Watanabe A

References (30)

Title : Renoprotective effects of a dipeptidyl peptidase 4 inhibitor in a mouse model of progressive renal fibrosis - Uchida_2017_Ren.Fail_39_340
Author(s) : Uchida T , Oda T , Matsubara H , Watanabe A , Takechi H , Oshima N , Sakurai Y , Kumagai H
Ref : Ren Fail , 39 :340 , 2017
Abstract : Although the effects of dipeptidyl peptidase 4 (DPP-4) inhibitors beyond their hypoglycemic action have been reported, whether these inhibitors have renoprotective effects in nondiabetic chronic kidney disease (CKD) is unclear. We examined the therapeutic effects of DPP-4 inhibition in mice with unilateral ureteral obstruction (UUO), a nondiabetic model of progressive renal fibrosis. After UUO surgery, mice were administered either the DPP-4 inhibitor alogliptin or a vehicle by oral gavage once a day for 10 days. Physiological parameters, degrees of renal fibrosis and inflammation, and molecules related to renal fibrosis and inflammation were then evaluated using sham-operated mice as controls. Positive area of alpha-smooth muscle actin was significantly smaller and expression of transforming growth factor beta messenger RNA was significantly lower in the alogliptin-treated group than in the vehicle-treated group. Renal total collagen content was also significantly lower in the alogliptin-treated group than in the vehicle-treated group. These results suggest that alogliptin exerted renoprotective antifibrotic effects. The positive area of F4/80 was significantly smaller and expression of CD68 messenger RNA was significantly lower in the alogliptin-treated group than in the vehicle-treated group, suggesting an anti-inflammatory action by the DPP-4 inhibitor. Compared to the results for the vehicle-treated group, expression of markers for M1 macrophages tended to be lower in the alogliptin-treated group, and the relative expression of M2 macrophages tended to be higher. These data indicate the various protective effects of DPP-4 inhibition in nondiabetic mice with UUO. DPP-4 inhibitors may therefore be promising therapeutic choices even for nondiabetic CKD patients.
ESTHER : Uchida_2017_Ren.Fail_39_340
PubMedSearch : Uchida_2017_Ren.Fail_39_340
PubMedID: 28118775

Title : Discovery of 1-oxa-4,9-diazaspiro[5.5]undecane-based trisubstituted urea derivatives as highly potent soluble epoxide hydrolase inhibitors and orally active drug candidates for treating of chronic kidney diseases - Kato_2014_Bioorg.Med.Chem.Lett_24_565
Author(s) : Kato Y , Fuchi N , Nishimura Y , Watanabe A , Yagi M , Nakadera Y , Higashi E , Yamada M , Aoki T , Kigoshi H
Ref : Bioorganic & Medicinal Chemistry Lett , 24 :565 , 2014
Abstract : We identified 1-oxa-4,9-diazaspiro[5.5]undecane-based trisubstituted ureas as highly potent soluble epoxide hydrolase (sEH) inhibitors and orally active agents for treating chronic kidney diseases. Compound 19 exhibited excellent sEH inhibitory activity and bioavailability. When administered orally at 30 mg/kg, 19 lowered serum creatinine in a rat model of anti-glomerular basement membrane glomerulonephritis but 2,8-diazaspiro[4.5]decane-based trisubstituted ureas did not. These results suggest that 19 is an orally active drug candidate for treating chronic kidney diseases.
ESTHER : Kato_2014_Bioorg.Med.Chem.Lett_24_565
PubMedSearch : Kato_2014_Bioorg.Med.Chem.Lett_24_565
PubMedID: 24373724

Title : Discovery of 2,8-diazaspiro[4.5]decane-based trisubstituted urea derivatives as highly potent soluble epoxide hydrolase inhibitors and orally active drug candidates for treating hypertension - Kato_2013_Bioorg.Med.Chem.Lett_23_5975
Author(s) : Kato Y , Fuchi N , Saburi H , Nishimura Y , Watanabe A , Yagi M , Nakadera Y , Higashi E , Yamada M , Aoki T
Ref : Bioorganic & Medicinal Chemistry Lett , 23 :5975 , 2013
Abstract : We identified 2,8-diazaspiro[4.5]decane-based trisubstituted urea derivatives as highly potent soluble epoxide hydrolase (sEH) inhibitors and orally active agents for treating hypertension. Docking studies using human and murine sEH X-ray crystal structures revealed steric hindrance around the side chain of Phe406 of murine sEH. The trifluoromethyl moiety (11) was replaced with a trifluoromethoxy moiety (12) to prevent steric clash, and improved murine sEH inhibitory activity was observed. The oral administration of 12, 20, and 37 at a dose of 30mg/kg reduced blood pressure in spontaneously hypertensive rat, but had little effect on blood pressure in normotensive rat.
ESTHER : Kato_2013_Bioorg.Med.Chem.Lett_23_5975
PubMedSearch : Kato_2013_Bioorg.Med.Chem.Lett_23_5975
PubMedID: 24035338

Title : Species differences in tissue distribution and enzyme activities of arylacetamide deacetylase in human, rat, and mouse - Kobayashi_2012_Drug.Metab.Dispos_40_671
Author(s) : Kobayashi Y , Fukami T , Nakajima A , Watanabe A , Nakajima M , Yokoi T
Ref : Drug Metabolism & Disposition: The Biological Fate of Chemicals , 40 :671 , 2012
Abstract : Human arylacetamide deacetylase (AADAC) is a major esterase responsible for the hydrolysis of clinical drugs such as flutamide, phenacetin, and rifampicin. Thus, AADAC is considered to be a relevant enzyme in preclinical drug development, but there is little information about species differences with AADAC. This study investigated the species differences in the tissue distribution and enzyme activities of AADAC. In human, AADAC mRNA was highly expressed in liver and the gastrointestinal tract, followed by bladder. In rat and mouse, AADAC mRNA was expressed in liver at the highest level, followed by the gastrointestinal tract and kidney. The expression levels in rat tissues were approximately 7- and 10-fold lower than those in human and mouse tissues, respectively. To compare the catalytic efficiency of AADAC among three species, each recombinant AADAC was constructed, and enzyme activities were evaluated by normalizing with the expression levels of AADAC. Flutamide and phenacetin hydrolase activities were detected by the recombinant AADAC of all species. In flutamide hydrolysis, liver microsomes of all species showed similar catalytic efficiencies, despite the lower AADAC mRNA expression in rat liver. In phenacetin hydrolysis, rat liver microsomes showed approximately 4- to 6.5-fold lower activity than human and mouse liver microsomes. High rifampicin hydrolase activity was detected only by recombinant human AADAC and human liver and jejunum microsomes. Taken together, the results of this study clarified the species differences in the tissue distribution and enzyme activities of AADAC and facilitate our understanding of species differences in drug hydrolysis.
ESTHER : Kobayashi_2012_Drug.Metab.Dispos_40_671
PubMedSearch : Kobayashi_2012_Drug.Metab.Dispos_40_671
PubMedID: 22207054
Gene_locus related to this paper: human-AADAC , mouse-aryla , ratno-aryla

