Research Topics
Genomes and Genes | Hideto TakamiSummaryAffiliation: Japan Agency for Marine-Earth Science and Technology Country: Japan Publications
| Collaborators
|
Detail Information
Publications
A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystemHideto Takami
Microbial Genome Research Group, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Japan
PLoS ONE 7:e30559. 2012..The habitat, physiology and phylogenetic position of Ca. 'A. autotrophicum' support the view that the first bacterial and archaeal lineages were H(2)-dependent acetogens and methanogenes living in hydrothermal environments...- Evaluation method for the potential functionome harbored in the genome and metagenomeHideto Takami
Microbial Genome Research Group, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima, Yokosuka, 237 0061, Japan
BMC Genomics 13:699. 2012..We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules... 
Biodiversity in deep-sea sites located near the south part of JapanH Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka
Extremophiles 3:97-102. 1999..No extremophilic strains isolated in this study showed growth at 60MPa, although a few of the other isolates grew slightly at this hydrostatic pressure...- Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilisH Takami
Japan Marine Science and Technology Center, Deep Sea Microorganisms Research Group, 2 15 Natsushima, Yokosuka, Kanagawa 237 0061, Japan
Nucleic Acids Res 28:4317-31. 2000..subtilis genome. Out of 11 sigma factors which belong to the extracytoplasmic function family, 10 are unique to B. halodurans, suggesting that they may have a role in the special mechanism of adaptation to an alkaline environment... - Replication origin region of the chromosome of alkaliphilic Bacillus halodurans C-125H Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Kanagawa, Japan
Biosci Biotechnol Biochem 63:1134-7. 1999..subtilis was not found in the corresponding region in the case of alkaliphilic Bacillus halodurans C-125... - Genetic analysis of the chromosome of alkaliphilic Bacillus halodurans C-125H Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Natsushima, Yokosuka, Japan
Extremophiles 3:227-33. 1999..halodurans C-125 and B. subtilis... - Reidentification of the keratinase-producing facultatively alkaliphilic Bacillus sp. AH-101 as Bacillus haloduransH Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka, Japan
Extremophiles 3:293-6. 1999..halodurans type strain (DSM497). Our findings demonstrate that strain AH-101 is a member of the species B. halodurans... - Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana TrenchHideto Takami
Microbial Genome Research Group, Japan Agency of Marine Earth Science and Technology, 2 15 Natsushima, Yokosuka 237 0061, Japan
Extremophiles 8:351-6. 2004..kaustophilus HTA426 genome, although the CDS organization in another lambda insert is identical to that in the HTA426 genome... - Reidentification of facultatively alkaliphilic Bacillus firmus OF4 as Bacillus pseudofirmus OF4H Takami
Deep sea Microorganisms Research Group DEEP STAR, Japan Marine Science and Technology Center JAMSTEC, Yokosuka, Japan
Extremophiles 4:19-22. 2000..pseudofirmus type strain (DSM 8715(T)). The findings support the conclusion that this alkaliphile strain is more closely related to B. pseudofirmus than to B. firmus, and we propose the future use of the designation B. pseudofirmus OF4... - Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilusHideto Takami
Microbial Genome Research Group, Japan Agency of Marine Earth Science and Technology, 2 15 Natsushima, Yokosuka, Kanagawa 237 0061, Japan
Nucleic Acids Res 32:6292-303. 2004..Further analysis revealed some asymmetric amino acid substitutions between the thermophiles and the mesophiles, which are possibly associated with the thermoadaptation of the organism... - Sequence analysis of a 32-kb region including the major ribosomal protein gene clusters from alkaliphilic Bacillus sp. strain C-125H Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Kanagawa, Japan
Biosci Biotechnol Biochem 63:452-5. 1999..Each ORF product showed more than 70% identity to those of B. subtilis. Gene organization in the region of str, S10, spc, and the alpha cluster was highly conserved among three strains, C-125, B. subtilis, and B. stearothermophilus... - Sequencing of three lambda clones from the genome of alkaliphilic Bacillus sp. strain C-125H Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka
Extremophiles 3:29-34. 1999..subtilis, although some gene clusters (ydh, yqi, yer, and yts) were conserved as operon units the same as in B. subtilis... - An improved physical and genetic map of the genome of alkaliphilic Bacillus sp. C-125H Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka
