Yoshida T

References (47)

Title : Differential contribution of canonical and noncanonical NLGN3 pathways to early social development and memory performance - Li_2024_Mol.Brain_17_16
Author(s) : Li LY , Imai A , Izumi H , Inoue R , Koshidaka Y , Takao K , Mori H , Yoshida T
Ref : Mol Brain , 17 :16 , 2024
Abstract : Neuroligin (NLGN) 3 is a postsynaptic cell adhesion protein organizing synapse formation through two different types of transsynaptic interactions, canonical interaction with neurexins (NRXNs) and a recently identified noncanonical interaction with protein tyrosine phosphatase (PTP) delta. Although, NLGN3 gene is known as a risk gene for neurodevelopmental disorders such as autism spectrum disorder (ASD) and intellectual disability (ID), the pathogenic contribution of the canonical NLGN3-NRXN and noncanonical NLGN3-PTPdelta pathways to these disorders remains elusive. In this study, we utilized Nlgn3 mutant mice selectively lacking the interaction with either NRXNs or PTPdelta and investigated their social and memory performance. Neither Nlgn3 mutants showed any social cognitive deficiency in the social novelty recognition test. However, the Nlgn3 mutant mice lacking the PTPdelta pathway exhibited significant decline in the social conditioned place preference (sCPP) at the juvenile stage, suggesting the involvement of the NLGN3-PTPdelta pathway in the regulation of social motivation and reward. In terms of learning and memory, disrupting the canonical NRXN pathway attenuated contextual fear conditioning while disrupting the noncanonical NLGN3-PTPdelta pathway enhanced it. Furthermore, disruption of the NLGN3-PTPdelta pathway negatively affected the remote spatial reference memory in the Barnes maze test. These findings highlight the differential contributions of the canonical NLGN3-NRXN and noncanonical NLGN3-PTPdelta synaptogenic pathways to the regulation of higher order brain functions associated with ASD and ID.
ESTHER : Li_2024_Mol.Brain_17_16
PubMedSearch : Li_2024_Mol.Brain_17_16
PubMedID: 38475840

Title : Epitope-tag-mediated synaptogenic activity in an engineered neurexin-1beta lacking the binding interface with neuroligin-1 - Hamid_2023_Biochem.Biophys.Res.Commun_658_141
Author(s) : Hamid SA , Imayasu M , Yoshida T , Tsutsui H
Ref : Biochemical & Biophysical Research Communications , 658 :141 , 2023
Abstract : Clustering of neurexin-1beta occurs through the formation of a trans-cellular complex with neuroligin-1, which promotes the generation of presynapse. While the extracellular region of neurexin-1beta functions to constitute the heterophilic binding interface with neuroligin-1, it has remained unclear whether the region could also play any key role in exerting the intracellular signaling for presynaptic differentiation. In this study, we generated neurexin-1beta lacking the binding site to neuroligin-1 and with a FLAG epitope at the N-terminus, and examined its activity in cultured neurons. The engineered protein still exhibited robust synaptogenic activities upon the epitope-mediated clustering, indicating that the region for complex formation and that for transmitting presynapse differentiation signals are structurally independent of each other. Using a fluorescence protein as an epitope, synaptogenesis was also induced by a gene-codable nanobody. The finding opens possibilities of neurexin-1beta as a platform for developing various molecular tools which may allow, for example, precise modifications of neural wirings under genetic control.
ESTHER : Hamid_2023_Biochem.Biophys.Res.Commun_658_141
PubMedSearch : Hamid_2023_Biochem.Biophys.Res.Commun_658_141
PubMedID: 37030069
Gene_locus related to this paper: human-NLGN1

