Hattori M

References (82)

Title : Genome analysis of a novel Bradyrhizobium sp. DOA9 carrying a symbiotic plasmid - Okazaki_2015_PLoS.One_10_e0117392
Author(s) : Okazaki S , Noisangiam R , Okubo T , Kaneko T , Oshima K , Hattori M , Teamtisong K , Songwattana P , Tittabutr P , Boonkerd N , Saeki K , Sato S , Uchiumi T , Minamisawa K , Teaumroong N
Ref : PLoS ONE , 10 :e0117392 , 2015
Abstract : Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. Genome analysis of DOA9 revealed that its genome comprised a single chromosome of 7.1 Mbp and a plasmid of 0.7 Mbp. The chromosome showed highest similarity with that of the nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene species. Unlike in other bradyrhizobia, the plasmid of DOA9 encodes genes related to symbiotic functions including nodulation, nitrogen fixation, and type III/IV protein secretion systems. The plasmid has also a lower GC content (60.1%) than the chromosome (64.4%). These features suggest that the plasmid could be the origin of the symbiosis island that is found in the genome of other bradyrhizobia. The nod genes of DOA9 exhibited low similarity with those of other strains. The nif gene cluster of DOA9 showed greatest similarity to those of photosynthetic bradyrhizobia. The type III/IV protein secretion systems of DOA9 are similar to those of nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation. Bradyrhizobium sp. DOA9 isolated from the legume Aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the Bradyrhizobiaceae. Genome analysis of DOA9 revealed that its genome comprised a single chromosome of 7.1 Mbp and a plasmid of 0.7 Mbp. The chromosome showed highest similarity with that of the nod gene-harboring soybean symbiont B. japonicum USDA110, whereas the plasmid showed highest similarity with pBBta01 of the nod gene-lacking photosynthetic strain BTAi1, which nodulates Aeschynomene species. Unlike in other bradyrhizobia, the plasmid of DOA9 encodes genes related to symbiotic functions including nodulation, nitrogen fixation, and type III/IV protein secretion systems. The plasmid has also a lower GC content (60.1%) than the chromosome (64.4%). These features suggest that the plasmid could be the origin of the symbiosis island that is found in the genome of other bradyrhizobia. The nod genes of DOA9 exhibited low similarity with those of other strains. The nif gene cluster of DOA9 showed greatest similarity to those of photosynthetic bradyrhizobia. The type III/IV protein secretion systems of DOA9 are similar to those of nod gene-harboring B. elkanii and photosynthetic BTAi1. The DOA9 genome exhibited intermediate characteristics between nod gene-harboring bradyrhizobia and nod gene-lacking photosynthetic bradyrhizobia, thus providing the evidence for the evolution of the Bradyrhizobiaceae during ecological adaptation.
ESTHER : Okazaki_2015_PLoS.One_10_e0117392
PubMedSearch : Okazaki_2015_PLoS.One_10_e0117392
PubMedID: 25710540
Gene_locus related to this paper: 9brad-a0a0r3chf0 , 9brad-a0a0s6v2v2

Title : Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes - Inoue_2015_Microbes.Environ_30_44
Author(s) : Inoue J , Oshima K , Suda W , Sakamoto M , Iino T , Noda S , Hongoh Y , Hattori M , Ohkuma M
Ref : Microbes Environ , 30 :44 , 2015
Abstract : Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 15093(T) and Geofilum rubicundum JCM 15548(T). In addition to these and previously reported 'Candidatus Azobacteroides pseudotrichonymphae' and Paludibacter propionicigenes, an extensive survey of the genome sequences of diverse Bacteroidetes members revealed the presence of a set of nif genes (nifHDKENB) in strains of Dysgonomonas gadei, Dysgonomonas capnocytophagoides, Saccharicrinis fermentans, and Alkaliflexus imshenetskii. These eight species belonged to and were distributed sporadically within the order Bacteroidales. Acetylene reduction activity was detected in the five species examined, strongly suggesting their diazotrophic nature. Phylogenetic analyses showed monophyletic clustering of the six Nif protein sequences in the eight Bacteroidales species, implying that nitrogen fixation is ancestral to Bacteroidales and has been retained in these species, but lost in many other lineages. The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.
ESTHER : Inoue_2015_Microbes.Environ_30_44
PubMedSearch : Inoue_2015_Microbes.Environ_30_44
PubMedID: 25736980
Gene_locus related to this paper: 9bact-a0a0e9lvi0 , 9bact-a0a0e9lzx7 , 9bace-a0a069d1v9 , 9bact-a0a0e9lyc6 , 9bace-a0a069d662

Title : Draft Genome Sequence of Streptomyces incarnatus NRRL8089, which Produces the Nucleoside Antibiotic Sinefungin - Oshima_2015_Genome.Announc_3_e00715
Author(s) : Oshima K , Hattori M , Shimizu H , Fukuda K , Nemoto M , Inagaki K , Tamura T
Ref : Genome Announc , 3 : , 2015
Abstract : A draft genome sequence of Streptomyces incarnatus NRRL8089, which produces the nucleoside antibiotic sinefungin, is described here. The genome contains 8,897,465 bp in 76 contigs and 8,266 predicted genes. Interestingly, the genome encodes an open reading frame for selenocysteine-containing formate dehydrogenase-O and the selenoprotein biosynthetic gene cluster selABCD.
ESTHER : Oshima_2015_Genome.Announc_3_e00715
PubMedSearch : Oshima_2015_Genome.Announc_3_e00715
PubMedID: 26159526
Gene_locus related to this paper: 9actn-a0a0g3ac56 , 9actn-a0a0g3anc9 , 9actn-a0a0g3awn7 , 9actn-a0a0g3avt9

Title : Complete Genome Sequence of a Phenanthrene Degrader, Mycobacterium sp. Strain EPa45 (NBRC 110737), Isolated from a Phenanthrene-Degrading Consortium - Kato_2015_Genome.Announc_3_e00782
Author(s) : Kato H , Ogawa N , Ohtsubo Y , Oshima K , Toyoda A , Mori H , Nagata Y , Kurokawa K , Hattori M , Fujiyama A , Tsuda M
Ref : Genome Announc , 3 : , 2015
Abstract : A phenanthrene degrader, Mycobacterium sp. EPa45, was isolated from a phenanthrene-degrading consortium. Here, we report the complete genome sequence of EPa45, which has a 6.2-Mb single circular chromosome. We propose a phenanthrene degradation pathway in EPa45 based on the complete genome sequence.
ESTHER : Kato_2015_Genome.Announc_3_e00782
PubMedSearch : Kato_2015_Genome.Announc_3_e00782
PubMedID: 26184940
Gene_locus related to this paper: 9myco-a0a0g3iim6 , 9myco-a0a0g3ijm3 , 9myco-a0a0g3ipv9 , 9myco-a0a0g3iuf8 , 9myco-a0a0g3ivy5 , 9myco-a0a0g3ihb1

Title : Autopsy-confirmed hippocampal-sparing Alzheimer's disease with delusional jealousy as initial manifestation - Fujishiro_2015_Psychogeriatrics_15_198
Author(s) : Fujishiro H , Iritani S , Hattori M , Sekiguchi H , Matsunaga S , Habuchi C , Torii Y , Umeda K , Ozaki N , Yoshida M , Fujita K
Ref : Psychogeriatrics , 15 :198 , 2015
Abstract : Alzheimer's disease (AD) is clinically characterized by gradual onset over years with worsening of cognition. The initial and most prominent cognitive deficit is commonly memory dysfunction. However, a subset of AD cases has less hippocampal atrophy than would be expected relative to the predominance of cortical atrophy. These hippocampal-sparing cases have distinctive clinical features, including the presence of focal cortical clinical syndromes. Given that previous studies have indicated that severe hippocampal atrophy corresponds to prominent loss of episodic memory, it is likely that memory impairment is initially absent in hippocampal-sparing AD cases. Here, we report on a patient with an 8-year history of delusional jealousy with insidious onset who was clinically diagnosed as possible AD and pathologically confirmed to have AD with relatively preserved neurons in the hippocampus. This patient had delusional jealousy with a long pre-dementia stage, which initially was characterized by lack of memory impairment. Head magnetic resonance imaging findings showed preserved hippocampal volume with bilateral enlarged ventricles and mild-to-moderate cortical atrophy. Head single-photon emission computed tomography revealed severely decreased regional cerebral blood flow in the right temporal lobe. The resolution of the delusion was attributed to pharmacotherapy by an acetylcholinesterase inhibitor, suggesting that the occurrence of delusional jealousy was due to the disease process of AD. Although the neural basis of delusional jealousy remains unclear, this hippocampal-sparing AD case may be classified as an atypical presentation of AD.
ESTHER : Fujishiro_2015_Psychogeriatrics_15_198
PubMedSearch : Fujishiro_2015_Psychogeriatrics_15_198
PubMedID: 25737011

Title : Draft Genome Sequences of Marine Flavobacterium Algibacter lectus Strains SS8 and NR4 - Takatani_2014_Genome.Announc_2_e01168
Author(s) : Takatani N , Nakanishi M , Meirelles P , Mino S , Suda W , Oshima K , Hattori M , Ohkuma M , Hosokawa M , Miyashita K , Thompson FL , Niwa A , Sawabe T
Ref : Genome Announc , 2 : , 2014
Abstract : Here, we present the draft genome sequences of a zeaxanthin-producing flavobacterium, Algibacter lectus strains SS8 and NR4, isolated from coastal sediment and rock surfaces in Hakodate, Japan, respectively. This genomic information represents the first Algibacter genome sequences, which will help us to elucidate the biology and evolution of Flavobacteriaceae bacteria.
ESTHER : Takatani_2014_Genome.Announc_2_e01168
PubMedSearch : Takatani_2014_Genome.Announc_2_e01168
PubMedID: 25395640
Gene_locus related to this paper: 9flao-a0a090w6b8 , 9flao-a0a090wm61

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 : Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen - Iguchi_2014_Genome.Biol.Evol_6_2096
Author(s) : Iguchi A , Nagaya Y , Pradel E , Ooka T , Ogura Y , Katsura K , Kurokawa K , Oshima K , Hattori M , Parkhill J , Sebaihia M , Coulthurst SJ , Gotoh N , Thomson NR , Ewbank JJ , Hayashi T
Ref : Genome Biol Evol , 6 :2096 , 2014
Abstract : Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multidrug resistance of this species. We show a remarkable intraspecies genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of approximately 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents.
ESTHER : Iguchi_2014_Genome.Biol.Evol_6_2096
PubMedSearch : Iguchi_2014_Genome.Biol.Evol_6_2096
PubMedID: 25070509
Gene_locus related to this paper: serma-a0a031rry9 , serma-a0a0a5sc46

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 : Draft Genome Sequences of Marinobacter similis A3d10T and Marinobacter salarius R9SW1T - Ivanova_2014_Genome.Announc_2_e00442
Author(s) : Ivanova EP , Ng HJ , Webb HK , Feng G , Oshima K , Hattori M , Ohkuma M , Sergeev AF , Mikhailov VV , Crawford RJ , Sawabe T
Ref : Genome Announc , 2 : , 2014
Abstract : Here, we present the draft genomes of Marinobacter similis A3d10(T), a potential plastic biodegrader, and Marinobacter salarius R9SW1(T), isolated from radioactive waters. This genomic information will contribute information on the genetic basis of the metabolic pathways for the degradation of both plastic and radionuclides.
ESTHER : Ivanova_2014_Genome.Announc_2_e00442
PubMedSearch : Ivanova_2014_Genome.Announc_2_e00442
PubMedID: 24855296
Gene_locus related to this paper: 9alte-a6f367

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 : Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability - Fukao_2013_PLoS.One_8_e60521
Author(s) : Fukao M , Oshima K , Morita H , Toh H , Suda W , Kim SW , Suzuki S , Yakabe T , Hattori M , Yajima N
Ref : PLoS ONE , 8 :e60521 , 2013
Abstract : We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes, and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and the stress response were present in L. brevis KB290 but not in the closely related L. brevis ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was essential for the strain's gastrointestinal tract tolerance and tendency to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains to detect low frequency variants, we evaluated genome stability. Deep sequencing of four periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and 37 minority variation sites, indicating long-term stability and providing a useful method for assessing the stability of industrial bacteria at the nucleotide level.
ESTHER : Fukao_2013_PLoS.One_8_e60521
PubMedSearch : Fukao_2013_PLoS.One_8_e60521
PubMedID: 23544154
Gene_locus related to this paper: lacba-q03sl1

Title : Genomic adaptation of the Lactobacillus casei group - Toh_2013_PLoS.One_8_e75073
Author(s) : Toh H , Oshima K , Nakano A , Takahata M , Murakami M , Takaki T , Nishiyama H , Igimi S , Hattori M , Morita H
Ref : PLoS ONE , 8 :e75073 , 2013
Abstract : Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the draft genome sequence of L. paracasei COM0101, all of which were isolated from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is distinct from other strains previously described as L. paracasei. The core genome of 10 completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes. Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334. Several genomic islands, including carbohydrate utilization gene clusters, were found at the same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was first identified in GG, was also found in other strains of the L. casei group, but several L. paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher number of proteins involved in carbohydrate utilization compared with intestinal lactobacilli, and extracellular adhesion proteins, several of which are absent in other strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L. paracasei strains, the complete genome sequences of L. casei will provide valuable insights into the evolution of the L. casei group.
ESTHER : Toh_2013_PLoS.One_8_e75073
PubMedSearch : Toh_2013_PLoS.One_8_e75073
PubMedID: 24116025
Gene_locus related to this paper: lacc3-q03b36 , laccb-b3wcx2 , lacrh-pepr , lacca-b5qt93 , lacca-k0n1x0 , lacpa-s2ter8 , lacpa-s2rz88

