Fujita N

References (39)

Title : Genome sequence of Aspergillus luchuensis NBRC 4314 - Yamada_2016_DNA.Res_23_507
Author(s) : Yamada O , Machida M , Hosoyama A , Goto M , Takahashi T , Futagami T , Yamagata Y , Takeuchi M , Kobayashi T , Koike H , Abe K , Asai K , Arita M , Fujita N , Fukuda K , Higa KI , Horikawa H , Ishikawa T , Jinno K , Kato Y , Kirimura K , Mizutani O , Nakasone K , Sano M , Shiraishi Y , Tsukahara M , Gomi K
Ref : DNA Research , 23 :507 , 2016
Abstract : Awamori is a traditional distilled beverage made from steamed Thai-Indica rice in Okinawa, Japan. For brewing the liquor, two microbes, local kuro (black) koji mold Aspergillus luchuensis and awamori yeast Saccharomyces cerevisiae are involved. In contrast, that yeasts are used for ethanol fermentation throughout the world, a characteristic of Japanese fermentation industries is the use of Aspergillus molds as a source of enzymes for the maceration and saccharification of raw materials. Here we report the draft genome of a kuro (black) koji mold, A. luchuensis NBRC 4314 (RIB 2604). The total length of nonredundant sequences was nearly 34.7 Mb, comprising approximately 2,300 contigs with 16 telomere-like sequences. In total, 11,691 genes were predicted to encode proteins. Most of the housekeeping genes, such as transcription factors and N-and O-glycosylation system, were conserved with respect to Aspergillus niger and Aspergillus oryzae An alternative oxidase and acid-stable alpha-amylase regarding citric acid production and fermentation at a low pH as well as a unique glutamic peptidase were also found in the genome. Furthermore, key biosynthetic gene clusters of ochratoxin A and fumonisin B were absent when compared with A. niger genome, showing the safety of A. luchuensis for food and beverage production. This genome information will facilitate not only comparative genomics with industrial kuro-koji molds, but also molecular breeding of the molds in improvements of awamori fermentation.
ESTHER : Yamada_2016_DNA.Res_23_507
PubMedSearch : Yamada_2016_DNA.Res_23_507
PubMedID: 27651094
Gene_locus related to this paper: 9euro-a0a146f3d2

Title : Complete Genome Sequence of Polypropylene Glycol- and Polyethylene Glycol-Degrading Sphingopyxis macrogoltabida Strain EY-1 - Ohtsubo_2015_Genome.Announc_3_e01399
Author(s) : Ohtsubo Y , Nagata Y , Numata M , Tsuchikane K , Hosoyama A , Yamazoe A , Tsuda M , Fujita N , Kawai F
Ref : Genome Announc , 3 : , 2015
Abstract : Strain EY-1 was isolated from a microbial consortium growing on a random polymer of ethylene oxide and propylene oxide. Strain EY-1 grew on polyethylene glycol and polypropylene glycol and identified as Sphingopyxis macrogoltabida. Here, we report the complete genome sequence of Sphingopyxis macrogoltabida EY-1. The genome of strain EY-1 is comprised of a 4.76-Mb circular chromosome, and five plasmids. The whole finishing was conducted in silico, with aids of computational tools GenoFinisher and AceFileViewer. Strain EY-1 is available from Biological Resource Center, National Institute of Technology and Evaluation (Tokyo, Japan) (NITE).
ESTHER : Ohtsubo_2015_Genome.Announc_3_e01399
PubMedSearch : Ohtsubo_2015_Genome.Announc_3_e01399
PubMedID: 26634754
Gene_locus related to this paper: sphmc-a0a0n9ujk2

Title : MR Prediction of Liver Function and Pathology Using Gd-EOB-DTPA: Effect of Liver Volume Consideration - Shimamoto_2015_Biomed.Res.Int_2015_141853
Author(s) : Shimamoto D , Nishie A , Asayama Y , Ushijima Y , Takayama Y , Fujita N , Shirabe K , Hida T , Kubo Y , Honda H
Ref : Biomed Res Int , 2015 :141853 , 2015
Abstract : Purpose. To evaluate whether the diagnostic performance of Gd-EOB-DTPA-enhanced MRI in evaluating liver function and pathology is improved by considering liver volume (LV). Methods. This retrospective study included 104 patients who underwent Gd-EOB-DTPA-enhanced MRI before liver surgery. For each patient, using the precontrast and hepatobiliary phase images, we calculated the increase rate of the liver-to-spleen signal intensity ratio (LSR), that is, the "DeltaLSR," and the increase rate of the liver-to-muscle signal intensity ratio (LMR), that is, the "DeltaLMR." DeltaLSR x LV and DeltaLMR x LV were also calculated. The correlation of each MR parameter with liver function data or liver pathology was assessed. The correlation coefficients were compared between DeltaLSR (DeltaLMR) and DeltaLSR (DeltaLMR) x LV. Results. The correlation coefficient between DeltaLSR (DeltaLMR) x LV and cholinesterase was significantly higher than that between DeltaLSR (DeltaLMR) and cholinesterase. The correlation coefficient between DeltaLSR (DeltaLMR) x LV and the degree of fibrosis or necroinflammatory activity was significantly lower than that between DeltaLSR (DeltaLMR) and the degree of fibrosis or necroinflammatory activity. Conclusion. The inclusion of liver volume may improve Gd-EOB-DTPA-based predictions of liver function, but not in predictions of liver pathology.
ESTHER : Shimamoto_2015_Biomed.Res.Int_2015_141853
PubMedSearch : Shimamoto_2015_Biomed.Res.Int_2015_141853
PubMedID: 26609519

Title : Draft genome sequence of marine-derived Streptomyces sp. TP-A0598, a producer of anti-MRSA antibiotic lydicamycins - Komaki_2015_Stand.Genomic.Sci_10_58
Author(s) : Komaki H , Ichikawa N , Hosoyama A , Fujita N , Igarashi Y
Ref : Stand Genomic Sci , 10 :58 , 2015
Abstract : Streptomyces sp. TP-A0598, isolated from seawater, produces lydicamycin, structurally unique type I polyketide bearing two nitrogen-containing five-membered rings, and four congeners TPU-0037-A, -B, -C, and -D. We herein report the 8 Mb draft genome sequence of this strain, together with classification and features of the organism and generation, annotation and analysis of the genome sequence. The genome encodes 7,240 putative ORFs, of which 4,450 ORFs were assigned with COG categories. Also, 66 tRNA genes and one rRNA operon were identified. The genome contains eight gene clusters involved in the production of polyketides and nonribosomal peptides. Among them, a PKS/NRPS gene cluster was assigned to be responsible for lydicamycin biosynthesis and a plausible biosynthetic pathway was proposed on the basis of gene function prediction. This genome sequence data will facilitate to probe the potential of secondary metabolism in marine-derived Streptomyces.
ESTHER : Komaki_2015_Stand.Genomic.Sci_10_58
PubMedSearch : Komaki_2015_Stand.Genomic.Sci_10_58
PubMedID: 26380643
Gene_locus related to this paper: 9actn-a0a0p4r772 , strpt-a0a1y2njq2 , 9actn-a0a0p4rci1

