Uchiyama I

References (12)

Title : Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1 - Takami_2017_DNA.Res_24_169
Author(s) : Takami H , Toyoda A , Uchiyama I , Itoh T , Takaki Y , Arai W , Nishi S , Kawai M , Shin-Ya K , Ikeda H
Ref : DNA Research , 24 :169 , 2017
Abstract : Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture. Thus, the strain was found more valuable than hitherto considered. In addition, M497-1 harbours 98 genes involved in the biosynthesis of various natural products, 16 of which are M497-1-specific across 4 Lysobacter species. A gene cluster starting at LEN_2603 through LEN_2673 among the 98 genes closely resembled the lysobactin biosynthesis gene cluster of Lysobacter sp. ATCC 53042. It is likely that M497-1 may produce lysobactin or related antibacterial compounds. Furthermore, comparative genomic analysis of M497-1 and four other Lysobacter species revealed that their core genome structure comprises 3,737 orthologous groups. Our findings are expected to advance further biotechnological application of Lysobacter spp. as a promising source of natural bioactive compounds.
ESTHER : Takami_2017_DNA.Res_24_169
PubMedSearch : Takami_2017_DNA.Res_24_169
PubMedID: 28065880
Gene_locus related to this paper: lysen-a0a1j1ebl3 , lysen-a0a1j1e5b0 , lysen-a0a0s2dfs0

Title : Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water - Nakai_2016_Genome.Announc_4_e00616
Author(s) : Nakai R , Fujisawa T , Nakamura Y , Nishide H , Uchiyama I , Baba T , Toyoda A , Fujiyama A , Naganuma T , Niki H
Ref : Genome Announc , 4 : , 2016
Abstract : Aurantimicrobium minutum type strain KNC(T) is a planktonic ultramicrobacterium isolated from river water in western Japan. Strain KNC(T) has an extremely small, streamlined genome of 1,622,386 bp comprising 1,575 protein-coding sequences. The genome annotation suggests that strain KNC(T) has an actinorhodopsin-based photometabolism.
ESTHER : Nakai_2016_Genome.Announc_4_e00616
PubMedSearch : Nakai_2016_Genome.Announc_4_e00616
PubMedID: 27365350
Gene_locus related to this paper: 9mico-a0a173lyl3

Title : High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes - Kawai_2014_Front.Microbiol_5_80
Author(s) : Kawai M , Futagami T , Toyoda A , Takaki Y , Nishi S , Hori S , Arai W , Tsubouchi T , Morono Y , Uchiyama I , Ito T , Fujiyama A , Inagaki F , Takami H
Ref : Front Microbiol , 5 :80 , 2014
Abstract : Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.
ESTHER : Kawai_2014_Front.Microbiol_5_80
PubMedSearch : Kawai_2014_Front.Microbiol_5_80
PubMedID: 24624126
Gene_locus related to this paper: 9zzzz-x0wci8 , 9zzzz-x1k9j7 , 9zzzz-x0se68 , 9zzzz-x0tpm6 , 9zzzz-x0tv89 , 9zzzz-x0ws69 , 9zzzz-x1tg33 , 9zzzz-x1anx0 , 9zzzz-x1m8t8 , 9zzzz-x1a5i7 , 9zzzz-x1k2t2 , 9zzzz-x0uzq5

Title : Chromosome painting in silico in a bacterial species reveals fine population structure - Yahara_2013_Mol.Biol.Evol_30_1454
Author(s) : Yahara K , Furuta Y , Oshima K , Yoshida M , Azuma T , Hattori M , Uchiyama I , Kobayashi I
Ref : Molecular Biology Evolution , 30 :1454 , 2013
Abstract : Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale.
ESTHER : Yahara_2013_Mol.Biol.Evol_30_1454
PubMedSearch : Yahara_2013_Mol.Biol.Evol_30_1454
PubMedID: 23505045