Title : Developmental synapse pathology triggered by maternal exposure to the herbicide glufosinate ammonium - Izumi_2023_Front.Mol.Neurosci_16_1298238
Author(s) : Izumi H , Demura M , Imai A , Ogawa R , Fukuchi M , Okubo T , Tabata T , Mori H , Yoshida T
Ref : Front Mol Neurosci , 16 :1298238 , 2023
Abstract : Environmental and genetic factors influence synapse formation. Numerous animal experiments have revealed that pesticides, including herbicides, can disturb normal intracellular signals, gene expression, and individual animal behaviors. However, the mechanism underlying the adverse outcomes of pesticide exposure remains elusive. Herein, we investigated the effect of maternal exposure to the herbicide glufosinate ammonium (GLA) on offspring neuronal synapse formation in vitro. Cultured cerebral cortical neurons prepared from mouse embryos with maternal GLA exposure demonstrated impaired synapse formation induced by synaptic organizer neuroligin 1 (NLGN1)-coated beads. Conversely, the direct administration of GLA to the neuronal cultures exhibited negligible effect on the NLGN1-induced synapse formation. The comparison of the transcriptomes of cultured neurons from embryos treated with maternal GLA or vehicle and a subsequent bioinformatics analysis of differentially expressed genes (DEGs) identified "nervous system development," including "synapse," as the top-ranking process for downregulated DEGs in the GLA group. In addition, we detected lower densities of parvalbumin (Pvalb)-positive neurons at the postnatal developmental stage in the medial prefrontal cortex (mPFC) of offspring born to GLA-exposed dams. These results suggest that maternal GLA exposure induces synapse pathology, with alterations in the expression of genes that regulate synaptic development via an indirect pathway distinct from the effect of direct GLA action on neurons.
ESTHER : Izumi_2023_Front.Mol.Neurosci_16_1298238
PubMedSearch : Izumi_2023_Front.Mol.Neurosci_16_1298238
PubMedID: 38098940

Title : Exposure to organophosphorus compounds of Japanese children and the indoor air quality in their residences - Yoshida_2022_Sci.Total.Environ__158020
Author(s) : Yoshida T , Mimura M , Sakon N
Ref : Sci Total Environ , :158020 , 2022
Abstract : Several organophosphorus compounds such as organophosphate pesticides (OPPs) and trialkylphosphates (TAPs) are suspected to inhibit cholinesterase activities, to affect endocrine systems or to possibly be carcinogenic. To evaluate their adverse effects on health with chronic exposure in the general population, especially in children, we measured the household exposure to OPPs and TAPs by Japanese children via all exposure pathways and the contribution of indoor air quality. First-morning void urine was collected from subjects aged 6 to 15 years (n = 132), and airborne organophosphorus compounds were sampled in the subject's bedroom for 24 h. Airborne levels of nine OPPs and three TAPs and their urinary metabolites were determined. No significant correlations were detected for any compounds between their airborne concentrations and the urinary excretion amounts of their corresponding metabolites. The estimated daily intakes were as follows (median, microg/kg b.w./d): chlorpyrifos, 0.042; diazinon, 0.067; tri-n-butylphosphate, 0.094. The 95th percentiles of the intakes for fenthion, fenitrothion and the above three compounds did not exceed their reference limit values, although one subject had a daily intake of tri-n-butylphosphate that was about twice its reference limit value. The concentration levels of the urinary metabolite of tri-n-butylphosphate in our subjects tended to be higher than those for children in many other countries. The fractions of the amounts absorbed by inhalation to the amounts absorbed via all of the exposure pathways was only 2.3 % (median) for tri-n-butylphosphate. Inhalation did not seem to contribute very much as an absorption pathway of the organophosphorus compounds in these Japanese children while they were at home. The exposure amounts of OPPs were not suggested to be high enough to adversely affect the health of these children at present on the basis of their daily intakes compared to their reference limit values.
ESTHER : Yoshida_2022_Sci.Total.Environ__158020
PubMedSearch : Yoshida_2022_Sci.Total.Environ__158020
PubMedID: 35973537

Title : Endoplasmic stress-inducing variants in carboxyl ester lipase and pancreatic cancer risk - Kawamoto_2022_Pancreatology__
Author(s) : Kawamoto M , Yoshida T , Tamura K , Dbouk M , Canto MI , Burkhart R , He J , Roberts NJ , Klein AP , Goggins M
Ref : Pancreatology , : , 2022
Abstract : BACKGROUND: Endoplasmic reticulum (ER) stress-inducing variants in several pancreatic secretory enzymes have been associated with pancreatic disease. Multiple variants in CEL, encoding carboxyl ester lipase, are known to cause maturity-onset diabetes of the young (MODY8) but have not been implicated in pancreatic cancer risk. METHODS: The prevalence of ER stress-inducing variants in the CEL gene was compared among pancreatic cancer cases vs. controls. Variants were identified by next-generation sequencing and confirmed by Sanger sequencing. Variants of uncertain significance (VUS) were assessed for their effect on the secretion of CEL protein and variants with reduced protein secretion were evaluated to determine if they induced endoplasmic reticulum stress. RESULTS: ER stress-inducing CEL variants were found in 34 of 986 cases with sporadic pancreatic ductal adenocarcinoma, and 21 of 1045 controls (P = 0.055). Most of the variants were either the CEL-HYB1 variant, the I488T variant, or the combined CEL-HYB1/I488T variant; one case had a MODY8 variant. CONCLUSION: This case/control analysis finds ER stress-inducing CEL variants are not associated with an increased likelihood of having pancreatic cancer.
ESTHER : Kawamoto_2022_Pancreatology__
PubMedSearch : Kawamoto_2022_Pancreatology__
PubMedID: 35995657

