Iida T

References (25)

Title : Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles - Matsumoto_2019_Emerg.Microbes.Infect_8_1043
Author(s) : Matsumoto Y , Kinjo T , Motooka D , Nabeya D , Jung N , Uechi K , Horii T , Iida T , Fujita J , Nakamura S
Ref : Emerg Microbes Infect , 8 :1043 , 2019
Abstract : The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.
ESTHER : Matsumoto_2019_Emerg.Microbes.Infect_8_1043
PubMedSearch : Matsumoto_2019_Emerg.Microbes.Infect_8_1043
PubMedID: 31287781
Gene_locus related to this paper: 9myco-a0a6n4vdv4

Title : New-onset diabetes mellitus after living-donor liver transplantation: association with graft synthetic function - Yagi_2017_Surg.Today_47_733
Author(s) : Yagi S , Kaido T , Iida T , Yoshizawa A , Okajima H , Uemoto S
Ref : Surg Today , 47 :733 , 2017
Abstract : BACKGROUND AND PURPOSE: It is now known that post-transplant graft function after deceased-donor liver transplantation and living-donor liver transplantation (LDLT) differ; however, there is no report assessing the relationship between graft function and the development of new-onset diabetes mellitus after transplantation (NODAT). We conducted this study to identify the predictive risk factors for NODAT, including graft function after LDLT.
METHODS: The subjects of this study were 175 adult recipients who underwent LDLT at Kyoto University Hospital between 2006 and 2010, and survived for more than 3 months (median observation period, 1046 days).
RESULTS: The 1-, 2-, and 3-year incidences of NODAT after LDLT were 26.1, 32.0, and 33.4%, respectively. Pre-transplant diabetes was associated with poor survival (p = 0.0048), whereas NODAT was not associated with patient survival. In the multivariate analysis, recipient age >/=40, a tacrolimus trough level >/=8 ng/mL 3 months after LDLT, and cholinesterase (ChE) <185 IU/L 3 months after LDLT were the independent risk factors for NODAT.
CONCLUSIONS: Poor graft synthetic function 3 months after LDLT as well as older age of the recipient and a higher tacrolimus concentration were strongly associated with NODAT development after LDLT.
ESTHER : Yagi_2017_Surg.Today_47_733
PubMedSearch : Yagi_2017_Surg.Today_47_733
PubMedID: 27837276

Title : Draft Genome Sequence of the Alkaliphilic and Xylanolytic Paenibacillus sp. Strain JCM 10914, Isolated from the Gut of a Soil-Feeding Termite - Ohkuma_2014_Genome.Announc_2_e01144
Author(s) : Ohkuma M , Yuki M , Oshima K , Suda W , Oshida Y , Kitamura K , Iida T , Hattori M
Ref : Genome Announc , 2 :e01144 , 2014
Abstract : Panibacillus sp. strain JCM 10914 is a xylanolytic alkaliphile isolated from the gut of a soil-feeding termite. Its draft genome sequence revealed various genes for hydrolytic enzymes and will facilitate studies on adaptation to the highly alkaline gut environment and its role in digesting soil organic matter in the gut.
ESTHER : Ohkuma_2014_Genome.Announc_2_e01144
PubMedSearch : Ohkuma_2014_Genome.Announc_2_e01144
PubMedID: 24459258
Gene_locus related to this paper: 9bacl-v9gd19 , 9bacl-v9g8w0

Title : Draft Genome Sequences of Three Strains of Bacteroides pyogenes Isolated from a Cat and Swine - Sakamoto_2014_Genome.Announc_2_e01242
Author(s) : Sakamoto M , Oshima K , Suda W , Kitamura K , Iida T , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Here, we report the draft genome sequences of Bacteroides pyogenes JCM 6294(T), JCM 6292, and JCM 10003, which were isolated from a cat and swine and were recently classified into a single species, B. pyogenes. Comparative analyses of these genomes revealed the diversification of B. pyogenes strains isolated from different animals.
ESTHER : Sakamoto_2014_Genome.Announc_2_e01242
PubMedSearch : Sakamoto_2014_Genome.Announc_2_e01242
PubMedID: 24482517
Gene_locus related to this paper: 9bace-w4pec1 , 9bace-w4paz4