Title : Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica - Okubo_2013_Appl.Environ.Microbiol_79_2542
Author(s) : Okubo T , Fukushima S , Itakura M , Oshima K , Longtonglang A , Teaumroong N , Mitsui H , Hattori M , Hattori R , Hattori T , Minamisawa K
Ref : Applied Environmental Microbiology , 79 :2542 , 2013
Abstract : Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58(T) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and fix) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica.
ESTHER : Okubo_2013_Appl.Environ.Microbiol_79_2542
PubMedSearch : Okubo_2013_Appl.Environ.Microbiol_79_2542
PubMedID: 23396330
Gene_locus related to this paper: 9brad-m4zgf0 , 9brad-m4z0c0 , 9brad-m4za51 , 9brad-m4zdq9 , 9brad-m4zbd2

Title : Complete Genome Sequence of Burkholderia sp. Strain RPE64, Bacterial Symbiont of the Bean Bug Riptortus pedestris - Shibata_2013_Genome.Announc_1_e00441
Author(s) : Shibata TF , Maeda T , Nikoh N , Yamaguchi K , Oshima K , Hattori M , Nishiyama T , Hasebe M , Fukatsu T , Kikuchi Y , Shigenobu S
Ref : Genome Announc , 1 :e00441 , 2013
Abstract : We isolated Burkholderia symbiont strain RPE64 from the bean bug Riptortus pedestris. Analysis of the complete 6.96-Mb genome, which consists of three chromosomes and two plasmids, will facilitate further understanding of insect-microbe symbiosis and the development of pest-control technologies.
ESTHER : Shibata_2013_Genome.Announc_1_e00441
PubMedSearch : Shibata_2013_Genome.Announc_1_e00441
PubMedID: 23833137
Gene_locus related to this paper: 9burk-r4wy41 , 9burk-a0a069nn99 , 9burk-r4wtx8 , 9burk-r4wsg0 , 9burk-r4x084 , 9burk-r4wsp2

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 : Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs - Okubo_2012_Microbes.Environ_27_306
Author(s) : Okubo T , Tsukui T , Maita H , Okamoto S , Oshima K , Fujisawa T , Saito A , Futamata H , Hattori R , Shimomura Y , Haruta S , Morimoto S , Wang Y , Sakai Y , Hattori M , Aizawa S , Nagashima KV , Masuda S , Hattori T , Yamashita A , Bao Z , Hayatsu M , Kajiya-Kanegae H , Yoshinaga I , Sakamoto K , Toyota K , Nakao M , Kohara M , Anda M , Niwa R , Jung-Hwan P , Sameshima-Saito R , Tokuda S , Yamamoto S , Yokoyama T , Akutsu T , Nakamura Y , Nakahira-Yanaka Y , Takada Hoshino Y , Hirakawa H , Mitsui H , Terasawa K , Itakura M , Sato S , Ikeda-Ohtsubo W , Sakakura N , Kaminuma E , Minamisawa K
Ref : Microbes Environ , 27 :306 , 2012
Abstract : Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
ESTHER : Okubo_2012_Microbes.Environ_27_306
PubMedSearch : Okubo_2012_Microbes.Environ_27_306
PubMedID: 22452844
Gene_locus related to this paper: 9brad-i0g2u8 , 9brad-i0gf89 , braja-pcaD , 9brad-i0fzh8 , 9brad-i0gfv2 , 9brad-i0g2y4

Title : Anammox organism KSU-1 expresses a NirK-type copper-containing nitrite reductase instead of a NirS-type with cytochrome cd1 - Hira_2012_FEBS.Lett_586_1658
Author(s) : Hira D , Toh H , Migita CT , Okubo H , Nishiyama T , Hattori M , Furukawa K , Fujii T
Ref : FEBS Letters , 586 :1658 , 2012
Abstract : Anaerobic ammonium oxidation (anammox) and denitrification are two distinct microbial reactions relevant to the global nitrogen cycle. The proposed initial step of the anammox reactions, reduction of nitrite to nitric oxide, has been postulated to be identical to that in denitrification catalyzed by the dissimilatory nitrite reductase of the cytochrome cd(1)-type. Here, we characterized the copper-containing nitrite reductase homolog encoded by nirK detected in the genome of an anammox bacterium strain KSU-1. We hypothesize that this NirK-type nitrite reductase, rather than a nitrite reductase of the cytochrome cd(1)-type (NirS), is likely to catalyze nitrite reduction in anammox organism KSU-1.
ESTHER : Hira_2012_FEBS.Lett_586_1658
PubMedSearch : Hira_2012_FEBS.Lett_586_1658
PubMedID: 22673575
Gene_locus related to this paper: 9plan-i3iq59 , 9plan-i3ile2 , 9bact-i3ijt8

Title : Complete genome sequence of Bacillus cereus NC7401, which produces high levels of the emetic toxin cereulide - Takeno_2012_J.Bacteriol_194_4767
Author(s) : Takeno A , Okamoto A , Tori K , Oshima K , Hirakawa H , Toh H , Agata N , Yamada K , Ogasawara N , Hayashi T , Shimizu T , Kuhara S , Hattori M , Ohta M
Ref : Journal of Bacteriology , 194 :4767 , 2012
Abstract : We report the complete and annotated genome sequence of Bacillus cereus NC7401, a representative of the strain group that causes emetic-type food poisoning. The emetic toxin, cereulide, is produced by a nonribosomal protein synthesis (NRPS) system that is encoded by a gene cluster on a large resident plasmid, pNCcld.
ESTHER : Takeno_2012_J.Bacteriol_194_4767
PubMedSearch : Takeno_2012_J.Bacteriol_194_4767
PubMedID: 22887669
Gene_locus related to this paper: bacce-c2zyv1

Title : A fluorescence-detection size-exclusion chromatography-based thermostability assay for membrane protein precrystallization screening - Hattori_2012_Structure_20_1293
Author(s) : Hattori M , Hibbs RE , Gouaux E
Ref : Structure , 20 :1293 , 2012
Abstract : Optimization of membrane protein stability under different solution conditions is essential for obtaining crystals that diffract to high resolution. Traditional methods that evaluate protein stability require large amounts of material and are, therefore, ill suited for medium- to high-throughput screening of membrane proteins. Here we present a rapid and efficient fluorescence-detection size-exclusion chromatography-based thermostability assay (FSEC-TS). In this method, the target protein is fused to GFP. Heated protein samples, treated with a panel of additives, are then analyzed by FSEC. FSEC-TS allows one to evaluate the thermostability of nanogram-to-microgram amounts of the target protein under a variety of conditions without purification. We applied this method to the Danio rerio P2X4 receptor and Caenorhabditis elegans GluCl to screen ligands, ions, and lipids, including newly designed cholesterol derivatives. In the case of GluCl, the screening results were used to obtain crystals of the receptor in the presence of lipids.
ESTHER : Hattori_2012_Structure_20_1293
PubMedSearch : Hattori_2012_Structure_20_1293
PubMedID: 22884106

Title : Complete genome sequence of Lactococcus lactis IO-1, a lactic acid bacterium that utilizes xylose and produces high levels of L-lactic acid - Kato_2012_J.Bacteriol_194_2102
Author(s) : Kato H , Shiwa Y , Oshima K , Machii M , Araya-Kojima T , Zendo T , Shimizu-Kadota M , Hattori M , Sonomoto K , Yoshikawa H
Ref : Journal of Bacteriology , 194 :2102 , 2012
Abstract : We report the complete genome sequence of Lactococcus lactis IO-1 (= JCM7638). It is a nondairy lactic acid bacterium, produces nisin Z, ferments xylose, and produces predominantly L-lactic acid at high xylose concentrations. From ortholog analysis with other five L. lactis strains, IO-1 was identified as L. lactis subsp. lactis.
ESTHER : Kato_2012_J.Bacteriol_194_2102
PubMedSearch : Kato_2012_J.Bacteriol_194_2102
PubMedID: 22461545
Gene_locus related to this paper: lacla-menX

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 : Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group - Nunoura_2011_Nucleic.Acids.Res_39_3204
Author(s) : Nunoura T , Takaki Y , Kakuta J , Nishi S , Sugahara J , Kazama H , Chee GJ , Hattori M , Kanai A , Atomi H , Takai K , Takami H
Ref : Nucleic Acids Research , 39 :3204 , 2011
Abstract : The domain Archaea has historically been divided into two phyla, the Crenarchaeota and Euryarchaeota. Although regarded as members of the Crenarchaeota based on small subunit rRNA phylogeny, environmental genomics and efforts for cultivation have recently revealed two novel phyla/divisions in the Archaea; the 'Thaumarchaeota' and 'Korarchaeota'. Here, we show the genome sequence of Candidatus 'Caldiarchaeum subterraneum' that represents an uncultivated crenarchaeotic group. A composite genome was reconstructed from a metagenomic library previously prepared from a microbial mat at a geothermal water stream of a sub-surface gold mine. The genome was found to be clearly distinct from those of the known phyla/divisions, Crenarchaeota (hyperthermophiles), Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest that this crenarchaeotic group can be considered as a novel archaeal phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like protein modifier system consisting of Ub, E1, E2 and small Zn RING finger family protein with structural motifs specific to eukaryotic system proteins, a system clearly distinct from the prokaryote-type system recently identified in Haloferax and Mycobacterium. 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.
ESTHER : Nunoura_2011_Nucleic.Acids.Res_39_3204
PubMedSearch : Nunoura_2011_Nucleic.Acids.Res_39_3204
PubMedID: 21169198
Gene_locus related to this paper: 9arch-e6n6u9

Title : Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation - Prakash_2011_Cell.Host.Microbe_10_273
Author(s) : Prakash T , Oshima K , Morita H , Fukuda S , Imaoka A , Kumar N , Sharma VK , Kim SW , Takahashi M , Saitou N , Taylor TD , Ohno H , Umesaki Y , Hattori M
Ref : Cell Host Microbe , 10 :273 , 2011
Abstract : Segmented filamentous bacteria (SFB) are noncultivable commensals inhabiting the gut of various vertebrate species and have been shown to induce Th17 cells in mice. We present the complete genome sequences of both rat and mouse SFB isolated from SFB-monocolonized hosts. The rat and mouse SFB genomes each harbor a single circular chromosome of 1.52 and 1.59 Mb encoding 1346 and 1420 protein-coding genes, respectively. The overall nucleotide identity between the two genomes is 86%, and the substitution rate was estimated to be similar to that of the free-living E. coli. SFB genomes encode typical genes for anaerobic fermentation and spore and flagella formation, but lack most of the amino acid biosynthesis enzymes, reminiscent of pathogenic Clostridia, exhibiting large dependency on the host. However, SFB lack most of the clostridial virulence-related genes. Comparative analysis with clostridial genomes suggested possible mechanisms for host responses and specific adaptations in the intestine.
ESTHER : Prakash_2011_Cell.Host.Microbe_10_273
PubMedSearch : Prakash_2011_Cell.Host.Microbe_10_273
PubMedID: 21925114
Gene_locus related to this paper: 9clot-g2ifk0

Title : Complete genome sequence and comparative analysis of the fish pathogen Lactococcus garvieae - Morita_2011_PLoS.One_6_e23184
Author(s) : Morita H , Toh H , Oshima K , Yoshizaki M , Kawanishi M , Nakaya K , Suzuki T , Miyauchi E , Ishii Y , Tanabe S , Murakami M , Hattori M
Ref : PLoS ONE , 6 :e23184 , 2011
Abstract : Lactococcus garvieae causes fatal haemorrhagic septicaemia in fish such as yellowtail. The comparative analysis of genomes of a virulent strain Lg2 and a non-virulent strain ATCC 49156 of L. garvieae revealed that the two strains shared a high degree of sequence identity, but Lg2 had a 16.5-kb capsule gene cluster that is absent in ATCC 49156. The capsule gene cluster was composed of 15 genes, of which eight genes are highly conserved with those in exopolysaccharide biosynthesis gene cluster often found in Lactococcus lactis strains. Sequence analysis of the capsule gene cluster in the less virulent strain L. garvieae Lg2-S, Lg2-derived strain, showed that two conserved genes were disrupted by a single base pair deletion, respectively. These results strongly suggest that the capsule is crucial for virulence of Lg2. The capsule gene cluster of Lg2 may be a genomic island from several features such as the presence of insertion sequences flanked on both ends, different GC content from the chromosomal average, integration into the locus syntenic to other lactococcal genome sequences, and distribution in human gut microbiomes. The analysis also predicted other potential virulence factors such as haemolysin. The present study provides new insights into understanding of the virulence mechanisms of L. garvieae in fish.
ESTHER : Morita_2011_PLoS.One_6_e23184
PubMedSearch : Morita_2011_PLoS.One_6_e23184
PubMedID: 21829716
Gene_locus related to this paper: lacgt-f9v7p0