Title : A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem - Takami_2012_PLoS.One_7_e30559
Author(s) : Takami H , Noguchi H , Takaki Y , Uchiyama I , Toyoda A , Nishi S , Chee GJ , Arai W , Nunoura T , Itoh T , Hattori M , Takai K
Ref : PLoS ONE , 7 :e30559 , 2012
Abstract : A nearly complete genome sequence of Candidatus 'Acetothermum autotrophicum', a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that Ca. 'A. autotrophicum' is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO(2) fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of Ca. 'A. autotrophicum' is a particularly ancient bacterial pathway. 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.
ESTHER : Takami_2012_PLoS.One_7_e30559
PubMedSearch : Takami_2012_PLoS.One_7_e30559
PubMedID: 22303444
Gene_locus related to this paper: 9bact-h5srl9 , 9chlr-h5sfm8

Title : Birth and death of genes linked to chromosomal inversion - Furuta_2011_Proc.Natl.Acad.Sci.U.S.A_108_1501
Author(s) : Furuta Y , Kawai M , Yahara K , Takahashi N , Handa N , Tsuru T , Oshima K , Yoshida M , Azuma T , Hattori M , Uchiyama I , Kobayashi I
Ref : Proc Natl Acad Sci U S A , 108 :1501 , 2011
Abstract : The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. The availability of closely related complete genome sequences helps to follow changes in gene contents and clarify their relationship to overall genome organization. Helicobacter pylori, bacteria in our stomach, are known for their extreme genome plasticity through mutation and recombination and will make a good target for such an analysis. In comparing their complete genome sequences, we found that gain and loss of genes (loci) for outer membrane proteins, which mediate host interaction, occurred at breakpoints of chromosomal inversions. Sequence comparison there revealed a unique mechanism of DNA duplication: DNA duplication associated with inversion. In this process, a DNA segment at one chromosomal locus is copied and inserted, in an inverted orientation, into a distant locus on the same chromosome, while the entire region between these two loci is also inverted. Recognition of this and three more inversion modes, which occur through reciprocal recombination between long or short sequence similarity or adjacent to a mobile element, allowed reconstruction of synteny evolution through inversion events in this species. These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells.
ESTHER : Furuta_2011_Proc.Natl.Acad.Sci.U.S.A_108_1501
PubMedSearch : Furuta_2011_Proc.Natl.Acad.Sci.U.S.A_108_1501
PubMedID: 21212362

Title : Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes - Kawai_2011_BMC.Microbiol_11_104
Author(s) : Kawai M , Furuta Y , Yahara K , Tsuru T , Oshima K , Handa N , Takahashi N , Yoshida M , Azuma T , Hattori M , Uchiyama I , Kobayashi I
Ref : BMC Microbiol , 11 :104 , 2011
Abstract : BACKGROUND: The genome of Helicobacter pylori, an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. The high incidence of stomach cancer in East Asia might be related to bacterial genotype. We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains.
RESULTS: A phylogenetic tree of concatenated well-defined core genes supported divergence of the East Asian lineage (hspEAsia; Japanese and Korean) from the European lineage ancestor, and then from the Amerind lineage ancestor. Phylogenetic profiling revealed a large difference in the repertoire of outer membrane proteins (including oipA, hopMN, babABC, sabAB and vacA-2) through gene loss, gain, and mutation. All known functions associated with molybdenum, a rare element essential to nearly all organisms that catalyzes two-electron-transfer oxidation-reduction reactions, appeared to be inactivated. Two pathways linking acetyl~CoA and acetate appeared intact in some Japanese strains. Phylogenetic analysis revealed greater divergence between the East Asian (hspEAsia) and the European (hpEurope) genomes in proteins in host interaction, specifically virulence factors (tipalpha), outer membrane proteins, and lipopolysaccharide synthesis (human Lewis antigen mimicry) enzymes. Divergence was also seen in proteins in electron transfer and translation fidelity (miaA, tilS), a DNA recombinase/exonuclease that recognizes genome identity (addA), and DNA/RNA hybrid nucleases (rnhAB). Positively selected amino acid changes between hspEAsia and hpEurope were mapped to products of cagA, vacA, homC (outer membrane protein), sotB (sugar transport), and a translation fidelity factor (miaA). Large divergence was seen in genes related to antibiotics: frxA (metronidazole resistance), def (peptide deformylase, drug target), and ftsA (actin-like, drug target).
CONCLUSIONS: These results demonstrate dramatic genome evolution within a species, especially in likely host interaction genes. The East Asian strains appear to differ greatly from the European strains in electron transfer and redox reactions. These findings also suggest a model of adaptive evolution through proteome diversification and selection through modulation of translational fidelity. The results define H. pylori East Asian lineages and provide essential information for understanding their pathogenesis and designing drugs and therapies that target them.
ESTHER : Kawai_2011_BMC.Microbiol_11_104
PubMedSearch : Kawai_2011_BMC.Microbiol_11_104
PubMedID: 21575176