Title : Functional analysis of FarA transcription factor in the regulation of the genes encoding lipolytic enzymes and hydrophobic surface binding protein for the degradation of biodegradable plastics in Aspergillus oryzae - Garrido_2012_J.Biosci.Bioeng_113_549
Author(s) : Garrido SM , Kitamoto N , Watanabe A , Shintani T , Gomi K
Ref : J Biosci Bioeng , 113 :549 , 2012
Abstract : FarA is a Zn(II)(2)Cys(6) transcription factor which upregulates genes required for growth on fatty acids in filamentous fungi like Aspergillus nidulans. FarA is also highly similar to the cutinase transcription factor CTF1 alpha of Fusarium solani which binds to the cutinase gene promoter in this plant pathogen. This study determines whether FarA transcriptional factor also works in the regulation of genes responsible for the production of cutinase for the degradation of a biodegradable plastic, poly-(butylene succinate-co-adipate) (PBSA), in Aspergillus oryzae. The wild-type and the farA gene disruption strains were grown in minimal agar medium with emulsified PBSA, and the wild-type showed clear zone around the colonies while the disruptants did not. Western blot analysis revealed that the cutinase protein CutL1 and a hydrophobic surface binding protein such as HsbA were produced by the wild-type but not by the disruptants. In addition, the expressions of cutL1, triacylglycerol lipase (tglA), and mono- and di-acylglycerol lipase (mdlB) genes as well as the hsbA gene were significantly lower in the disruptants compared to the wild-type. These results indicated that the FarA transcriptional factor would be implicated in the expression of cutL1 and hsbA genes that are required for the degradation of PBSA as well as lipolytic genes such as mdlB and tglA for lipid hydrolysis.
ESTHER : Garrido_2012_J.Biosci.Bioeng_113_549
PubMedSearch : Garrido_2012_J.Biosci.Bioeng_113_549
PubMedID: 22280964

Title : Human arylacetamide deacetylase is responsible for deacetylation of rifamycins: rifampicin, rifabutin, and rifapentine - Nakajima_2011_Biochem.Pharmacol_82_1747
Author(s) : Nakajima A , Fukami T , Kobayashi Y , Watanabe A , Nakajima M , Yokoi T
Ref : Biochemical Pharmacology , 82 :1747 , 2011
Abstract : Rifamycins such as rifampicin, rifabutin, and rifapentine are used for the treatment of tuberculosis and induce various drug-metabolizing enzymes. Rifamycins have been reported to be mainly deacetylated by esterase(s) expressed in human liver microsomes (HLM) to 25-deacetylrifamycins, but the responsible enzyme remained to be determined. In this study, we found that recombinant human arylacetamide deacetylase (AADAC) could efficiently deacetylate rifamycins, whereas human carboxylesterases, which are enzymes responsible for the hydrolysis of many prodrugs, showed no activity. The involvement of AADAC in the deacetylation of rifamycins in HLM was verified by the similarities of the K(m) and K(i) values and the inhibitory characteristics between recombinant AADAC and HLM. Rifamycins exhibited potent cytotoxicity to HepG2 cells, but their 25-deacetylated metabolites did not. Luciferase assay using a reporter plasmid containing CYP3A4 direct repeat 3 and everted repeat 6 motifs revealed that 25-deacetylrifamycins have lesser potency to transactivate CYP3A4 compared with the parent drugs. Supporting these results, HepG2 cells infected with a recombinant adenovirus expressing human AADAC showed low cytotoxicity and induction potency of CYP3A4 by rifamycins. In addition, CYP3A4 induction in human hepatocytes by rifamycins was increased by transfecting siRNA for human AADAC. Thus, we found that human AADAC was the enzyme responsible for the deacetylation of rifamycins and would affect the induction rate of drug-metabolizing enzymes by rifamycins and their induced hepatotoxicity.
ESTHER : Nakajima_2011_Biochem.Pharmacol_82_1747
PubMedSearch : Nakajima_2011_Biochem.Pharmacol_82_1747
PubMedID: 21856291
Gene_locus related to this paper: human-AADAC

Title : Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T - Kaneko_2011_Genes.(Basel)_2_763
Author(s) : Kaneko T , Maita H , Hirakawa H , Uchiike N , Minamisawa K , Watanabe A , Sato S
Ref : Genes (Basel) , 2 :763 , 2011
Abstract : The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.
ESTHER : Kaneko_2011_Genes.(Basel)_2_763
PubMedSearch : Kaneko_2011_Genes.(Basel)_2_763
PubMedID: 24710291
Gene_locus related to this paper: braja-pcaD , brajp-g7d382 , brajp-g7daf5 , brajp-g7daf6 , brajp-g7dfn9 , brajp-g7dbr2 , brajp-g7dmu1 , brajp-g7dnh7

Title : Arylacetamide deacetylase is a determinant enzyme for the difference in hydrolase activities of phenacetin and acetaminophen - Watanabe_2010_Drug.Metab.Dispos_38_1532
Author(s) : Watanabe A , Fukami T , Takahashi S , Kobayashi Y , Nakagawa N , Nakajima M , Yokoi T
Ref : Drug Metabolism & Disposition: The Biological Fate of Chemicals , 38 :1532 , 2010
Abstract : Phenacetin was withdrawn from the market because it caused renal failure in some patients. Many reports indicated that the nephrotoxicity of phenacetin is associated with the hydrolyzed metabolite, p-phenetidine. Acetaminophen (APAP), the major metabolite of phenacetin, is also hydrolyzed to p-aminophenol, which is a nephrotoxicant. However, APAP is safely prescribed if used in normal therapeutic doses. This background prompted us to investigate the difference between phenacetin and APAP hydrolase activities in human liver. In this study, we found that phenacetin is efficiently hydrolyzed in human liver microsomes (HLM) [CL(int) 1.08 +/- 0.02 microl/(min . mg)], whereas APAP is hardly hydrolyzed [0.02 +/- 0.00 microl/(min . mg)]. To identify the esterase involved in their hydrolysis, the activities were measured using recombinant human carboxylesterase (CES) 1A1, CES2, and arylacetamide deacetylase (AADAC). Among these, AADAC showed a K(m) value (1.82 +/- 0.02 mM) similar to that of HLM (3.30 +/- 0.16 mM) and the highest activity [V(max) 6.03 +/- 0.14 nmol/(min . mg)]. In contrast, APAP was poorly hydrolyzed by the three esterases. The large contribution of AADAC to phenacetin hydrolysis was demonstrated by the prediction with a relative activity factor. In addition, the phenacetin hydrolase activity by AADAC was activated by flutamide (5-fold) as well as that in HLM (4-fold), and the activity in HLM was potently inhibited by eserine, a strong inhibitor of AADAC. In conclusion, we found that AADAC is the principal enzyme responsible for the phenacetin hydrolysis, and the difference of hydrolase activity between phenacetin and APAP is largely due to the substrate specificity of AADAC.
ESTHER : Watanabe_2010_Drug.Metab.Dispos_38_1532
PubMedSearch : Watanabe_2010_Drug.Metab.Dispos_38_1532
PubMedID: 20542992

Title : Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510 - Kaneko_2010_DNA.Res_17_37
Author(s) : Kaneko T , Minamisawa K , Isawa T , Nakatsukasa H , Mitsui H , Kawaharada Y , Nakamura Y , Watanabe A , Kawashima K , Ono A , Shimizu Y , Takahashi C , Minami C , Fujishiro T , Kohara M , Katoh M , Nakazaki N , Nakayama S , Yamada M , Tabata S , Sato S
Ref : DNA Research , 17 :37 , 2010
Abstract : We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3,311,395 bp) and six plasmids, designated as pAB510a (1,455,109 bp), pAB510b (723,779 bp), pAB510c (681,723 bp), pAB510d (628,837 bp), pAB510e (537,299 bp), and pAB510f (261,596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N(2) fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C(4)-dicarboxylate during its symbiotic relationship with the host plant.
ESTHER : Kaneko_2010_DNA.Res_17_37
PubMedSearch : Kaneko_2010_DNA.Res_17_37
PubMedID: 20047946
Gene_locus related to this paper: azos1-d3nrk5 , azos1-d3ns85 , azos1-d3nsh5 , azos1-d3nt15 , azos1-d3ntk4 , azos1-d3nv04 , azos1-d3nx23 , azos1-d3ny33 , azos1-d3p0k9 , azos1-d3p0n8 , azos1-d3p1p1 , azos1-d3p2z0 , azos1-d3p4h2 , azos1-d3p4k9 , azos1-d3p5e7 , azos1-d3p281 , azos1-d3p626