Title : Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses - Lertwattanasakul_2015_Biotechnol.Biofuels_8_47
Author(s) : Lertwattanasakul N , Kosaka T , Hosoyama A , Suzuki Y , Rodrussamee N , Matsutani M , Murata M , Fujimoto N , Suprayogi , Tsuchikane K , Limtong S , Fujita N , Yamada M
Ref : Biotechnol Biofuels , 8 :47 , 2015
Abstract : BACKGROUND: High-temperature fermentation technology with thermotolerant microbes has been expected to reduce the cost of bioconversion of cellulosic biomass to fuels or chemicals. Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. These capabilities have been found to exceed those of the traditional ethanol producer Saccharomyces cerevisiae or lignocellulose-bioconvertible ethanologenic Scheffersomyces stipitis. RESULTS: The complete genome sequence of K. marxianus DMKU 3-1042 as one of the most thermotolerant strains in the same species has been determined. A comparison of its genomic information with those of other yeasts and transcriptome analysis revealed that the yeast bears beneficial properties of temperature resistance, wide-range bioconversion ability, and production of recombinant proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature, and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30 degrees C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions. CONCLUSIONS: This study reveals many gene resources for the ability to assimilate various sugars in addition to species-specific genes in K. marxianus, and the molecular basis of its attractive traits for industrial applications including high-temperature fermentation. Especially, the thermotolerance trait may be achieved by an integrated mechanism consisting of various strategies. Gene resources and transcriptome data of the yeast are particularly useful for fundamental and applied researches for innovative applications.
ESTHER : Lertwattanasakul_2015_Biotechnol.Biofuels_8_47
PubMedSearch : Lertwattanasakul_2015_Biotechnol.Biofuels_8_47
PubMedID: 25834639
Gene_locus related to this paper: klumd-w0tha9

Title : Complete Genome Sequence of Polyvinyl Alcohol-Degrading Strain Sphingopyxis sp. 113P3 (NBRC 111507) - Ohtsubo_2015_Genome.Announc_3_e01169
Author(s) : Ohtsubo Y , Nagata Y , Numata M , Tsuchikane K , Hosoyama A , Yamazoe A , Tsuda M , Fujita N , Kawai F
Ref : Genome Announc , 3 :e01169 , 2015
Abstract : Strain 113P3 was isolated from activated sludge and identified as a polyvinyl alcohol (PVA)-degrading Pseudomonas species; it was later reidentified as Sphingopyxis species. Only three genes are directly relevant to the metabolism of PVA and comprise the pva operon, which was deposited as accession no. AB190228. Here, we report the complete genome sequence of strain 113P3, which has been conserved as a stock culture (NBRC 111507) at the Biological Resource Center, National Institute of Technology and Evaluation (NITE) (Tokyo, Japan). The genome of strain 113P3 is composed of a 4.4-Mb circular chromosome and a 243-kb plasmid. The whole finishing was conducted in silico except for four PCRs. The sequence corresponding to AB190288 exists on the chromosome.
ESTHER : Ohtsubo_2015_Genome.Announc_3_e01169
PubMedSearch : Ohtsubo_2015_Genome.Announc_3_e01169
PubMedID: 26472829
Gene_locus related to this paper: sphs1-a0a0m4cze0

Title : Complete Genome Sequence of the Thermophilic Polychlorinated Biphenyl Degrader Geobacillus sp. Strain JF8 (NBRC 109937) - Shintani_2014_Genome.Announc_2_e01213
Author(s) : Shintani M , Ohtsubo Y , Fukuda K , Hosoyama A , Ohji S , Yamazoe A , Fujita N , Nagata Y , Tsuda M , Hatta T , Kimbara K
Ref : Genome Announc , 2 : , 2014
Abstract : Geobacillus sp. strain JF8 (NBRC 109937) utilizes biphenyl and naphthalene as sole carbon sources and degrades polychlorinated biphenyl (PCB) at 60 degrees C. Here, we report the complete nucleotide sequence of the JF8 genome (a 3,446,630-bp chromosome and a 39,678-bp plasmid). JF8 has the smallest genome among the known PCB degraders.
ESTHER : Shintani_2014_Genome.Announc_2_e01213
PubMedSearch : Shintani_2014_Genome.Announc_2_e01213
PubMedID: 24459274
Gene_locus related to this paper: geotn-a4isp0 , 9baci-s5yvc0 , 9baci-s5yzj8

Title : Complete Genome Sequence of an Alkane Degrader, Alcanivorax sp. Strain NBRC 101098 - Miura_2014_Genome.Announc_2_e00766
Author(s) : Miura T , Tsuchikane K , Numata M , Hashimoto M , Hosoyama A , Ohji S , Yamazoe A , Fujita N
Ref : Genome Announc , 2 : , 2014
Abstract : Alcanivorax sp. strain NBRC 101098 was isolated from seawater in Japan. Strain NBRC 101098 is able to degrade various types of n-alkanes. Here, we report the complete genome of strain NBRC 101098.
ESTHER : Miura_2014_Genome.Announc_2_e00766
PubMedSearch : Miura_2014_Genome.Announc_2_e00766
PubMedID: 25125640
Gene_locus related to this paper: 9gamm-a0a068q136

Title : Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species - Komaki_2014_BMC.Genomics_15_323
Author(s) : Komaki H , Ichikawa N , Hosoyama A , Takahashi-Nakaguchi A , Matsuzawa T , Suzuki K , Fujita N , Gonoi T
Ref : BMC Genomics , 15 :323 , 2014
Abstract : BACKGROUND: Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primarily because of the clinical importance of the strains, some Nocardia genomes have been sequenced, and genome sequences have accumulated. Genome sizes of Nocardia strains are similar to those of Streptomyces strains, the producers of most antibiotics. In the present work, we compared secondary metabolite biosynthesis gene clusters of type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) among genomes of representative Nocardia species/strains based on domain organization and amino acid sequence homology.
RESULTS: Draft genome sequences of Nocardia asteroides NBRC 15531(T), Nocardia otitidiscaviarum IFM 11049, Nocardia brasiliensis NBRC 14402(T), and N. brasiliensis IFM 10847 were read and compared with published complete genome sequences of Nocardia farcinica IFM 10152, Nocardia cyriacigeorgica GUH-2, and N. brasiliensis HUJEG-1. Genome sizes are as follows: N. farcinica, 6.0 Mb; N. cyriacigeorgica, 6.2 Mb; N. asteroides, 7.0 Mb; N. otitidiscaviarum, 7.8 Mb; and N. brasiliensis, 8.9 - 9.4 Mb. Predicted numbers of PKS-I, NRPS, and PKS-I/NRPS hybrid clusters ranged between 4-11, 7-13, and 1-6, respectively, depending on strains, and tended to increase with increasing genome size. Domain and module structures of representative or unique clusters are discussed in the text. CONCLUSION: We conclude the following: 1) genomes of Nocardia strains carry as many PKS-I and NRPS gene clusters as those of Streptomyces strains, 2) the number of PKS-I and NRPS gene clusters in Nocardia strains varies substantially depending on species, and N. brasiliensis strains carry the largest numbers of clusters among the species studied, 3) the seven Nocardia strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied, and 4) different N. brasiliensis strains have some different gene clusters of PKS-I/NRPS, although the rest of the clusters are common within the N. brasiliensis strains. Genome sequencing suggested that Nocardia strains are highly promising resources in the search of novel secondary metabolites.
ESTHER : Komaki_2014_BMC.Genomics_15_323
PubMedSearch : Komaki_2014_BMC.Genomics_15_323
PubMedID: 24884595
Gene_locus related to this paper: 9noca-k0el65 , 9noca-k0eub3 , 9noca-k0ev09 , nocas-u5e4p8 , 9noca-a0a034uhh9 , 9noca-a0a034ud25 , 9noca-a0a034u924 , 9noca-a0a034uiv2 , 9noca-a0a034ufr8 , 9noca-a0a034ubl9 , 9noca-a0a034ulh7 , 9noca-a0a034unm1 , nocas-u5emb6 , nocas-u5eg51 , nocas-u5eht1