Title : Complete genome sequence of Macrococcus caseolyticus strain JCSCS5402, [corrected] reflecting the ancestral genome of the human-pathogenic staphylococci - Baba_2009_J.Bacteriol_191_1180
Author(s) : Baba T , Kuwahara-Arai K , Uchiyama I , Takeuchi F , Ito T , Hiramatsu K
Ref : Journal of Bacteriology , 191 :1180 , 2009
Abstract : We isolated the methicillin-resistant Macrococcus caseolyticus strain JCSC5402 from animal meat in a supermarket and determined its whole-genome nucleotide sequence. This is the first report on the genome analysis of a macrococcal species that is evolutionarily closely related to the human pathogens Staphylococcus aureus and Bacillus anthracis. The essential biological pathways of M. caseolyticus are similar to those of staphylococci. However, the species has a small chromosome (2.1 MB) and lacks many sugar and amino acid metabolism pathways and a plethora of virulence genes that are present in S. aureus. On the other hand, M. caseolyticus possesses a series of oxidative phosphorylation machineries that are closely related to those in the family Bacillaceae. We also discovered a probable primordial form of a Macrococcus methicillin resistance gene complex, mecIRAm, on one of the eight plasmids harbored by the M. caseolyticus strain. This is the first finding of a plasmid-encoding methicillin resistance gene. Macrococcus is considered to reflect the genome of ancestral bacteria before the speciation of staphylococcal species and may be closely associated with the origin of the methicillin resistance gene complex of the notorious human pathogen methicillin-resistant S. aureus.
ESTHER : Baba_2009_J.Bacteriol_191_1180
PubMedSearch : Baba_2009_J.Bacteriol_191_1180
PubMedID: 19074389
Gene_locus related to this paper: maccj-b9e7p5 , maccj-b9e9x1 , maccj-b9eah3 , maccj-b9eas3 , maccj-b9ebj0

Title : The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution - Nakayama_2008_DNA.Res_15_185
Author(s) : Nakayama K , Yamashita A , Kurokawa K , Morimoto T , Ogawa M , Fukuhara M , Urakami H , Ohnishi M , Uchiyama I , Ogura Y , Ooka T , Oshima K , Tamura A , Hattori M , Hayashi T
Ref : DNA Research , 15 :185 , 2008
Abstract : Scrub typhus ('Tsutsugamushi' disease in Japanese) is a mite-borne infectious disease. The causative agent is Orientia tsutsugamushi, an obligate intracellular bacterium belonging to the family Rickettsiaceae of the subdivision alpha-Proteobacteria. In this study, we determined the complete genome sequence of O. tsutsugamushi strain Ikeda, which comprises a single chromosome of 2 008 987 bp and contains 1967 protein coding sequences (CDSs). The chromosome is much larger than those of other members of Rickettsiaceae, and 46.7% of the sequence was occupied by repetitive sequences derived from an integrative and conjugative element, 10 types of transposable elements, and seven types of short repeats of unknown origins. The massive amplification and degradation of these elements have generated a huge number of repeated genes (1196 CDSs, categorized into 85 families), many of which are pseudogenes (766 CDSs), and also induced intensive genome shuffling. By comparing the gene content with those of other family members of Rickettsiacea, we identified the core gene set of the family Rickettsiaceae and found that, while much more extensive gene loss has taken place among the housekeeping genes of Orientia than those of Rickettsia, O. tsutsugamushi has acquired a large number of foreign genes. The O. tsutsugamushi genome sequence is thus a prominent example of the high plasticity of bacterial genomes, and provides the genetic basis for a better understanding of the biology of O. tsutsugamushi and the pathogenesis of 'Tsutsugamushi' disease.
ESTHER : Nakayama_2008_DNA.Res_15_185
PubMedSearch : Nakayama_2008_DNA.Res_15_185
PubMedID: 18508905
Gene_locus related to this paper: oriti-b3cqy7