Title : Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice - Yoshida_2021_Nat.Commun_12_1848
Author(s) : Yoshida T , Yamagata A , Imai A , Kim J , Izumi H , Nakashima S , Shiroshima T , Maeda A , Iwasawa-Okamoto S , Azechi K , Osaka F , Saitoh T , Maenaka K , Shimada T , Fukata Y , Fukata M , Matsumoto J , Nishijo H , Takao K , Tanaka S , Okabe S , Tabuchi K , Uemura T , Mishina M , Mori H , Fukai S
Ref : Nat Commun , 12 :1848 , 2021
Abstract : Neuroligin 3 (NLGN3) and neurexins (NRXNs) constitute a canonical transsynaptic cell-adhesion pair, which has been implicated in autism. In autism spectrum disorder (ASD) development of sociality can be impaired. However, the molecular mechanism underlying NLGN3-mediated social development is unclear. Here, we identify non-canonical interactions between NLGN3 and protein tyrosine phosphatase delta (PTPdelta) splice variants, competing with NRXN binding. NLGN3-PTPdelta complex structure revealed a splicing-dependent interaction mode and competition mechanism between PTPdelta and NRXNs. Mice carrying a NLGN3 mutation that selectively impairs NLGN3-NRXN interaction show increased sociability, whereas mice where the NLGN3-PTPdelta interaction is impaired exhibit impaired social behavior and enhanced motor learning, with imbalance in excitatory/inhibitory synaptic protein expressions, as reported in the Nlgn3 R451C autism model. At neuronal level, the autism-related Nlgn3 R451C mutation causes selective impairment in the non-canonical pathway. Our findings suggest that canonical and non-canonical NLGN3 pathways compete and regulate the development of sociality.
ESTHER : Yoshida_2021_Nat.Commun_12_1848
PubMedSearch : Yoshida_2021_Nat.Commun_12_1848
PubMedID: 33758193
Gene_locus related to this paper: mouse-3neur

Title : Difference in substrate specificity of carboxylesterase and arylacetamide deacetylase between dogs and humans - Yoshida_2018_Eur.J.Pharm.Sci_111_167
Author(s) : Yoshida T , Fukami T , Kurokawa T , Gotoh S , Oda A , Nakajima M
Ref : Eur J Pharm Sci , 111 :167 , 2018
Abstract : Carboxylesterase (CES) and arylacetamide deacetylase (AADAC) are the major enzymes responsible for the hydrolysis of various clinical drugs. Our recent study demonstrated that the identity of the responsible hydrolase can be roughly surmised based on the chemical structures of compounds in humans. Dogs are used for preclinical studies in drug development, but the substrate specificities of dog CES and AADAC remain to be clarified. The purpose of this study is to characterize their substrate specificities. We prepared recombinant dog CES1, CES2, and AADAC. p-Nitrophenyl acetate, a general substrate for esterases, was hydrolyzed by dog CES1 and AADAC, while it was not hydrolyzed by CES2. CES2 protein was not substantially detected in the recombinant system or in the dog liver and intestinal microsomes by Western blot using anti-human CES2 antibodies. In silico analyses demonstrated slight differences in the three-dimensional structures of dog CES2 and human CES2, indicating that dog CES2 might be unstable or inactive. By evaluating the hydrolase activities of 22 compounds, which are known to be substrates of human CES and/or AADAC, we found that the activities of dog recombinant CES1 and AADAC as well as dog tissue preparations for nearly all compounds were lower than those of human enzymes. The dog enzymes that were responsible for the hydrolysis of most compounds corresponded to the human enzymes, but the following differences were observed: oseltamivir, irinotecan, and rifampicin were not hydrolyzed in the dog liver or by any of the recombinant esterases and procaine, a human CES2 substrate, was hydrolyzed by dog CES1. In conclusion, the present study could provide new finding to facilitate our understanding of species differences in drug hydrolysis, which can facilitate drug development and drug safety evaluation.
ESTHER : Yoshida_2018_Eur.J.Pharm.Sci_111_167
PubMedSearch : Yoshida_2018_Eur.J.Pharm.Sci_111_167
PubMedID: 28966098
Gene_locus related to this paper: canfa-CESDD1 , canfa-f1p6w8 , canlf-e2r2h2

