Hiroyuki Ogata

Summary

Affiliation: Centre National de la Recherche Scientifique
Country: France

Publications

  1. pmc Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus
    Hiroyuki Ogata
    Harmful Algal Bloom Division, National Research Institute of Inland Sea, Fisheries Research Agency, 2 17 5 Maruishi, Hatsukaichi, Hiroshima 739 0452, Japan
    Virol J 6:178. 2009
  2. pmc Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell
    Peter von Dassow
    Evolution du Plancton et PaleOceans, Station Biologique de Roscoff, CNRS UPMC UMR7144, 29682 Roscoff, France
    Genome Biol 10:R114. 2009
  3. pmc Restricted changes in major surface protein-2 (msp2) transcription after prolonged in vitro passage of Anaplasma phagocytophilum
    Diana G Scorpio
    Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    BMC Microbiol 4:1. 2004
  4. pmc Metagrowth: a new resource for the building of metabolic hypotheses in microbiology
    Hiroyuki Ogata
    Information Genomique et Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Nucleic Acids Res 33:D321-4. 2005
  5. pmc Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment
    Hiroyuki Ogata
    Information Genomique et Structurale, CNRS UPR2589, Institut de Microbiologie de la Mediterranee, Parc Scientifique de Luminy, Aix Marseille Universite, Marseille Cedex 9, France
    ISME J 5:1143-51. 2011
  6. pmc The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
    PLoS Biol 3:e248. 2005
  7. pmc Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique UPR 2589, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
    PLoS Genet 2:e76. 2006
  8. pmc Unique genes in giant viruses: regular substitution pattern and anomalously short size
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory CNRS UPR 2589, IBSM Parc Scientifique de Luminy, Case 934 13288 Marseille Cedex 9, France
    Genome Res 17:1353-61. 2007
  9. pmc Protein coding palindromes are a unique but recurrent feature in Rickettsia
    Hiroyuki Ogata
    Information Génétique and Structurale, CNRS AVENTIS UMR 1889, 13402 Marseille Cedex 20, France
    Genome Res 12:808-16. 2002
  10. pmc A new example of viral intein in Mimivirus
    Hiroyuki Ogata
    Information Genomique et Structurale, UPR2589 CNRS, IBSM, IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Virol J 2:8. 2005