Extremophiles 3:21-8. 1999..subtilis in the AscI linking clones were positioned on the physical map. The oriC region of the C-125 chromosome was identified by southern blot analysis with a DNA probe containing the gyrB region... - Wide-range distribution of insertion sequences identified in B. halodurans among bacilli and a new transposon disseminated in alkaliphilic and thermophilic bacilliHideto Takami
Microbial Genome Research Group, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima, Yokosuka 237 0061, Japan
DNA Res 11:153-62. 2004..Three ISs (IS652, IS653, and IS660) and a group II intron (Bh.Int) were widely dispersed in other Bacillus species without a correlation with the phylogenetic placement based on 16S rDNA sequences... - Identification and distribution of new insertion sequences in the genome of alkaliphilic Bacillus halodurans C-125H Takami
Deep Sea Research Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
J Bacteriol 183:4345-56. 2001..It is evident, however, that not all IS elements have transposed and caused rearrangements of the genome in the past 17 years during which strain C-125 was subcultured under neutral and alkaline conditions... - Microbial flora in the deepest sea mud of the Mariana TrenchH Takami
Deep sea Microorganism Research Group, Japan Marine Science and Technology Center, Yokoruka, Japan
FEMS Microbiol Lett 152:279-85. 1997..Phylogenetic analysis of Mariana isolates based on 16S rDNA sequences revealed that a wide range of taxa were represented... - Analysis of the genome of an alkaliphilic Bacillus strain from an industrial point of viewH Takami
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka
Extremophiles 4:99-108. 2000..Through genome analysis, it became apparent that the genome organization of alkaliphilic Bacillus halodurans C-125 is totally different from that of B. subtilis orthologues... - Isolation and characterization of toluene-sensitive mutants from Pseudomonas putida IH-2000H Hirayama
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Kanagawa, Japan
FEMS Microbiol Lett 169:219-25. 1998..Our findings indicate that cyo is an important gene for toluene tolerance, although its role is still unclear... - Identification and distribution of new insertion sequences in the genome of the extremely halotolerant and alkaliphilic Oceanobacillus iheyensis HTE831Yoshihiro Takaki
Microbial Genome Research Group, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima, Yokosuka 237 0061, Japan
DNA Res 11:233-45. 2004..Most of the ISs and the group II intron widely distributed throughout the genome were inserted in noncoding regions, while two ISs (IS667-08 and IS668-02) and Oi.Int-04 were inserted in the coding regions... - Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environmentsHideto Takami
Japan Marine Science and Technology Center, Microbial Genome Research Group, 2 15 Natsushima, Yokosuka, Kanagawa 237 0061, Japan
Nucleic Acids Res 30:3927-35. 2002..This second genome sequence of an alkaliphilic Bacillus-related species will be useful in understanding life in highly alkaline environments and microbial diversity within the ubiquitous bacilli... - Housekeeping recA gene interrupted by group II intron in the thermophilic Geobacillus kaustophilusGab Joo Chee
Microbial Genome Research Group, XBR, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima Yokosuka 237 0061, Japan
Gene 363:211-20. 2005..Int1. It is suggested that the amelioration of Gk.Int1 intron has occurred recently, and that it is still in the process of evolution to the recipient genome... - Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya RidgeJ Lu
Microbial Genome Research Group, DEEPSTAR, Japan Marine Science and Technology Center, 2-15 Natsushima, 237-0061, Yokosuka, Japan
FEMS Microbiol Lett 205:291-7. 2001.... - Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal groupTakuro Nunoura
Subsurface Geobiology and Advanced Research Project, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
Nucleic Acids Res 39:3204-23. 2011..The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea... - Characterization of alkaliphilic Bacillus strains used in industry: proposal of five novel speciesYuichi Nogi
Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
Int J Syst Evol Microbiol 55:2309-15. 2005..nov. (type strain N-4T=JCM 9156T=DSM 2522T), Bacillus akibai sp. nov. (type strain 1139T=JCM 9157T=ATCC 43226T) and Bacillus mannanilyticus sp. nov. (type strain AM-001T=JCM 10596T=DSM 16130T)... - Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragmentsTakuro Nunoura
Subground Animalcule Retrieval SUGAR Program, Extremebiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima cho, Jokosuka, Japan