Title : Structural insights into modulation and selectivity of transsynaptic neurexin-LRRTM interaction - Yamagata_2018_Nat.Commun_9_3964
Author(s) : Yamagata A , Goto-Ito S , Sato Y , Shiroshima T , Maeda A , Watanabe M , Saitoh T , Maenaka K , Terada T , Yoshida T , Uemura T , Fukai S
Ref : Nat Commun , 9 :3964 , 2018
Abstract : Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Neurexins (Nrxns) and heparan sulfate proteoglycans have been identified as presynaptic ligands for LRRTMs. Specifically, LRRTM1 and LRRTM2 bind to the Nrxn splice variant lacking an insert at the splice site 4 (S4). Here, we report the crystal structure of the Nrxn1beta-LRRTM2 complex at 3.4 A resolution. The Nrxn1beta-LRRTM2 interface involves Ca(2+)-mediated interactions and overlaps with the Nrxn-neuroligin interface. Together with structure-based mutational analyses at the molecular and cellular levels, the present structural analysis unveils the mechanism of selective binding between Nrxn and LRRTM1/2 and its modulation by the S4 insertion of Nrxn.
ESTHER : Yamagata_2018_Nat.Commun_9_3964
PubMedSearch : Yamagata_2018_Nat.Commun_9_3964
PubMedID: 30262834

Title : Improvement of Visuo-spatial Function Assessed by Raven's Colored Progressive Matrices in Dementia with Lewy Bodies by Donepezil Treatment - Yoshino_2017_Clin.Psychopharmacol.Neurosci_15_243
Author(s) : Yoshino Y , Mori T , Yoshida T , Toyota Y , Shimizu H , Iga JI , Nishitani S , Ueno SI
Ref : Clin Psychopharmacol Neurosci , 15 :243 , 2017
Abstract : Objective: Donepezil is used to improve cognitive impairment of dementia with Lewy bodies (DLB). Visuo-spatial dysfunction is a well-known symptom of DLB. Non-verbal Raven's Colored Progressive Matrices (RCPM) were used to assess both visual perception and reasoning ability in DLB subjects treated with donepezil. Methods: Twenty-one DLB patients (mean age, 78.7+/-4.5 years) were enrolled. RCPM assessment was performed at the time of starting donepezil and within one year after starting donepezil. Results: There were significant improvements of RCPM in the total scores between one year donepezil treatment (p=0.013), in both Set A score (p=0.002) and Set AB score (p=0.015), but trend in the Set B score (p=0.083). Conclusion: Donepezil is useful for improving visuo-spatial impairment in DLB, but not for problem-solving impairment.
ESTHER : Yoshino_2017_Clin.Psychopharmacol.Neurosci_15_243
PubMedSearch : Yoshino_2017_Clin.Psychopharmacol.Neurosci_15_243
PubMedID: 28783933