Title : Draft Genome Sequences of Psychrobacter Strains JCM 18900, JCM 18901, JCM 18902, and JCM 18903, Isolated Preferentially from Frozen Aquatic Organisms - Kudo_2014_Genome.Announc_2_e00280
Author(s) : Kudo T , Kidera A , Kida M , Kawauchi A , Shimizu R , Nakahara T , Zhang X , Yamada A , Amano M , Hamada Y , Taniyama S , Arakawa O , Yoshida A , Oshima K , Suda W , Kuwahara H , Nogi Y , Kitamura K , Yuki M , Iida T , Moriya S , Inoue T , Hongoh Y , Hattori M , Ohkuma M
Ref : Genome Announc , 2 :e00280 , 2014
Abstract : Four Psychrobacter strains, JCM 18900, JCM 18901, JCM 18902, and JCM 18903, related to either Psychrobacter nivimaris or Psychrobacter cibarius, were isolated from frozen marine animals. The genome information of these four strains will be useful for studies of their physiology and adaptation properties to frozen conditions.
ESTHER : Kudo_2014_Genome.Announc_2_e00280
PubMedSearch : Kudo_2014_Genome.Announc_2_e00280
PubMedID: 24699965
Gene_locus related to this paper: 9gamm-x0q9t6 , 9gamm-x0r0h9 , 9gamm-x0rb73 , 9gamm-x0qpg3 , 9gamm-x0rx94 , 9gamm-x0rpe0

Title : Draft Genome Sequence of Bacteroides reticulotermitis Strain JCM 10512T, Isolated from the Gut of a Termite - Yuki_2014_Genome.Announc_2_e00072
Author(s) : Yuki M , Oshima K , Suda W , Sakamoto M , Iida T , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Here we report the draft genome sequence of Bacteroides reticulotermitis strain JCM 10512(T), a xylanolytic and cellulolytic bacterium isolated from the gut of a wood-feeding termite. The genome information will facilitate the study of this strain for biomass degradation and adaptation to the gut environment.
ESTHER : Yuki_2014_Genome.Announc_2_e00072
PubMedSearch : Yuki_2014_Genome.Announc_2_e00072
PubMedID: 24526645
Gene_locus related to this paper: 9bace-w4uxt1 , 9bace-w4uy17 , 9bace-w4uuy7

Title : Draft Genome Sequences of Three Alkaliphilic Bacillus Strains, Bacillus wakoensis JCM 9140T, Bacillus akibai JCM 9157T, and Bacillus hemicellulosilyticus JCM 9152T - Yuki_2014_Genome.Announc_2_e01258
Author(s) : Yuki M , Oshima K , Suda W , Oshida Y , Kitamura K , Iida T , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Here, we report the draft genome sequences of the type strains of three cellulolytic or hemicellulolytic alkaliphilic Bacillus species: Bacillus wakoensis, Bacillus akibai, and Bacillus hemicellulosilyticus. The genome information for these three strains will be useful for studies of alkaliphilic Bacillus species, their evolution, and biotechnological applications for their enzymes.
ESTHER : Yuki_2014_Genome.Announc_2_e01258
PubMedSearch : Yuki_2014_Genome.Announc_2_e01258
PubMedID: 24482522
Gene_locus related to this paper: 9baci-w4q973 , baca3-w4qlz5 , 9baci-w4qj07 , 9baci-w4q8b8 , baca3-w4qp70 , 9baci-w4qcm9 , baca3-w4qrq6

Title : Draft Genome Sequence of the Boron-Tolerant and Moderately Halotolerant Bacterium Gracilibacillus boraciitolerans JCM 21714T - Ahmed_2014_Genome.Announc_2_e00097
Author(s) : Ahmed I , Oshima K , Suda W , Kitamura K , Iida T , Ohmori Y , Fujiwara T , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Gracilibacillus boraciitolerans JCM 21714(T) has been characterized as a highly boron-tolerant and moderately halotolerant bacterium. Here, we report the draft genome sequence of this strain. The genome sequence facilitates an understanding of the biochemical functions of boron and provides a base to identify the gene(s) involved in the boron tolerance mechanism of the strain.
ESTHER : Ahmed_2014_Genome.Announc_2_e00097
PubMedSearch : Ahmed_2014_Genome.Announc_2_e00097
PubMedID: 24558242
Gene_locus related to this paper: 9baci-w4vi05 , 9baci-w4vjh3 , 9baci-w4vgr7