Title : Complete genomic sequence of the O-desmethylangolensin-producing bacterium Clostridium rRNA cluster XIVa strain SY8519, isolated from adult human intestine - Yokoyama_2011_J.Bacteriol_193_5568
Author(s) : Yokoyama S , Oshima K , Nomura I , Hattori M , Suzuki T
Ref : Journal of Bacteriology , 193 :5568 , 2011
Abstract : The O-desmethylangolensin-producing Clostridium rRNA cluster XIVa strain SY8519 was isolated from the intestinal flora of a healthy human as a key isoflavonoid-metabolizing bacterium. Here, we report the finished and annotated genomic sequence of this organism.
ESTHER : Yokoyama_2011_J.Bacteriol_193_5568
PubMedSearch : Yokoyama_2011_J.Bacteriol_193_5568
PubMedID: 21914882
Gene_locus related to this paper: closs-f7v5q6 , closs-f7v6v0

Title : Selective cholinesterase inhibition by lanostane triterpenes from fruiting bodies of Ganoderma lucidum - Lee_2011_Bioorg.Med.Chem.Lett_21_6603
Author(s) : Lee I , Ahn B , Choi J , Hattori M , Min B , Bae K
Ref : Bioorganic & Medicinal Chemistry Lett , 21 :6603 , 2011
Abstract : Two new lanostane triterpenes, named methyl ganoderate A acetonide (1) and n-butyl ganoderate H (2), were isolated from the fruiting bodies of Ganoderma lucidum together with 16 known compounds (3-18). Extensive spectroscopic and chemical studies established the structures of these compounds as methyl 7beta,15alpha-isopropylidenedioxy-3,11,23-trioxo-5alpha-lanost-8-en-26-oate (1) and n-butyl 12beta-acetoxy-3beta-hydroxy-7,11,15,23-tetraoxo-5alpha-lanost-8-en-26-oate (2). Because new compounds exhibiting specific anti-acetylcholinesterase activity are being sought as possible drug candidates for the treatment of Alzheimer's and related neurodegenerative diseases, compounds 1-18 were examined for their inhibitory activities against acetylcholinesterase and butyrylcholinesterase. All of the compounds exhibited moderate acetylcholinesterase-inhibitory activity, with IC(50) values ranging from 9.40 to 31.03muM. In contrast, none of the compounds except lucidadiol (13) and lucidenic acid N (14) exhibited butyrylcholinesterase-inhibitory activity at concentrations up to 200muM. These results indicate that these lanostane triterpenes are preferential inhibitors of acetylcholinesterase and may be suitable drug candidates.
ESTHER : Lee_2011_Bioorg.Med.Chem.Lett_21_6603
PubMedSearch : Lee_2011_Bioorg.Med.Chem.Lett_21_6603
PubMedID: 21924611

Title : Complete genomic sequence of the equol-producing bacterium Eggerthella sp. strain YY7918, isolated from adult human intestine - Yokoyama_2011_J.Bacteriol_193_5570
Author(s) : Yokoyama S , Oshima K , Nomura I , Hattori M , Suzuki T
Ref : Journal of Bacteriology , 193 :5570 , 2011
Abstract : Eggerthella sp. strain YY7918 was isolated from the intestinal flora of a healthy human. It metabolizes daidzein (a soybean isoflavonoid) and produces S-equol, which has stronger estrogenic activities than daidzein. Here, we report the finished and annotated genomic sequence of this organism.
ESTHER : Yokoyama_2011_J.Bacteriol_193_5570
PubMedSearch : Yokoyama_2011_J.Bacteriol_193_5570
PubMedID: 21914883
Gene_locus related to this paper: eegsy-f7uz47

Title : Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell - Toh_2011_J.Bacteriol_193_6411
Author(s) : Toh H , Sharma VK , Oshima K , Kondo S , Hattori M , Ward FB , Free A , Taylor TD
Ref : Journal of Bacteriology , 193 :6411 , 2011
Abstract : Arcobacter butzleri strain ED-1 is an exoelectrogenic epsilonproteobacterium isolated from the anode biofilm of a microbial fuel cell. Arcobacter sp. strain L dominates the liquid phase of the same fuel cell. Here we report the finished and annotated genome sequences of these organisms.
ESTHER : Toh_2011_J.Bacteriol_193_6411
PubMedSearch : Toh_2011_J.Bacteriol_193_6411
PubMedID: 22038970
Gene_locus related to this paper: 9prot-e6l4v2 , 9prot-g2hv40 , 9prot-a0a0g9kwp1 , 9prot-g2hwt3

Title : Bifidobacteria can protect from enteropathogenic infection through production of acetate - Fukuda_2011_Nature_469_543
Author(s) : Fukuda S , Toh H , Hase K , Oshima K , Nakanishi Y , Yoshimura K , Tobe T , Clarke JM , Topping DL , Suzuki T , Taylor TD , Itoh K , Kikuchi J , Morita H , Hattori M , Ohno H
Ref : Nature , 469 :543 , 2011
Abstract : The human gut is colonized with a wide variety of microorganisms, including species, such as those belonging to the bacterial genus Bifidobacterium, that have beneficial effects on human physiology and pathology. Among the most distinctive benefits of bifidobacteria are modulation of host defence responses and protection against infectious diseases. Nevertheless, the molecular mechanisms underlying these effects have barely been elucidated. To investigate these mechanisms, we used mice associated with certain bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic Escherichia coli O157:H7, together with an integrated 'omics' approach. Here we show that genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We found that this effect can be attributed, at least in part, to increased production of acetate and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal defence mediated by epithelial cells and thereby protects the host against lethal infection.
ESTHER : Fukuda_2011_Nature_469_543
PubMedSearch : Fukuda_2011_Nature_469_543
PubMedID: 21270894
Gene_locus related to this paper: bifli-c2gxu7 , biflo-BL0073 , biflo-BL0336 , biflo-BL0581 , biflo-BL0582 , biflo-BL0682 , biflo-BL0787 , biflo-BL0807 , biflo-BL1109 , biflo-BL1514 , biflo-PAP , biflo-PTRB , bifln-c2gtr2

Title : Complete genome sequence of the denitrifying and N(2)O-reducing bacterium Pseudogulbenkiania sp. strain NH8B - Ishii_2011_J.Bacteriol_193_6395
Author(s) : Ishii S , Tago K , Nishizawa T , Oshima K , Hattori M , Senoo K
Ref : Journal of Bacteriology , 193 :6395 , 2011
Abstract : Pseudogulbenkiania sp. strain NH8B is a Neisseriales bacterium isolated from an agricultural field. This strain has strong denitrification and N(2)O reduction activities. Here, we report the finished and annotated genome sequence of this organism.
ESTHER : Ishii_2011_J.Bacteriol_193_6395
PubMedSearch : Ishii_2011_J.Bacteriol_193_6395
PubMedID: 22038961
Gene_locus related to this paper: pseul-g2j1k1 , pseul-g2iue3 , pseul-g2j5g5

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 : The Selaginella genome identifies genetic changes associated with the evolution of vascular plants - Banks_2011_Science_332_960
Author(s) : Banks JA , Nishiyama T , Hasebe M , Bowman JL , Gribskov M , dePamphilis C , Albert VA , Aono N , Aoyama T , Ambrose BA , Ashton NW , Axtell MJ , Barker E , Barker MS , Bennetzen JL , Bonawitz ND , Chapple C , Cheng C , Correa LG , Dacre M , DeBarry J , Dreyer I , Elias M , Engstrom EM , Estelle M , Feng L , Finet C , Floyd SK , Frommer WB , Fujita T , Gramzow L , Gutensohn M , Harholt J , Hattori M , Heyl A , Hirai T , Hiwatashi Y , Ishikawa M , Iwata M , Karol KG , Koehler B , Kolukisaoglu U , Kubo M , Kurata T , Lalonde S , Li K , Li Y , Litt A , Lyons E , Manning G , Maruyama T , Michael TP , Mikami K , Miyazaki S , Morinaga S , Murata T , Mueller-Roeber B , Nelson DR , Obara M , Oguri Y , Olmstead RG , Onodera N , Petersen BL , Pils B , Prigge M , Rensing SA , Riano-Pachon DM , Roberts AW , Sato Y , Scheller HV , Schulz B , Schulz C , Shakirov EV , Shibagaki N , Shinohara N , Shippen DE , Sorensen I , Sotooka R , Sugimoto N , Sugita M , Sumikawa N , Tanurdzic M , Theissen G , Ulvskov P , Wakazuki S , Weng JK , Willats WW , Wipf D , Wolf PG , Yang L , Zimmer AD , Zhu Q , Mitros T , Hellsten U , Loque D , Otillar R , Salamov A , Schmutz J , Shapiro H , Lindquist E , Lucas S , Rokhsar D , Grigoriev IV
Ref : Science , 332 :960 , 2011
Abstract : Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
ESTHER : Banks_2011_Science_332_960
PubMedSearch : Banks_2011_Science_332_960
PubMedID: 21551031
Gene_locus related to this paper: selml-d8qua5 , selml-d8qva1 , selml-d8qyh7 , selml-d8qza0 , selml-d8r5d4 , selml-d8r6d4 , selml-d8r504 , selml-d8r506 , selml-d8rbi1 , selml-d8rbs1 , selml-d8rck8 , selml-d8rf38 , selml-d8rkl6 , selml-d8rpr1 , selml-d8rpy0 , selml-d8ru47 , selml-d8ry54 , selml-d8rzp6 , selml-d8rzy7 , selml-d8s0c9 , selml-d8s0u3 , selml-d8s2t1 , selml-d8s3z8 , selml-d8s401 , selml-d8sba6 , selml-d8sch9 , selml-d8spq2 , selml-d8sq37 , selml-d8ssx7 , selml-d8swp2 , selml-d8t7a3 , selml-d8t8v4 , selml-d8taz4 , selml-d8tdq6 , selml-d8rai8 , selml-d8qt54 , selml-d8r2d8 , selml-d8rmd3 , selml-d8rra9 , selml-d8slg4 , selml-d8swp0 , selml-d8s7i0 , selml-d8qz37 , selml-d8sz00 , selml-d8s776 , selml-d8qw15 , selml-d8ska7 , selml-d8t0c4 , selml-d8r194 , selml-d8s5m8 , selml-d8s7r2 , selml-d8ta80 , selml-d8ru55

Title : Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2 - Toh_2010_J.Bacteriol_192_1165
Author(s) : Toh H , Oshima K , Toyoda A , Ogura Y , Ooka T , Sasamoto H , Park SH , Iyoda S , Kurokawa K , Morita H , Itoh K , Taylor TD , Hayashi T , Hattori M
Ref : Journal of Bacteriology , 192 :1165 , 2010
Abstract : Escherichia coli SE15 (O150:H5) is a human commensal bacterium recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B2, which includes the majority of extraintestinal pathogenic E. coli. Here, we report the finished and annotated genome sequence of this organism.
ESTHER : Toh_2010_J.Bacteriol_192_1165
PubMedSearch : Toh_2010_J.Bacteriol_192_1165
PubMedID: 20008064
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C2429 , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-YfhR , ecos5-d2nhh3 , yerpe-YBTT , ecolx-f4suw9

Title : Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids - Yano_2010_J.Bacteriol_192_4337
Author(s) : Yano H , Miyakoshi M , Ohshima K , Tabata M , Nagata Y , Hattori M , Tsuda M
Ref : Journal of Bacteriology , 192 :4337 , 2010
Abstract : To understand the mechanisms for structural diversification of Pseudomonas-derived toluene-catabolic (TOL) plasmids, the complete sequence of a self-transmissible plasmid pDK1 with a size of 128,921 bp from Pseudomonas putida HS1 was determined. Comparative analysis revealed that (i) pDK1 consisted of a 75.6-kb IncP-7 plasmid backbone and 53.2-kb accessory gene segments that were bounded by transposon-associated regions, (ii) the genes for conjugative transfer of pDK1 were highly similar to those of MOB(H) group of mobilizable plasmids, and (iii) the toluene-catabolic (xyl) gene clusters of pDK1 were derived through homologous recombination, transposition, and site-specific recombination from the xyl gene clusters homologous to another TOL plasmid, pWW53. The minireplicons of pDK1 and its related IncP-7 plasmids, pWW53 and pCAR1, that contain replication and partition genes were maintained in all of six Pseudomonas strains tested, but not in alpha- or betaproteobacterial strains. The recipient host range of conjugative transfer of pDK1 was, however, limited to two Pseudomonas strains. These results indicate that IncP-7 plasmids are essentially narrow-host-range and self-transmissible plasmids that encode MOB(H) group-related transfer functions and that the host range of IncP-7-specified conjugative transfer was, unlike the situation in other well-known plasmids, narrower than that of its replication.
ESTHER : Yano_2010_J.Bacteriol_192_4337
PubMedSearch : Yano_2010_J.Bacteriol_192_4337
PubMedID: 20581207