Title : Arylacetamide Deacetylase is Responsible for Activation of Prasugrel in Human and Dog - Kurokawa_2016_Drug.Metab.Dispos_44_409
Author(s) : Kurokawa T , Fukami T , Yoshida T , Nakajima M
Ref : Drug Metabolism & Disposition: The Biological Fate of Chemicals , 44 :409 , 2016
Abstract : Prasugrel, a thienopyridine anti-platelet agent, is pharmacologically activated by hydrolysis and hydroxylation. It is efficiently hydrolyzed in the intestine after oral administration, and the enzyme responsible for the hydrolysis in humans was demonstrated to be carboxylesterase (CES)2. Prasugrel hydrolase activity is detected in dog intestines, where CES enzymes are absent; therefore, this prompted us to investigate the involvement of an enzyme(s) other than CES. Human arylacetamide deacetylase (AADAC) is highly expressed in the small intestine, catalyzing the hydrolysis of several clinical drugs containing small acyl moieties. In the present study, we investigated whether AADAC catalyzes prasugrel hydrolysis. Recombinant human AADAC was shown to catalyze prasugrel hydrolysis with a CLint value of 50.0 +/- 1.2 ml/min/mg protein with a similar Km value to human intestinal and liver microsomes, whereas the CLint values of human CES1 and CES2 were 4.6 +/- 0.1 and 6.6 +/- 0.3 ml/min/mg protein, respectively. Inhibition studies using various chemical inhibitors and the relative activity factor approach suggested that the contribution of AADAC to prasugrel hydrolysis in human intestine is comparable to that of CES2. In dog intestine, the expression of AADAC, but not CES1 and CES2, was confirmed by measuring the marker hydrolase activities of each human esterase. The similar Km values and inhibition profiles between recombinant dog AADAC and small intestinal microsomes suggest that AADAC is a major enzyme responsible for prasugrel hydrolysis in dog intestine. Collectively, we found that AADAC largely contributes to prasugrel hydrolysis in both human and dog intestine.
ESTHER : Kurokawa_2016_Drug.Metab.Dispos_44_409
PubMedSearch : Kurokawa_2016_Drug.Metab.Dispos_44_409
PubMedID: 26718653

Title : Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-y lcarbonyl]thiazolidine): a highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes - Yoshida_2012_Bioorg.Med.Chem_20_5705
Author(s) : Yoshida T , Akahoshi F , Sakashita H , Kitajima H , Nakamura M , Sonda S , Takeuchi M , Tanaka Y , Ueda N , Sekiguchi S , Ishige T , Shima K , Nabeno M , Abe Y , Anabuki J , Soejima A , Yoshida K , Takashina Y , Ishii S , Kiuchi S , Fukuda S , Tsutsumiuchi R , Kosaka K , Murozono T , Nakamaru Y , Utsumi H , Masutomi N , Kishida H , Miyaguchi I , Hayashi Y
Ref : Bioorganic & Medicinal Chemistry , 20 :5705 , 2012
Abstract : Dipeptidyl peptidase IV (DPP-4) inhibition is suitable mechanism for once daily oral dosing regimen because of its low risk of hypoglycemia. We explored linked bicyclic heteroarylpiperazines substituted at the gamma-position of the proline structure in the course of the investigation of l-prolylthiazolidines. The efforts led to the discovery of a highly potent, selective, long-lasting and orally active DPP-4 inhibitor, 3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl carbonyl]thiazolidine (8 g), which has a unique structure characterized by five consecutive rings. An X-ray co-crystal structure of 8 g in DPP-4 demonstrated that the key interaction between the phenyl ring on the pyrazole and the S(2) extensive subsite of DPP-4 not only boosted potency, but also increased selectivity. Compound 8 g, at 0.03 mg/kg or higher doses, significantly inhibited the increase of plasma glucose levels after an oral glucose load in Zucker fatty rats. Compound 8 g (teneligliptin) has been approved for the treatment of type 2 diabetes in Japan.
ESTHER : Yoshida_2012_Bioorg.Med.Chem_20_5705
PubMedSearch : Yoshida_2012_Bioorg.Med.Chem_20_5705
PubMedID: 22959556
Gene_locus related to this paper: human-DPP4

Title : Fused bicyclic heteroarylpiperazine-substituted L-prolylthiazolidines as highly potent DPP-4 inhibitors lacking the electrophilic nitrile group - Yoshida_2012_Bioorg.Med.Chem_20_5033
Author(s) : Yoshida T , Akahoshi F , Sakashita H , Sonda S , Takeuchi M , Tanaka Y , Nabeno M , Kishida H , Miyaguchi I , Hayashi Y
Ref : Bioorganic & Medicinal Chemistry , 20 :5033 , 2012
Abstract : Hypoglycemic agents with a mechanism of depeptidyl peptidase IV (DPP-4) inhibition are suitable for once daily oral dosing. It is difficult to strike a balance between inhibitory activity and duration of action in plasma for inhibitors bearing an electrophilic nitrile group. We explored fused bicyclic heteroarylpiperazine substituted at the gamma-position of the proline structure in the investigation of L-prolylthiazolidines lacking the electrophilic nitrile. Among them, 2-trifluoroquinolyl compound 8g is the most potent, long-lasting DPP-4 inhibitor (IC(50) = 0.37 nmol/L) with high selectivity against other related peptidases. X-ray crystal structure determination of 8g indicates that CH-pi interactions generated between the quinolyl ring and the guanidinyl group of Arg358 enhances the DPP-4 inhibitory activity and selectivity.
ESTHER : Yoshida_2012_Bioorg.Med.Chem_20_5033
PubMedSearch : Yoshida_2012_Bioorg.Med.Chem_20_5033
PubMedID: 22824762
Gene_locus related to this paper: human-DPP4