Title : Draft Genome Sequences of Cyclodextrin-Producing Alkaliphilic Bacillus Strains JCM 19045, JCM 19046, and JCM 19047 - Kudo_2014_Genome.Announc_2_e00211
Author(s) : Kudo T , Sakamoto K , Akinaga M , Kawauchi A , Nakahara T , Zhang X , Yamada A , Oshima K , Suda W , Kuwahara H , Nakamura N , Nogi Y , Kitamura K , Yuki M , Iida T , Moriya S , Inoue T , Hongoh Y , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Bacillus strains JCM 19045, JCM 19046, and JCM 19047 are alkaliphiles that produce beta-cyclodextrin from starch. They are related to Bacillus xiaoxiensis and Bacillus lehensis. The genome information for these three strains will be useful for studies of the physiological role of cyclodextrin and cyclodextrin production.
ESTHER : Kudo_2014_Genome.Announc_2_e00211
PubMedSearch : Kudo_2014_Genome.Announc_2_e00211
PubMedID: 24652985
Gene_locus related to this paper: 9baci-a0a060lzd7 , 9baci-w7yjr4 , 9baci-w7zpe5 , 9baci-w8a608 , 9baci-w7zad0

Title : Draft Genome Sequences of Geomicrobium sp. Strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, Isolated from Aquatic Samples - Kudo_2014_Genome.Announc_2_e00622
Author(s) : Kudo T , Nakahara T , Zhang X , Taniyama S , Arakawa O , Murase S , Nakata H , Oshima K , Suda W , Kitamura K , Iida T , Oshida Y , Inoue T , Hongoh Y , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Haloalkaliphilic strains JCM 19037, JCM 19038, JCM 19039, and JCM 19055, closely related to Geomicrobium sediminis, were isolated from aquatic samples, and their draft genome sequences were determined. The genome information of these four strains will be useful for studies of their physiology and ecology.
ESTHER : Kudo_2014_Genome.Announc_2_e00622
PubMedSearch : Kudo_2014_Genome.Announc_2_e00622
PubMedID: 24948772
Gene_locus related to this paper: 9bacl-a0a061nv39 , 9bacl-a0a061nsm4 , 9bacl-a0a061ndf6 , 9bacl-a0a061nlu5 , 9bacl-a0a061ntb4 , 9bacl-a0a061nnc9 , 9bacl-a0a061pf66

Title : Draft Genome Sequences of Two Lactobacillus Strains, L. farraginis JCM 14108T and L. composti JCM 14202T, Isolated from Compost of Distilled Shochu Residue - Yuki_2014_Genome.Announc_2_e00257
Author(s) : Yuki M , Oshima K , Suda W , Kitahara M , Kitamura K , Iida T , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Here, we report the draft genome sequences of two type strains of Lactobacillus, Lactobacillus farraginis JCM 14108(T) and Lactobacillus composti JCM 14202(T), isolated from the compost of distilled shochu residue. Their genome information will be useful for studies of ecological and physiological functions of these Lactobacillus species.
ESTHER : Yuki_2014_Genome.Announc_2_e00257
PubMedSearch : Yuki_2014_Genome.Announc_2_e00257
PubMedID: 24675866
Gene_locus related to this paper: 9laco-x0pb49 , 9laco-x0psi7

Title : Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated from a Cellulose-Degrading Bacterial Community - Yuki_2014_Genome.Announc_2_e00110
Author(s) : Yuki M , Oshima K , Suda W , Sakamoto M , Kitamura K , Iida T , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Here, we report the draft genome sequence of a fibrolytic bacterium, Clostridium straminisolvens JCM 21531(T), isolated from a cellulose-degrading bacterial community. The genome information of this strain will be useful for studies on the degradation enzymes and functional interactions with other members in the community.
ESTHER : Yuki_2014_Genome.Announc_2_e00110
PubMedSearch : Yuki_2014_Genome.Announc_2_e00110
PubMedID: 24558248
Gene_locus related to this paper: 9firm-w4vb95 , 9firm-w4v5w9

Title : Draft Genome Sequences of Vibrio sp. Strains Isolated from Tetrodotoxin-Bearing Scavenging Gastropod - Kudo_2014_Genome.Announc_2_e00623
Author(s) : Kudo T , Kawauchi A , Nakahara T , Zhang X , Taniyama S , Takatani T , Arakawa O , Oshima K , Suda W , Kitamura K , Iida T , Iino T , Inoue T , Hongoh Y , Hattori M , Ohkuma M
Ref : Genome Announc , 2 : , 2014
Abstract : Vibrio sp. strains JCM 18905 and JCM 19053 were isolated from a tetrodotoxin (TTX)-bearing scavenging gastropod, and Vibrio sp. strain JCM 18904 was isolated from a sea cucumber. All these are closely related to Vibrio alginolyticus. Their comparative genome information is useful for studies of TTX production in bacteria.
ESTHER : Kudo_2014_Genome.Announc_2_e00623
PubMedSearch : Kudo_2014_Genome.Announc_2_e00623
PubMedID: 24948773