Title : Preoperative butyrylcholinesterase level as an independent predictor of overall survival in clear cell renal cell carcinoma patients treated with nephrectomy - Koie_2014_ScientificWorldJournal_2014_948305
Author(s) : Koie T , Ohyama C , Mikami J , Iwamura H , Fujita N , Sato T , Kojima Y , Fukushi K , Yamamoto H , Imai A , Hatakeyama S , Yoneyama T , Hashimoto Y , Kitayama M , Hirota K
Ref : ScientificWorldJournal , 2014 :948305 , 2014
Abstract : The prognostic factors for the overall survival (OS) of clear cell renal cell carcinoma (ccRCC) patients treated with nephrectomy are not well defined. In the present study, we investigated the prognostic significance of preoperative butyrylcholinesterase (BChE) levels in 400 ccRCC patients undergoing radical or partial nephrectomy from 1992 to 2013 at our institution. Univariate and multivariate analyses were performed to determine the clinical factors associated with OS. Among the enrolled patients, 302 were diagnosed with organ-confined disease only (T1-2N0M0), 16 with lymph node metastases, and 56 with distant metastases. The median preoperative BChE level was 250 U/L (normal range, 168-470 U/L), and median follow-up period was 36 months. The 3-year OS rate in patients with preoperative BChE levels of >/=100 U/L was significantly higher than in those with levels of <100 U/L (89.3% versus 77.7%, P = 0.004). On univariate analysis, performance status; anemia; hypoalbuminemia; preoperative levels of BChE, corrected calcium, and C-reactive protein; and distant metastasis status were significantly associated with OS. Multivariate analysis revealed that preoperative BChE levels and distant metastasis status were significantly associated with OS. Our findings suggest a possible role of preoperative BChE levels as an independent predictor of OS after nephrectomy in ccRCC patients.
ESTHER : Koie_2014_ScientificWorldJournal_2014_948305
PubMedSearch : Koie_2014_ScientificWorldJournal_2014_948305
PubMedID: 24741368

Title : The Complete Genome Sequence of Pseudomonas putida NBRC 14164T Confirms High Intraspecies Variation - Ohji_2014_Genome.Announc_2_e00029
Author(s) : Ohji S , Yamazoe A , Hosoyama A , Tsuchikane K , Ezaki T , Fujita N
Ref : Genome Announc , 2 : , 2014
Abstract : Pseudomonas putida has attracted much interest for its environmental, industrial, biotechnological, and clinical importance. Here, we report the complete genome sequence of the type strain P. putida NBRC 14164. This genome sequence will assist to further elucidate the molecular mechanisms of the characteristic traits among strains belonging to the species P. putida.
ESTHER : Ohji_2014_Genome.Announc_2_e00029
PubMedSearch : Ohji_2014_Genome.Announc_2_e00029
PubMedID: 24526630
Gene_locus related to this paper: psepu-PIP , psepu-PP3943 , psepu-PP4249 , psepu-q9wwz4

Title : Complete Genome Sequence of a Dimethyl Sulfide-Utilizing Bacterium, Acinetobacter guillouiae Strain 20B (NBRC 110550) - Yee_2014_Genome.Announc_2_e01048
Author(s) : Yee L , Hosoyama A , Ohji S , Tsuchikane K , Shimodaira J , Yamazoe A , Fujita N , Suzuki-Minakuchi C , Nojiri H
Ref : Genome Announc , 2 : , 2014
Abstract : Acinetobacter guillouiae strain 20B can utilize dimethyl sulfide (DMS) as the sole sulfur source and degrade chloroethylenes. We report here the complete 4,648,418-bp genome sequence for this strain, which contains 4,367 predicted coding sequences (CDSs), including a well-characterized DMS degradative operon.
ESTHER : Yee_2014_Genome.Announc_2_e01048
PubMedSearch : Yee_2014_Genome.Announc_2_e01048
PubMedID: 25323718
Gene_locus related to this paper: acigi-n8ybk0 , acigi-n8tiz0 , acigi-a0a077l572 , acigi-a0a077l147 , acigi-n8wvi6

Title : Complete Genome Sequence of Polychlorinated Biphenyl Degrader Comamonas testosteroni TK102 (NBRC 109938) - Fukuda_2014_Genome.Announc_2_e00865
Author(s) : Fukuda K , Hosoyama A , Tsuchikane K , Ohji S , Yamazoe A , Fujita N , Shintani M , Kimbara K
Ref : Genome Announc , 2 : , 2014
Abstract : Comamonas testosteroni TK102 (NBRC 109938; JCM 19603) can utilize biphenyl as a sole carbon source and degrade polychlorinated biphenyls (PCBs). The complete nucleotide sequence of the TK102 genome was determined. TK102 possesses several integrative and conjugative element-like regions, and one of them carries biphenyl-degradative genes.
ESTHER : Fukuda_2014_Genome.Announc_2_e00865
PubMedSearch : Fukuda_2014_Genome.Announc_2_e00865
PubMedID: 25212615
Gene_locus related to this paper: comte-a0h7e1 , comte-d8d186

Title : Draft Genome Sequences of Elizabethkingia meningoseptica - Matyi_2013_Genome.Announc_1_E00444
Author(s) : Matyi SA , Hoyt PR , Hosoyama A , Yamazoe A , Fujita N , Gustafson JE
Ref : Genome Announc , 1 : , 2013
Abstract : Elizabethkingia meningoseptica is ubiquitous in nature, exhibits a multiple-antibiotic resistance phenotype, and causes rare opportunistic infections. We now report two draft genome sequences of E. meningoseptica type strains that were sequenced independently in two laboratories.
ESTHER : Matyi_2013_Genome.Announc_1_E00444
PubMedSearch : Matyi_2013_Genome.Announc_1_E00444
PubMedID: 23846266
Gene_locus related to this paper: elime-r9cjk2 , elime-r9ck83

Title : Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand - Matsumoto_2013_Int.J.Syst.Evol.Microbiol_63_3404
Author(s) : Matsumoto A , Kasai H , Matsuo Y , Shizuri Y , Ichikawa N , Fujita N , Omura S , Takahashi Y
Ref : Int J Syst Evol Microbiol , 63 :3404 , 2013
Abstract : Bacterial strains YM16-303(T) and YM16-304(T) were isolated from a sample of seashore sand using a medium with an artificial seawater base. Both isolates grew slowly on marine agar, and were found to be Gram-reaction-positive, aerobic, non-motile and rod-shaped. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glycine, alanine and hydroxyglutamic acid, and the acyl type of the muramic acid was glycolyl. The predominant menaquinone was MK-9(H8). The 16S rRNA gene sequences of strains YM16-303(T) and YM16-304(T) were most similar to that of Ilumatobacter fluminis YM22-133(T), and phylogenetic analyses also indicated that they belong to the genus Ilumatobacter. Ilumatobacter fluminis YM22-133(T) and strains YM16-303(T) and YM16-304(T) should be classified as distinct species in the genus Ilumatobacter, however, since the 16S rRNA gene sequence similarity between them was low and the major cellular fatty acids and some physiological properties were different. Moreover, average nucleotide identity and maximal unique exact matches index values also supported the conclusion that they represent different species. On the basis of the above analyses, two novel species, Ilumatobacter nonamiense sp. nov. (type strain YM16-303(T) = NBRC 109120(T) = KCTC 29139(T)) and Ilumatobacter coccineum sp. nov. (type strain YM16-304(T) = NBRC 103263(T) = KCTC 29153(T)), are proposed. The order Acidimicrobiales, which contains the genus Ilumatobacter, currently includes six genera and only six species, and they are phylogenetically very far from each other. Phylogenetic analyses revealed that strains YM16-303(T) and YM16-304(T) clustered with closely related uncultured actinobacteria but not Ilumatobacter fluminis YM22-133(T), suggesting that many uncultured bacteria related to these isolates exist in the environment. This is the first report on interspecies relationships in the order Acidimicrobiales.
ESTHER : Matsumoto_2013_Int.J.Syst.Evol.Microbiol_63_3404
PubMedSearch : Matsumoto_2013_Int.J.Syst.Evol.Microbiol_63_3404
PubMedID: 23524358
Gene_locus related to this paper: 9actn-m5a1u1 , 9actn-m5ata2 , 9actn-m5a3u3 , 9actn-m5a4d8