Environ Microbiol 7:1967-84. 2005..The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota... - Alternative splicing by participation of the group II intron ORF in extremely halotolerant and alkaliphilic Oceanobacillus iheyensisGab Joo Chee
Microbial Genome Research Group, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima, Yokosuka 237 0061, Japan
Microbes Environ 26:54-60. 2011..These findings imply that alternative 5' splicing which causes a functional change of ligated exons presumably has influenced past adaptations of O. iheyensis to various environmental changes... - Molecular cloning, nucleotide sequence and expression of the structural gene for a thermostable alkaline protease from Bacillus sp. no. AH-101H Takami
Department of Bioengineering, Tokyo Institute of Technology, Kanagawa, Japan
Appl Microbiol Biotechnol 38:101-8. 1992..AH-101 protease, however, was distinct among the proteases from alkaliphilic bacilli in showing the lowest homology to the others... - Molecular cloning, nucleotide sequence, and expression of the structural gene for alkaline serine protease from alkaliphilic Bacillus sp. 221H Takami
Department of Bioengineering, Tokyo Institute of Technology, Kanagawa, Japan
Biosci Biotechnol Biochem 56:1455-60. 1992.... - An alkali-inducible flotillin-like protein from Bacillus halodurans C-125Hui Min Zhang
Extremobiosphere Research Center, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima, Yokosuka, Kanagawa 237 0061, Japan
Protein J 24:125-31. 2005..halodurans by mass spectrometry and Western blotting. Interestingly, BH3500 was expressed strongly in alkaline conditions at both transcriptional and translational levels, which implies that it is one of the alkali-inducible proteins... - Characterization and comparative study of the rrn operons of alkaliphilic Bacillus halodurans C-125K Nakasone
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka
Extremophiles 4:209-14. 2000..subtilis revealed that the ITS regions in C-125 were much longer than those in B. subtilis. There was no substantial difference in the length of potential promoter sequences in B. halodurans and B. subtilis... - Isolation and transposon mutagenesis of a Pseudomonas putida KT2442 toluene-resistant variant: involvement of an efflux system in solvent resistanceF Fukumori
DEEPSTAR Group, Japan Marine Science and Technology Center, Yokosuka
Extremophiles 2:395-400. 1998..These observations indicate that a multidrug efflux system plays a major role in the organic solvent resistance of P. putida TOL. However, several other genes may also be involved... - Characterization of alpha-maltotetraohydrolase produced by Pseudomonas sp. MS300 isolated from the deepest site of the mariana trenchH Kobayashi
Japan Marine Science and Technology Center, Deep sea Microorganism Research Group, Yokosuka, Japan
Extremophiles 2:401-7. 1998..8 for one and 8.9 for the other. MS300 produced more amylase under high hydrostatic pressure than under atmospheric pressure. Strain MS300 may be active in the deep sea at a depth of 10,897 m... - Cloning and expression of the gene encoding RNA polymerase alpha subunit from alkaliphilic Bacillus sp. strain C-125K Nakasone
Deep Star Group, Japan Marine Science and Technology Center, Kanagawa, Japan
FEMS Microbiol Lett 168:269-76. 1998..coli cells and purified to near homogeneity... - Outer membrane changes in a toluene-sensitive mutant of toluene-tolerant Pseudomonas putida IH-2000H Kobayashi
Deep Sea Microorganisms Research Group, Japan Marine Science and Technology Center, Yokosuka 237 0061, Japan
J Bacteriol 181:4493-8. 1999..These changes in the outer membrane would cause an increase in cell surface hydrophobicity, and mutant No. 32 is considered to be sensitive to toluene... - Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific OceanT Nagahama
Deep sea Microorganism Research Group, Japan Marine Science and Technology Center JAMSTEC, Yokosuka
Antonie Van Leeuwenhoek 80:101-10. 2001..Some strains assigned to known species on the basis of phenotypic features should be regarded as new species as suggested by the results of molecular analysis... - Effects of hydrostatic pressure and temperature on growth and lipid composition of the inner membrane of barotolerant Pseudomonas sp. BT1 isolated from the deep-seaH Kaneko
Deep Star Group, Japan Marine Science and Technology Center, Yokosuka, Japan
Biosci Biotechnol Biochem 64:72-9. 2000.... - Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1Yoshihiro Takaki
Microbial Genome Research Group, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa 237 0061, Japan
DNA Res 17:123-37. 2010..desulfuricans SSM1 thriving in the physically and chemically fluctuating environments near hydrothermal vents. This is the first genome sequence from the phylum Deferribacteres... 