Title : The GAF-like-domain-containing transcriptional regulator DfdR is a sensor protein for dibenzofuran and several hydrophobic aromatic compounds - Iida_2009_J.Bacteriol_191_123
Author(s) : Iida T , Waki T , Nakamura K , Mukouzaka Y , Kudo T
Ref : Journal of Bacteriology , 191 :123 , 2009
Abstract : Dibenzofuran (DF) is one of the dioxin carbon skeletal compounds used as a model to study the microbial degradation of dioxins. This study analyzed the transcriptional regulation of the DF dioxygenase genes dfdA1 to dfdA4 in the DF-utilizing actinomycetes Rhodococcus sp. strain YK2 and Terrabacter sp. strain YK3. An open reading frame designated dfdR was detected downstream of the dfdC genes. The C-terminal part of the DfdR amino acid sequence has high levels of similarity to several LuxR-type DNA binding helix-turn-helix domains, and a GAF domain sequence in the central part was detected by a domain search analysis. A derivative of YK2 with dfdR disrupted was not able to utilize DF and did not exhibit DF-dependent dfdA1 transcriptional induction ability, and these dysfunctions were compensated for by introduction of dfdR. Promoter analysis of dfdA1 in Rhodococcus strains indicated that activation of the dfdA1 promoter (P(dfdA1)) was dependent on dfdR and DF and not on a metabolite of the DF pathway. The cell extract of a Rhodococcus strain that heterologously expressed DfdR showed electrophoretic mobility shift (EMS) activity for the P(dfdA1) DNA fragment in a DF-dependent manner. In addition, P(dfdA1) activation and EMS activity were observed with hydrophobic aromatic compounds comprising two or more aromatic rings, suggesting that DfdR has broad effector molecule specificity for several hydrophobic aromatic compounds.
ESTHER : Iida_2009_J.Bacteriol_191_123
PubMedSearch : Iida_2009_J.Bacteriol_191_123
PubMedID: 18952799
Gene_locus related to this paper: rhosp-DFDC

Title : Genomic taxonomy of Vibrios - Thompson_2009_BMC.Evol.Biol_9_258
Author(s) : Thompson CC , Vicente AC , Souza RC , Vasconcelos AT , Vesth T , Alves N, Jr. , Ussery DW , Iida T , Thompson FL
Ref : BMC Evol Biol , 9 :258 , 2009
Abstract : BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, < or = 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. CONCLUSION: The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.
ESTHER : Thompson_2009_BMC.Evol.Biol_9_258
PubMedSearch : Thompson_2009_BMC.Evol.Biol_9_258
PubMedID: 19860885
Gene_locus related to this paper: vibal-q1v7b5 , vibal-q1v7d0 , vibal-q1v463 , vibal-q1v627 , vibal-q1v697 , vibal-q1va42 , vibal-q1vai8 , vibal-q1vap1 , vibal-q1vbx2 , vibal-q1vfw6 , vibch-a6xrz3 , vibch-VC2718 , vibch-VCA0688 , vibch-y1892 , vibch-y2276 , vibha-d0x5c8 , vibha-d0x7p9 , vibha-d0xb11 , vibha-d0xgc5 , vibcb-a7mwv0 , vibhb-a7mzs1 , vibhb-a7n5i4 , vibhb-bioh , vibmi-d2y908 , vibmi-d2ygk2 , vibpa-PHAC , vibpa-VPA0468 , vibpa-VPA1467 , vibpa-VPA1496 , vibpa-VPA1595 , vibal-d0wu09 , vibha-d0xda8 , vibmi-u4zh77 , 9vibr-k5u9q4 , vibmi-g0sil5

Title : Analysis of two gene clusters involved in the degradation of 4-fluorophenol by Arthrobacter sp. strain IF1 - Ferreira_2009_Appl.Environ.Microbiol_75_7767
Author(s) : Ferreira MI , Iida T , Hasan SA , Nakamura K , Fraaije MW , Janssen DB , Kudo T
Ref : Applied Environmental Microbiology , 75 :7767 , 2009
Abstract : Arthrobacter sp. strain IF1 is able to grow on 4-fluorophenol (4-FP) as a sole source of carbon and energy. To clone the 4-FP degradation genes, DNA libraries were constructed and screened with a probe obtained by PCR using primers designed on the basis of conserved regions of aromatic two-component monooxygenases. Sequencing of positive clones yielded two gene clusters, each harboring a gene encoding a monooxygenase with high sequence similarity to the oxygenase component of 4-nitrophenol and 4-chlorophenol monooxygenase systems. Both these monooxygenase genes were differentially expressed during growth on 4-FP, as revealed by Northern blotting and reverse transcription-PCR. One cluster also contained a gene for a flavin reductase. The monooxygenase and reductase were purified from Escherichia coli cells expressing the corresponding genes, and together they catalyzed NADH-dependent hydroxylation and dehalogenation of 4-halophenols. The results indicate that strain IF1 transforms 4-FP to hydroquinone by a two-component monooxygenase system of which one component provides reduced flavin adenine dinucleotide at the expense of NADH and the other catalyzes para-hydroxylation of 4-FP and other 4-substituted phenols.
ESTHER : Ferreira_2009_Appl.Environ.Microbiol_75_7767
PubMedSearch : Ferreira_2009_Appl.Environ.Microbiol_75_7767
PubMedID: 19837837
Gene_locus related to this paper: 9micc-d1mys5