Title : Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus - Takami_2004_Nucleic.Acids.Res_32_6292
Author(s) : Takami H , Takaki Y , Chee GJ , Nishi S , Shimamura S , Suzuki H , Matsui S , Uchiyama I
Ref : Nucleic Acids Research , 32 :6292 , 2004
Abstract : We present herein the first complete genome sequence of a thermophilic Bacillus-related species, Geobacillus kaustophilus HTA426, which is composed of a 3.54 Mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. Upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the G.kaustophilus genome were found to be unique to that species. We were able to find the first prokaryotic sperm protamine P1 homolog, polyamine synthase, polyamine ABC transporter and RNA methylase in the 839 unique genes; these may contribute to thermophily by stabilizing the nucleic acids. Contrasting results were obtained from the principal component analysis (PCA) of the amino acid composition and synonymous codon usage for highlighting the thermophilic signature of the G.kaustophilus genome. Only in the PCA of the amino acid composition were the Bacillus-related species located near, but were distinguishable from, the borderline distinguishing thermophiles from mesophiles on the second principal axis. Further analysis revealed some asymmetric amino acid substitutions between the thermophiles and the mesophiles, which are possibly associated with the thermoadaptation of the organism.
ESTHER : Takami_2004_Nucleic.Acids.Res_32_6292
PubMedSearch : Takami_2004_Nucleic.Acids.Res_32_6292
PubMedID: 15576355
Gene_locus related to this paper: bac25-mglp , geoka-q5kva3 , geoka-q5kvf2 , geoka-q5kvx7 , geoka-q5kvz7 , geoka-q5kzv8 , geoka-q5l1a6 , geoka-q5l1d4 , geoka-q5l1n0 , geoka-q5l1u3 , geoka-q5l3h0 , geotn-a4isp0 , geoka-g5eba9

Title : Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments - Takami_2002_Nucleic.Acids.Res_30_3927
Author(s) : Takami H , Takaki Y , Uchiyama I
Ref : Nucleic Acids Research , 30 :3927 , 2002
Abstract : Oceanobacillus iheyensis HTE831 is an alkaliphilic and extremely halotolerant Bacillus-related species isolated from deep-sea sediment. We present here the complete genome sequence of HTE831 along with analyses of genes required for adaptation to highly alkaline and saline environments. The genome consists of 3.6 Mb, encoding many proteins potentially associated with roles in regulation of intracellular osmotic pressure and pH homeostasis. The candidate genes involved in alkaliphily were determined based on comparative analysis with three Bacillus species and two other Gram-positive species. Comparison with the genomes of other major Gram-positive bacterial species suggests that the backbone of the genus Bacillus is composed of approximately 350 genes. 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.
ESTHER : Takami_2002_Nucleic.Acids.Res_30_3927
PubMedSearch : Takami_2002_Nucleic.Acids.Res_30_3927
PubMedID: 12235376
Gene_locus related to this paper: oceih-DHBF , oceih-OB0234 , oceih-OB0300 , oceih-OB0444 , oceih-OB0462 , oceih-OB0555 , oceih-OB0606 , oceih-OB0639 , oceih-OB0706 , oceih-OB0923 , oceih-OB0925 , oceih-OB0963 , oceih-OB0990 , oceih-OB1045 , oceih-OB1074 , oceih-OB1081 , oceih-OB1195 , oceih-OB1231 , oceih-OB1264 , oceih-OB2095 , oceih-OB2324 , oceih-OB2429 , oceih-OB2431 , oceih-OB2463 , oceih-OB2742 , oceih-OB2952 , oceih-OB3344 , oceih-OB3377