Title : Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli - Ogura_2009_Proc.Natl.Acad.Sci.U.S.A_106_17939
Author(s) : Ogura Y , Ooka T , Iguchi A , Toh H , Asadulghani M , Oshima K , Kodama T , Abe H , Nakayama K , Kurokawa K , Tobe T , Hattori M , Hayashi T
Ref : Proc Natl Acad Sci U S A , 106 :17939 , 2009
Abstract : Among the various pathogenic Escherichia coli strains, enterohemorrhagic E. coli (EHEC) is the most devastating. Although serotype O157:H7 strains are the most prevalent, strains of different serotypes also possess similar pathogenic potential. Here, we present the results of a genomic comparison between EHECs of serotype O157, O26, O111, and O103, as well as 21 other, fully sequenced E. coli/Shigella strains. All EHECs have much larger genomes (5.5-5.9 Mb) than the other strains and contain surprisingly large numbers of prophages and integrative elements (IEs). The gene contents of the 4 EHECs do not follow the phylogenetic relationships of the strains, and they share virulence genes for Shiga toxins and many other factors. We found many lambdoid phages, IEs, and virulence plasmids that carry the same or similar virulence genes but have distinct evolutionary histories, indicating that independent acquisition of these mobile genetic elements has driven the evolution of each EHEC. Particularly interesting is the evolution of the type III secretion system (T3SS). We found that the T3SS of EHECs is composed of genes that were introduced by 3 different types of genetic elements: an IE referred to as the locus of enterocyte effacement, which encodes a central part of the T3SS; SpLE3-like IEs; and lambdoid phages carrying numerous T3SS effector genes and other T3SS-related genes. Our data demonstrate how E. coli strains of different phylogenies can independently evolve into EHECs, providing unique insights into the mechanisms underlying the parallel evolution of complex virulence systems in bacteria.
ESTHER : Ogura_2009_Proc.Natl.Acad.Sci.U.S.A_106_17939
PubMedSearch : Ogura_2009_Proc.Natl.Acad.Sci.U.S.A_106_17939
PubMedID: 19815525
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C2429 , ecoli-C4836 , ecoli-d7xp23 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-Z1341 , ecoli-Z1930 , ecoli-Z2445 , ecoli-YfhR , yerpe-YBTT

Title : Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific content - Maruyama_2009_BMC.Genomics_10_358
Author(s) : Maruyama F , Kobata M , Kurokawa K , Nishida K , Sakurai A , Nakano K , Nomura R , Kawabata S , Ooshima T , Nakai K , Hattori M , Hamada S , Nakagawa I
Ref : BMC Genomics , 10 :358 , 2009
Abstract : BACKGROUND: Streptococcus mutans is the major pathogen of dental caries, and it occasionally causes infective endocarditis. While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood. RESULTS: We have sequenced the complete genome of S. mutans serotype c strain NN2025, and compared it with the genome of UA159. The NN2025 genome is composed of 2,013,587 bp, and the two strains show highly conserved core-genome. However, comparison of the two S. mutans strains showed a large genomic inversion across the replication axis producing an X-shaped symmetrical DNA dot plot. This phenomenon was also observed between other streptococcal species, indicating that streptococcal genetic rearrangements across the replication axis play an important role in Streptococcus genetic shuffling. We further confirmed the genomic diversity among 95 clinical isolates using long-PCR analysis. Genomic diversity in S. mutans appears to occur frequently between insertion sequence (IS) elements and transposons, and these diversity regions consist of restriction/modification systems, antimicrobial peptide synthesis systems, and transporters. S. mutans may preferentially reject the phage infection by clustered regularly interspaced short palindromic repeats (CRISPRs). In particular, the CRISPR-2 region, which is highly divergent between strains, in NN2025 has long repeated spacer sequences corresponding to the streptococcal phage genome. CONCLUSION: These observations suggest that S. mutans strains evolve through chromosomal shuffling and that phage infection is not needed for gene acquisition. In contrast, S. pyogenes tolerates phage infection for acquisition of virulence determinants for niche adaptation.
ESTHER : Maruyama_2009_BMC.Genomics_10_358
PubMedSearch : Maruyama_2009_BMC.Genomics_10_358
PubMedID: 19656368
Gene_locus related to this paper: strmn-c6spx6 , strmu-BGLB , strmu-SMU.118C , strmu-SMU.643 , strmu-SMU.1314 , strmu-SMU.1443C , strmu-SMU.1678

Title : Complete genome sequence of the probiotic Lactobacillus rhamnosus ATCC 53103 - Morita_2009_J.Bacteriol_191_7630
Author(s) : Morita H , Toh H , Oshima K , Murakami M , Taylor TD , Igimi S , Hattori M
Ref : Journal of Bacteriology , 191 :7630 , 2009
Abstract : Lactobacillus rhamnosus is a facultatively heterofermentative lactic acid bacterium and is frequently isolated from human gastrointestinal mucosa of healthy individuals. L. rhamnosus ATCC 53103, isolated from a healthy human intestinal flora, is one of the most widely used and well-documented probiotics. Here, we report the finished and annotated genome sequence of this organism.
ESTHER : Morita_2009_J.Bacteriol_191_7630
PubMedSearch : Morita_2009_J.Bacteriol_191_7630
PubMedID: 19820099
Gene_locus related to this paper: lacrg-c7tei3 , lacrh-B2CZF3 , lacrh-b5qmk1 , lacrh-pepr , lacrh-pepx , lacrl-pip

Title : Systematic identification and sequence analysis of the genomic islands of the enteropathogenic Escherichia coli strain B171-8 by the combined use of whole-genome PCR scanning and fosmid mapping - Ogura_2008_J.Bacteriol_190_6948
Author(s) : Ogura Y , Abe H , Katsura K , Kurokawa K , Asadulghani M , Iguchi A , Ooka T , Nakayama K , Yamashita A , Hattori M , Tobe T , Hayashi T
Ref : Journal of Bacteriology , 190 :6948 , 2008
Abstract : Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) are diarrheagenic pathogens that colonize the intestinal tract through the formation of attaching and effacing lesions, induced by effectors translocated via a type III secretion system (T3SS) encoded on the locus of enterocyte effacement (LEE). In EHEC O157, numerous virulence factors, including around 40 T3SS effectors, have been identified. Most of them are encoded on genomic islands (GEIs) such as prophages and integrative elements. For EPEC, however, no systematic search of GEIs and virulence-related genes carried therein has been done, and only a limited number of virulence factors have been identified so far. In this study, we performed a systemic and genome-wide survey of the GEIs in strain B171-8, one of the prototype strains of EPEC, by the combined use of whole-genome PCR scanning and fosmid mapping and identified 22 large GEIs, including nine lambda-like prophages, three P2-like prophages, the LEE, and three additional integrative elements. On these prophages and integrative elements, we found genes for a set of T3SS proteins, a total of 33 T3SS effectors or effector homologues, and 12 other virulence factors which include five nonfimbrial adhesins. Most of the T3SS effector families identified are also present in EHEC O157, but B171-8 possesses a significantly smaller number of effectors. Not only the presence or absence of Shiga toxin genes but also the difference in the T3SS effector repertoire should be considered in analyzing the pathogenicity of EPEC and EHEC strains.
ESTHER : Ogura_2008_J.Bacteriol_190_6948
PubMedSearch : Ogura_2008_J.Bacteriol_190_6948
PubMedID: 18757547
Gene_locus related to this paper: ecoli-Z1930

Title : Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult - Oshima_2008_DNA.Res_15_375
Author(s) : Oshima K , Toh H , Ogura Y , Sasamoto H , Morita H , Park SH , Ooka T , Iyoda S , Taylor TD , Hayashi T , Itoh K , Hattori M
Ref : DNA Research , 15 :375 , 2008
Abstract : We sequenced and analyzed the genome of a commensal Escherichia coli (E. coli) strain SE11 (O152:H28) recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B1. SE11 harbored a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes. None of the SE11 genes had sequence similarity to known genes encoding phage- and plasmid-borne virulence factors found in pathogenic E. coli strains. The comparative genome analysis with the laboratory strain K-12 MG1655 identified 62 poorly conserved genes between these two non-pathogenic strains and 1186 genes absent in MG1655. These genes in SE11 were mostly encoded in large insertion regions on the chromosome or in the plasmids, and were notably abundant in genes of fimbriae and autotransporters, which are cell surface appendages that largely contribute to the adherence ability of bacteria to host cells and bacterial conjugation. These data suggest that SE11 may have evolved to acquire and accumulate the functions advantageous for stable colonization of intestinal cells, and that the adhesion-associated functions are important for the commensality of E. coli in human gut habitat.
ESTHER : Oshima_2008_DNA.Res_15_375
PubMedSearch : Oshima_2008_DNA.Res_15_375
PubMedID: 18931093
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-Z1930 , ecoli-Z2445 , ecoli-YfhR

Title : Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production - Morita_2008_DNA.Res_15_151
Author(s) : Morita H , Toh H , Fukuda S , Horikawa H , Oshima K , Suzuki T , Murakami M , Hisamatsu S , Kato Y , Takizawa T , Fukuoka H , Yoshimura T , Itoh K , O'Sullivan DJ , McKay LL , Ohno H , Kikuchi J , Masaoka T , Hattori M
Ref : DNA Research , 15 :151 , 2008
Abstract : Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol. We determined the complete genome sequences of the reuterin-producing L. reuteri JCM 1112(T) and its closely related species Lactobacillus fermentum IFO 3956. Both are in the same phylogenetic group within the genus Lactobacillus. Comparative genome analysis revealed that L. reuteri JCM 1112(T) has a unique cluster of 58 genes for the biosynthesis of reuterin and cobalamin (vitamin B(12)). The 58-gene cluster has a lower GC content and is apparently inserted into the conserved region, suggesting that the cluster represents a genomic island acquired from an anomalous source. Two-dimensional nuclear magnetic resonance (2D-NMR) with (13)C(3)-glycerol demonstrated that L. reuteri JCM 1112(T) could convert glycerol to reuterin in vivo, substantiating the potential of L. reuteri JCM 1112(T) to produce reuterin in the intestine. Given that glycerol is shown to be naturally present in feces, the acquired ability to produce reuterin and cobalamin is an adaptive evolutionary response that likely contributes to the probiotic properties of L. reuteri.
ESTHER : Morita_2008_DNA.Res_15_151
PubMedSearch : Morita_2008_DNA.Res_15_151
PubMedID: 18487258
Gene_locus related to this paper: lacfe-c0wz89 , lacre-a5vi88 , lacre-b3xl59 , lacre-b3xl60 , lacre-b3xlh0 , lacre-b3xps7 , lacre-q4jle7 , lacre-q4jlf2 , lacre-q4jll5 , lacre-q6wu85 , lacrj-b2g622

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 : Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis - Naito_2008_DNA.Res_15_215
Author(s) : Naito M , Hirakawa H , Yamashita A , Ohara N , Shoji M , Yukitake H , Nakayama K , Toh H , Yoshimura F , Kuhara S , Hattori M , Hayashi T
Ref : DNA Research , 15 :215 , 2008
Abstract : The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of chronic periodontitis. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. Here, we present the whole genome sequence of P. gingivalis ATCC 33277, which is classified as a less-virulent strain. We identified 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, we identified 461 ATCC 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements were observed between the two strains: 175 regions in which genomic rearrangements have occurred were identified. Thirty-five of those genomic rearrangements were inversion or translocation and 140 were simple insertion, deletion, or replacement. Both strains contained large numbers of mobile elements, such as insertion sequences, miniature inverted-repeat transposable elements (MITEs), and conjugative transposons, which are frequently associated with genomic rearrangements. These findings indicate that the mobile genetic elements have been deeply involved in the extensive genome rearrangement of P. gingivalis and the occurrence of many of the strain-specific CDSs. We also describe here a very unique feature of MITE400, which we renamed MITEPgRS (MITE of P. gingivalis with Repeating Sequences).
ESTHER : Naito_2008_DNA.Res_15_215
PubMedSearch : Naito_2008_DNA.Res_15_215
PubMedID: 18524787
Gene_locus related to this paper: porgi-DPP , porgi-q7mub3 , porgi-q7muw6 , porgi-q7mwa7 , porgi-q7mx03

Title : Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen - Goto_2008_DNA.Res_15_39
Author(s) : Goto T , Yamashita A , Hirakawa H , Matsutani M , Todo K , Ohshima K , Toh H , Miyamoto K , Kuhara S , Hattori M , Shimizu T , Akimoto S
Ref : DNA Research , 15 :39 , 2008
Abstract : Finegoldia magna (formerly Peptostreptococcus magnus), a member of the Gram-positive anaerobic cocci (GPAC), is a commensal bacterium colonizing human skin and mucous membranes. Moreover, it is also recognized as an opportunistic pathogen responsible for various infectious diseases. Here, we report the complete genome sequence of F. magna ATCC 29328. The genome consists of a 1,797,577 bp circular chromosome and an 189,163 bp plasmid (pPEP1). The metabolic maps constructed based on the genome information confirmed that most F. magna strains cannot ferment most sugars, except fructose, and have various aminopeptidase activities. Three homologs of albumin-binding protein, a known virulence factor useful for antiphagocytosis, are encoded on the chromosome, and one albumin-binding protein homolog is encoded on the plasmid. A unique feature of the genome is that F. magna encodes many sortase genes, of which substrates may be involved in bacterial pathogenesis, such as antiphagocytosis and adherence to the host cell. The plasmid pPEP1 encodes seven sortase and seven substrate genes, whereas the chromosome encodes four sortase and 19 substrate genes. These plasmid-encoded sortases may play important roles in the pathogenesis of F. magna by enriching the variety of cell wall anchored surface proteins.
ESTHER : Goto_2008_DNA.Res_15_39
PubMedSearch : Goto_2008_DNA.Res_15_39
PubMedID: 18263572