Title : Polychlorinated biphenyl\/biphenyl degrading gene clusters in Rhodococcus sp. K37, HA99, and TA431 are different from well-known bph gene clusters of Rhodococci - Taguchi_2007_Biosci.Biotechnol.Biochem_71_1136
Author(s) : Taguchi K , Motoyama M , Iida T , Kudo T
Ref : Biosci Biotechnol Biochem , 71 :1136 , 2007
Abstract : Four kinds of polychlorinated biphenyl (PCB)-degrading Rhodococcus sp. (TA421, TA431, HA99, and K37) have been isolated from termite ecosystem and under alkaline condition. The bph gene cluster involved in the degradation of PCB/biphenyl has been analyzed in strain TA421. This gene cluster was highly homologous to bph gene clusters in R. globerulus P6 and Rhodococcus sp. RHA1. In this study, we cloned and analyzed the bph gene cluster essential to PCB/biphenyl degradation from R. rhodochrous K37. The order of the genes and the sequence were different in K37 than in P6, RHA1, and TA421. The bphC8(K37) gene was more homologous to the meta-cleavage enzyme involved in phenanthrene metabolism than bphC genes involved in biphenyl metabolism. Two other Rhodococcus strains (HA99 and TA431) had PCB/biphenyl degradation gene clusters similar to that in K37. These findings suggest that these bph gene clusters evolved separately from the well-known bph gene clusters of PCB/biphenyl degraders.
ESTHER : Taguchi_2007_Biosci.Biotechnol.Biochem_71_1136
PubMedSearch : Taguchi_2007_Biosci.Biotechnol.Biochem_71_1136
PubMedID: 17485846
Gene_locus related to this paper: rhoer-a3kd02

Title : Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast - Buker_2007_Nat.Struct.Mol.Biol_14_200
Author(s) : Buker SM , Iida T , Buhler M , Villen J , Gygi SP , Nakayama J , Moazed D
Ref : Nat Struct Mol Biol , 14 :200 , 2007
Abstract : The RNA-induced transcriptional silencing (RITS) complex, containing Ago1, Chp1, Tas3 and centromeric small interfering RNAs (siRNAs), is required for heterochromatic gene silencing at centromeres. Here, we identify a second fission yeast Argonaute complex (Argonaute siRNA chaperone, ARC), which contains, in addition to Ago1, two previously uncharacterized proteins, Arb1 and Arb2, both of which are required for histone H3 Lys9 (H3-K9) methylation, heterochromatin assembly and siRNA generation. Furthermore, whereas siRNAs in the RITS complex are mostly single-stranded, siRNAs associated with ARC are mostly double-stranded, indicating that Arb1 and Arb2 inhibit the release of the siRNA passenger strand from Ago1. Consistent with this observation, purified Arb1 inhibits the slicer activity of Ago1 in vitro, and purified catalytically inactive Ago1 contains only double-stranded siRNA. Finally, we show that slicer activity is required for the siRNA-dependent association of Ago1 with chromatin and for the spreading of histone H3-K9 methylation.
ESTHER : Buker_2007_Nat.Struct.Mol.Biol_14_200
PubMedSearch : Buker_2007_Nat.Struct.Mol.Biol_14_200
PubMedID: 17310250