Title : Whole genome sequencing of meticillin-resistant Staphylococcus aureus - Kuroda_2001_Lancet_357_1225
Author(s) : Kuroda M , Ohta T , Uchiyama I , Baba T , Yuzawa H , Kobayashi I , Cui L , Oguchi A , Aoki K , Nagai Y , Lian J , Ito T , Kanamori M , Matsumaru H , Maruyama A , Murakami H , Hosoyama A , Mizutani-Ui Y , Takahashi NK , Sawano T , Inoue R , Kaito C , Sekimizu K , Hirakawa H , Kuhara S , Goto S , Yabuzaki J , Kanehisa M , Yamashita A , Oshima K , Furuya K , Yoshino C , Shiba T , Hattori M , Ogasawara N , Hayashi H , Hiramatsu K
Ref : Lancet , 357 :1225 , 2001
Abstract : BACKGROUND: Staphylococcus aureus is one of the major causes of community-acquired and hospital-acquired infections. It produces numerous toxins including superantigens that cause unique disease entities such as toxic-shock syndrome and staphylococcal scarlet fever, and has acquired resistance to practically all antibiotics. Whole genome analysis is a necessary step towards future development of countermeasures against this organism.
METHODS: Whole genome sequences of two related S aureus strains (N315 and Mu50) were determined by shot-gun random sequencing. N315 is a meticillin-resistant S aureus (MRSA) strain isolated in 1982, and Mu50 is an MRSA strain with vancomycin resistance isolated in 1997. The open reading frames were identified by use of GAMBLER and GLIMMER programs, and annotation of each was done with a BLAST homology search, motif analysis, and protein localisation prediction. FINDINGS: The Staphylococcus genome was composed of a complex mixture of genes, many of which seem to have been acquired by lateral gene transfer. Most of the antibiotic resistance genes were carried either by plasmids or by mobile genetic elements including a unique resistance island. Three classes of new pathogenicity islands were identified in the genome: a toxic-shock-syndrome toxin island family, exotoxin islands, and enterotoxin islands. In the latter two pathogenicity islands, clusters of exotoxin and enterotoxin genes were found closely linked with other gene clusters encoding putative pathogenic factors. The analysis also identified 70 candidates for new virulence factors. INTERPRETATION: The remarkable ability of S aureus to acquire useful genes from various organisms was revealed through the observation of genome complexity and evidence of lateral gene transfer. Repeated duplication of genes encoding superantigens explains why S aureus is capable of infecting humans of diverse genetic backgrounds, eliciting severe immune reactions. Investigation of many newly identified gene products, including the 70 putative virulence factors, will greatly improve our understanding of the biology of staphylococci and the processes of infectious diseases caused by S aureus.
ESTHER : Kuroda_2001_Lancet_357_1225
PubMedSearch : Kuroda_2001_Lancet_357_1225
PubMedID: 11418146
Gene_locus related to this paper: staau-LIP , staau-lipas , staau-MW0741 , staau-MW2456 , staau-q6gfm6 , staau-SA0011 , staau-SA0569 , staau-SA0572 , staau-SA0897 , staau-SA1143 , staau-SA2240 , staau-SA2306 , staau-SA2367 , staau-SA2422 , staau-SAV0321 , staau-SAV0446 , staau-SAV0457 , staau-SAV0655 , staau-SAV1014 , staau-SAV1765 , staau-SAV1793 , staau-SAV2188 , staau-SAV2350 , staau-SAV2484 , staau-SAV2594