Title : Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350 - Ohnishi_2008_J.Bacteriol_190_4050
Author(s) : Ohnishi Y , Ishikawa J , Hara H , Suzuki H , Ikenoya M , Ikeda H , Yamashita A , Hattori M , Horinouchi S
Ref : Journal of Bacteriology , 190 :4050 , 2008
Abstract : We determined the complete genome sequence of Streptomyces griseus IFO 13350, a soil bacterium producing an antituberculosis agent, streptomycin, which is the first aminoglycoside antibiotic, discovered more than 60 years ago. The linear chromosome consists of 8,545,929 base pairs (bp), with an average G+C content of 72.2%, predicting 7,138 open reading frames, six rRNA operons (16S-23S-5S), and 66 tRNA genes. It contains extremely long terminal inverted repeats (TIRs) of 132,910 bp each. The telomere's nucleotide sequence and secondary structure, consisting of several palindromes with a loop sequence of 5'-GGA-3', are different from those of typical telomeres conserved among other Streptomyces species. In accordance with the difference, the chromosome has pseudogenes for a conserved terminal protein (Tpg) and a telomere-associated protein (Tap), and a novel pair of Tpg and Tap proteins is instead encoded by the TIRs. Comparisons with the genomes of two related species, Streptomyces coelicolor A3(2) and Streptomyces avermitilis, clarified not only the characteristics of the S. griseus genome but also the existence of 24 Streptomyces-specific proteins. The S. griseus genome contains 34 gene clusters or genes for the biosynthesis of known or unknown secondary metabolites. Transcriptome analysis using a DNA microarray showed that at least four of these clusters, in addition to the streptomycin biosynthesis gene cluster, were activated directly or indirectly by AdpA, which is a central transcriptional activator for secondary metabolism and morphogenesis in the A-factor (a gamma-butyrolactone signaling molecule) regulatory cascade in S. griseus.
ESTHER : Ohnishi_2008_J.Bacteriol_190_4050
PubMedSearch : Ohnishi_2008_J.Bacteriol_190_4050
PubMedID: 18375553
Gene_locus related to this paper: strgg-b1vku3 , strgg-b1vl52 , strgg-b1vlg6 , strgg-b1vm48 , strgg-b1vmn5 , strgg-b1vms2 , strgg-b1vmu0 , strgg-b1vn62 , strgg-b1vn76 , strgg-b1vnq8 , strgg-b1vp88 , strgg-b1vpj5.1 , strgg-b1vpj5.2 , strgg-b1vpn6 , strgg-b1vr06 , strgg-b1vr99 , strgg-b1vs60 , strgg-b1vsh1 , strgg-b1vsw0 , strgg-b1vt13 , strgg-b1vtd3 , strgg-b1vu88 , strgg-b1vw73 , strgg-b1vwl8 , strgg-b1vwx6 , strgg-b1vyg6 , strgg-b1vyh0 , strgg-b1vyj0 , strgg-b1vz78 , strgg-b1vzt4 , strgg-b1vzw6 , strgg-b1w1l1 , strgg-b1w1m6 , strgg-b1w2r7 , strgg-b1w3q4 , strgg-b1w4m3 , strgg-b1w5d5 , strgg-b1w5v0 , strgg-b1w021 , strgg-b1w150 , strgg-b1w151 , strgg-b1w254 , strgg-b1w1b1 , strgg-b1vkv5 , strgg-b1vqn4 , strgg-b1vv39

Title : Human chromosome 11 DNA sequence and analysis including novel gene identification - Taylor_2006_Nature_440_497
Author(s) : Taylor TD , Noguchi H , Totoki Y , Toyoda A , Kuroki Y , Dewar K , Lloyd C , Itoh T , Takeda T , Kim DW , She X , Barlow KF , Bloom T , Bruford E , Chang JL , Cuomo CA , Eichler E , Fitzgerald MG , Jaffe DB , LaButti K , Nicol R , Park HS , Seaman C , Sougnez C , Yang X , Zimmer AR , Zody MC , Birren BW , Nusbaum C , Fujiyama A , Hattori M , Rogers J , Lander ES , Sakaki Y
Ref : Nature , 440 :497 , 2006
Abstract : Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.
ESTHER : Taylor_2006_Nature_440_497
PubMedSearch : Taylor_2006_Nature_440_497
PubMedID: 16554811
Gene_locus related to this paper: human-PRCP

Title : Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host - Toh_2006_Genome.Res_16_149
Author(s) : Toh H , Weiss BL , Perkin SA , Yamashita A , Oshima K , Hattori M , Aksoy S
Ref : Genome Res , 16 :149 , 2006
Abstract : Sodalis glossinidius is a maternally transmitted endosymbiont of tsetse flies (Glossina spp.), an insect of medical and veterinary significance. Analysis of the complete sequence of Sodalis' chromosome (4,171,146 bp, encoding 2,432 protein coding sequences) indicates a reduced coding capacity of 51%. Furthermore, the chromosome contains 972 pseudogenes, an inordinately high number compared with that of other bacterial species. A high proportion of these pseudogenes are homologs of known proteins that function either in defense or in the transport and metabolism of carbohydrates and inorganic ions, suggesting Sodalis' degenerative adaptations to the immunity and restricted nutritional status of the host. Sodalis possesses three chromosomal symbiosis regions (SSR): SSR-1, SSR-2, and SSR-3, with gene inventories similar to the Type-III secretion system (TTSS) ysa from Yersinia enterolitica and SPI-1 and SPI-2 from Salmonella, respectively. While core components of the needle structure have been conserved, some of the effectors and regulators typically associated with these systems in pathogenic microbes are modified or eliminated in Sodalis. Analysis of SSR-specific invA transcript abundance in Sodalis during host development indicates that the individual symbiosis regions may exhibit different temporal expression profiles. In addition, the Sodalis chromosome encodes a complete flagella structure, key components of which are expressed in immature host developmental stages. These features may be important for the transmission and establishment of symbiont infections in the intra-uterine progeny. The data suggest that Sodalis represents an evolutionary intermediate transitioning from a free-living to a mutualistic lifestyle.
ESTHER : Toh_2006_Genome.Res_16_149
PubMedSearch : Toh_2006_Genome.Res_16_149
PubMedID: 16365377
Gene_locus related to this paper: sodgm-q2nqh6 , sodgm-q2nqt2 , sodgm-q2nss6 , sodgm-q2nt34 , sodgm-q2nth7 , sodgm-q2nue4 , sodgm-q2nvf1 , sodgm-q2nwd0

Title : Interfacial behavior of fatty-acylated sericin prepared by lipase-catalyzed solid-phase synthesis - Ogino_2006_Biosci.Biotechnol.Biochem_70_66
Author(s) : Ogino M , Tanaka R , Hattori M , Yoshida T , Yokote Y , Takahashi K
Ref : Biosci Biotechnol Biochem , 70 :66 , 2006
Abstract : Fatty-acylated sericin {1:0.7 molar ratio of sericin (Mr 18,700) to oleic acid} was prepared by lipase-catalyzed solid-phase synthesis in n-hexane containing oleic acid to endow sericin with interfacial properties. Acylation with oleic acid was confirmed by 1H-NMR. The fatty-acylated sericin exhibited superior emulsifying activity index and emulsion stability in the presence of 0-0.5 M NaCl, in a temperature range of 30-80 degrees C and pH range of 2-7, as compared with the control sericin. The fatty-acylated sericin (1:0.4 molar ratio) prepared by using low-molecular-weight sericin (Mr 5,000) also exhibited superior emulsifying properties. The affinity of the fatty-acylated sericin to a hydrophobic surface as evaluated by a biomolecular interaction analyzer was about twice as much as that of the control sericin. The fatty-acylated sericin showed retarded water vaporization, similar to the control sericin, indicating good retention of moistness, and was adsorbed four times as much to defatted wool with little desorption as compared with the control sericin.
ESTHER : Ogino_2006_Biosci.Biotechnol.Biochem_70_66
PubMedSearch : Ogino_2006_Biosci.Biotechnol.Biochem_70_66
PubMedID: 16428822

Title : Genome sequence of the cat pathogen, Chlamydophila felis - Azuma_2006_DNA.Res_13_15
Author(s) : Azuma Y , Hirakawa H , Yamashita A , Cai Y , Rahman MA , Suzuki H , Mitaku S , Toh H , Goto S , Murakami T , Sugi K , Hayashi H , Fukushi H , Hattori M , Kuhara S , Shirai M
Ref : DNA Research , 13 :15 , 2006
Abstract : Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent) is a worldwide spread pathogen for pneumonia and conjunctivitis in cats. Herein, we determined the entire genomic DNA sequence of the Japanese C. felis strain Fe/C-56 to understand the mechanism of diseases caused by this pathogen. The C. felis genome is composed of a circular 1,166,239 bp chromosome encoding 1005 protein-coding genes and a 7552 bp circular plasmid. Comparison of C. felis gene contents with other Chlamydia species shows that 795 genes are common in the family Chlamydiaceae species and 47 genes are specific to C. felis. Phylogenetic analysis of the common genes reveals that most of the orthologue sets exhibit a similar divergent pattern but 14 C. felis genes accumulate more mutations, implicating that these genes may be involved in the evolutional adaptation to the C. felis-specific niche. Gene distribution and orthologue analyses reveal that two distinctive regions, i.e. the plasticity zone and frequently gene-translocated regions (FGRs), may play important but different roles for chlamydial genome evolution. The genomic DNA sequence of C. felis provides information for comprehension of diseases and elucidation of the chlamydial evolution.
ESTHER : Azuma_2006_DNA.Res_13_15
PubMedSearch : Azuma_2006_DNA.Res_13_15
PubMedID: 16766509
Gene_locus related to this paper: chlff-q253e0 , chlff-q254l8

Title : Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection - Kuroda_2005_Proc.Natl.Acad.Sci.U.S.A_102_13272
Author(s) : Kuroda M , Yamashita A , Hirakawa H , Kumano M , Morikawa K , Higashide M , Maruyama A , Inose Y , Matoba K , Toh H , Kuhara S , Hattori M , Ohta T
Ref : Proc Natl Acad Sci U S A , 102 :13272 , 2005
Abstract : Staphylococcus saprophyticus is a uropathogenic Staphylococcus frequently isolated from young female outpatients presenting with uncomplicated urinary tract infections. We sequenced the whole genome of S. saprophyticus type strain ATCC 15305, which harbors a circular chromosome of 2,516,575 bp with 2,446 ORFs and two plasmids. Comparative genomic analyses with the strains of two other species, Staphylococcus aureus and Staphylococcus epidermidis, as well as experimental data, revealed the following characteristics of the S. saprophyticus genome. S. saprophyticus does not possess any virulence factors found in S. aureus, such as coagulase, enterotoxins, exoenzymes, and extracellular matrix-binding proteins, although it does have a remarkable paralog expansion of transport systems related to highly variable ion contents in the urinary environment. A further unique feature is that only a single ORF is predictable as a cell wall-anchored protein, and it shows positive hemagglutination and adherence to human bladder cell associated with initial colonization in the urinary tract. It also shows significantly high urease activity in S. saprophyticus. The uropathogenicity of S. saprophyticus can be attributed to its genome that is needed for its survival in the human urinary tract by means of novel cell wall-anchored adhesin and redundant uro-adaptive transport systems, together with urease.
ESTHER : Kuroda_2005_Proc.Natl.Acad.Sci.U.S.A_102_13272
PubMedSearch : Kuroda_2005_Proc.Natl.Acad.Sci.U.S.A_102_13272
PubMedID: 16135568
Gene_locus related to this paper: stas1-q4a0b8 , stas1-q4a0z3 , stas1-q4a018 , stas1-q4a076 , stas1-q4a169 , stas1-q49uw5 , stas1-q49vf8 , stas1-q49vg1 , stas1-q49vk0 , stas1-q49w07 , stas1-q49w20 , stas1-q49we3 , stas1-q49wg7 , stas1-q49ws3 , stas1-q49x95 , stas1-q49xp4 , stas1-q49yj4 , stas1-q49zd4 , stas1-q49zs7

Title : DNA sequence and analysis of human chromosome 18 - Nusbaum_2005_Nature_437_551
Author(s) : Nusbaum C , Zody MC , Borowsky ML , Kamal M , Kodira CD , Taylor TD , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Abouelleil A , Allen NR , Anderson S , Bloom T , Bugalter B , Butler J , Cook A , Decaprio D , Engels R , Garber M , Gnirke A , Hafez N , Hall JL , Norman CH , Itoh T , Jaffe DB , Kuroki Y , Lehoczky J , Lui A , Macdonald P , Mauceli E , Mikkelsen TS , Naylor JW , Nicol R , Nguyen C , Noguchi H , O'Leary SB , O'Neill K , Piqani B , Smith CL , Talamas JA , Topham K , Totoki Y , Toyoda A , Wain HM , Young SK , Zeng Q , Zimmer AR , Fujiyama A , Hattori M , Birren BW , Sakaki Y , Lander ES
Ref : Nature , 437 :551 , 2005
Abstract : Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.
ESTHER : Nusbaum_2005_Nature_437_551
PubMedSearch : Nusbaum_2005_Nature_437_551
PubMedID: 16177791
Gene_locus related to this paper: human-LIPG