Title : Synthesis of phenserine analogues and evaluation of their cholinesterase inhibitory activities - Shinada_2012_Bioorg.Med.Chem_20_4901
Author(s) : Shinada M , Narumi F , Osada Y , Matsumoto K , Yoshida T , Higuchi K , Kawasaki T , Tanaka H , Satoh M
Ref : Bioorganic & Medicinal Chemistry , 20 :4901 , 2012
Abstract : Phenserine is a potentially attractive drug for Alzheimer's disease. In order to further expand SAR study for inhibitions of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), the methyl group at the 3a-position of phenserine was replaced with an alkyl or alkenyl group, and its phenylcarbamoyl moiety was substituted at the o- or p-position. The synthetic methodology for these phenserine analogues includes the efficient cascade reactions for introduction of the 3a-substituent and assembly of the quaternary carbon center followed by reductive cyclization to the key pyrroloindoline structure. The bulkiness of the substituent at 3a-position of phenserine derivatives tends to reduce the inhibitory effect on AChE activity in the following order: methyl > ethyl > vinyl > propyl approximately allyl > reverse-prenyl groups. Among the series synthesized, the 3a-ethyl derivative demonstrated the highest AChE selectivity. In construct, the 3a-reverse-prenyl derivative indicated modest BuChE selectivity.
ESTHER : Shinada_2012_Bioorg.Med.Chem_20_4901
PubMedSearch : Shinada_2012_Bioorg.Med.Chem_20_4901
PubMedID: 22831800

Title : Association of carboxylesterase 1A genotypes with irinotecan pharmacokinetics in Japanese cancer patients - Sai_2010_Br.J.Clin.Pharmacol_70_222
Author(s) : Sai K , Saito Y , Tatewaki N , Hosokawa M , Kaniwa N , Nishimaki-Mogami T , Naito M , Sawada J , Shirao K , Hamaguchi T , Yamamoto N , Kunitoh H , Tamura T , Yamada Y , Ohe Y , Yoshida T , Minami H , Ohtsu A , Matsumura Y , Saijo N , Okuda H
Ref : British Journal of Clinical Pharmacology , 70 :222 , 2010
Abstract : WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT Association of UDP-glucuronosyltransferase 1A1 (UGT1A1) genetic polymorphisms *6 and *28 with reduced clearance of SN-38 and severe neutropenia in irinotecan therapy was demonstrated in Japanese cancer patients. * The detailed gene structure of CES1 has been characterized. * Possible functional SNPs in the promoter region have been reported. WHAT THIS STUDY ADDS * Association of functional CES1 gene number with AUC ratio [(SN-38 + SN-38G)/irinotecan], an in vivo index of CES activity, was observed in patients with irinotecan monotherapy. * No significant effects of major CES1 SNPs on irinotecan PK were detected. AIMS Human carboxylesterase 1 (CES1) hydrolyzes irinotecan to produce an active metabolite SN-38 in the liver. The human CES1 gene family consists of two functional genes, CES1A1 (1A1) and CES1A2 (1A2), which are located tail-to-tail on chromosome 16q13-q22.1 (CES1A2-1A1). The pseudogene CES1A3 (1A3) and a chimeric CES1A1 variant (var1A1) are also found as polymorphic isoforms of 1A2 and 1A1, respectively. In this study, roles of CES1 genotypes and major SNPs in irinotecan pharmacokinetics were investigated in Japanese cancer patients. METHODS CES1A diplotypes [combinations of haplotypes A (1A3-1A1), B (1A2-1A1), C (1A3-var1A1) and D (1A2-var1A1)] and the major SNPs (-75T>G and -30G>A in 1A1, and -816A>C in 1A2 and 1A3) were determined in 177 Japanese cancer patients. Associations of CES1 genotypes, number of functional CES1 genes (1A1, 1A2 and var1A1) and major SNPs, with the AUC ratio of (SN-38 + SN-38G)/irinotecan, a parameter of in vivo CES activity, were analyzed for 58 patients treated with irinotecan monotherapy. RESULTS The median AUC ratio of patients having three or four functional CES1 genes (diplotypes A/B, A/D or B/C, C/D, B/B and B/D; n= 35) was 1.24-fold of that in patients with two functional CES1 genes (diplotypes A/A, A/C and C/C; n= 23) [median (25th-75th percentiles): 0.31 (0.25-0.38) vs. 0.25 (0.20-0.32), P= 0.0134]. No significant effects of var1A1 and the major SNPs examined were observed. CONCLUSION This study suggests a gene-dose effect of functional CES1A genes on SN-38 formation in irinotecan-treated Japanese cancer patients.
ESTHER : Sai_2010_Br.J.Clin.Pharmacol_70_222
PubMedSearch : Sai_2010_Br.J.Clin.Pharmacol_70_222
PubMedID: 20653675
Gene_locus related to this paper: human-CES1