Unique substrate specificity of a thermostable glycosyl hydrolase from an uncultured Anaerolinea, derived from bacterial mat on a subsurface geothermal water streamMasaaki Konishi
Institute of Biogeoscience, Japan Agency for Marine Earth Science and Technology, 2 15 Natsushima cho, Yokosuka 237 0061, Japan
Biotechnol Lett 34:1887-93. 2012..It was optimally active at 65 °C and from pH 4 to 8. rGH showed hydrolytic activity for α-1,1, α-1,2 and α-1,6 linkages, including isomaltose, but not α-1,4 and β-linkages...- The Hadal Amphipod Hirondellea gigas possessing a unique cellulase for digesting wooden debris buried in the deepest seafloorHideki Kobayashi
Institute of Biogeosciences, Japan Agency for Marine Earth Science and Technology, Yokosuka, Japan
PLoS ONE 7:e42727. 2012..These results strongly suggested that H. gigas adapted to its extreme oligotrophic hadal oceanic environment by evolving digestive enzymes capable of digesting sunken wooden debris... - Lactobacillus hayakitensis sp. nov., isolated from intestines of healthy thoroughbredsHidetoshi Morita
School of Veterinary Medicine, Azabu University, 1 17 71 Fuchinobe, Sagamihara, Kanagawa 229 8501, Japan
Int J Syst Evol Microbiol 57:2836-9. 2007..salivarius and L. aviarius confirmed that KBL13(T) represents a novel species, for which the name Lactobacillus hayakitensis sp. nov. is proposed. The type strain is KBL13(T) (=JCM 14209(T)=DSM 18933(T))... - Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomesKen Kurokawa
Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
DNA Res 14:169-81. 2007..In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes... - Characterization of a new rhamnogalacturonan acetyl esterase from Bacillus halodurans C-125 with a new putative carbohydrate binding domainJosé Navarro-Fernández
Department of Biochemistry and Molecular Biology A, Faculty of Biology, University of Murcia, Campus Espinardo, E 30071 Murcia, Spain
J Bacteriol 190:1375-82. 2008..Furthermore, the enzyme possesses a putative substrate binding region at the N terminus of the protein which has never been described to date for any RGAE... - Characterization of endo-beta-N-acetylglucosaminidase from alkaliphilic Bacillus halodurans C-125Kiyotaka Fujita
Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
Biosci Biotechnol Biochem 68:1059-66. 2004..Although the C-terminal tail region is not essential for enzyme activity, the sequence is also conserved among endo-beta-N-acetylglucosaminidases of various origins... - The BH1999 protein of Bacillus halodurans C-125 is gentisyl-coenzyme A thioesteraseZhihao Zhuang
Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA
J Bacteriol 186:393-9. 2004..A comparative study of these two enzymes showed that they differ greatly in the rate contribution made by the catalytic aspartate, in the pH dependence of catalysis, and in substrate specificity... - Characterization and structural modeling of a novel thermostable glycine oxidase from Geobacillus kaustophilus HTA426Irene Martínez-Martínez
Department of Biochemistry and Molecular Biology A, Faculty of Biology, University of Murcia, Campus Espinardo, E 30071 Murcia, Spain
Proteins 70:1429-41. 2008..The comparison between the possible topology of GOXK with that of GOXB showed changes at the putative interactions between monomers for the building of the tetrameric oligomerization...