Title : Human arylacetamide deacetylase is a principal enzyme in flutamide hydrolysis - Watanabe_2009_Drug.Metab.Dispos_37_1513
Author(s) : Watanabe A , Fukami T , Nakajima M , Takamiya M , Aoki Y , Yokoi T
Ref : Drug Metabolism & Disposition: The Biological Fate of Chemicals , 37 :1513 , 2009
Abstract : Flutamide, an antiandrogen drug, is widely used for the treatment of prostate cancer. The initial metabolic pathways of flutamide are hydroxylation and hydrolysis. It was recently reported that the hydrolyzed product, 4-nitro-3-(trifluoromethyl)phenylamine (FLU-1), is further metabolized to N-hydroxy FLU-1, an assumed hepatotoxicant. However, the esterase responsible for the flutamide hydrolysis has not been characterized. In the present study, we found that human arylacetamide deacetylase (AADAC) efficiently hydrolyzed flutamide using recombinant AADAC expressed in COS7 cells. In contrast, carboxylesterase1 (CES1) and CES2, which are responsible for the hydrolysis of many drugs, could not hydrolyze flutamide. AADAC is specifically expressed in the endoplasmic reticulum. Flutamide hydrolase activity was highly detected in human liver microsomes (K(m), 794 +/- 83 microM; V(max), 1.1 +/- 0.0 nmol/min/mg protein), whereas the activity was extremely low in human liver cytosol. The flutamide hydrolase activity in human liver microsomes was strongly inhibited by bis-(p-nitrophenyl)phosphate [corrected], diisopropylphosphorofluoride, and physostigmine sulfate (eserine) but moderately inhibited by sodium fluoride, phenylmethylsulfonyl fluoride, and disulfiram. The same inhibition pattern was obtained with the recombinant AADAC. Moreover, human liver and jejunum microsomes showing AADAC expression could hydrolyze flutamide, but human pulmonary and renal microsomes, which do not express AADAC, showed slight activity. In human liver microsomal samples (n = 50), the flutamide hydrolase activities were significantly correlated with the expression levels of AADAC protein (r = 0.66, p < 0.001). In conclusion, these results clearly showed that flutamide is exclusively hydrolyzed by AADAC. AADAC would be an important enzyme responsible for flutamide-induced hepatotoxicity.
ESTHER : Watanabe_2009_Drug.Metab.Dispos_37_1513
PubMedSearch : Watanabe_2009_Drug.Metab.Dispos_37_1513
PubMedID: 19339378
Gene_locus related to this paper: human-AADAC

Title : Human homolog of NOTUM, overexpressed in hepatocellular carcinoma, is regulated transcriptionally by beta-catenin\/TCF - Torisu_2008_Cancer.Sci_99_1139
Author(s) : Torisu Y , Watanabe A , Nonaka A , Midorikawa Y , Makuuchi M , Shimamura T , Sugimura H , Niida A , Akiyama T , Iwanari H , Kodama T , Zeniya M , Aburatani H
Ref : Cancer Sci , 99 :1139 , 2008
Abstract : The Drosophila Notum gene, which is regulated by the Wingless pathway, encodes a secreted hydrolase that modifies heparan sulfate proteoglycans. In comparative analysis of the gene expression profiles in primary human hepatocellular carcinomas (HCC) and normal organs, we observed that the human ortholog of Drosophila Notum was overexpressed markedly in a subset of HCC, but expressed rarely in adult normal tissues. Immunoblotting confirmed the overexpression of NOTUM protein in 12 of 40 primary HCC cases (30%). High levels of NOTUM protein were significantly associated with intracellular (nuclear or cytoplasmic) accumulation of beta-catenin protein: all 10 HCC with high intracellular beta-catenin also had high NOTUM expression, whereas only 2 of 30 cases (6.7%) without intracellular beta-catenin had high NOTUM expression (P < 0.00001). NOTUM expression in HepG2 cells was downregulated significantly by induction of a dominant-negative mutant of TCF4, a beta-catenin partner. In vivo binding of the beta-catenin/TCF complex to the NOTUM promoter was demonstrated by chromatin immunoprecipitation in HepG2 and SW480 cells, where canonical Wnt signaling is activated constitutively. These findings provide evidence that NOTUM is a novel target of beta-catenin/TCF4 and is upregulated in Wnt/beta-catenin signaling-activated HCC.
ESTHER : Torisu_2008_Cancer.Sci_99_1139
PubMedSearch : Torisu_2008_Cancer.Sci_99_1139
PubMedID: 18429952

Title : Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843 - Kaneko_2007_DNA.Res_14_247
Author(s) : Kaneko T , Nakajima N , Okamoto S , Suzuki I , Tanabe Y , Tamaoki M , Nakamura Y , Kasai F , Watanabe A , Kawashima K , Kishida Y , Ono A , Shimizu Y , Takahashi C , Minami C , Fujishiro T , Kohara M , Katoh M , Nakazaki N , Nakayama S , Yamada M , Tabata S , Watanabe MM
Ref : DNA Research , 14 :247 , 2007
Abstract : The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome.
ESTHER : Kaneko_2007_DNA.Res_14_247
PubMedSearch : Kaneko_2007_DNA.Res_14_247
PubMedID: 18192279
Gene_locus related to this paper: micae-a8yde8 , micae-a8yen2 , micae-a8yma5 , micae-MCYC , mican-b0jqg0 , mican-b0jqq0 , mican-b0jsa2 , mican-b0jxh1 , mican-b0jux6 , mican-b0jyg0

Title : Synthesis and Herbicidal Activity of New 1-Alkyl-3-aryloxypyrazole-4-carboxamide Derivatives - Ohno_2004_J.Pestic.Sci_29_96
Author(s) : Ohno R , Watanabe A , Nagaoka M , Ueda T , Sakurai H , Hori M , Hirai K
Ref : Journal of Pesticide Science , 29 :96 , 2004
Abstract : A series of novel 1-alkyl-3-aryloxypyrazole-4-carboxamide derivatives were synthesized and their herbicidal activity and crop safety examined under flooded conditions. Introduction of an aryloxy group at the 3-position of the pyrazole ring was accomplished with a nucleophilic substitution reaction of 3-hydroxypyrazoles with halobenzenes which were activated by electron-withdrawing groups such as a nitro group. The 3-trifluoromethylphenoxy analogs provided good results. The level of activity also varied with the N-substituents of the carbamoyl group, especially the 2,4-difluorophenyl group which provided the best combination of herbicidal activity and crop selectivity. Among the compounds synthesized, N-(2,4-difluorophenyl)-1-ethyl-3-(3-trifluoromethylphenoxy)pyrazole-4-carboxamide (KPP-856) showed good herbicidal activity against various annual lowland weeds and excellent crop safety at 33 g a.i./ha.
ESTHER : Ohno_2004_J.Pestic.Sci_29_96
PubMedSearch : Ohno_2004_J.Pestic.Sci_29_96
PubMedID:

Title : Synthesis and Herbicidal Activity of New Pyrazole-4-carboxamide Derivatives - Ohno_2004_J.Pestic.Sci_29_15
Author(s) : Ohno R , Watanabe A , Matsukawa T , Ueda T , Sakurai H , Hori M , Hirai K
Ref : Journal of Pesticide Science , 29 :15 , 2004
Abstract : A series of novel 3-(substituted alkoxy)pyrazole-4-carboxamide derivatives were synthesized, and their herbicidal activity against various weeds and crop safety were examined under flooded conditions. The herbicidal activity was primarily influenced by the substituent at the 3-position of the pyrazole ring. The benzyloxy group, the meta-position of which was substituted with an electron-withdrawing group, particularly with a trifluoromethyl group, was most efficient in enhancing the bleaching activity. The level of activity also varied with the N-substituent of the carbamoyl group, with N-ethoxycarbamoyl group providing the best combination of herbicidal activity and selectivity. Among the compounds synthesized, N-ethoxy-1-methyl-3-(3-trifluoromethylbenzyloxy)pyrazole-4-carboxamide (KPP-297), which showed good herbicidal activity against various annual lowland weeds and excellent crop safety at just of 100 g a.i./ha, was considered to be the most promising rice herbicide.
ESTHER : Ohno_2004_J.Pestic.Sci_29_15
PubMedSearch : Ohno_2004_J.Pestic.Sci_29_15
PubMedID:

Title : Loss of imprinting of PEG1\/MEST in lung cancer cell lines - Nakanishi_2004_Oncol.Rep_12_1273
Author(s) : Nakanishi H , Suda T , Katoh M , Watanabe A , Igishi T , Kodani M , Matsumoto S , Nakamoto M , Shigeoka Y , Okabe T , Oshimura M , Shimizu E
Ref : Oncol Rep , 12 :1273 , 2004
Abstract : Paternally expressed imprinted gene 1/mesoderm-specific transcript (PEG1/MEST) is an imprinted gene expressed from the paternal allele. Recently, frequent loss of imprinting (LOI) of PEG1/MEST has been reported in lung adenocarcinomas. It is suggested that the LOI may be involved in pathogenesis of lung adenocarcinoma. In the present study, incidence of LOI of PEG1/MEST was examined in lung cancer cell lines, including small cell lung cancer (SCLC). Among 50 cell lines tested, 20 cell lines were heterozygous for the AflIII site of the PEG1/MEST gene. In these heterozygotes, biallelic expression was observed in 9 cell lines (45%), monoallelic in 11 (55%). In cell lines of non-small cell lung cancer (NSCLC), 62% (8 of 13) exhibited biallelic expression. In SCLC, only 1 of 7 cell lines (14%) showed biallelic expression. LOI of PEG1/MEST in the NSCLC cell line is significantly frequent compared with that in SCLC cell lines (p=0.043). This result supports the possibility that LOI may be related to tumorigenesis and malignant transformation, especially in NSCLC.
ESTHER : Nakanishi_2004_Oncol.Rep_12_1273
PubMedSearch : Nakanishi_2004_Oncol.Rep_12_1273
PubMedID: 15547750

Title : Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids - Nakamura_2003_DNA.Res_10_137
Author(s) : Nakamura Y , Kaneko T , Sato S , Mimuro M , Miyashita H , Tsuchiya T , Sasamoto S , Watanabe A , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Nakazaki N , Shimpo S , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 10 :137 , 2003
Abstract : The nucleotide sequence of the entire genome of a cyanobacterium Gloeobacter violaceus PCC 7421 was determined. The genome of G. violaceus was a single circular chromosome 4,659,019 bp long with an average GC content of 62%. No plasmid was detected. The chromosome comprises 4430 potential protein-encoding genes, one set of rRNA genes, 45 tRNA genes representing 44 tRNA species and genes for tmRNA, B subunit of RNase P, SRP RNA and 6Sa RNA. Forty-one percent of the potential protein-encoding genes showed sequence similarity to genes of known function, 37% to hypothetical genes, and the remaining 22% had no apparent similarity to reported genes. Comparison of the assigned gene components with those of other cyanobacteria has unveiled distinctive features of the G. violaceus genome. Genes for PsaI, PsaJ, PsaK, and PsaX for Photosystem I and PsbY, PsbZ and Psb27 for Photosystem II were missing, and those for PsaF, PsbO, PsbU, and PsbV were poorly conserved. cpcG for a rod core linker peptide for phycobilisomes and nblA related to the degradation of phycobilisomes were also missing. Potential signal peptides of the presumptive products of petJ and petE for soluble electron transfer catalysts were less conserved than the remaining portions. These observations may be related to the fact that photosynthesis in G. violaceus takes place not in thylakoid membranes but in the cytoplasmic membrane. A large number of genes for sigma factors and transcription factors in the LuxR, LysR, PadR, TetR, and MarR families could be identified, while those for major elements for circadian clock, kaiABC were not found. These differences may reflect the phylogenetic distance between G. violaceus and other cyanobacteria.
ESTHER : Nakamura_2003_DNA.Res_10_137
PubMedSearch : Nakamura_2003_DNA.Res_10_137
PubMedID: 14621292
Gene_locus related to this paper: glovi-GLL0053 , glovi-GLL0778 , glovi-GLL1217 , glovi-GLL1281 , glovi-GLL1310 , glovi-GLL1435 , glovi-GLL2002 , glovi-gll2009 , glovi-GLL2335 , glovi-GLL2500 , glovi-GLL3208 , glovi-GLL3677 , glovi-GLL4259 , glovi-GLR0796 , glovi-GLR1368 , glovi-GLR1422 , glovi-GLR2241 , glovi-GLR2809 , glovi-GLR3058 , glovi-GLR3329 , glovi-GLR3546 , glovi-GLR3833 , glovi-q7ncx6 , glovi-q7nd10 , glovi-q7ndi8 , glovi-q7ndy7 , glovi-q7nek8 , glovi-q7net1 , glovi-q7new7 , glovi-q7ney7 , glovi-q7nfx3 , glovi-q7nga2 , glovi-q7ngw1 , glovi-q7nj78 , glovi-q7nj91 , glovi-q7nj98 , glovi-q7njx8 , glovi-q7njz2 , glovi-q7nkk7 , glovi-q7nly3 , glovi-q7nm82 , glovi-q7nmt4 , glovi-q7nmz0 , glovi-q7nn33 , glovi-q7nn46 , glovi-q7nn64 , glovi-q7nny4 , glovi-q7np81 , glovi-q7npc6

Title : Complete genome structure of Gloeobacter violaceus PCC 7421, a cyanobacterium that lacks thylakoids (supplement) -
Author(s) : Nakamura Y , Kaneko T , Sato S , Mimuro M , Miyashita H , Tsuchiya T , Sasamoto S , Watanabe A , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Nakazaki N , Shimpo S , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 10 :181 , 2003
PubMedID: 14621296
Gene_locus related to this paper: glovi-gll2009