Title : Lateral transfer of the lux gene cluster - Kasai_2007_J.Biochem_141_231
Author(s) : Kasai S , Okada K , Hoshino A , Iida T , Honda T
Ref : J Biochem , 141 :231 , 2007
Abstract : The lux operon is an uncommon gene cluster. To find the pathway through which the operon has been transferred, we sequenced the operon and both flanking regions in four typical luminous species. In Vibrio cholerae NCIMB 41, a five-gene cluster, most genes of which were highly similar to orthologues present in Gram-positive bacteria, along with the lux operon, is inserted between VC1560 and VC1563, on chromosome 1. Because this entire five-gene cluster is present in Photorhabdus luminescens TT01, about 1.5 Mbp upstream of the operon, we deduced that the operon and the gene cluster were transferred from V. cholerae to an ancestor of Pr. luminescens. Because in both V. fischeri and Shewanella hanedai, luxR and luxI were found just upstream of the operon, we concluded that the operon was transferred from either species to the other. Because most of the genes flanking the operon were highly similar to orthologues present on chromosome 2 of vibrios, we speculated that the operon of most species is located on this chromosome. The undigested genomic DNAs of five luminous species were analysed by pulsed-field gel electrophoresis and Southern hybridization. In all the species except V. cholerae, the operons are located on chromosome 2.
ESTHER : Kasai_2007_J.Biochem_141_231
PubMedSearch : Kasai_2007_J.Biochem_141_231
PubMedID: 17169972
Gene_locus related to this paper: phopo-luxd , sheha-a0zsg8 , sheha-LUXD

Title : Isolation and characterization of a gene cluster for dibenzofuran degradation in a new dibenzofuran-utilizing bacterium, Paenibacillus sp. strain YK5 - Iida_2006_Arch.Microbiol_184_305
Author(s) : Iida T , Nakamura K , Izumi A , Mukouzaka Y , Kudo T
Ref : Arch Microbiol , 184 :305 , 2006
Abstract : Spore-forming bacterial strains capable of utilizing dibenzofuran (DF) as a sole source of carbon and energy were isolated. Characteristics of the isolates justified their classification into the genus Paenibacillus, and their closest relative was P. naphthalenovorans. Degenerate primers for aromatic hydrocarbon dioxygenase alpha subunit (AhDOa) genes and genomic DNA of the strain YK5 were used for gene isolation. The nucleotide sequences of clones of the PCR products revealed that the strain YK5 carries at least five different AhDOa genes. Northern hybridization analysis showed that one of the AhDOa genes was transcribed under DF-containing culture conditions. A gene cluster encoding the AhDOa was isolated. The genes predicted to encode extradiol dioxygenase (dbfB) and hydrolase (dbfC) were found to be an upstream of genes encoding the alpha and beta subunit of the AhDO (dbfA1 and dbfA2, respectively); the latter two gene products showed 60 and 53% identity to the amino acid sequences of DbfA1 and DbfA2 of Terrabacter sp. DBF63, respectively. Two Paenibacillus validus JCM 9077 strains transformed with the dbf gene clusters acquired the ability to convert DF to 2,2',3-trihydroxybiphenyl (THBP) and salicylic acid (SAL). These results suggest that the enzymes encoded by the gene cluster isolated in this study are involved in DF metabolism in YK5.
ESTHER : Iida_2006_Arch.Microbiol_184_305
PubMedSearch : Iida_2006_Arch.Microbiol_184_305
PubMedID: 16284749
Gene_locus related to this paper: 9bacl-q2wga4

Title : Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V cholerae - Makino_2003_Lancet_361_743
Author(s) : Makino K , Oshima K , Kurokawa K , Yokoyama K , Uda T , Tagomori K , Iijima Y , Najima M , Nakano M , Yamashita A , Kubota Y , Kimura S , Yasunaga T , Honda T , Shinagawa H , Hattori M , Iida T
Ref : Lancet , 361 :743 , 2003
Abstract : Background Vibrio parahaemolyticus, a gram-negative marine bacterium, is a worldwide cause of food-borne gastroenteritis. V parahaemolyticus strains of a few specific serotypes, probably derived from a common clonal ancestor, have lately caused a pandemic of gastroenteritis. The organism is phylogenetically close to V cholerae, the causative agent of cholera. METHODS: The whole genome sequence of a clinical V parahaemolyticus strain RIMD2210633 was established by shotgun sequencing. The coding sequences were identified by use of Gambler and Glimmer programs. Comparative analysis with the V cholerae genome was undertaken with MUMmer. FINDINGS: The genome consisted of two circular chromosomes of 3288558 bp and 1877212 bp; it contained 4832 genes. Comparison of the V parahaemolyticus genome with that of V cholerae showed many rearrangements within and between the two chromosomes. Genes for the type III secretion system (TTSS) were identified in the genome of V parahaemolyticus; V cholerae does not have these genes. INTERPRETATION: The TTSS is a central virulence factor of diarrhoea-causing bacteria such as shigella, salmonella, and enteropathogenic Escherichia coli, which cause gastroenteritis by invading or intimately interacting with intestinal epithelial cells. Our results suggest that V parahaemolyticus and V cholerae use distinct mechanisms to establish infection. This finding explains clinical features of V parahaemolyticus infections, which commonly include inflammatory diarrhoea and in some cases systemic manifestations such as septicaemia, distinct from those of V cholerae infections, which are generally associated with non-inflammatory diarrhoea.
ESTHER : Makino_2003_Lancet_361_743
PubMedSearch : Makino_2003_Lancet_361_743
PubMedID: 12620739
Gene_locus related to this paper: vibpa-PHAC , vibpa-VP0148 , vibpa-VP0409 , vibpa-VP0429 , vibpa-VP0626 , vibpa-VP0693 , vibpa-VP0837 , vibpa-VP0869 , vibpa-VP0930 , vibpa-VP1025 , vibpa-VP1181 , vibpa-VP1677 , vibpa-VP1678 , vibpa-VP2790 , vibpa-VP2974 , vibpa-VPA0054 , vibpa-VPA0070 , vibpa-VPA0081 , vibpa-VPA0167 , vibpa-VPA0468 , vibpa-VPA0859 , vibpa-VPA0997 , vibpa-VPA1061 , vibpa-VPA1249 , vibpa-VPA1467 , vibpa-VPA1496 , vibpa-VPA1595 , vibpa-y674 , vibpa-y969