Title : [Preparedness response to hazard and toxic incidents and food terrorism] - Yoshida_2008_Yakugaku.Zasshi_128_851
Author(s) : Yoshida T
Ref : Yakugaku Zasshi , 128 :851 , 2008
Abstract : The nerve gas sarin has been responsible for tragic disasters in Matsumoto city, Nagano in 1994 and in the Tokyo subway system in 1995, which was a terrorist attack against non-military citizens. These chemical weapons exposures shocked the world, and have become sources of social concern. Thereafter there were several toxic substance-evoked incidents in Japan, specifically a poisoning due to curry containing arsenite at Wakayama city and foods and drinks containing other toxic chemicals. Following these tragic events, the Japanese government started to prepare a risk and medical management system for countering chemical and biological terrorism by developing a network of nationwide highly-sophisticated analytical instruments in police research institutes and emergency hospitals. Various ministries and National Research Institutes also provide information, guidelines and treatments for chemical and biological agents. In the event of an emergency such as a mass chemical exposure or mass food poisoning, information on "when, where, who, whom, what, how" should be reported rapidly and accurately to the first responding national organizations, such as police and fire departments, health care centers, and hospitals. Pharmaceutical scientists and pharmacists have been educated and trained on the handling of toxic chemical substances as well as drugs, and thus in the case of an event, they can become advisers for risk assessment and the analysis of drugs and chemicals. Japan has experienced food- and drink-poisonings as terrorism-like attacks. Poisonings caused by the herbicide paraquat and other pesticides including organophosphate insecticides, potassium cyanate and the above-mentioned arsenite-poisoned curry food have occurred. Because of easy access to internet-aided purchases of toxic substances and the import and export of foods, we must pay attention to possible massive exposures through foods and develop emergency management measures to counter them.
ESTHER : Yoshida_2008_Yakugaku.Zasshi_128_851
PubMedSearch : Yoshida_2008_Yakugaku.Zasshi_128_851
PubMedID: 18520132

Title : Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii - Kuwahara_2007_Curr.Biol_17_881
Author(s) : Kuwahara H , Yoshida T , Takaki Y , Shimamura S , Nishi S , Harada M , Matsuyama K , Takishita K , Kawato M , Uematsu K , Fujiwara Y , Sato T , Kato C , Kitagawa M , Kato I , Maruyama T
Ref : Current Biology , 17 :881 , 2007
Abstract : Although dense animal communities at hydrothermal vents and cold seeps rely on symbioses with chemoautotrophic bacteria [1, 2], knowledge of the mechanisms underlying these chemosynthetic symbioses is still fragmentary because of the difficulty in culturing the symbionts and the hosts in the laboratory. Deep-sea Calyptogena clams harbor thioautotrophic bacterial symbionts in their gill epithelial cells [1, 2]. They have vestigial digestive tracts and nutritionally depend on their symbionts [3], which are vertically transmitted via eggs [4]. To clarify the symbionts' metabolic roles in the symbiosis and adaptations to intracellular conditions, we present the complete genome sequence of the symbiont of Calyptogena okutanii. The genome is a circular chromosome of 1,022,154 bp with 31.6% guanine + cytosine (G + C) content, and is the smallest reported genome in autotrophic bacteria. It encodes 939 protein-coding genes, including those for thioautotrophy and for the syntheses of almost all amino acids and various cofactors. However, transporters for these substances to the host cell are apparently absent. Genes that are unnecessary for an intracellular lifestyle, as well as some essential genes (e.g., ftsZ for cytokinesis), appear to have been lost from the symbiont genome. Reductive evolution of the genome might be ongoing in the vertically transmitted Calyptogena symbionts.
ESTHER : Kuwahara_2007_Curr.Biol_17_881
PubMedSearch : Kuwahara_2007_Curr.Biol_17_881
PubMedID: 17493812
Gene_locus related to this paper: vesoh-a5cvz2