Title : Complete Genome Sequence of the Carbazole Degrader Pseudomonas resinovorans Strain CA10 (NBRC 106553) - Shintani_2013_Genome.Announc_1_e00488
Author(s) : Shintani M , Hosoyama A , Ohji S , Tsuchikane K , Takarada H , Yamazoe A , Fujita N , Nojiri H
Ref : Genome Announc , 1 :e00488 , 2013
Abstract : Pseudomonas resinovorans strain CA10 can grow on carbazole as its sole carbon and nitrogen source. Here, we report the complete nucleotide sequence of the CA10 genome (a 6,285,863-bp chromosome and a 198,965-bp plasmid). CA10 carries a larger number of genes that are potentially responsible for aromatic hydrocarbon metabolism than do other previously sequenced Pseudomonas spp.
ESTHER : Shintani_2013_Genome.Announc_1_e00488
PubMedSearch : Shintani_2013_Genome.Announc_1_e00488
PubMedID: 23887915
Gene_locus related to this paper: psere-s6ale3 , psere-s6ans1 , psere-s6aji0 , psere-s6aev9 , psere-s6amt1 , psere-s6agn4

Title : Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls - Masai_2012_J.Bacteriol_194_534
Author(s) : Masai E , Kamimura N , Kasai D , Oguchi A , Ankai A , Fukui S , Takahashi M , Yashiro I , Sasaki H , Harada T , Nakamura S , Katano Y , Narita-Yamada S , Nakazawa H , Hara H , Katayama Y , Fukuda M , Yamazaki S , Fujita N
Ref : Journal of Bacteriology , 194 :534 , 2012
Abstract : Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls and monoaryls, and the catabolic genes for these compounds are useful for the production of industrially valuable metabolites from lignin. Here we report the complete nucleotide sequence of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and the 148,801-bp-long plasmid.
ESTHER : Masai_2012_J.Bacteriol_194_534
PubMedSearch : Masai_2012_J.Bacteriol_194_534
PubMedID: 22207743
Gene_locus related to this paper: 9sphn-g2itm4 , 9sphn-g2iml3 , sphsk-g2ijj5

Title : Complete genome sequence of phototrophic betaproteobacterium Rubrivivax gelatinosus IL144 - Nagashima_2012_J.Bacteriol_194_3541
Author(s) : Nagashima S , Kamimura A , Shimizu T , Nakamura-Isaki S , Aono E , Sakamoto K , Ichikawa N , Nakazawa H , Sekine M , Yamazaki S , Fujita N , Shimada K , Hanada S , Nagashima KV
Ref : Journal of Bacteriology , 194 :3541 , 2012
Abstract : Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in freshwater ponds, sewage ditches, activated sludge, and food processing wastewater. There have not been many studies on photosynthetic betaproteobacteria. Here we announce the complete genome sequence of the best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC 100245).
ESTHER : Nagashima_2012_J.Bacteriol_194_3541
PubMedSearch : Nagashima_2012_J.Bacteriol_194_3541
PubMedID: 22689232
Gene_locus related to this paper: rubgi-i0hxc6

Title : Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7 - Akao_2011_DNA.Res_18_423
Author(s) : Akao T , Yashiro I , Hosoyama A , Kitagaki H , Horikawa H , Watanabe D , Akada R , Ando Y , Harashima S , Inoue T , Inoue Y , Kajiwara S , Kitamoto K , Kitamoto N , Kobayashi O , Kuhara S , Masubuchi T , Mizoguchi H , Nakao Y , Nakazato A , Namise M , Oba T , Ogata T , Ohta A , Sato M , Shibasaki S , Takatsume Y , Tanimoto S , Tsuboi H , Nishimura A , Yoda K , Ishikawa T , Iwashita K , Fujita N , Shimoi H
Ref : DNA Research , 18 :423 , 2011
Abstract : The term 'sake yeast' is generally used to indicate the Saccharomyces cerevisiae strains that possess characteristics distinct from others including the laboratory strain S288C and are well suited for sake brewery. Here, we report the draft whole-genome shotgun sequence of a commonly used diploid sake yeast strain, Kyokai no. 7 (K7). The assembled sequence of K7 was nearly identical to that of the S288C, except for several subtelomeric polymorphisms and two large inversions in K7. A survey of heterozygous bases between the homologous chromosomes revealed the presence of mosaic-like uneven distribution of heterozygosity in K7. The distribution patterns appeared to have resulted from repeated losses of heterozygosity in the ancestral lineage of K7. Analysis of genes revealed the presence of both K7-acquired and K7-lost genes, in addition to numerous others with segmentations and terminal discrepancies in comparison with those of S288C. The distribution of Ty element also largely differed in the two strains. Interestingly, two regions in chromosomes I and VII of S288C have apparently been replaced by Ty elements in K7. Sequence comparisons suggest that these gene conversions were caused by cDNA-mediated recombination of Ty elements. The present study advances our understanding of the functional and evolutionary genomics of the sake yeast.
ESTHER : Akao_2011_DNA.Res_18_423
PubMedSearch : Akao_2011_DNA.Res_18_423
PubMedID: 21900213
Gene_locus related to this paper: yeast-YDR428C , yeast-hda1

Title : Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales - Sakai_2011_PLoS.One_6_e22898
Author(s) : Sakai S , Takaki Y , Shimamura S , Sekine M , Tajima T , Kosugi H , Ichikawa N , Tasumi E , Hiraki AT , Shimizu A , Kato Y , Nishiko R , Mori K , Fujita N , Imachi H , Takai K
Ref : PLoS ONE , 6 :e22898 , 2011
Abstract : We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50), which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50) CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50), further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.
ESTHER : Sakai_2011_PLoS.One_6_e22898
PubMedSearch : Sakai_2011_PLoS.One_6_e22898
PubMedID: 21829548

Title : Complete genome sequence of NBRC 3288, a unique cellulose-nonproducing strain of Gluconacetobacter xylinus isolated from vinegar - Ogino_2011_J.Bacteriol_193_6997
Author(s) : Ogino H , Azuma Y , Hosoyama A , Nakazawa H , Matsutani M , Hasegawa A , Otsuyama K , Matsushita K , Fujita N , Shirai M
Ref : Journal of Bacteriology , 193 :6997 , 2011
Abstract : Gluconacetobacter xylinus is involved in the industrial production of cellulose. We have determined the genome sequence of G. xylinus NBRC 3288, a cellulose-nonproducing strain. Comparative analysis of genomes of G. xylinus NBRC 3288 with those of the cellulose-producing strains clarified the genes important for cellulose production in Gluconacetobacter.
ESTHER : Ogino_2011_J.Bacteriol_193_6997
PubMedSearch : Ogino_2011_J.Bacteriol_193_6997
PubMedID: 22123756
Gene_locus related to this paper: kommn-g2i1m7

Title : Whole-genome analysis of Salmonella enterica serovar Typhimurium T000240 reveals the acquisition of a genomic island involved in multidrug resistance via IS1 derivatives on the chromosome - Izumiya_2011_Antimicrob.Agents.Chemother_55_623
Author(s) : Izumiya H , Sekizuka T , Nakaya H , Taguchi M , Oguchi A , Ichikawa N , Nishiko R , Yamazaki S , Fujita N , Watanabe H , Ohnishi M , Kuroda M
Ref : Antimicrobial Agents & Chemotherapy , 55 :623 , 2011
Abstract : Salmonella enterica serovar Typhimurium is frequently associated with life-threatening systemic infections, and the recent global emergence of multidrug resistance in S. enterica isolates from agricultural and clinical settings has raised concerns. In this study, we determined the whole-genome sequence of fluoroquinolone-resistant S. enterica serovar Typhimurium T000240 strain (DT12) isolated from human gastroenteritis in 2000. Comparative genome analysis revealed that T000240 displays high sequence similarity to strain LT2, which was originally isolated in 1940, indicating that progeny of LT2 might be reemerging. T000240 possesses a unique 82-kb genomic island, designated as GI-DT12, which is composed of multidrug resistance determinants, including a Tn2670-like composite transposon (class 1 integron [intI1, bla(oxa-30), aadA1, qacEDelta1, and sul1], mercury resistance proteins, and chloramphenicol acetyltransferase), a Tn10-like tetracycline resistance protein (tetA), the aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron transporter (sitABCD). Since GI-DT12 is flanked by IS1 derivatives, IS1-mediated recombination likely played a role in the acquisition of this genomic island through horizontal gene transfer. The aminoglycoside-(3)-N-acetyltransferase (aac(3)) gene and a class 1 integron harboring the dfrA1 gene cassette responsible for gentamicin and trimethoprim resistance, respectively, were identified on plasmid pSTMDT12_L and appeared to have been acquired through homologous recombination with IS26. This study represents the first characterization of the unique genomic island GI-DT12 that appears to be associated with possible IS1-mediated recombination in S. enterica serovar Typhimurium. It is expected that future whole-genome studies will aid in the characterization of the horizontal gene transfer events for the emerging S. enterica serovar Typhimurium strains.
ESTHER : Izumiya_2011_Antimicrob.Agents.Chemother_55_623
PubMedSearch : Izumiya_2011_Antimicrob.Agents.Chemother_55_623
PubMedID: 21098248
Gene_locus related to this paper: salty-ycfp