Title : Isolation and characterization of dibenzofuran-degrading actinomycetes: analysis of multiple extradiol dioxygenase genes in dibenzofuran-degrading Rhodococcus species - Iida_2002_Biosci.Biotechnol.Biochem_66_1462
Author(s) : Iida T , Mukouzaka Y , Nakamura K , Yamaguchi I , Kudo T
Ref : Biosci Biotechnol Biochem , 66 :1462 , 2002
Abstract : Sixteen actinomycetes capable of utilizing dibenzofuran as a sole source of carbon and energy were isolated, including Rhodococcus, Microbacterium, and Terrabacter genera. Heretofore, no dibenzofuran-utilizing strain belonging to the genus Microbacterium has been reported. Five extradiol dioxygenase genes (dfdB, and edil to 4) of the strain Rhodococcus sp. YK2 were cloned and analyzed. The nucleotide sequence of dfdB gene was almost identical to the bphC1 gene of Terrabacter sp. DPO360, which was involved in dibenzofuran metabolism in this strain. Southern and Northern hybridization analyses using these extradiol dioxygenase genes as probes suggest that the dfdB gene in YK2 was conserved in diverse dibenzofuran-utilizing actinomycetes; also, the dfdB gene was the only expressed gene among five extradiol dioxygenase genes in the medium containing DF as a sole carbon source. These results suggest that the dfdB gene is important for dibenzofuran metabolism not only in the strain YK2, but also in diverse dibenzofuran-degrading actinomycetes.
ESTHER : Iida_2002_Biosci.Biotechnol.Biochem_66_1462
PubMedSearch : Iida_2002_Biosci.Biotechnol.Biochem_66_1462
PubMedID: 12224629
Gene_locus related to this paper: rhosp-DFDC , rhosp-ORF1

Title : Plasmid-borne genes code for an angular dioxygenase involved in dibenzofuran degradation by Terrabacter sp. strain YK3 - Iida_2002_Appl.Environ.Microbiol_68_3716
Author(s) : Iida T , Mukouzaka Y , Nakamura K , Kudo T
Ref : Applied Environmental Microbiology , 68 :3716 , 2002
Abstract : The genes responsible for angular dioxygenation of dibenzofuran in actinomycetes were cloned by using a degenerate set of PCR primers designed by using conserved sequences of the dioxygenase alpha subunit genes. One sequence of alpha subunit genes was commonly amplified from four dibenzofuran-utilizing actinomycetes: Terrabacter sp. strains YK1 and YK3, Rhodococcus sp. strain YK2, and Microbacterium sp. strain YK18. A 5.2-kb PstI fragment encoding the alpha and beta subunits of the terminal dioxygenase, ferredoxin, and ferredoxin reductase (designated dfdA1 to dfdA4, respectively) was cloned from the large circular plasmid pYK3 isolated from Terrabacter sp. strain YK3. We confirmed that transcription of the dfdA1 gene was induced by dibenzofuran in Terrabacter sp. strain YK3. Southern blot hybridization analysis revealed that this type of dioxygenase gene is distributed among diverse dibenzofuran-utilizing actinomycetes. However, genes homologous to dfdA1 were not detected in dibenzofuran utilization-deficient mutants of Terrabacter, Rhodococcus, and Microbacterium species. When the dfdA1 to dfdA4 genes were introduced into a non-dibenzofuran-degrading mutant of Rhodococcus sp. strain YK2, strain YK2-RD2, which had spontaneously lost the gene homologous to dfdA1, the ability to degrade dibenzofuran was restored. Analysis of the breakdown products indicated that DfdA has angular dioxygenase activity. This dfdA transformant degraded several aromatic compounds, indicating that the novel angular dioxygenase possesses broad substrate specificity.
ESTHER : Iida_2002_Appl.Environ.Microbiol_68_3716
PubMedSearch : Iida_2002_Appl.Environ.Microbiol_68_3716
PubMedID: 12147464
Gene_locus related to this paper: rhosp-DFDC