Title : DNA sequence and comparative analysis of chimpanzee chromosome 22 - Watanabe_2004_Nature_429_382
Author(s) : Watanabe H , Fujiyama A , Hattori M , Taylor TD , Toyoda A , Kuroki Y , Noguchi H , BenKahla A , Lehrach H , Sudbrak R , Kube M , Taenzer S , Galgoczy P , Platzer M , Scharfe M , Nordsiek G , Blocker H , Hellmann I , Khaitovich P , Paabo S , Reinhardt R , Zheng HJ , Zhang XL , Zhu GF , Wang BF , Fu G , Ren SX , Zhao GP , Chen Z , Lee YS , Cheong JE , Choi SH , Wu KM , Liu TT , Hsiao KJ , Tsai SF , Kim CG , S OO , Kitano T , Kohara Y , Saitou N , Park HS , Wang SY , Yaspo ML , Sakaki Y
Ref : Nature , 429 :382 , 2004
Abstract : Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.
ESTHER : Watanabe_2004_Nature_429_382
PubMedSearch : Watanabe_2004_Nature_429_382
PubMedID: 15164055
Gene_locus related to this paper: pantr-a0a2j8lmv7

Title : Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism - Ueda_2004_Nucleic.Acids.Res_32_4937
Author(s) : Ueda K , Yamashita A , Ishikawa J , Shimada M , Watsuji TO , Morimura K , Ikeda H , Hattori M , Beppu T
Ref : Nucleic Acids Research , 32 :4937 , 2004
Abstract : Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57 Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the genome is closest to that of Firmicutes, a phylum consisting of low G + C Gram-positive bacteria. This provides evidence for the presence of an undefined category in the Gram-positive bacterial group. The presence of both spo and related genes and microscopic observation indicate that S.thermophilum is the first high G + C organism that forms endospores. The S.thermophilum genome is also characterized by the widespread insertion of class C group II introns, which are oriented in the same direction as chromosomal replication. The genome has many membrane transporters, a number of which are involved in the uptake of peptides and amino acids. The genes involved in primary metabolism are largely identified, except those that code several biosynthetic enzymes and carbonic anhydrase. The organism also has a variety of respiratory systems including Nap nitrate reductase, which has been found only in Gram-negative bacteria. Overall, these features suggest that S.thermophilum is adaptable to and thus lives in various environments, such that its growth requirement could be a substance or a physiological condition that is generally available in the natural environment rather than a highly specific substance that is present only in a limited niche. The genomic information from S.thermophilum offers new insights into microbial diversity and evolutionary sciences, and provides a framework for characterizing the molecular basis underlying microbial commensalism.
ESTHER : Ueda_2004_Nucleic.Acids.Res_32_4937
PubMedSearch : Ueda_2004_Nucleic.Acids.Res_32_4937
PubMedID: 15383646
Gene_locus related to this paper: symth-metx , symth-q67kd5 , symth-q67kg6 , symth-q67kl6 , symth-q67km7 , symth-q67lu3 , symth-q67mi3 , symth-q67mk6 , symth-q67mr3 , symth-q67n56 , symth-q67nt3 , symth-q67pl6 , symth-q67qv2 , symth-q67r02 , symth-q67r99 , symth-q67ra1 , symth-q67ri0 , symth-q67rl1 , symth-q67ru9 , symth-q67s20 , symth-q67sr9 , symth-q67sv7 , symth-q67t46

Title : Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation - Kuwahara_2004_Proc.Natl.Acad.Sci.U.S.A_101_14919
Author(s) : Kuwahara T , Yamashita A , Hirakawa H , Nakayama H , Toh H , Okada N , Kuhara S , Hattori M , Hayashi T , Ohnishi Y
Ref : Proc Natl Acad Sci U S A , 101 :14919 , 2004
Abstract : Bacteroides are predominant human colonic commensals, but the principal pathogenic species, Bacteroides fragilis (BF), lives closely associated with the mucosal surface, whereas a second major species, Bacteroides thetaiotaomicron (BT), concentrates within the colon. We find corresponding differences in their genomes, based on determination of the genome sequence of BF and comparative analysis with BT. Both species have acquired two mechanisms that contribute to their dominance among the colonic microbiota: an exceptional capability to use a wide range of dietary polysaccharides by gene amplification and the capacity to create variable surface antigenicities by multiple DNA inversion systems. However, the gene amplification for polysaccharide assimilation is more developed in BT, in keeping with its internal localization. In contrast, external antigenic structures can be changed more systematically in BF. Thereby, at the mucosal surface, where microbes encounter continuous attack by host defenses, BF evasion of the immune system is favored, and its colonization and infectious potential are increased.
ESTHER : Kuwahara_2004_Proc.Natl.Acad.Sci.U.S.A_101_14919
PubMedSearch : Kuwahara_2004_Proc.Natl.Acad.Sci.U.S.A_101_14919
PubMedID: 15466707
Gene_locus related to this paper: bacfn-q5lh43 , bacfr-q64mh3 , bacfr-q64n33 , bacfr-q64qs3 , bacfr-q64t24 , bacfr-q64uj8 , bacfr-q64vl4 , bacfr-q64vx6 , bacfr-q64wh2 , bacfr-q64xp9 , bacfr-q64yv4 , bacfr-q650j0

Title : The complete genomic sequence of Nocardia farcinica IFM 10152 - Ishikawa_2004_Proc.Natl.Acad.Sci.U.S.A_101_14925
Author(s) : Ishikawa J , Yamashita A , Mikami Y , Hoshino Y , Kurita H , Hotta K , Shiba T , Hattori M
Ref : Proc Natl Acad Sci U S A , 101 :14925 , 2004
Abstract : We determined the genomic sequence of Nocardia farcinica IFM 10152, a clinical isolate, and revealed the molecular basis of its versatility. The genome consists of a single circular chromosome of 6,021,225 bp with an average G+C content of 70.8% and two plasmids of 184,027 (pNF1) and 87,093 (pNF2) bp with average G+C contents of 67.2% and 68.4%, respectively. The chromosome encoded 5,674 putative protein-coding sequences, including many candidate genes for virulence and multidrug resistance as well as secondary metabolism. Analyses of paralogous protein families suggest that gene duplications have resulted in a bacterium that can survive not only in soil environments but also in animal tissues, resulting in disease.
ESTHER : Ishikawa_2004_Proc.Natl.Acad.Sci.U.S.A_101_14925
PubMedSearch : Ishikawa_2004_Proc.Natl.Acad.Sci.U.S.A_101_14925
PubMedID: 15466710
Gene_locus related to this paper: 9arch-q5nw20 , nocfa-metx , nocfa-q5ymb5 , nocfa-q5yml0 , nocfa-q5ymz1 , nocfa-q5yn12 , nocfa-q5yn81 , nocfa-q5yna6 , nocfa-q5ynd1 , nocfa-q5yne7 , nocfa-q5ynm0 , nocfa-q5ynw9 , nocfa-q5ynx0 , nocfa-q5yp07 , nocfa-q5yp18 , nocfa-q5yp33 , nocfa-q5yp46 , nocfa-q5yp51 , nocfa-q5ypg5 , nocfa-q5yph7 , nocfa-q5ypm0 , nocfa-q5ypu9 , nocfa-q5ypw3 , nocfa-q5yqi7 , nocfa-q5yql3 , nocfa-q5yqp8 , nocfa-q5yqw8 , nocfa-q5yqy4 , nocfa-q5yr00 , nocfa-q5yr19 , nocfa-q5yrc7 , nocfa-q5yrg2 , nocfa-q5yrn9 , nocfa-q5yrp2 , nocfa-q5yrp3 , nocfa-q5yrq8 , nocfa-q5yrt6 , nocfa-q5yrv3 , nocfa-q5yrz4 , nocfa-q5ys96 , nocfa-q5ys98 , nocfa-q5ysa6 , nocfa-q5ysq0 , nocfa-q5yt17 , nocfa-q5ytb0 , nocfa-q5ytg1 , nocfa-q5ytn3 , nocfa-q5ytr2 , nocfa-q5ytw9 , nocfa-q5ytz8 , nocfa-q5yua9 , nocfa-q5yub8 , nocfa-q5yuk6 , nocfa-q5yum4 , nocfa-q5yun2 , nocfa-q5yun5 , nocfa-q5yun7 , nocfa-q5yuq2 , nocfa-q5yur6 , nocfa-q5yus3 , nocfa-q5yus4 , nocfa-q5yv08 , nocfa-q5yv27 , nocfa-q5yvb8 , nocfa-q5yvi0 , nocfa-q5yvk3 , nocfa-q5yvr2 , nocfa-q5yvw8 , nocfa-q5yvz9 , nocfa-q5yw34 , nocfa-q5yw53 , nocfa-q5ywe0 , nocfa-q5ywh1 , nocfa-q5ywp2 , nocfa-q5ywt3 , nocfa-q5yx25 , nocfa-q5yx42 , nocfa-q5yx67 , nocfa-q5yxc9 , nocfa-q5yxd4 , nocfa-q5yxg3 , nocfa-q5yxx4 , nocfa-q5yy59 , nocfa-q5yyb5 , nocfa-q5yz80 , nocfa-q5yz86 , nocfa-q5yz89 , nocfa-q5yz97 , nocfa-q5yza2 , nocfa-q5yzd7 , nocfa-q5yzg2 , nocfa-q5yzh3 , nocfa-q5yzi0 , nocfa-q5yzq7 , nocfa-q5yzu6 , nocfa-q5z0b7 , nocfa-q5z0l3 , nocfa-q5z0s0 , nocfa-q5z0u1 , nocfa-q5z1b6 , nocfa-q5z1d9 , nocfa-q5z1g6 , nocfa-q5z1t3 , nocfa-q5z1t8 , nocfa-q5z1x5 , nocfa-q5z1x6 , nocfa-q5z1x7 , nocfa-q5z1x8 , nocfa-q5z2c2 , nocfa-q5z2d3 , nocfa-q5z2d5 , nocfa-q5z2e7 , nocfa-q5z2m6 , nocfa-q5z2s1 , nocfa-q5z2x4 , nocfa-q5z2x8 , nocfa-q5z2z7 , nocfa-q5z3c1 , nocfa-q5z3e1 , nocfa-q5z3g0 , nocfa-q5z3g3 , nocfa-q5z3g5 , nocfa-q5z3g6 , nocfa-q5z3g7 , nocfa-q5z3g8 , nocfa-q5z3q1 , nocfa-q5z3z4 , nocfa-q5z200 , nocfa-q5z339 , nocfa-q5ynw5 , nocfa-q5ynd9 , nocfa-q5yp20

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 : Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis - Ikeda_2003_Nat.Biotechnol_21_526
Author(s) : Ikeda H , Ishikawa J , Hanamoto A , Shinose M , Kikuchi H , Shiba T , Sakaki Y , Hattori M , Omura S
Ref : Nat Biotechnol , 21 :526 , 2003
Abstract : Species of the genus Streptomyces are of major pharmaceutical interest because they synthesize a variety of bioactive secondary metabolites. We have determined the complete nucleotide sequence of the linear chromosome of Streptomyces avermitilis. S. avermitilis produces avermectins, a group of antiparasitic agents used in human and veterinary medicine. The genome contains 9,025,608 bases (average GC content, 70.7%) and encodes at least 7,574 potential open reading frames (ORFs). Thirty-five percent of the ORFs (2,664) constitute 721 paralogous families. Thirty gene clusters related to secondary metabolite biosynthesis were identified, corresponding to 6.6% of the genome. Comparison with Streptomyces coelicolor A3(2) revealed that an internal 6.5-Mb region in the S. avermitilis genome was highly conserved with respect to gene order and content, and contained all known essential genes but showed perfectly asymmetric structure at the oriC center. In contrast, the terminal regions were not conserved and preferentially contained nonessential genes.
ESTHER : Ikeda_2003_Nat.Biotechnol_21_526
PubMedSearch : Ikeda_2003_Nat.Biotechnol_21_526
PubMedID: 12692562
Gene_locus related to this paper: strav-cah , strav-GEOB , strav-PCAL , strav-Q93HH8 , strav-SAV38 , strav-SAV141 , strav-SAV154 , strav-SAV297 , strav-SAV298 , strav-SAV433 , strav-SAV469 , strav-SAV512 , strav-SAV519 , strav-SAV541 , strav-SAV569 , strav-SAV620 , strav-SAV819 , strav-SAV875 , strav-SAV888 , strav-SAV906 , strav-SAV923 , strav-SAV974 , strav-SAV1231 , strav-SAV1256 , strav-SAV1457 , strav-SAV1549 , strav-SAV1585 , strav-SAV1746 , strav-SAV1898 , strav-SAV1906 , strav-SAV1959 , strav-SAV1968 , strav-SAV1973 , strav-SAV2099 , strav-SAV2105 , strav-SAV2113 , strav-SAV2604 , strav-SAV2722 , strav-SAV3039 , strav-SAV3080 , strav-SAV3081 , strav-SAV3092 , strav-SAV3099 , strav-SAV3144 , strav-SAV3359 , strav-SAV3461 , strav-SAV3624 , strav-SAV3810 , strav-SAV3854 , strav-SAV4041 , strav-SAV4252 , strav-SAV4410 , strav-SAV4434 , strav-SAV4531 , strav-SAV4564 , strav-SAV4596 , strav-SAV4674 , strav-SAV4779 , strav-SAV4863 , strav-SAV4922 , strav-SAV4968 , strav-SAV5173 , strav-SAV5300 , strav-SAV5344 , strav-SAV5668 , strav-SAV5711 , strav-SAV5844 , strav-SAV5965 , strav-SAV6079 , strav-SAV6138 , strav-SAV6422 , strav-SAV6559 , strav-SAV6609 , strav-SAV7067 , strav-SAV7089 , strav-SAV7110 , strav-SAV7198 , strav-SAV7423 , strav-SAV7455 , strav-SAV7475 , strav-SLPD , straw-AVEG , straw-pepx , straw-q82bb0 , straw-q82en5 , straw-q82et1 , straw-q93hc9 , straw-SAV1543 , straw-SAV2023