Title : Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1 - Takaki_2010_DNA.Res_17_123
Author(s) : Takaki Y , Shimamura S , Nakagawa S , Fukuhara Y , Horikawa H , Ankai A , Harada T , Hosoyama A , Oguchi A , Fukui S , Fujita N , Takami H , Takai K
Ref : DNA Research , 17 :123 , 2010
Abstract : The complete genome sequence of the thermophilic sulphur-reducing bacterium, Deferribacter desulfuricans SMM1, isolated from a hydrothermal vent chimney has been determined. The genome comprises a single circular chromosome of 2,234,389 bp and a megaplasmid of 308,544 bp. Many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within Deltaproteobacteria. The reconstructed central metabolisms showed a heterotrophic lifestyle primarily driven by C1 to C3 organics, e.g. formate, acetate, and pyruvate, and also suggested that the inability of autotrophy via a reductive tricarboxylic acid cycle may be due to the lack of ATP-dependent citrate lyase. In addition, the genome encodes numerous genes for chemoreceptors, chemotaxis-like systems, and signal transduction machineries. These signalling networks may be linked to this bacterium's versatile energy metabolisms and may provide ecophysiological advantages for D. desulfuricans SSM1 thriving in the physically and chemically fluctuating environments near hydrothermal vents. This is the first genome sequence from the phylum Deferribacteres.
ESTHER : Takaki_2010_DNA.Res_17_123
PubMedSearch : Takaki_2010_DNA.Res_17_123
PubMedID: 20189949
Gene_locus related to this paper: defds-d3pdu6 , defds-metxa

Title : Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae - Ichikawa_2010_DNA.Res_17_393
Author(s) : Ichikawa N , Oguchi A , Ikeda H , Ishikawa J , Kitani S , Watanabe Y , Nakamura S , Katano Y , Kishi E , Sasagawa M , Ankai A , Fukui S , Hashimoto Y , Kamata S , Otoguro M , Tanikawa S , Nihira T , Horinouchi S , Ohnishi Y , Hayakawa M , Kuzuyama T , Arisawa A , Nomoto F , Miura H , Takahashi Y , Fujita N
Ref : DNA Research , 17 :393 , 2010
Abstract : Kitasatospora setae NBRC 14216(T) (=KM-6054(T)) is known to produce setamycin (bafilomycin B1) possessing antitrichomonal activity. The genus Kitasatospora is morphologically similar to the genus Streptomyces, although they are distinguishable from each other on the basis of cell wall composition and the 16S rDNA sequence. We have determined the complete genome sequence of K. setae NBRC 14216(T) as the first Streptomycetaceae genome other than Streptomyces. The genome is a single linear chromosome of 8,783,278 bp with terminal inverted repeats of 127,148 bp, predicted to encode 7569 protein-coding genes, 9 rRNA operons, 1 tmRNA and 74 tRNA genes. Although these features resemble those of Streptomyces, genome-wide comparison of orthologous genes between K. setae and Streptomyces revealed smaller extent of synteny. Multilocus phylogenetic analysis based on amino acid sequences unequivocally placed K. setae outside the Streptomyces genus. Although many of the genes related to morphological differentiation identified in Streptomyces were highly conserved in K. setae, there were some differences such as the apparent absence of the AmfS (SapB) class of surfactant protein and differences in the copy number and variation of paralogous components involved in cell wall synthesis.
ESTHER : Ichikawa_2010_DNA.Res_17_393
PubMedSearch : Ichikawa_2010_DNA.Res_17_393
PubMedID: 21059706
Gene_locus related to this paper: kitsk-e4n1a1 , kitsk-e4n2t9 , kitsk-e4n4j8 , kitsk-e4n6l6 , kitsk-e4n9v4 , kitsk-e4n533 , kitsk-e4n648 , kitsk-e4na97 , kitsk-e4nas1 , kitsk-e4nas4 , kitsk-e4nf33 , kitsk-e4ngi3 , kitsk-e4nj77 , kitsk-e4ngr7 , kitsk-e4n1n8 , kitsk-e4n5j9 , kitsk-e4ndj5 , kitsk-e4ni45 , kitsk-e4nik2

Title : Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39 - Fujisawa_2010_DNA.Res_17_85
Author(s) : Fujisawa T , Narikawa R , Okamoto S , Ehira S , Yoshimura H , Suzuki I , Masuda T , Mochimaru M , Takaichi S , Awai K , Sekine M , Horikawa H , Yashiro I , Omata S , Takarada H , Katano Y , Kosugi H , Tanikawa S , Ohmori K , Sato N , Ikeuchi M , Fujita N , Ohmori M
Ref : DNA Research , 17 :85 , 2010
Abstract : A filamentous non-N(2)-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an important organism for industrial applications and as a food supply. Almost the complete genome of A. platensis NIES-39 was determined in this study. The genome structure of A. platensis is estimated to be a single, circular chromosome of 6.8 Mb, based on optical mapping. Annotation of this 6.7 Mb sequence yielded 6630 protein-coding genes as well as two sets of rRNA genes and 40 tRNA genes. Of the protein-coding genes, 78% are similar to those of other organisms; the remaining 22% are currently unknown. A total 612 kb of the genome comprise group II introns, insertion sequences and some repetitive elements. Group I introns are located in a protein-coding region. Abundant restriction-modification systems were determined. Unique features in the gene composition were noted, particularly in a large number of genes for adenylate cyclase and haemolysin-like Ca(2+)-binding proteins and in chemotaxis proteins. Filament-specific genes were highlighted by comparative genomic analysis.
ESTHER : Fujisawa_2010_DNA.Res_17_85
PubMedSearch : Fujisawa_2010_DNA.Res_17_85
PubMedID: 20203057
Gene_locus related to this paper: spima-b5w3f7 , spipl-d4zug2 , spipl-d4zvx0 , spipl-d4zwi8 , spipl-d4zxa2 , spipl-d5a1w9 , artpn-d4zwi5 , artma-b5w601 , artpn-d5a0k5

Title : Complete genome sequence of the representative gamma-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26 - Nagata_2010_J.Bacteriol_192_5852
Author(s) : Nagata Y , Ohtsubo Y , Endo R , Ichikawa N , Ankai A , Oguchi A , Fukui S , Fujita N , Tsuda M
Ref : Journal of Bacteriology , 192 :5852 , 2010
Abstract : Sphingobium japonicum strain UT26 utilizes gamma-hexachlorocyclohexane (gamma-HCH), a man-made chlorinated pesticide that causes serious environmental problems due to its toxicity and long persistence, as a sole source of carbon and energy. Here, we report the complete genome sequence of UT26, which consists of two chromosomes and three plasmids. The 15 lin genes involved in gamma-HCH degradation are dispersed on the two chromosomes and one of the three plasmids.
ESTHER : Nagata_2010_J.Bacteriol_192_5852
PubMedSearch : Nagata_2010_J.Bacteriol_192_5852
PubMedID: 20817768
Gene_locus related to this paper: psepa-q6vpf3 , sphju-d4z1p3 , sphju-d4z3u6 , sphpi-linb , sphju-d4yyy8