Collaborators

Detail Information

Publications42

  1. pmc Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus
    Hiroyuki Ogata
    Harmful Algal Bloom Division, National Research Institute of Inland Sea, Fisheries Research Agency, 2 17 5 Maruishi, Hatsukaichi, Hiroshima 739 0452, Japan
    Virol J 6:178. 2009
    ....
  2. pmc Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell
    Peter von Dassow
    Evolution du Plancton et PaleOceans, Station Biologique de Roscoff, CNRS UPMC UMR7144, 29682 Roscoff, France
    Genome Biol 10:R114. 2009
    ..huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism...
  3. pmc Restricted changes in major surface protein-2 (msp2) transcription after prolonged in vitro passage of Anaplasma phagocytophilum
    Diana G Scorpio
    Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    BMC Microbiol 4:1. 2004
    ..Thus, Msp2 profiles and msp2 transcripts of low passage A. phagocytophilum Webster strain, initially comprised of a single abundant msp2 transcript, were re-examined after > or = 20 in vitro passages without immune selection...
  4. pmc Metagrowth: a new resource for the building of metabolic hypotheses in microbiology
    Hiroyuki Ogata
    Information Genomique et Structurale, CNRS UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Nucleic Acids Res 33:D321-4. 2005
    ..The web interface of Metagrowth helps users to design new axenic culture media eventually suitable for those bacteria. Metagrowth is accessible at http://igs-server.cnrs-mrs.fr/axenic/...
  5. pmc Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment
    Hiroyuki Ogata
    Information Genomique et Structurale, CNRS UPR2589, Institut de Microbiologie de la Mediterranee, Parc Scientifique de Luminy, Aix Marseille Universite, Marseille Cedex 9, France
    ISME J 5:1143-51. 2011
    ..Giruses thus seem to represent a major source of the underexplored diversity of the MutS family in the microbial world...
  6. pmc The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, UPR 2589, IBSM, CNRS, Marseille Cedex, France
    PLoS Biol 3:e248. 2005
    ..Our study demonstrates that complete genome sequencing is the fastest approach to reveal phenotypic characters of recently cultured obligate intracellular bacteria...
  7. pmc Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique UPR 2589, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
    PLoS Genet 2:e76. 2006
    ....
  8. pmc Unique genes in giant viruses: regular substitution pattern and anomalously short size
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory CNRS UPR 2589, IBSM Parc Scientifique de Luminy, Case 934 13288 Marseille Cedex 9, France
    Genome Res 17:1353-61. 2007
    ..We propose that their characteristic features are the consequences of the specific evolutionary forces shaping the viral gene repertoires in the context of their parasitic lifestyles...
  9. pmc Protein coding palindromes are a unique but recurrent feature in Rickettsia
    Hiroyuki Ogata
    Information Génétique and Structurale, CNRS AVENTIS UMR 1889, 13402 Marseille Cedex 20, France
    Genome Res 12:808-16. 2002
    ..This comprehensive study of Rickettsia repeats confirms and extends our previous observations and further indicates a significant role of selfish DNAs in the creation and modification of proteins...
  10. pmc A new example of viral intein in Mimivirus
    Hiroyuki Ogata
    Information Genomique et Structurale, UPR2589 CNRS, IBSM, IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Virol J 2:8. 2005
    ..After their discovery, inteins have been quickly identified in all domains of life, but only once to date in the genome of a eukaryote-infecting virus...
  11. pmc Reductive genome evolution from the mother of Rickettsia
    Guillaume Blanc
    Structural and Genomic Information Laboratory, Institut de Biologie Structurale et Microbiologie, Parc Scientifique de Luminy, Marseille, France
    PLoS Genet 3:e14. 2007
    ....
  12. ncbi request reprint Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity
    Chantal Abergel
    Information Génomique and Structurale, CNRS UPR 2589, IBSM, Marseille Cedex, France
    Mol Biol Evol 23:2112-22. 2006
    ....
  13. pmc Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome
    Guillaume Blanc
    Structural and Genomic Information Laboratory, CNRS UPR 2589, Institut de Biologie Structurale et Microbiologie, IFR 88, Parc Scientifique de Luminy, 13288 Marseille Cedex 9, France
    Genome Res 17:1657-64. 2007
    ..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...
  14. pmc Marine mimivirus relatives are probably large algal viruses
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Virol J 5:12. 2008
    ..The existence of mimivirus relatives was first suggested by the analysis of the Sargasso Sea metagenomic data...
  15. ncbi request reprint Molecular evolution of rickettsia surface antigens: evidence of positive selection
    Guillaume Blanc
    Information Genomique et Structurale, UPR 2589, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