Title : Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution - Nakagawa_2003_Genome.Res_13_1042
Author(s) : Nakagawa I , Kurokawa K , Yamashita A , Nakata M , Tomiyasu Y , Okahashi N , Kawabata S , Yamazaki K , Shiba T , Yasunaga T , Hayashi H , Hattori M , Hamada S
Ref : Genome Res , 13 :1042 , 2003
Abstract : Group Astreptococcus (GAS) is a gram-positive bacterial pathogen that causes various suppurative infections and nonsuppurative sequelae. Since the late 1980s, streptococcal toxic-shock like syndrome (STSS) and severe invasive GAS infections have been reported globally. Here we sequenced the genome of serotype M3 strain SSI-1, isolated from an STSS patient in Japan, and compared it with those of other GAS strains. The SSI-1 genome is composed of 1,884,275 bp, and 1.7 Mb of the sequence is highly conserved relative to strain SF370 (serotype M1) and MGAS8232 (serotype M18), and almost completely conserved relative to strain MGAS315 (serotype M3). However, a large genomic rearrangement has been shown to occur across the replication axis between the homologous rrn-comX1 regions and between two prophage-coding regions across the replication axis. Atotal of 1 Mb of chromosomal DNA is inverted across the replication axis. Interestingly, the recombinations between the prophage regions are within the phage genes, and the genes encoding superantigens and mitogenic factors are interchanged between two prophages. This genomic rearrangement occurs in 65% of clinical isolates (64/94) collected after 1990, whereas it is found in only 25% of clinical isolates (7/28) collected before 1985. These observations indicate that streptococcal phages represent important plasticity regions in the GAS chromosome where recombination between homologous phage genes can occur and result not only in new phage derivatives, but also in large chromosomal rearrangements.
ESTHER : Nakagawa_2003_Genome.Res_13_1042
PubMedSearch : Nakagawa_2003_Genome.Res_13_1042
PubMedID: 12799345
Gene_locus related to this paper: strpy-ESTA , strpy-PEPXP , strpy-SPY1308

Title : Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia - Akman_2002_Nat.Genet_32_402
Author(s) : Akman L , Yamashita A , Watanabe H , Oshima K , Shiba T , Hattori M , Aksoy S
Ref : Nat Genet , 32 :402 , 2002
Abstract : Many insects that rely on a single food source throughout their developmental cycle harbor beneficial microbes that provide nutrients absent from their restricted diet. Tsetse flies, the vectors of African trypanosomes, feed exclusively on blood and rely on one such intracellular microbe for nutritional provisioning and fecundity. As a result of co-evolution with hosts over millions of years, these mutualists have lost the ability to survive outside the sheltered environment of their host insect cells. We present the complete annotated genome of Wigglesworthia glossinidia brevipalpis, which is composed of one chromosome of 697,724 base pairs (bp) and one small plasmid, called pWig1, of 5,200 bp. Genes involved in the biosynthesis of vitamin metabolites, apparently essential for host nutrition and fecundity, have been retained. Unexpectedly, this obligate's genome bears hallmarks of both parasitic and free-living microbes, and the gene encoding the important regulatory protein DnaA is absent.
ESTHER : Akman_2002_Nat.Genet_32_402
PubMedSearch : Akman_2002_Nat.Genet_32_402
PubMedID: 12219091
Gene_locus related to this paper: wigbr-BIOH

Title : Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater - Shimizu_2002_Proc.Natl.Acad.Sci.U.S.A_99_996
Author(s) : Shimizu T , Ohtani K , Hirakawa H , Ohshima K , Yamashita A , Shiba T , Ogasawara N , Hattori M , Kuhara S , Hayashi H
Ref : Proc Natl Acad Sci U S A , 99 :996 , 2002
Abstract : Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium that causes life-threatening gas gangrene and mild enterotoxaemia in humans, although it colonizes as normal intestinal flora of humans and animals. The organism is known to produce a variety of toxins and enzymes that are responsible for the severe myonecrotic lesions. Here we report the complete 3,031,430-bp sequence of C. perfringens strain 13 that comprises 2,660 protein coding regions and 10 rRNA genes, showing pronounced low overall G + C content (28.6%). The genome contains typical anaerobic fermentation enzymes leading to gas production but no enzymes for the tricarboxylic acid cycle or respiratory chain. Various saccharolytic enzymes were found, but many enzymes for amino acid biosynthesis were lacking in the genome. Twenty genes were newly identified as putative virulence factors of C. perfringens, and we found a total of five hyaluronidase genes that will also contribute to virulence. The genome analysis also proved an efficient method for finding four members of the two-component VirR/VirS regulon that coordinately regulates the pathogenicity of C. perfringens. Clearly, C. perfringens obtains various essential materials from the host by producing several degradative enzymes and toxins, resulting in massive destruction of the host tissues.
ESTHER : Shimizu_2002_Proc.Natl.Acad.Sci.U.S.A_99_996
PubMedSearch : Shimizu_2002_Proc.Natl.Acad.Sci.U.S.A_99_996
PubMedID: 11792842
Gene_locus related to this paper: clope-CPE0307 , clope-CPE0432 , clope-CPE1581 , clope-CPE1596 , clope-CPE1989 , clope-CPE2231 , clope-CPE2312 , clope-lipa , clope-LIPB , clope-PLDB

Title : The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans - Sasaki_2002_Nucleic.Acids.Res_30_5293
Author(s) : Sasaki Y , Ishikawa J , Yamashita A , Oshima K , Kenri T , Furuya K , Yoshino C , Horino A , Shiba T , Sasaki T , Hattori M
Ref : Nucleic Acids Research , 30 :5293 , 2002
Abstract : The complete genomic sequence of an intracellular bacterial pathogen, Mycoplasma penetrans HF-2 strain, was determined. The HF-2 genome consists of a 1 358 633 bp single circular chromosome containing 1038 predicted coding sequences (CDSs), one set of rRNA genes and 30 tRNA genes. Among the 1038 CDSs, 264 predicted proteins are common to the Mycoplasmataceae sequenced thus far and 463 are M.penetrans specific. The genome contains the two-component system but lacks the essential cellular gene, uridine kinase. The relatively large genome of M.penetrans HF-2 among mycoplasma species may be accounted for by both its rich core proteome and the presence of a number of paralog families corresponding to 25.4% of all CDSs. The largest paralog family is the p35 family, which encodes surface lipoproteins including the major antigen, P35. A total of 44 genes for p35 and p35 homologs were identified and 30 of them form one large cluster in the chromosome. The genetic tree of p35 paralogs suggests the occurrence of dynamic chromosomal rearrangement in paralog formation during evolution. Thus, M.penetrans HF-2 may have acquired diverse repertoires of antigenic variation-related genes to allow its persistent infection in humans.
ESTHER : Sasaki_2002_Nucleic.Acids.Res_30_5293
PubMedSearch : Sasaki_2002_Nucleic.Acids.Res_30_5293
PubMedID: 12466555
Gene_locus related to this paper: mycpe-MYPE3930 , mycpe-MYPE5460 , mycpe-MYPE8330 , mycpe-MYPE9300 , mycpe-q8eve6

Title : Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites - Omura_2001_Proc.Natl.Acad.Sci.U.S.A_98_12215
Author(s) : Omura S , Ikeda H , Ishikawa J , Hanamoto A , Takahashi C , Shinose M , Takahashi Y , Horikawa H , Nakazawa H , Osonoe T , Kikuchi H , Shiba T , Sakaki Y , Hattori M
Ref : Proc Natl Acad Sci U S A , 98 :12215 , 2001
Abstract : Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is commercially important in human and veterinary medicine. The major interest in this genus Streptomyces is the diversity of its production of secondary metabolites as an industrial microorganism. A major factor in its prominence as a producer of the variety of secondary metabolites is its possession of several metabolic pathways for biosynthesis. Here we report sequence analysis of S. avermitilis, covering 99% of its genome. At least 8.7 million base pairs exist in the linear chromosome; this is the largest bacterial genome sequence, and it provides insights into the intrinsic diversity of the production of the secondary metabolites of Streptomyces. Twenty-five kinds of secondary metabolite gene clusters were found in the genome of S. avermitilis. Four of them are concerned with the biosyntheses of melanin pigments, in which two clusters encode tyrosinase and its cofactor, another two encode an ochronotic pigment derived from homogentiginic acid, and another polyketide-derived melanin. The gene clusters for carotenoid and siderophore biosyntheses are composed of seven and five genes, respectively. There are eight kinds of gene clusters for type-I polyketide compound biosyntheses, and two clusters are involved in the biosyntheses of type-II polyketide-derived compounds. Furthermore, a polyketide synthase that resembles phloroglucinol synthase was detected. Eight clusters are involved in the biosyntheses of peptide compounds that are synthesized by nonribosomal peptide synthetases. These secondary metabolite clusters are widely located in the genome but half of them are near both ends of the genome. The total length of these clusters occupies about 6.4% of the genome.
ESTHER : Omura_2001_Proc.Natl.Acad.Sci.U.S.A_98_12215
PubMedSearch : Omura_2001_Proc.Natl.Acad.Sci.U.S.A_98_12215
PubMedID: 11572948
Gene_locus related to this paper: strav-cah , strav-GEOB , strav-OLMA7 , strav-OLMC , strav-PCAL , strav-PTEA5 , strav-PTEH , strav-Q93GY0 , strav-Q93GY7 , strav-Q93H00 , strav-Q93H03 , strav-Q93H41 , strav-Q93H55 , strav-Q93H68 , strav-Q93H73 , strav-Q93HG2 , strav-Q93HH2 , strav-Q93HH8 , strav-Q93HI2 , strav-SAV38 , strav-SAV141 , strav-SAV154 , strav-SAV297 , strav-SAV298 , strav-SAV299 , strav-SAV433 , strav-SAV469 , strav-SAV512 , strav-SAV519 , strav-SAV541 , strav-SAV569 , strav-SAV620 , strav-SAV819 , strav-SAV875 , strav-SAV888 , strav-SAV906 , strav-SAV923 , strav-SAV974 , strav-SAV1231 , strav-SAV1256 , strav-SAV1457 , strav-SAV1549 , strav-SAV1585 , strav-SAV1746 , strav-SAV1898 , strav-SAV1906 , strav-SAV1959 , strav-SAV1968 , strav-SAV1973 , strav-SAV2099 , strav-SAV2105 , strav-SAV2113 , strav-SAV2604 , strav-SAV2722 , strav-SAV3039 , strav-SAV3080 , strav-SAV3081 , strav-SAV3092 , strav-SAV3099 , strav-SAV3144 , strav-SAV3359 , strav-SAV3461 , strav-SAV3624 , strav-SAV3810 , strav-SAV3854 , strav-SAV4041 , strav-SAV4252 , strav-SAV4410 , strav-SAV4434 , strav-SAV4531 , strav-SAV4564 , strav-SAV4596 , strav-SAV4674 , strav-SAV4779 , strav-SAV4863 , strav-SAV4922 , strav-SAV4968 , strav-SAV5173 , strav-SAV5300 , strav-SAV5344 , strav-SAV5668 , strav-SAV5711 , strav-SAV5844 , strav-SAV5965 , strav-SAV6079 , strav-SAV6138 , strav-SAV6422 , strav-SAV6559 , strav-SAV6609 , strav-SAV7067 , strav-SAV7089 , strav-SAV7110 , strav-SAV7198 , strav-SAV7423 , strav-SAV7455 , strav-SAV7475 , strav-SLPD , straw-AVEG , straw-pepx , straw-q82bb0 , straw-q82en5 , straw-q82et1 , straw-q93hc9 , straw-SAV1543 , straw-SAV2023 , strax-Q93H72

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 : 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