Title : Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria - Nakazawa_2009_Genome.Res_19_1801
Author(s) : Nakazawa H , Arakaki A , Narita-Yamada S , Yashiro I , Jinno K , Aoki N , Tsuruyama A , Okamura Y , Tanikawa S , Fujita N , Takeyama H , Matsunaga T
Ref : Genome Res , 19 :1801 , 2009
Abstract : Magnetotactic bacteria are ubiquitous microorganisms that synthesize intracellular magnetite particles (magnetosomes) by accumulating Fe ions from aquatic environments. Recent molecular studies, including comprehensive proteomic, transcriptomic, and genomic analyses, have considerably improved our hypotheses of the magnetosome-formation mechanism. However, most of these studies have been conducted using pure-cultured bacterial strains of alpha-proteobacteria. Here, we report the whole-genome sequence of Desulfovibrio magneticus strain RS-1, the only isolate of magnetotactic microorganisms classified under delta-proteobacteria. Comparative genomics of the RS-1 and four alpha-proteobacterial strains revealed the presence of three separate gene regions (nuo and mamAB-like gene clusters, and gene region of a cryptic plasmid) conserved in all magnetotactic bacteria. The nuo gene cluster, encoding NADH dehydrogenase (complex I), was also common to the genomes of three iron-reducing bacteria exhibiting uncontrolled extracellular and/or intracellular magnetite synthesis. A cryptic plasmid, pDMC1, encodes three homologous genes that exhibit high similarities with those of other magnetotactic bacterial strains. In addition, the mamAB-like gene cluster, encoding the key components for magnetosome formation such as iron transport and magnetosome alignment, was conserved only in the genomes of magnetotactic bacteria as a similar genomic island-like structure. Our findings suggest the presence of core genetic components for magnetosome biosynthesis; these genes may have been acquired into the magnetotactic bacterial genomes by multiple gene-transfer events during proteobacterial evolution.
ESTHER : Nakazawa_2009_Genome.Res_19_1801
PubMedSearch : Nakazawa_2009_Genome.Res_19_1801
PubMedID: 19675025
Gene_locus related to this paper: desmr-c4xjz8 , desmr-c4xl23 , desmr-c4xq70 , desmr-c4xqs3 , desmr-c4xr42 , desmr-c4xr97 , desmr-metxa

Title : Patients achieving clearance of HCV with interferon therapy recover from decreased retinol-binding protein 4 levels - Iwasa_2009_J.Viral.Hepat_16_716
Author(s) : Iwasa M , Hara N , Miyachi H , Tanaka H , Takeo M , Fujita N , Kobayashi Y , Kojima Y , Kaito M , Takei Y
Ref : J Viral Hepat , 16 :716 , 2009
Abstract : Retinol-binding protein 4 (RBP4) is a recently identified adipokine that is elevated in the blood in several insulin-resistant states. We investigated the association between plasma RBP4 and histological and biochemical characteristics of chronic hepatitis C (CHC), as well as changes in RBP4 levels following interferon therapy. Eighty-one patients with CHC infected with genotype 1 received treatment with peginterferon plus ribavirin. Histological data were available for 41 out of 81 patients before treatment, and the degree of fibrosis, inflammation and steatosis was assessed. Plasma levels of RBP4 were determined in serial samples (before, at the end of treatment, and at 6 months post-treatment). RBP4 levels were lower in CHC patients than in control subjects (34.6 +/- 12.3 microg/mL vs 46.2 +/- 10.5 microg/mL; P
ESTHER : Iwasa_2009_J.Viral.Hepat_16_716
PubMedSearch : Iwasa_2009_J.Viral.Hepat_16_716
PubMedID: 19302338

Title : Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus - Azuma_2009_Nucleic.Acids.Res_37_5768
Author(s) : Azuma Y , Hosoyama A , Matsutani M , Furuya N , Horikawa H , Harada T , Hirakawa H , Kuhara S , Matsushita K , Fujita N , Shirai M
Ref : Nucleic Acids Research , 37 :5768 , 2009
Abstract : Acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. To clarify the mutability, Acetobacter pasteurianus NBRC 3283, which forms a multi-phenotype cell complex, was subjected to genome DNA sequencing. The genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-Mb chromosome and six plasmids. There were three single nucleotide mutations and five transposon insertions in 32 isolates from the cell complex. The A. pasteurianus hyper-mutability was applied for breeding a temperature-resistant strain grown at an unviable high-temperature (42 degrees C). The genomic DNA sequence of a heritable mutant showing temperature resistance was analyzed by mutation mapping, illustrating that a 92-kb deletion and three single nucleotide mutations occurred in the genome during the adaptation. Alpha-proteobacteria including A. pasteurianus consists of many intracellular symbionts and parasites, and their genomes show increased evolution rates and intensive genome reduction. However, A. pasteurianus is assumed to be a free-living bacterium, it may have the potentiality to evolve to fit in natural niches of seasonal fruits and flowers with other organisms, such as yeasts and lactic acid bacteria.
ESTHER : Azuma_2009_Nucleic.Acids.Res_37_5768
PubMedSearch : Azuma_2009_Nucleic.Acids.Res_37_5768
PubMedID: 19638423
Gene_locus related to this paper: acepa-c7jn35 , acepa-c7k2x1 , acepa-c7kgx1 , acepa-c7kzj8 , acepa-este2 , acepa-h1uu55 , acepa-c7jpi3 , acep3-c7jf97

Title : Complete genome sequence of the soil actinomycete Kocuria rhizophila - Takarada_2008_J.Bacteriol_190_4139
Author(s) : Takarada H , Sekine M , Kosugi H , Matsuo Y , Fujisawa T , Omata S , Kishi E , Shimizu A , Tsukatani N , Tanikawa S , Fujita N , Harayama S
Ref : Journal of Bacteriology , 190 :4139 , 2008
Abstract : The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent bacterial group for which only a limited amount of genomic information is currently available. K. rhizophila is also important in industrial applications; e.g., it is commonly used as a standard quality control strain for antimicrobial susceptibility testing. Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC 103217) revealed a single circular chromosome (2,697,540 bp; G+C content of 71.16%) containing 2,357 predicted protein-coding genes. Most of the predicted proteins (87.7%) were orthologous to actinobacterial proteins, and the genome showed fairly good conservation of synteny with taxonomically related actinobacterial genomes. On the other hand, the genome seems to encode much smaller numbers of proteins necessary for secondary metabolism (one each of nonribosomal peptide synthetase and type III polyketide synthase), transcriptional regulation, and lateral gene transfer, reflecting the small genome size. The presence of probable metabolic pathways for the transformation of phenolic compounds generated from the decomposition of plant materials, and the presence of a large number of genes associated with membrane transport, particularly amino acid transporters and drug efflux pumps, may contribute to the organism's utilization of root exudates, as well as the tolerance to various organic compounds.
ESTHER : Takarada_2008_J.Bacteriol_190_4139
PubMedSearch : Takarada_2008_J.Bacteriol_190_4139
PubMedID: 18408034
Gene_locus related to this paper: kocrd-b2ggb9 , kocrd-b2gh24 , kocrd-b2ghy5 , kocrd-b2gi73 , kocrd-b2gih2 , kocrd-b2gix1 , kocrd-b2gjc9 , kocrd-b2gk02 , kocrd-b2gk84 , kocrd-b2gkb8 , kocrd-b2gl03