Title : Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803 - Kaneko_2003_DNA.Res_10_221
Author(s) : Kaneko T , Nakamura Y , Sasamoto S , Watanabe A , Kohara M , Matsumoto M , Shimpo S , Yamada M , Tabata S
Ref : DNA Research , 10 :221 , 2003
Abstract : The genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803 consists of a single chromosome and several plasmids of different sizes, and the nucleotide sequences of the chromosome and three small plasmids (5.2 kb, 2.4 kb, and 2.3 kb) have already been sequenced. We newly determined the nucleotide sequences of four large plasmids, which have been identified in our laboratory (pSYSM:120 kb, pSYSX:106 kb, pSYSA:103 kb, and pSYSG:44 kb). Computer-aided analysis was performed to explore the genetic information carried by these plasmids. A total of 397 potential protein-encoding genes were predicted, but little information was obtained about the functional relationship of plasmids to host cell, as a large portion of the predicted genes (77%) were of unknown function. The occurrence of the potential genes on plasmids was divergent, and parA was the only gene common to all four large plasmids. The distribution data of a Cyanobacterium-specific sequence (HIP1: 5'-GCGATCGC-3') suggested that respective plasmids could have originated from different cyanobacterial strains.
ESTHER : Kaneko_2003_DNA.Res_10_221
PubMedSearch : Kaneko_2003_DNA.Res_10_221
PubMedID: 14686584
Gene_locus related to this paper: syny3-q6zeq0 , 9sync-m1mb45

Title : Complete genome structure of the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 - Nakamura_2002_DNA.Res_9_123
Author(s) : Nakamura Y , Kaneko T , Sato S , Ikeuchi M , Katoh H , Sasamoto S , Watanabe A , Iriguchi M , Kawashima K , Kimura T , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Nakazaki N , Shimpo S , Sugimoto M , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 9 :123 , 2002
Abstract : The entire genome of a thermophilic unicellular cyanobacterium, Thermosynechococcus elongatus BP-1, was sequenced. The genome consisted of a circular chromosome 2,593,857 bp long, and no plasmid was detected. A total of 2475 potential protein-encoding genes, one set of rRNA genes, 42 tRNA genes representing 42 tRNA species and 4 genes for small structural RNAs were assigned to the chromosome by similarity search and computer prediction. The translated products of 56% of the potential protein-encoding genes showed sequence similarity to experimentally identified and predicted proteins of known function, and the products of 34% of these genes showed sequence similarity to the translated products of hypothetical genes. The remaining 10% lacked significant similarity to genes for predicted proteins in the public DNA databases. Sixty-three percent of the T. elongatus genes showed significant sequence similarity to those of both Synechocystis sp. PCC 6803 and Anabaena sp. PCC 7120, while 22% of the genes were unique to this species, indicating a high degree of divergence of the gene information among cyanobacterial strains. The lack of genes for typical fatty acid desaturases and the presence of more genes for heat-shock proteins in comparison with other mesophilic cyanobacteria may be genomic features of thermophilic strains. A remarkable feature of the genome is the presence of 28 copies of group II introns, 8 of which contained a presumptive gene for maturase/reverse transcriptase. A trace of genome rearrangement mediated by the group II introns was also observed.
ESTHER : Nakamura_2002_DNA.Res_9_123
PubMedSearch : Nakamura_2002_DNA.Res_9_123
PubMedID: 12240834
Gene_locus related to this paper: theeb-q8dg48 , theeb-TLL0292 , theeb-TLL0340 , theeb-TLL0918 , theeb-TLL0989 , theeb-TLL1717 , theeb-TLL2163 , theeb-TLR0492 , theeb-TLR1045 , theeb-TLR1157 , theeb-TLR1274 , theeb-TLR1393 , theeb-TLR1423 , theeb-TLR1685 , theeb-TLR1725 , theeb-TLR1892 , theeb-TLR1982 , theeb-TLR2038 , theeb-TLR2066

Title : Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 - Kaneko_2002_DNA.Res_9_189
Author(s) : Kaneko T , Nakamura Y , Sato S , Minamisawa K , Uchiumi T , Sasamoto S , Watanabe A , Idesawa K , Iriguchi M , Kawashima K , Kohara M , Matsumoto M , Shimpo S , Tsuruoka H , Wada T , Yamada M , Tabata S
Ref : DNA Research , 9 :189 , 2002
Abstract : The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by Gottfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.
ESTHER : Kaneko_2002_DNA.Res_9_189
PubMedSearch : Kaneko_2002_DNA.Res_9_189
PubMedID: 12597275
Gene_locus related to this paper: braja-BLL0118 , braja-BLL0272 , braja-BLL0546 , braja-BLL0558 , braja-BLL0837 , braja-BLL0839 , braja-BLL1016 , braja-BLL1128 , braja-BLL1234 , braja-BLL1350 , braja-BLL1401 , braja-BLL2323 , braja-BLL2387 , braja-BLL2443 , braja-BLL2527 , braja-BLL2884 , braja-BLL2902 , braja-BLL3246 , braja-BLL3359 , braja-BLL3416 , braja-BLL3418 , braja-BLL3470 , braja-BLL3759 , braja-BLL3777 , braja-BLL4001 , braja-BLL4189 , braja-BLL4284 , braja-BLL4335 , braja-BLL4360 , braja-BLL4548 , braja-BLL4985 , braja-BLL4989 , braja-BLL4997 , braja-BLL5160 , braja-BLL5514 , braja-BLL5588 , braja-BLL5740 , braja-bll6073 , braja-BLL6264 , braja-BLL6275 , braja-BLL6428 , braja-bll6463 , braja-BLL6574 , braja-BLL6577 , braja-BLL6614 , braja-bll6820 , braja-BLL6841 , braja-BLL6890 , braja-BLL6974 , braja-BLL7123 , braja-BLL7368 , braja-BLL7370 , braja-BLL7497 , braja-BLL7506 , braja-BLL7509 , braja-BLL7545 , braja-BLL7692 , braja-BLL7862 , braja-BLL8011 , braja-BLL8277 , braja-BLR0230 , braja-BLR0418 , braja-BLR0711 , braja-BLR0899 , braja-BLR0908 , braja-BLR1078 , braja-BLR1197 , braja-BLR1251 , braja-BLR2261 , braja-BLR2321 , braja-BLR2487 , braja-BLR2879 , braja-BLR2885 , braja-BLR2889 , braja-BLR2982 , braja-BLR3322 , braja-BLR3456 , braja-BLR3519 , braja-blr3732 , braja-BLR3878 , braja-BLR4157 , braja-BLR4181 , braja-BLR5346 , braja-BLR5359 , braja-BLR6083 , braja-BLR6127 , braja-BLR6186 , braja-BLR6271 , braja-BLR6465 , braja-BLR6576 , braja-BLR6677 , braja-BLR6703 , braja-BLR6960 , braja-BLR6965 , braja-BLR7068 , braja-BLR7144 , braja-BLR7443 , braja-BLR7556 , braja-BLR7622 , braja-BLR7741 , braja-BLR7809 , braja-BLR7810 , braja-BLR7894 , braja-BLR8188 , braja-dhaa , braja-EPHA , braja-EPHB , braja-ID587 , braja-ID930 , braja-METX , braja-pcaD , braja-PIP , braja-PLDB , braja-PTRB , braja-q89c18 , braja-q89c36 , braja-q89mj3 , braja-q89ql9 , braja-q89y23

Title : Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110 (supplement) -
Author(s) : Kaneko T , Nakamura Y , Sato S , Minamisawa K , Uchiumi T , Sasamoto S , Watanabe A , Idesawa K , Iriguchi M , Kawashima K , Kohara M , Matsumoto M , Shimpo S , Tsuruoka H , Wada T , Yamada M , Tabata S
Ref : DNA Research , 9 :225 , 2002
PubMedID: 12597279
Gene_locus related to this paper: braja-bll6463 , braja-bll6820 , braja-EPHB , braja-ID930 , braja-pcaD