    Mol Biol Evol 22:2073-83. 2005
    ....
  16. pmc Comparative genomics of multidrug resistance in Acinetobacter baumannii
    Pierre Edouard Fournier
    Information Genomique et Structurale, Institute for Structural Biology and Microbiology, IBSM, Marseille, France
    PLoS Genet 2:e7. 2006
    ..Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance...
  17. doi request reprint Identification of a new phospholipase D in Carica papaya latex
    Slim Abdelkafi
    CNRS, Aix Marseille Universite, Enzymologie Interfaciale et Physiologie de la Lipolyse, Marseille, France
    Gene 499:243-9. 2012
    ..05 kDa. From sequence analysis, CpPLD1 was identified as a PLD belonging to the plant phosphatidylcholine phosphatidohydrolase family...
  18. ncbi request reprint Genome-based design of a cell-free culture medium for Tropheryma whipplei
    Patricia Renesto
    Unite des Rickettsies, CNRS UMR 6020, Faculte de Medecine, 27 Boulevard Jean Moulin, 13385, Marseille, France
    Lancet 362:447-9. 2003
    ..Genomic information can, therefore, provide sufficient clues for designing axenic media for fastidious and uncultured pathogens...
  19. ncbi request reprint Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation
    Clarisse Rovery
    Unite des Rickettsies, CNRS UMR 6020, IFR48, Faculte de Medecine, 27, Bd Jean Moulin, Marseille, France
    Res Microbiol 156:211-8. 2005
    ..Bioinformatics analysis of these possibly encoded proteins is also reported...
  20. ncbi request reprint Mimivirus and the emerging concept of "giant" virus
    Jean Michel Claverie
    Information Genomique et Structurale, CNRS UPR 2589, IBSM, Parc Scientifique de Luminy, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Virus Res 117:133-44. 2006
    ..We propose to introduce the word "girus" to recognize the intermediate status of these giant DNA viruses, the genome complexity of which makes them closer to small parasitic prokaryotes than to regular viruses...
  21. pmc Taxonomic distribution of large DNA viruses in the sea
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Université de la Méditerranée Parc Scientifique de Luminy, Avenue de Luminy, FR 13288 Marseille, France
    Genome Biol 9:R106. 2008
    ..In this study, we used a new approach--'phylogenetic mapping'--to obtain a comprehensive picture of the taxonomic distribution of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition metagenomic data set...
  22. pmc Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR2589, Mediterranean Institute of Microbiology IFR 88, Universite de la Mediterranee, Parc Scientifique de Luminy, Marseille, France
    Genome Res 19:1441-9. 2009
    ....
  23. pmc Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses
    Adam Monier
    Structural and Genomic Information Laboratory, CNRS UPR 2589, Institute for Structural Biology and Microbiology, Parc Scientifique de Luminy, 163 Avenue de Luminy, FR 13288, Marseille Cedex 09, France
    BMC Genomics 8:456. 2007
    ..We then interpreted their compositional heterogeneity in terms of possible causes, including strand asymmetry, gene function/expression, and horizontal transfer...
  24. pmc Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids
    Takashi Yoshida
    Structural and Genomic Information Laboratory, CNRS UPR 2589, Aix Marseille University, Mediterranean Institute of Microbiology, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France
    Virol J 8:427. 2011
    ..Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes...
  25. doi request reprint Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges
    Jean Michel Claverie
    Structural and Genomic Information Laboratory, CNRS UPR 2589, IFR 88, Parc Scientifique de Luminy, Case 934, Marseille, France
    J Invertebr Pathol 101:172-80. 2009
    ....
  26. pmc Multispacer typing of Rickettsia prowazekii enabling epidemiological studies of epidemic typhus
    Yong Zhu
    Unite des Rickettsies, CNRS UMR 6020, IFR 48, Faculte de Medecine, Universite de la Mediterranee, Marseille, France
    J Clin Microbiol 43:4708-12. 2005
    ..This may help to discriminate between natural and intentional outbreaks. Our study supports the usefulness of MST as a versatile method for rickettsial strain genotyping...
  27. pmc Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
    Pascal Hingamp
    CNRS, Aix Marseille Universite, Laboratoire Information Génomique et Structurale UMR 7256, Mediterranean Institute of Microbiology FR 3479, Marseille, France
    ISME J 7:1678-95. 2013
    ....
  28. ncbi request reprint The insertion of palindromic repeats in the evolution of proteins
    Jean Michel Claverie
    Information Genetique et Structurale, CNRS AVENTIS UMR 1889, Institut de Biologie Structurale et Microbiologie, Marseille, France
    Trends Biochem Sci 28:75-80. 2003
    ..Based on previous results and theories on the coding potential of palindromic elements, we speculate that their insertion and mobility might have played a significant role in the early stages of protein evolution...