Title : Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4 - Sekine_2006_Environ.Microbiol_8_334
Author(s) : Sekine M , Tanikawa S , Omata S , Saito M , Fujisawa T , Tsukatani N , Tajima T , Sekigawa T , Kosugi H , Matsuo Y , Nishiko R , Imamura K , Ito M , Narita H , Tago S , Fujita N , Harayama S
Ref : Environ Microbiol , 8 :334 , 2006
Abstract : Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The strain harbours one linear plasmid, pREL1 (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637 bp), all with some sequence similarities to other Rhodococcus plasmids. For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames, respectively, were predicted. Linear plasmid pREL1 has several regions homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis of pREL1 and pBD2 identified common metal-resistance genes on both, but pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme constituents some of which are quite different from those of other organisms. The alkane hydroxylase consisted of a cytochrome P450 monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin reductase) sequence. A zinc-containing alcohol dehydrogenase further oxydizes alkanols, alkane oxidation products catalysed by alkane hydroxylase. Of the circular plasmids, the pREC1 sequence is partially similar to the sequence of pREAT701, the virulence plasmid found in Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes for beta-oxidation of fatty acids. Thus, joint actions of enzymes encoded by pREL1 and pREC1 may enable efficient mineralization of alkanes.
ESTHER : Sekine_2006_Environ.Microbiol_8_334
PubMedSearch : Sekine_2006_Environ.Microbiol_8_334
PubMedID: 16423019
Gene_locus related to this paper: rhosp-AHY95170 , rhoe4-c0zm41 , rhoe4-c0zny8 , rhoe4-c0zp51 , rhoe4-c0zp80 , rhoe4-c0zpm5 , rhoe4-c0zq56 , rhoe4-c0zq93 , rhoe4-c0zri5 , rhoe4-c0zse4 , rhoe4-c0ztk5 , rhoe4-c0ztv6 , rhoe4-c0ztz5 , rhoe4-c0zw14 , rhoe4-c0zyp1 , rhoe4-c1a1s7 , rhoe4-c1a149 , rhoe4-c1a168 , rhoe4-q3l9i4 , rhoe4-q3l9v3 , rhoe4-q3l9y4 , rhoe4-q3l922 , rhoe4-q3la05 , rhoer-c3jd87 , rhoer-c3jdh1 , rhoer-c3jfg3 , rhoer-c3jfu1 , rhoer-c3jfv6 , rhoer-c3jfw7 , rhoer-c3jg26 , rhoer-c3jgc0 , rhoer-c3jgr8 , rhoer-c3ji24 , rhoer-c3jif3 , rhoer-c3jif5 , rhoer-c3jif6 , rhoer-c3jiw5 , rhoer-c3jl72 , rhoer-c3jle6 , rhoer-c3jmu4 , rhoer-c3jqd8 , rhoer-c3jqd9 , rhoer-c3jqg3 , rhoer-c3jqn9 , rhoer-c3jqs1 , rhoer-c3jr01 , rhoer-c3jrb8 , rhoer-c3jt01 , rhoer-c3jtx3 , rhoer-c3jtx4 , rhoer-c3jvx6 , rhoer-c3jwe1 , rhoer-c3jwn8 , rhosp-bphD2 , rhoe4-c0zua7

Title : Efficacy of long-term dietary restriction of total calories, fat, iron, and protein in patients with chronic hepatitis C virus - Iwasa_2004_Nutrition_20_368
Author(s) : Iwasa M , Iwata K , Kaito M , Ikoma J , Yamamoto M , Takeo M , Kuroda M , Fujita N , Kobayashi Y , Adachi Y
Ref : Nutrition , 20 :368 , 2004
Abstract : OBJECTIVES: A diet restrictive in total calories, fat, iron, and protein intake reduces serum alanine aminotransferase levels in patients with long-term hepatitis C virus infection. However, whether long-term dietary therapy causes adverse effects such as malnutrition and anemia due to a shortage of energy intake is not clear. We evaluated the balance of energy intake and changes in physical and hematologic indices of nutrition after a long-term dietary therapy.
METHODS: Twenty-two patients with long-term hepatitis C virus infection that did not respond to or who were able or unwilling to take interferon therapy were enrolled in this study. Our prescriptions included 7 mg/d or less of iron, 30 kcal. kg(-1). d(-1) of energy, 1.1 to 1.2 g. kg(-1). d(-1) of protein, and a fat energy fraction of 20%. Patients were followed for 24 mo.
RESULTS: Mean body fat percentage was 24.6% at entry and was significantly reduced after the diet prescription. Mean serum ferritin decreased significantly from 376 ng/mL at entry to 141 ng/mL after 24 mo. Mean serum alanine aminotransferase levels decreased significantly from 66 to 49 IU/L. Mean levels of hemoglobin, serum albumin, and cholinesterase did not change significantly during the follow-up period.
CONCLUSIONS: These results suggest that restriction of energy, fat, iron, and protein intakes is safely tolerated, so its long-term use should be recommended to patients with long-term infection with hepatitis C virus.
ESTHER : Iwasa_2004_Nutrition_20_368
PubMedSearch : Iwasa_2004_Nutrition_20_368
PubMedID: 15043853

Title : [A case of acute distigmine bromide intoxication in the therapeutic dosage for treatment of underactive neurogenic bladder] - Tada_2004_No.To.Shinkei_56_415
Author(s) : Tada M , Fujita N , Umeda M , Koike H , Nagai H
Ref : No To Shinkei , 56 :415 , 2004
Abstract : Distigmine bromide (Ubretid) is a long-acting anti-cholinesterase, widely used for the treatment of underactive neurogenic bladder and myasthenia gravis. Our study concerns a 73-year-old man treated with a potentially life-threatening cholinergic state due to distigmine bromide. He had been administered distigmine bromide orally for over two years at a daily dosage of 10 mg as a treatment for underactive neurogenic bladder. He suddenly developed diarrhea and consciousness disturbance during treatment of his urinary tract infection. Bradycardia and miosis were noted. Blood examination revealed extremely low levels of the plasma cholinesterase activity. The condition was diagnosed as distigmine bromide intoxication. All cholinergic symptoms disappeared in several days after the administration of distigmine bromide was terminated. Cholinergic crisis due to overdosage with anticholinesterases is well known, and the myasthenic patients are usually supervised in the early stages of dosage regulation to guard against the possibility of cholinergic crisis. However the use of oral distigmine bromide, even in therapeutic doses for urinary retention, could result in cholinergic crisis. We therefore conclude that extreme caution must be used in administering distigmine bromide.
ESTHER : Tada_2004_No.To.Shinkei_56_415
PubMedSearch : Tada_2004_No.To.Shinkei_56_415
PubMedID: 15279199

Title : Identification of the cpdA gene encoding cyclic 3',5'-adenosine monophosphate phosphodiesterase in Escherichia coli - Imamura_1996_J.Biol.Chem_271_25423
Author(s) : Imamura R , Yamanaka K , Ogura T , Hiraga S , Fujita N , Ishihama A , Niki H
Ref : Journal of Biological Chemistry , 271 :25423 , 1996
Abstract : We have identified a gene, cpdA, located at 66.2 min of the chromosome of Escherichia coli that encodes cyclic 3',5'-adenosine monophosphate phosphodiesterase (cAMP phosphodiesterase, EC). The expression of beta-galactosidase, which is a product of the lacZ gene, was repressed in cells that harbored multiple copies of the plasmid carrying the cpdA gene. Northern blotting showed that the transcription of the lacZ gene was inhibited in these cells. Multiple copies of the cpdA gene decreased the intracellular concentration of cAMP, which is a positive regulator for transcription of the lacZ gene. We found that the purified CpdA protein repressed in vitro transcription from the lacP1 promoter by decreasing cAMP. In addition, we showed that the CpdA protein hydrolyzed cAMP to 5'-adenosine monophosphate and that its activity was activated by iron. Our results suggested that regulation of intracellular concentration of cAMP is dependent not only on synthesis of cAMP but also on hydrolysis of cAMP by cAMP phosphodiesterase.
ESTHER : Imamura_1996_J.Biol.Chem_271_25423
PubMedSearch : Imamura_1996_J.Biol.Chem_271_25423
PubMedID: 8810311
Gene_locus related to this paper: ecoli-yqia