Title : Acetylcholinesterase distribution and refractory constipation - a new criterion for diagnosis and management - Kobayashi_2002_Pediatr.Surg.Int_18_349
Author(s) : Kobayashi H , Li Z , Yamataka A , Lane GJ , Yokota H , Watanabe A , Miyano T
Ref : Pediatr Surg Int , 18 :349 , 2002
Abstract : To describe manifestations of acetylcholinesterase (AchE) activity in the bowel of patients presenting with refractory constipation and correlate them with outcome, rectal biopsy specimens (RBS) from 165 patients who presented with refractory constipation between 1988 and 1999 were examined. Age at biopsy ranged from 4 days to 17 years; 45 subjects were excluded because they satisfied diagnostic criteria for Hirschsprung's disease, intestinal neuronal dysplasia, or hypoganglionosis. Thirty-five autopsy subjects were used as controls. All RBS were compared and AchE activity was assessed in the lamina propria (LP), muscularis mucosae (MM), and around the submucosal vessels (V). Variations in AchE distribution were classified as grade I (no AchE-positive nerve fibers in the LP or MM), grade II (some positive fibers in the LP or MM), grade III (moderate positive fibers in the LP or MM), grade IV (many positive fibers in the LP, MM, or V), or grade V (fibrillar, foamy, or amorphous staining for AchE). All grade I (11/120) and V (12/120) subjects achieved normal bowel control with laxatives alone and all grade II subjects (58/120) did with laxatives and enemas. Grade III subjects (34/120) required addition of cisapride. All grade IV subjects (5/120) were unresponsive to conservative management and 4/5 were found to have a megarectum, which was treated surgically. AchE distribution correlated well with eventual outcome and requirement for surgery. AchE distribution could also be used to classify bowel motility disorders, and we suggest the term AchE-positive disease be used to describe them.
ESTHER : Kobayashi_2002_Pediatr.Surg.Int_18_349
PubMedSearch : Kobayashi_2002_Pediatr.Surg.Int_18_349
PubMedID: 12415353

Title : Pentaketide melanin biosynthesis in Aspergillus fumigatus requires chain-length shortening of a heptaketide precursor - Tsai_2001_J.Biol.Chem_276_29292
Author(s) : Tsai HF , Fujii I , Watanabe A , Wheeler MH , Chang YC , Yasuoka Y , Ebizuka Y , Kwon-Chung KJ
Ref : Journal of Biological Chemistry , 276 :29292 , 2001
Abstract : Chain lengths and cyclization patterns of microbial polyketides are generally determined by polyketide synthases alone. Fungal polyketide melanins are often derived from a pentaketide 1,8-dihydroxynaphthalene, and pentaketide synthases are used for synthesis of the upstream pentaketide precursor, 1,3,6,8-tetrahydroxynaphthalene (1,3,6,8-THN). However, Aspergillus fumigatus, a human fungal pathogen, uses a heptaketide synthase (Alb1p) to synthesize its conidial pigment through a pentaketide pathway similar to that which produces 1,8-dihydroxynaphthalene-melanin. In this study we demonstrate that a novel protein, Ayg1p, is involved in the formation of 1,3,6,8-THN by chain-length shortening of a heptaketide precursor in A. fumigatus. Deletion of the ayg1 gene prevented the accumulation of 1,3,6,8-THN suggesting the involvement of ayg1 in 1,3,6,8-THN production. Genetic analyses of double-gene deletants suggested that Ayg1p catalyzes a novel biosynthetic step downstream of Alb1p and upstream of Arp2p (1,3,6,8-THN reductase). Further genetic and biochemical analyses of the reconstituted strains carrying alb1, ayg1, or alb1 + ayg1 indicated that Ayg1p is essential for synthesis of 1,3,6,8-THN in addition to Alb1p. Cell-free enzyme assays, using the crude Ayg1p protein extract, revealed that Ayg1p enzymatically shortened the heptaketide product of Alb1p to 1,3,6,8-THN. Thus, the protein Ayg1p facilitates the participation of a heptaketide synthase in a pentaketide pathway via a novel polyketide-shortening mechanism in A. fumigatus.
ESTHER : Tsai_2001_J.Biol.Chem_276_29292
PubMedSearch : Tsai_2001_J.Biol.Chem_276_29292
PubMedID: 11350964
Gene_locus related to this paper: aspfu-AYG1

Title : Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 - Kaneko_2001_DNA.Res_8_205
Author(s) : Kaneko T , Nakamura Y , Wolk CP , Kuritz T , Sasamoto S , Watanabe A , Iriguchi M , Ishikawa A , Kawashima K , Kimura T , Kishida Y , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakazaki N , Shimpo S , Sugimoto M , Takazawa M , Yamada M , Yasuda M , Tabata S
Ref : DNA Research , 8 :205 , 2001
Abstract : The nucleotide sequence of the entire genome of a filamentous cyanobacterium, Anabaena sp. strain PCC 7120, was determined. The genome of Anabaena consisted of a single chromosome (6,413,771 bp) and six plasmids, designated pCC7120alpha (408,101 bp), pCC7120beta (186,614 bp), pCC7120gamma (101,965 bp), pCC7120delta (55,414 bp), pCC7120epsilon (40,340 bp), and pCC7120zeta (5,584 bp). The chromosome bears 5368 potential protein-encoding genes, four sets of rRNA genes, 48 tRNA genes representing 42 tRNA species, and 4 genes for small structural RNAs. The predicted products of 45% of the potential protein-encoding genes showed sequence similarity to known and predicted proteins of known function, and 27% to translated products of hypothetical genes. The remaining 28% lacked significant similarity to genes for known and predicted proteins in the public DNA databases. More than 60 genes involved in various processes of heterocyst formation and nitrogen fixation were assigned to the chromosome based on their similarity to the reported genes. One hundred and ninety-five genes coding for components of two-component signal transduction systems, nearly 2.5 times as many as those in Synechocystis sp. PCC 6803, were identified on the chromosome. Only 37% of the Anabaena genes showed significant sequence similarity to those of Synechocystis, indicating a high degree of divergence of the gene information between the two cyanobacterial strains.
ESTHER : Kaneko_2001_DNA.Res_8_205
PubMedSearch : Kaneko_2001_DNA.Res_8_205
PubMedID: 11759840
Gene_locus related to this paper: anasp-ALL0111 , anasp-ALL0193 , anasp-ALL0254 , anasp-ALL0316 , anasp-ALL0955 , anasp-ALL0969 , anasp-ALL1161 , anasp-ALL1205 , anasp-ALL1353 , anasp-ALL1695 , anasp-ALL2050 , anasp-ALL2056 , anasp-ALL2058 , anasp-ALL2068 , anasp-ALL2529 , anasp-ALL2533 , anasp-ALL2753 , anasp-ALL2761 , anasp-ALL3898 , anasp-ALL4221 , anasp-ALL4875 , anasp-ALL8511 , anasp-ALR0039 , anasp-ALR0079 , anasp-ALR0130 , anasp-ALR0235 , anasp-ALR0851 , anasp-ALR1077 , anasp-ALR1270 , anasp-ALR1352 , anasp-ALR1362 , anasp-ALR1709 , anasp-ALR2045 , noss1-ALR3140 , anasp-ALR3514 , anasp-ALR3685 , anasp-ALR3911 , anasp-ALR4625 , anasp-ALR5028 , anasp-AROE , anasp-q8ymv5 , anasp-q8yxx2 , anasp-y1448 , noss1-ALL3113 , noss1-ALL4967 , noss1-ALR4786 , noss1-q8yrg0 , noss1-y2406

