii and Rickettsia prowazekii, we compared the usefulness of three types of sequences for typing of R. conorii isolates: (i) 5 variable coding genes comprising the 16S ribosomal DNA, gltA, ompB, and sca4 (gene D) genes, which are present in both genomes, and the ompA gene, which is degraded in R. prowazekii; (ii) 28 genes degraded in R. conorii but intact in R. prowazekii, including 23 split and 5 remnant genes; and (iii) 27 conserved and 25 variable intergenic spacers. The 4 conserved and 23 split genes as well as the 27 conserved intergenic spacers each had identical sequences in 34 human and 5 tick isolates of R. conorii. Analysis of the ompA sequences identified three genotypes of R. conorii. The variable intergenic spacers were significantly more variable than conserved genes, split genes, remnant genes, and conserved spacers (P < 10(-2) in all cases). Four of the variable intergenic spacers (dksA-xerC, mppA-purC, rpmE-tRNA(fMet), and tRNA(Gly)-tRNA(Tyr)) had highly variable sequences; when they were combined for typing, multispacer typing (MST) identified 27 different genotypes in the 39 R. conorii isolates. Two batches from the same R. conorii strain, Malish (Seven), with different culture passage histories were found to exhibit the same MST type. MST was more discriminatory for strain genotyping than multiple gene sequencing (P < 10(-2)). Phylogenetic analysis based on MST sequences was concordant with the geographic origins of R. conorii isolates. Our study supports the usefulness of MST for strain genotyping. This tool may be useful for tracing a strain and identifying its source during outbreaks, including those resulting from bioterrorism.
ESTHER : Fournier_2004_J.Clin.Microbiol_42_5757
PubMedSearch : Fournier_2004_J.Clin.Microbiol_42_5757
PubMedID: 15583310

Title : Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome - Raoult_2003_Genome.Res_13_1800
Author(s) : Raoult D , Ogata H , Audic S , Robert C , Suhre K , Drancourt M , Claverie JM
Ref : Genome Res , 13 :1800 , 2003
Abstract : The human pathogen Tropheryma whipplei is the only known reduced genome species (<1 Mb) within the Actinobacteria [high G+C Gram-positive bacteria]. We present the sequence of the 927303-bp circular genome of T. whipplei Twist strain, encoding 808 predicted protein-coding genes. Specific genome features include deficiencies in amino acid metabolisms, the lack of clear thioredoxin and thioredoxin reductase homologs, and a mutation in DNA gyrase predicting a resistance to quinolone antibiotics. Moreover, the alignment of the two available T. whipplei genome sequences (Twist vs. TW08/27) revealed a large chromosomal inversion the extremities of which are located within two paralogous genes. These genes belong to a large cell-surface protein family defined by the presence of a common repeat highly conserved at the nucleotide level. The repeats appear to trigger frequent genome rearrangements in T. whipplei, potentially resulting in the expression of different subsets of cell surface proteins. This might represent a new mechanism for evading host defenses. The T. whipplei genome sequence was also compared to other reduced bacterial genomes to examine the generality of previously detected features. The analysis of the genome sequence of this previously largely unknown human pathogen is now guiding the development of molecular diagnostic tools and more convenient culture conditions.
ESTHER : Raoult_2003_Genome.Res_13_1800
PubMedSearch : Raoult_2003_Genome.Res_13_1800
PubMedID: 12902375
Gene_locus related to this paper: trowh-PTRB , trowh-TW083.1 , trowh-TWT693

Title : A giant virus in amoebae -
Author(s) : La Scola B , Audic S , Robert C , Jungang L , de Lamballerie X , Drancourt M , Birtles R , Claverie JM , Raoult D
Ref : Science , 299 :2033 , 2003
PubMedID: 12663918
Gene_locus related to this paper: mimiv-q5uq83 , mimiv-q5uqk4 , mimiv-q5urb6

Title : Mechanisms of evolution in Rickettsia conorii and R. prowazekii - Ogata_2001_Science_293_2093
Author(s) : Ogata H , Audic S , Renesto-Audiffren P , Fournier PE , Barbe V , Samson D , Roux V , Cossart P , Weissenbach J , Claverie JM , Raoult D
Ref : Science , 293 :2093 , 2001
Abstract : Rickettsia conorii is an obligate intracellular bacterium that causes Mediterranean spotted fever in humans. We determined the 1,268,755-nucleotide complete genome sequence of R. conorii, containing 1374 open reading frames. This genome exhibits 804 of the 834 genes of the previously determined R. prowazekii genome plus 552 supplementary open reading frames and a 10-fold increase in the number of repetitive elements. Despite these differences, the two genomes exhibit a nearly perfect colinearity that allowed the clear identification of different stages of gene alterations with gene remnants and 37 genes split in 105 fragments, of which 59 are transcribed. A 38-kilobase sequence inversion was dated shortly after the divergence of the genus.
ESTHER : Ogata_2001_Science_293_2093
PubMedSearch : Ogata_2001_Science_293_2093
PubMedID: 11557893
Gene_locus related to this paper: ricco-PTRB , ricco-RC0464 , ricco-RC0603 , ricco-RC0617 , ricco-RC0713 , ricco-RC1147 , ricco-RC1296 , ricpr-RP681 , ricco-RC1136