Title : Expression of the four subunits of the Torpedo californica nicotinic acetylcholine receptor in Saccharomyces cerevisiae - Jansen_1989_J.Biol.Chem_264_15022
Author(s) : Jansen KU , Conroy WG , Claudio T , Fox TD , Fujita N , Hamill O , Lindstrom JM , Luther M , Nelson N , Ryan KA , Sweet MT , Hess GP
Ref : Journal of Biological Chemistry , 264 :15022 , 1989
Abstract : Yeast expression vectors were constructed containing complementary DNA encoding the alpha-, beta-, gamma-, and delta-subunits of the Torpedo californica nicotinic acetylcholine receptor under the control of the Saccharomyces cerevisiae alcohol dehydrogenase promoter. All four plasmids were integrated into the yeast genome of a single yeast cell. The resulting yeast strain synthesized polypeptides novel to yeast that had the molecular weights and antigenic properties similar to the authentic T. californica receptor alpha-, gamma, and delta-subunits. The beta-subunit polypeptide could not be detected in this yeast strain, even though the poly(A)+ RNA from this strain contained all the information necessary for the expression of functional acetylcholine receptors in Xenopus laevis oocytes. The replacement of the beta-subunit mRNA 5'-untranslated leader and its N-terminal signal sequence by the corresponding alpha-subunit sequences, however, resulted in the expression of the beta-subunit polypeptide in yeast grown at 5 degrees C.
ESTHER : Jansen_1989_J.Biol.Chem_264_15022
PubMedSearch : Jansen_1989_J.Biol.Chem_264_15022
PubMedID: 2670931

Title : Biosynthesis of the Torpedo californica acetylcholine receptor alpha subunit in yeast - Fujita_1986_Science_231_1284
Author(s) : Fujita N , Nelson N , Fox TD , Claudio T , Lindstrom JM , Riezman H , Hess GP
Ref : Science , 231 :1284 , 1986
Abstract : Yeast cells were transformed with a plasmid containing complementary DNA encoding the alpha subunit of the Torpedo californica acetylcholine receptor. These cells synthesized a protein that had the expected molecular weight, antigenic specificity, and ligand-binding properties of the alpha subunit. The subunit was inserted into the yeast plasma membrane, demonstrating that yeast has the apparatus to express a membrane-bound receptor protein and to insert such a foreign protein into its plasma membrane. The alpha subunit constituted approximately 1 percent of the total yeast membrane. The alpha subunit constituted approximately 1 percent of the total yeast membrane proteins, and its density was about the same in the plasma membrane of yeast and in the receptor-rich electric organ of Electrophorus electricus. In view of the available technology for obtaining large quantities of yeast proteins, it may now be possible to obtain amplified amounts of interesting membrane-bound proteins for physical and biochemical studies.
ESTHER : Fujita_1986_Science_231_1284
PubMedSearch : Fujita_1986_Science_231_1284
PubMedID: 3511531

Title : Expression of cDNAs for acetylcholine receptor subunits in the yeast cell plasma membrane - Fujita_1986_Biochem.Soc.Symp_52_41
Author(s) : Fujita N , Sweet MT , Fox TD , Nelson N , Claudio T , Lindstrom JM , Hess GP
Ref : Biochemical Society Symposium , 52 :41 , 1986
Abstract : Yeast cells transformed with a plasmid containing cDNA encoding the alpha or delta subunit of the Torpedo californica acetylcholine receptor synthesize a protein. The expected molecular mass, antigenic specificity, and ligand-binding properties (in the case of the alpha subunit) of the subunits in yeast are similar to those of the subunits in T. californica membranes. The subunits are inserted into the yeast plasma membrane, demonstrating for the first time that yeast has the apparatus to express and insert foreign proteins into its plasma membrane. The alpha subunit constitutes approximately 1% of the yeast membrane proteins, and its density is about the same in the plasma membrane of yeast as in the receptor-rich electric organ of Electrophorus electricus. In view of the widely available technology for obtaining large quantities of yeast proteins, yeast cells may prove ideal for amplifying the amounts of interesting membrane-bound proteins available so that physical and biochemical studies can be made easily.
ESTHER : Fujita_1986_Biochem.Soc.Symp_52_41
PubMedSearch : Fujita_1986_Biochem.Soc.Symp_52_41
PubMedID: 3579969

Title : Acetylcholine receptor: characterization of the voltage-dependent regulatory (inhibitory) site for acetylcholine in membrane vesicles from Torpedo californica electroplax - Takeyasu_1986_Biochemistry_25_1770
Author(s) : Takeyasu K , Shiono S , Udgaonkar JB , Fujita N , Hess GP
Ref : Biochemistry , 25 :1770 , 1986
Abstract : Evidence for a voltage-dependent regulatory (inhibitory) site on the nicotinic acetylcholine receptor to which acetylcholine binds was obtained in membrane vesicles prepared from the Torpedo californica electric organ. Two rate coefficients, JA and alpha, which pertain to the receptor-controlled ion flux, were measured. A 1000-fold concentration range of acetylcholine was used in a transmembrane voltage (Vm) range from 0 to -48 mV under a voltage-clamped condition at pH 7.4, 1 degrees C. The following observations were made. (i) At low acetylcholine concentrations, the value of JA, the rate coefficient for ion translocation by the active (nondesensitized) state of the receptor, increased with increasing concentration. (ii) JA decreased at high acetylcholine concentrations. (iii) In contrast, alpha, the rate coefficient for receptor desensitization, did not show such a decrease. (iv) When the transmembrane potential of the vesicle membrane was changed to more negative values, the value of KR (the dissociation constant for binding of acetylcholine to the regulatory site) decreased by a factor of approximately 9 for a 25 mV change in Vm, while KI (the dissociation constant for binding of acetylcholine to the receptor site that controls channel opening) did not show such a change and has a value of 80 microM. When Vm is -48 mV, KR has a value of 8 microM. (v) The effect of a transmembrane voltage on the regulatory site was reversible and occurred within the time resolution (5 ms) of the quench-flow technique used in the measurements.
ESTHER : Takeyasu_1986_Biochemistry_25_1770
PubMedSearch : Takeyasu_1986_Biochemistry_25_1770
PubMedID: 3707909

Title : Regulatory properties of acetylcholine receptor: evidence for two different inhibitory sites, one for acetylcholine and the other for a noncompetitive inhibitor of receptor function (procaine) - Shiono_1984_Biochemistry_23_6889
Author(s) : Shiono S , Takeyasu K , Udgaonkar JB , Delcour AH , Fujita N , Hess GP
Ref : Biochemistry , 23 :6889 , 1984
Abstract : Does the acetylcholine receptor have a specific regulatory (inhibitory) site for the natural receptor ligand acetylcholine? This paper deals with this question. The inhibition of acetylcholine-receptor function by diverse organic cations including local anesthetics such as procaine has been well documented. Evidence indicates that these compounds are noncompetitive inhibitors, enter the open-channel form of the receptor, and block it and that the extent of this blockage depends on the transmembrane voltage of the cell. Recently we reported that in the electroplax of Electrophorus electricus the receptor-controlled transmembrane ion flux is inhibited by acetylcholine in a voltage-dependent, noncompetitive manner. We report here that the Torpedo californica receptor also has an inhibitory site for acetylcholine. The question of whether acetylcholine, which is an organic cation, binds to the same site as other organic cations such as the noncompetitive inhibitor procaine is important and is addressed. The results reported here of chemical kinetic investigations, with receptor-rich E. electricus and T. californica membrane vesicles, indicate that the inhibition of receptor function by acetylcholine and by a local anesthetic, procaine, involves two different receptor sites. The existence of a specific inhibitory site for the natural receptor-ligand acetylcholine suggests that this site can play an important role in the modulation of receptor function and in the regulation of transmission of signals between cells.
ESTHER : Shiono_1984_Biochemistry_23_6889
PubMedSearch : Shiono_1984_Biochemistry_23_6889
PubMedID: 6529587