Title : Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12 - Hayashi_2001_DNA.Res_8_11
Author(s) : Hayashi T , Makino K , Ohnishi M , Kurokawa K , Ishii K , Yokoyama K , Han CG , Ohtsubo E , Nakayama K , Murata T , Tanaka M , Tobe T , Iida T , Takami H , Honda T , Sasakawa C , Ogasawara N , Yasunaga T , Kuhara S , Shiba T , Hattori M , Shinagawa H
Ref : DNA Research , 8 :11 , 2001
Abstract : Escherichia coli O157:H7 is a major food-borne infectious pathogen that causes diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. Here we report the complete chromosome sequence of an O157:H7 strain isolated from the Sakai outbreak, and the results of genomic comparison with a benign laboratory strain, K-12 MG1655. The chromosome is 5.5 Mb in size, 859 Kb larger than that of K-12. We identified a 4.1-Mb sequence highly conserved between the two strains, which may represent the fundamental backbone of the E. coli chromosome. The remaining 1.4-Mb sequence comprises of O157:H7-specific sequences, most of which are horizontally transferred foreign DNAs. The predominant roles of bacteriophages in the emergence of O157:H7 is evident by the presence of 24 prophages and prophage-like elements that occupy more than half of the O157:H7-specific sequences. The O157:H7 chromosome encodes 1632 proteins and 20 tRNAs that are not present in K-12. Among these, at least 131 proteins are assumed to have virulence-related functions. Genome-wide codon usage analysis suggested that the O157:H7-specific tRNAs are involved in the efficient expression of the strain-specific genes. A complete set of the genes specific to O157:H7 presented here sheds new insight into the pathogenicity and the physiology of O157:H7, and will open a way to fully understand the molecular mechanisms underlying the O157:H7 infection.
ESTHER : Hayashi_2001_DNA.Res_8_11
PubMedSearch : Hayashi_2001_DNA.Res_8_11
PubMedID: 11258796
Gene_locus related to this paper: ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-entf , ecoli-fes , ecoli-MCMK , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-Z0347 , ecoli-Z1341 , ecoli-Z1930 , ecoli-Z2445 , ecoli-YfhR

Title : Complete nucleotide sequences of 93-kb and 3.3-kb plasmids of an enterohemorrhagic Escherichia coli O157:H7 derived from Sakai outbreak - Makino_1998_DNA.Res_5_1
Author(s) : Makino K , Ishii K , Yasunaga T , Hattori M , Yokoyama K , Yutsudo CH , Kubota Y , Yamaichi Y , Iida T , Yamamoto K , Honda T , Han CG , Ohtsubo E , Kasamatsu M , Hayashi T , Kuhara S , Shinagawa H
Ref : DNA Research , 5 :1 , 1998
Abstract : Enterohemorrhagic Escherichia coli (EHEC) O157:H7, derived from an outbreak in Sakai city, Japan in 1996, possesses two kinds of plasmids: a 93-kb plasmid termed pO157, found in clinical EHEC isolates world-wide and a 3.3-kb plasmid termed pOSAK1, prevalent in EHEC strains isolated in Japan. Complete nucleotide sequences of both plasmids have been determined, and the putative functions of the encoded proteins and the cis-acting DNA sequences have been analyzed. pO157 shares strikingly similar genes and DNA sequences with F-factor and the transmissible drug-resistant plasmid R100 for DNA replication, copy number control, plasmid segregation, conjugative functions and stable maintenance in the host, although it is defective in DNA transfer by conjugation due to the truncation and deletion of the required genes and DNA sequences. In addition, it encodes several proteins implicated in EHEC pathogenicity such as an EHEC hemolysin (HlyA), a catalase-peroxidase (KatP), a serine protease (EspP) and type II secretion system. pOSAK1 possesses a ColE1-like replication system, and the DNA sequence is extremely similar to that of a drug-resistant plasmid, NTP16, derived from Salmonella typhimurium except that it lacks drug resistance transposons.
ESTHER : Makino_1998_DNA.Res_5_1
PubMedSearch : Makino_1998_DNA.Res_5_1
PubMedID: 9628576
Gene_locus related to this paper: ecoli-ypt1