Title : Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS - Shigenobu_2000_Nature_407_81
Author(s) : Shigenobu S , Watanabe H , Hattori M , Sakaki Y , Ishikawa H
Ref : Nature , 407 :81 , 2000
Abstract : Almost all aphid species (Homoptera, Insecta) have 60-80 huge cells called bacteriocytes, within which are round-shaped bacteria that are designated Buchnera. These bacteria are maternally transmitted to eggs and embryos through host generations, and the mutualism between the host and the bacteria is so obligate that neither can reproduce independently. Buchnera is a close relative of Escherichia coli, but it contains more than 100 genomic copies per cell, and its genome size is only a seventh of that of E. coli. Here we report the complete genome sequence of Buchnera sp. strain APS, which is composed of one 640,681-base-pair chromosome and two small plasmids. There are genes for the biosyntheses of amino acids essential for the hosts in the genome, but those for non-essential amino acids are missing, indicating complementarity and syntrophy between the host and the symbiont. In addition, Buchnera lacks genes for the biosynthesis of cell-surface components, including lipopolysaccharides and phospholipids, regulator genes and genes involved in defence of the cell. These results indicate that Buchnera is completely symbiotic and viable only in its limited niche, the bacteriocyte.
ESTHER : Shigenobu_2000_Nature_407_81
PubMedSearch : Shigenobu_2000_Nature_407_81
PubMedID: 10993077

Title : The DNA sequence of human chromosome 21 - Hattori_2000_Nature_405_311
Author(s) : Hattori M , Fujiyama A , Taylor TD , Watanabe H , Yada T , Park HS , Toyoda A , Ishii K , Totoki Y , Choi DK , Groner Y , Soeda E , Ohki M , Takagi T , Sakaki Y , Taudien S , Blechschmidt K , Polley A , Menzel U , Delabar J , Kumpf K , Lehmann R , Patterson D , Reichwald K , Rump A , Schillhabel M , Schudy A , Zimmermann W , Rosenthal A , Kudoh J , Schibuya K , Kawasaki K , Asakawa S , Shintani A , Sasaki T , Nagamine K , Mitsuyama S , Antonarakis SE , Minoshima S , Shimizu N , Nordsiek G , Hornischer K , Brant P , Scharfe M , Schon O , Desario A , Reichelt J , Kauer G , Blocker H , Ramser J , Beck A , Klages S , Hennig S , Riesselmann L , Dagand E , Haaf T , Wehrmeyer S , Borzym K , Gardiner K , Nizetic D , Francis F , Lehrach H , Reinhardt R , Yaspo ML
Ref : Nature , 405 :311 , 2000
Abstract : Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.
ESTHER : Hattori_2000_Nature_405_311
PubMedSearch : Hattori_2000_Nature_405_311
PubMedID: 10830953
Gene_locus related to this paper: human-LIPI

Title : Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA - Shirai_2000_Nucleic.Acids.Res_28_2311
Author(s) : Shirai M , Hirakawa H , Kimoto M , Tabuchi M , Kishi F , Ouchi K , Shiba T , Ishii K , Hattori M , Kuhara S , Nakazawa T
Ref : Nucleic Acids Research , 28 :2311 , 2000
Abstract : Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia and bronchitis. There are many reports of an association between C.PNEUMONIAE: infection and atherosclerosis. We determined the whole genome sequence of C.PNEUMONIAE: strain J138 isolated in Japan in 1994 and compared it with the sequence of strain CWL029 isolated in the USA before 1987. The J138 circular chromosome consists of 1 226 565 nt (40.7% G+C) with 1072 likely protein-coding genes that is 3665 nt shorter than the CWL029 genome. Plasmids, phage- or transposon-like sequences were not identified. The overall genomic organization, gene order and predicted proteomes of the two strains are very similar, suggesting a high level of structural and functional conservation between the two unrelated isolates. The most conspicuous differences in the J138 genome relative to the CWL029 genome are the absence of five DNA segments, ranging in size from 89 to 1649 nt, and the presence of three DNA segments, ranging from 27 to 84 nt. The complex organization of these 'different zones' may be attributable to a unique system of recombination.
ESTHER : Shirai_2000_Nucleic.Acids.Res_28_2311
PubMedSearch : Shirai_2000_Nucleic.Acids.Res_28_2311
PubMedID: 10871362
Gene_locus related to this paper: chlpn-CPJ0152 , chlpn-CPJ0342 , chlpn-CPN0161 , chlpn-CPN0271 , chlpn-q9jrv1 , chlpn-q9js10 , chlpn-q9k1u7 , chlpn-q9z6x9

Title : Comparative analysis of the whole set of rRNA operons between an enterohemorrhagic Escherichia coli O157:H7 Sakai strain and an Escherichia coli K-12 strain MG1655 - Ohnishi_2000_Syst.Appl.Microbiol_23_315
Author(s) : Ohnishi M , Murata T , Nakayama K , Kuhara S , Hattori M , Kurokawa K , Yasunaga T , Yokoyama K , Makino K , Shinagawa H , Hayashi T
Ref : Syst Appl Microbiol , 23 :315 , 2000
Abstract : Two primer sets for direct sequence determination of all seven rRNA operons (rrn) of Escherichia coli have been developed; one is for specific-amplification of each rrn operon and the other is for direct sequencing of the amplified operons. Using these primer sets, we determined the nucleotide sequences of seven rrn operons, including promoter and terminator regions, of an enterohemorrhagic E. coli (EHEC) O157:H7 Sakai strain. To elucidate the intercistronic or intraspecific variation of rrn operons, their sequences were compared with those for the K-12 rrn operons. The rrn genes and the internal transcribed spacer regions showed a higher similarity to each other in each strain than between the corresponding operons of the two strains. However, the degree of intercistronic homogeneity was much higher in the EHEC strain than in K-12. In contrast, promoter and terminator regions in each operons were conserved between the corresponding operons of the two strains, which exceeded intercistronic similarity.
ESTHER : Ohnishi_2000_Syst.Appl.Microbiol_23_315
PubMedSearch : Ohnishi_2000_Syst.Appl.Microbiol_23_315
PubMedID: 11108008

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

Title : Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer - Ho_1997_Nature_385_89
Author(s) : Ho YS , Swenson L , Derewenda U , Serre L , Wei Y , Dauter Z , Hattori M , Adachi T , Aoki J , Arai H , Inoue K , Derewenda ZS
Ref : Nature , 385 :89 , 1997
Abstract : The platelet-activating factor PAF (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) is a potent lipid first messenger active in general cell activation, fertilization, inflammatory and allergic reactions, asthma, HIV pathogenesis, carcinogenesis, and apoptosis. There is substantial evidence that PAF is involved in intracellular signalling, but the pathways are poorly understood. Inactivation of PAF is carried out by specific intra- and extracellular acetylhydrolases (PAF-AHs), a subfamily of phospholipases A2 that remove the sn-2 acetyl group. Mammalian brain contains at least three intracellular isoforms, of which PAF-AH(Ib) is the best characterized. This isoform contains a heterodimer of two homologous catalytic subunits alpha1 and alpha2, each of relative molecular mass 26K, and a non-catalytic 45K beta-subunit, a homologue of the beta-subunit of trimeric G proteins. We now report the crystal structure of the bovine alpha1 subunit of PAF-AH(Ib) at 1.7 A resolution in complex with a reaction product, acetate. The tertiary fold of this protein is closely reminiscent of that found in p21(ras) and other GTPases. The active site is made up of a trypsin-like triad of Ser 47, His 195 and Asp 192. Thus, the intact PAF-AH(Ib) molecule is an unusual G-protein-like (alpha1/alpha2)beta trimer.
ESTHER : Ho_1997_Nature_385_89
PubMedSearch : Ho_1997_Nature_385_89
PubMedID: 8985254

Title : cDNA cloning and expression of intracellular platelet-activating factor (PAF) acetylhydrolase II. Its homology with plasma PAF acetylhydrolase - Hattori_1996_J.Biol.Chem_271_33032
Author(s) : Hattori K , Adachi H , Matsuzawa A , Yamamoto K , Tsujimoto M , Aoki J , Hattori M , Arai H , Inoue K
Ref : Journal of Biological Chemistry , 271 :33032 , 1996
Abstract : Platelet-activating factor (PAF) acetylhydrolase, which inactivates PAF by removing the acetyl group at the sn-2 position, is widely distributed in plasma and tissues. We previously demonstrated that tissue cytosol contains at least two types of PAF acetylhydrolase, isoforms Ib and II, and that isoform Ib is a heterotrimer comprising 45-, 30-, and 29-kDa subunits, whereas isoform II is a 40-kDa monomer. In this study, we isolated cDNA clones of bovine and human PAF acetylhydrolase isoform II. From the longest open reading frame of the cloned cDNAs, both bovine and human PAF acetylhydrolases II are predicted to contain 392 amino acid residues and to exhibit 88% identity with each other at the amino acid level. Both enzymes contain a Gly-X-Ser-X-Gly motif that is characteristic of lipases and serine esterases. Expression of isoform II cDNA in COS7 cells resulted in a marked increase in PAF acetylhydrolase activity. An immunoblot study using an established monoclonal antibody against the bovine enzyme revealed that the recombinant protein exists in the membranous fraction as well as the soluble fraction. Isoform II is expressed most abundantly in the liver and kidney in cattle, but low levels were also observed in other tissues. The amino acid sequence deduced from the cDNA of isoform II had no homology with any subunit of isoform Ib. Interestingly, however, the amino acid sequence of isoform II showed 41% identity with that of plasma PAF acetylhydrolase. Combined with previous data demonstrating that isoform II shows similar substrate specificity to plasma PAF acetylhydrolase, these results indicate that tissue type isoform II and the plasma enzyme may share a common physiologic function.
ESTHER : Hattori_1996_J.Biol.Chem_271_33032
PubMedSearch : Hattori_1996_J.Biol.Chem_271_33032
PubMedID: 8955149
Gene_locus related to this paper: bovin-paf2 , human-PAFAH2

Title : Cloning and expression of a cDNA encoding the beta-subunit (30-kDa subunit) of bovine brain platelet-activating factor acetylhydrolase - Hattori_1995_J.Biol.Chem_270_31345
Author(s) : Hattori M , Adachi H , Aoki J , Tsujimoto M , Arai H , Inoue K
Ref : Journal of Biological Chemistry , 270 :31345 , 1995
Abstract : Bovine brain platelet-activating factor (PAF) acetylhydrolase isoform Ib is a heterotrimeric enzyme. Its gamma-subunit (which, formerly, we called the 29-kDa subunit) acts as a catalytic subunit, whereas the alpha-subunit (45 kDa) is the bovine homolog of the product of human LIS-1, the causative gene of Miller-Dieker lissencephaly, indicating that this intracellular PAF acetylhydrolase plays a key role in brain development. In the current study, we cloned the cDNA for the beta-subunit (30 kDa) of bovine brain PAF acetylhydrolase Ib. The predicted 229-amino acid sequence was homologous (63.2% identity) to that of the gamma-subunit, especially (86% identity) in the catalytic and PAF receptor homologous domains. The recombinant beta-protein produced in Escherichia coli showed significant PAF acetylhydrolase activity. A mutant protein, in which Ser48, which corresponds to the active serine residue of the gamma-subunit, was replaced with cysteine showed no enzymatic activity, suggesting Ser48 is the active serine residue. Although the beta- and gamma-subunits form a heterocomplex in the native enzyme, both recombinant beta- and gamma-proteins exist as a homodimer. The purified recombinant beta-protein was labeled readily with [1,3-H]diisopropyl fluorophosphate, whereas the beta-subunit in the native complex was only labeled with higher concentrations of [1,3-3H]diisopropyl fluorophosphate to a lesser extent than the gamma-subunit. Combined with our previous data, the present study demonstrated that bovine brain PAF acetylhydrolase Ib is a unique enzyme possessing two catalytic subunits and another, possibly regulatory, subunit.
ESTHER : Hattori_1995_J.Biol.Chem_270_31345
PubMedSearch : Hattori_1995_J.Biol.Chem_270_31345
PubMedID: 8537406

Title : The catalytic subunit of bovine brain platelet-activating factor acetylhydrolase is a novel type of serine esterase - Hattori_1994_J.Biol.Chem_269_23150
Author(s) : Hattori M , Adachi H , Tsujimoto M , Arai H , Inoue K
Ref : Journal of Biological Chemistry , 269 :23150 , 1994
Abstract : Platelet-activating factor (PAF) acetylhydrolase is the key enzyme in PAF inactivation. We recently purified one isoform of the enzyme from a bovine brain soluble fraction and revealed it as a heterotrimeric enzyme consisting of 29-, 30-, and 45-kDa subunits. Among them, the 29-kDa subunit possesses an active serine residue since diisopropyl fluorophosphate (DFP), an inhibitor of the enzyme, labeled only this subunit (Hattori, M., Arai, H., and Inoue, K. (1993) J. Biol. Chem. 268, 18748-18753). In the current study, we cloned the cDNA for the 29-kDa catalytic subunit. The predicted sequence of 232 amino acids is unique and is not homologous with those of any other proteins reported so far. When transfected into either Escherichia coli or COS7 cells, the cDNA produced PAF acetylhydrolase activity in both types of cells, indicating that this subunit alone is enough for catalysis. The recombinant 29-kDa protein was also inhibited and labeled by DFP. Furthermore, we isolated and sequenced the [3H]DFP-labeled peptide fragment, revealing that Ser47 is the active serine residue. The sequence surrounding it is different from the consensus sequence of the serine esterase family. Interestingly, the sequence of about 30 amino acids located 6 residues downstream from the active serine site exhibits significant homology to the first transmembrane region of the PAF receptor. These data demonstrate that the catalytic subunit of brain PAF acetylhydrolase is a novel type of serine esterase.
ESTHER : Hattori_1994_J.Biol.Chem_269_23150
PubMedSearch : Hattori_1994_J.Biol.Chem_269_23150
PubMedID: 8083218