Title : Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti - Kaneko_2000_DNA.Res_7_331
Author(s) : Kaneko T , Nakamura Y , Sato S , Asamizu E , Kato T , Sasamoto S , Watanabe A , Idesawa K , Ishikawa A , Kawashima K , Kimura T , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Mochizuki Y , Nakayama S , Nakazaki N , Shimpo S , Sugimoto M , Takeuchi C , Yamada M , Tabata S
Ref : DNA Research , 7 :331 , 2000
Abstract : The complete nucleotide sequence of the genome of a symbiotic bacterium Mesorhizobium loti strain MAFF303099 was determined. The genome of M. loti consisted of a single chromosome (7,036,071 bp) and two plasmids, designated as pMLa (351,911 bp) and pMLb (208, 315 bp). The chromosome comprises 6752 potential protein-coding genes, two sets of rRNA genes and 50 tRNA genes representing 47 tRNA species. Fifty-four percent of the potential protein genes showed sequence similarity to genes of known function, 21% to hypothetical genes, and the remaining 25% had no apparent similarity to reported genes. A 611-kb DNA segment, a highly probable candidate of a symbiotic island, was identified, and 30 genes for nitrogen fixation and 24 genes for nodulation were assigned in this region. Codon usage analysis suggested that the symbiotic island as well as the plasmids originated and were transmitted from other genetic systems. The genomes of two plasmids, pMLa and pMLb, contained 320 and 209 potential protein-coding genes, respectively, for a variety of biological functions. These include genes for the ABC-transporter system, phosphate assimilation, two-component system, DNA replication and conjugation, but only one gene for nodulation was identified.
ESTHER : Kaneko_2000_DNA.Res_7_331
PubMedSearch : Kaneko_2000_DNA.Res_7_331
PubMedID: 11214968
Gene_locus related to this paper: meslo-acoc , meslo-EphB , meslo-est , meslo-lipest , meslo-MLL0014 , meslo-MLL0351 , meslo-MLL0537 , meslo-mll0601 , meslo-MLL0618 , meslo-MLL1209 , meslo-MLL1226 , meslo-mll1328 , meslo-MLL1329 , meslo-MLL1495 , meslo-MLL1869 , meslo-mll1900 , meslo-MLL2018 , meslo-MLL2072 , meslo-mll2481 , meslo-mll2689 , meslo-MLL2788 , meslo-MLL3556 , meslo-MLL3568 , meslo-MLL3682 , meslo-mll3776 , meslo-MLL4497 , meslo-MLL4552 , meslo-MLL5128 , meslo-mll5179 , meslo-mll5392 , meslo-MLL5717 , meslo-mll5743 , meslo-MLL6746 , meslo-MLL6752 , meslo-mll6871 , meslo-MLL7643 , meslo-mll7742 , meslo-MLL9722 , meslo-MLR0094 , meslo-mlr0145 , meslo-mlr0170 , meslo-MLR0240 , meslo-mlr0493 , meslo-MLR0937 , meslo-mlr0978 , meslo-MLR0992 , meslo-MLR1612 , meslo-mlr1789 , meslo-mlr1864 , meslo-mlr2176 , meslo-MLR2262 , meslo-mlr2612 , meslo-mlr2710 , meslo-mlr3034 , meslo-MLR3538 , meslo-mlr3816 , meslo-mlr4436 , meslo-MLR4903 , meslo-MLR5045 , meslo-MLR5063 , rhilo-dhaa , meslo-MLR6087 , meslo-MLR6657 , meslo-mlr6682 , meslo-mlr6683 , meslo-MLR6684 , meslo-MLR6787 , meslo-MLR6993 , meslo-mlr6999 , meslo-mlr7206 , meslo-mlr7232 , meslo-mlr7803 , meslo-MLR9053 , meslo-mlr9622 , meslo-mlr9641 , rhilo-MLL0076 , rhilo-MLL1824 , rhilo-MLL7123 , rhilo-MLL8374 , rhilo-MLR1247 , rhilo-MLR2444 , rhilo-MLR4383 , rhilo-MLR8175 , rhilo-q98nf6 , rhilo-q98nf8 , rhilo-q988i9

Title : Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana - Tabata_2000_Nature_408_823
Author(s) : Tabata S , Kaneko T , Nakamura Y , Kotani H , Kato T , Asamizu E , Miyajima N , Sasamoto S , Kimura T , Hosouchi T , Kawashima K , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Naruo K , Okumura S , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Sato S , de la Bastide M , Huang E , Spiegel L , Gnoj L , O'Shaughnessy A , Preston R , Habermann K , Murray J , Johnson D , Rohlfing T , Nelson J , Stoneking T , Pepin K , Spieth J , Sekhon M , Armstrong J , Becker M , Belter E , Cordum H , Cordes M , Courtney L , Courtney W , Dante M , Du H , Edwards J , Fryman J , Haakensen B , Lamar E , Latreille P , Leonard S , Meyer R , Mulvaney E , Ozersky P , Riley A , Strowmatt C , Wagner-McPherson C , Wollam A , Yoakum M , Bell M , Dedhia N , Parnell L , Shah R , Rodriguez M , See LH , Vil D , Baker J , Kirchoff K , Toth K , King L , Bahret A , Miller B , Marra M , Martienssen R , McCombie WR , Wilson RK , Murphy G , Bancroft I , Volckaert G , Wambutt R , Dusterhoft A , Stiekema W , Pohl T , Entian KD , Terryn N , Hartley N , Bent E , Johnson S , Langham SA , McCullagh B , Robben J , Grymonprez B , Zimmermann W , Ramsperger U , Wedler H , Balke K , Wedler E , Peters S , van Staveren M , Dirkse W , Mooijman P , Lankhorst RK , Weitzenegger T , Bothe G , Rose M , Hauf J , Berneiser S , Hempel S , Feldpausch M , Lamberth S , Villarroel R , Gielen J , Ardiles W , Bents O , Lemcke K , Kolesov G , Mayer K , Rudd S , Schoof H , Schueller C , Zaccaria P , Mewes HW , Bevan M , Fransz P
Ref : Nature , 408 :823 , 2000
Abstract : The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.
ESTHER : Tabata_2000_Nature_408_823
PubMedSearch : Tabata_2000_Nature_408_823
PubMedID: 11130714
Gene_locus related to this paper: arath-At5g11650 , arath-At5g16120 , arath-at5g18630 , arath-AT5G20520 , arath-At5g21950 , arath-AT5G27320 , arath-CXE15 , arath-F1N13.220 , arath-F14F8.240 , arath-q3e9e4 , arath-q8lae9 , arath-Q8LFB7 , arath-q9ffg7 , arath-q9fij5 , arath-Q9LVU7 , arath-q66gm8 , arath-SCPL34 , arath-B9DFR3 , arath-a0a1p8bcz0