  29. ncbi request reprint Phylogenetic classification of Bartonella species by comparing groEL sequences
    Zaher Zeaiter
    Unite des Rickettsies, CNRS UPRES A 6020, Faculte de Medecine, Marseille, France
    Int J Syst Evol Microbiol 52:165-71. 2002
    ..In addition, the groEL gene was shown to be useful in subtyping six B. henselae isolates into three variants: Houston, Marseille and Fizz...
  30. doi request reprint Microbiology. How to infect a Mimivirus
    Hiroyuki Ogata
    Structural and Genomic Information Laboratory, CNRSUPR 2589, IFR 88, Universite de la Mediterranee, Parc Scientifique de Luminy, FR 13288 Marseille, France
    Science 321:1305-6. 2008
  31. pmc Genotyping, Orientalis-like Yersinia pestis, and plague pandemics
    Michel Drancourt
    Universite de la Mediterranee, Marseille, France
    Emerg Infect Dis 10:1585-92. 2004
    ..pestis Orientalis. These data indicate that Y. pestis caused cases of Justinian plague. The two historical plague pandemics were likely caused by Orientalis-like strains...
  32. doi request reprint Identification and biochemical characterization of a GDSL-motif carboxylester hydrolase from Carica papaya latex
    Slim Abdelkafi
    CNRS, Aix Marseille Universite, Enzymologie Interfaciale et Physiologie de la Lipolyse, Marseille, France
    Biochim Biophys Acta 1791:1048-56. 2009
    ....
  33. doi request reprint Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay
    Lucie Bittner
    CNRS, UMR7144 and Université Pierre et Marie Curie, Team EPPO, Station Biologique de Roscoff, Place Georges Tessier, Roscoff, France
    Mol Ecol 22:87-101. 2013
    ..8-3 μm). Overall, this study emphasized several technical and theoretical barriers inherent to the exploration of the large and largely unknown diversity of unicellular eukaryotes...
  34. ncbi request reprint Discovery of protein-coding palindromic repeats in Wolbachia
    Hiroyuki Ogata
    Trends Microbiol 13:253-5. 2005
  35. pmc Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products
    Patricia Renesto
    Unite des Rickettsies, CNRS UMR 6020, IFR 48, Faculte de Medecine, 27 Boulevard Jean Moulin, 13385 Marseille, France
    J Virol 80:11678-85. 2006
    ..Thus, anonymous and unique genes constituting the majority of the mimivirus gene complement encode bona fide proteins that are likely to participate in well-integrated processes...
  36. pmc Tropheryma whipplei Twist: a human pathogenic Actinobacteria with a reduced genome
    Didier Raoult
    Unite des Rickettsies, Faculte de Medecine, CNRS UMR6020, Universite de la Mediterranee, 13385 Marseille Cedex 05, France
    Genome Res 13:1800-9. 2003
    ..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...
  37. ncbi request reprint The 1.2-megabase genome sequence of Mimivirus
    Didier Raoult
    Unite des Rickettsies, Faculte de Medecine, CNRS UMR6020, Universite de la Mediterranee, 13385 Marseille Cedex 05, France
    Science 306:1344-50. 2004
    ..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...
  38. ncbi request reprint Identification of two putative rickettsial adhesins by proteomic analysis
    Patricia Renesto
    Unite des Rickettsies, CNRS UMR 6020, IFR 48, Faculte de Medecine, 27 Boulevard Jean Moulin, 13385 Marseille, France
    Res Microbiol 157:605-12. 2006
    ..Both proteins are highly conserved within the Rickettsia genus and might play a critical role in their pathogenicity. These data may have important implications for the development of future vaccines against rickettsial infections...
  39. pmc Use of highly variable intergenic spacer sequences for multispacer typing of Rickettsia conorii strains
    Pierre Edouard Fournier
    Unite des Rickettsies, IFR 48, CNRS UMR 6020, Faculte de Medecine, Universite de la Mediterranee, 27 Blvd Jean Moulin, 13385 Marseille Cedex 5, France
    J Clin Microbiol 42:5757-66. 2004
    ..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...
  40. ncbi request reprint Phylogenetic study of Rickettsia species using sequences of the autotransporter protein-encoding gene sca2
    Maxime Ngwamidiba
    Unite des Rickettsies, IFR 48, CNRS UMR 6020, Faculte de Medecine, Universite de la Mediterranee, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
    Ann N Y Acad Sci 1063:94-9. 2005
    ..rickettsii, R. massiliae, R. akari, and typhus groups, which were supported by significant bootstrap values...
  41. ncbi request reprint Some lessons from Rickettsia genomics
    Patricia Renesto
    Unite des Rickettsies, CNRS UMR 6020, IFR 48, Faculté de Médecine Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
    FEMS Microbiol Rev 29:99-117. 2005
    ..Environmental adaptation of Rickettsia is also discussed...
  42. pmc Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies
    Takashi Yoshida
    Department of Marine Bioscience, Fukui Prefectural University, 1 1 Gakuencho, Obama, Fukui 917 0003, Japan
    J Bacteriol 190:1762-72. 2008
    ..This phage genome study suggests that light is central in the phage-cyanobacterium relationships where the viruses use diverse genetic strategies to control their host's photosynthesis...