Title : Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana - Salanoubat_2000_Nature_408_820
Author(s) : Salanoubat M , Lemcke K , Rieger M , Ansorge W , Unseld M , Fartmann B , Valle G , Blocker H , Perez-Alonso M , Obermaier B , Delseny M , Boutry M , Grivell LA , Mache R , Puigdomenech P , de Simone V , Choisne N , Artiguenave F , Robert C , Brottier P , Wincker P , Cattolico L , Weissenbach J , Saurin W , Quetier F , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Benes V , Wurmbach E , Drzonek H , Erfle H , Jordan N , Bangert S , Wiedelmann R , Kranz H , Voss H , Holland R , Brandt P , Nyakatura G , Vezzi A , D'Angelo M , Pallavicini A , Toppo S , Simionati B , Conrad A , Hornischer K , Kauer G , Lohnert TH , Nordsiek G , Reichelt J , Scharfe M , Schon O , Bargues M , Terol J , Climent J , Navarro P , Collado C , Perez-Perez A , Ottenwalder B , Duchemin D , Cooke R , Laudie M , Berger-Llauro C , Purnelle B , Masuy D , de Haan M , Maarse AC , Alcaraz JP , Cottet A , Casacuberta E , Monfort A , Argiriou A , Flores M , Liguori R , Vitale D , Mannhaupt G , Haase D , Schoof H , Rudd S , Zaccaria P , Mewes HW , Mayer KF , Kaul S , Town CD , Koo HL , Tallon LJ , Jenkins J , Rooney T , Rizzo M , Walts A , Utterback T , Fujii CY , Shea TP , Creasy TH , Haas B , Maiti R , Wu D , Peterson J , Van Aken S , Pai G , Militscher J , Sellers P , Gill JE , Feldblyum TV , Preuss D , Lin X , Nierman WC , Salzberg SL , White O , Venter JC , Fraser CM , Kaneko T , Nakamura Y , Sato S , Kato T , Asamizu E , Sasamoto S , Kimura T , Idesawa K , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : Nature , 408 :820 , 2000
Abstract : Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
ESTHER : Salanoubat_2000_Nature_408_820
PubMedSearch : Salanoubat_2000_Nature_408_820
PubMedID: 11130713
Gene_locus related to this paper: arath-MES17 , arath-AT3G12150 , arath-At3g61680 , arath-AT3g62590 , arath-CXE12 , arath-eds1 , arath-SCP25 , arath-F1P2.110 , arath-F1P2.140 , arath-F11F8.28 , arath-F14D17.80 , arath-F16B3.4 , arath-SCP27 , arath-At3g50790 , arath-At3g05600 , arath-PAD4 , arath-At3g51000 , arath-SCP16 , arath-gid1 , arath-GID1B , arath-Q9LUG8 , arath-Q84JS1 , arath-Q9SFF6 , arath-q9m236 , arath-q9sr22 , arath-q9sr23 , arath-SCP7 , arath-SCP14 , arath-SCP15 , arath-SCP17 , arath-SCP36 , arath-SCP37 , arath-SCP39 , arath-SCP40 , arath-SCP49 , arath-T19F11.2

Title : Synthesis of a new class of camptothecin derivatives, the long-chain fatty acid esters of 10-hydroxycamptothecin, as a potent prodrug candidate, and their in vitro metabolic conversion by carboxylesterases - Takayama_1998_Bioorg.Med.Chem.Lett_8_415
Author(s) : Takayama H , Watanabe A , Hosokawa M , Chiba K , Satoh T , Aimi N
Ref : Bioorganic & Medicinal Chemistry Lett , 8 :415 , 1998
Abstract : Five (20S)-10-hydroxycamptothecin derivatives carrying the long-chain fatty acid esters were prepared for the development of a new class of prodrug-type agents. In vitro experiments using three kinds of purified carboxylesterase isozymes from the liver microsomes of rat, pig, and human demonstrated that these derivatives were efficiently metabolized by enzymes compared with CPT-11.
ESTHER : Takayama_1998_Bioorg.Med.Chem.Lett_8_415
PubMedSearch : Takayama_1998_Bioorg.Med.Chem.Lett_8_415
PubMedID: 9871589

Title : Ca2+ sensitizer Org-30029 reverses acidosis- and BDM-induced contractile depression in canine myocardium - Watanabe_1996_Am.J.Physiol_271_H1829
Author(s) : Watanabe A , Tomoike H , Endoh M
Ref : American Journal of Physiology , 271 :H1829 , 1996
Abstract : Effects of the Ca2+ sensitizer N-hydroxy-5,6-dimethoxy-benzo[b]thiophene-2-carboximidamide hydrochloride (Org-30029) on the myocardial contractile depression induced by acidosis and 2,3-butanedione monoxime (BDM) were investigated in aequorin-loaded canine ventricular myocardium. The peak Ca2+ transient-peak force relation during administration of Org-30029 (10(-4) to 10(-3) M) was shifted to the left and upward compared with the relation for elevation of the extracellular Ca2+ concentration ([Ca2+]o) (2.5-12.5 mM). Acidosis (pH 6.6) depressed the force with a small increase in the peak Ca2+ transient. BDM (3 mM) depressed the force with no change in the peak and duration of the Ca2+ transient, indicating that BDM may inhibit selectively the cross-bridge interaction. During acidosis or in the presence of BDM, elevation of [Ca2+]o increased the peak Ca2+ transient to the same extent as that in the control, but the force was inhibited. In contrast, Org-30029 increased the force to a level equivalent to the control with a slight change in the peak Ca2+ transient. In addition, during acidosis, Org-30029 (10(-3) M) increased the force in association with a slight decrease in the peak Ca2+ transient. Thus Org-30029 can reverse the myocardial contractile depression induced by a decrease in the Ca2+ sensitivity of myofilaments, as occurs in pathophysiological situations such as acidosis in cardiac ischemia. Org-30029 may exert the Ca(2+)-sensitizing effect by an increase in the affinity of troponin C for Ca2+ and by a direct action on the cross-bridge interaction.
ESTHER : Watanabe_1996_Am.J.Physiol_271_H1829
PubMedSearch : Watanabe_1996_Am.J.Physiol_271_H1829
PubMedID: 8945898

Title : Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions - Kaneko_1996_DNA.Res_3_109
Author(s) : Kaneko T , Sato S , Kotani H , Tanaka A , Asamizu E , Nakamura Y , Miyajima N , Hirosawa M , Sugiura M , Sasamoto S , Kimura T , Hosouchi T , Matsuno A , Muraki A , Nakazaki N , Naruo K , Okumura S , Shimpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : DNA Research , 3 :109 , 1996
Abstract : The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome. The entire sequence was assembled from the sequences of the physical map-based contigs of cosmid clones and of lambda clones and long PCR products which were used for gap-filling. The accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire genome. The authenticity of the assembled sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA using the assembled sequence data. To predict the potential protein-coding regions, analysis of open reading frames (ORFs), analysis by the GeneMark program and similarity search to databases were performed. As a result, a total of 3,168 potential protein genes were assigned on the genome, in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed similarity to reported and hypothetical genes, respectively. The remaining 1,426 (45.0%) had no apparent similarity to any genes in databases. Among the potential protein genes assigned, 128 were related to the genes participating in photosynthetic reactions. The sum of the sequences coding for potential protein genes occupies 87% of the genome length. By adding rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and RNA-coding regions. A notable feature on the gene organization of the genome was that 99 ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were found spread all over the genome, and at least 26 of them appeared to remain intact. The result implies that rearrangement of the genome occurred frequently during and after establishment of this species.
ESTHER : Kaneko_1996_DNA.Res_3_109
PubMedSearch : Kaneko_1996_DNA.Res_3_109
PubMedID: 8905231
Gene_locus related to this paper: synsp-ester , synsp-PHBC , synsp-prxc , synsp-Q55130 , synsp-SLL0482 , synsp-sll0553 , synsp-SLL0992 , synsp-sll1305 , synsp-SLL1969 , synsp-SLR0825 , synsp-slr1235 , synsp-SLR1506 , synsp-SLR1771 , synsp-SLR1807 , synsp-slr1827 , synsp-slr1916 , synsp-slr1917 , synsp-slr1932 , synsp-SLR1944 , synsp-SLR2053 , synsp-todF , syny3-dlhh , syny3-P73192 , syny3-p73194 , syny3-y249 , syny3-y264