Title : Lead optimization of [(S)-gamma-(arylamino)prolyl]thiazolidine focused on gamma-substituent: Indoline compounds as potent DPP-IV inhibitors - Sakashita_2007_Bioorg.Med.Chem_15_641
Author(s) : Sakashita H , Akahoshi F , Yoshida T , Kitajima H , Hayashi Y , Ishii S , Takashina Y , Tsutsumiuchi R , Ono S
Ref : Bioorganic & Medicinal Chemistry , 15 :641 , 2007
Abstract : Dipeptidyl peptidase IV (DPP-IV) inhibitors are looked to as a potential new antidiabetic agent class. A series of [(S)-gamma-(arylamino)prolyl]thiazolidine compounds in which the electrophilic nitrile is removed are chemically stable DPP-IV inhibitors. To discover a structure for the gamma-substituent of the proline moiety more suitable for interacting with the S(2) pocket of DPP-IV, optimization focused on the gamma-substituent was carried out. The indoline compound 22e showed a DPP-IV-inhibitory activity 100-fold more potent than that of the prolylthiazolidine 10 and comparable to that of NVP-DPP728. It also displayed improved inhibitory selectivity for DPP-IV over DPP8 and DPP9 compared to compound 10. Indoline compounds such as 22e have a rigid conformation with double restriction of the aromatic moiety by proline and indoline structures to promote interaction with the binding site in the S(2) pocket of DPP-IV. The double restriction effect provides a potent inhibitory activity which compensates for the decrease in activity caused by removing the electrophilic nitrile.
ESTHER : Sakashita_2007_Bioorg.Med.Chem_15_641
PubMedSearch : Sakashita_2007_Bioorg.Med.Chem_15_641
PubMedID: 17113301

Title : [(S)-gamma-(4-Aryl-1-piperazinyl)-l-prolyl]thiazolidines as a novel series of highly potent and long-lasting DPP-IV inhibitors - Yoshida_2007_Bioorg.Med.Chem.Lett_17_2618
Author(s) : Yoshida T , Sakashita H , Akahoshi F , Hayashi Y
Ref : Bioorganic & Medicinal Chemistry Lett , 17 :2618 , 2007
Abstract : In the search for an inhibitor of dipeptidyl peptidase IV (DPP-IV) highly potent both in vitro and in vivo, we synthesized a series of L-prolylthiazolidine-based DPP-IV inhibitors having 4-arylpiperazine or 4-arylpiperidine at the gamma-position of the proline structure. Of these compounds, the 4-(5-nitro-2-pyridyl)piperazine analog 21e showed a sub-nanomolar (IC(50)=0.92 nmol/L) DPP-IV inhibitory activity and a long-lasting in vivo DPP-IV inhibition profile.
ESTHER : Yoshida_2007_Bioorg.Med.Chem.Lett_17_2618
PubMedSearch : Yoshida_2007_Bioorg.Med.Chem.Lett_17_2618
PubMedID: 17317162
Gene_locus related to this paper: human-DPP4

Title : Haplotypes and a novel defective allele of CES2 found in a Japanese population - Kim_2007_Drug.Metab.Dispos_35_1865
Author(s) : Kim SR , Sai K , Tanaka-Kagawa T , Jinno H , Ozawa S , Kaniwa N , Saito Y , Akasawa A , Matsumoto K , Saito H , Kamatani N , Shirao K , Yamamoto N , Yoshida T , Minami H , Ohtsu A , Saijo N , Sawada J
Ref : Drug Metabolism & Disposition: The Biological Fate of Chemicals , 35 :1865 , 2007
Abstract : Human carboxylesterase 2 (hCE-2) is a member of the serine esterase superfamily and is responsible for hydrolysis of a wide variety of xenobiotic and endogenous esters. hCE-2 also activates an anticancer drug, irinotecan (7-ethyl-10-[4-(1-piperidino)-1-piperidino]-carbonyloxycamptothecin, CPT-11), into its active metabolite, 7-ethyl-10-hydroxycamptothecin (SN-38). In this study, a comprehensive haplotype analysis of the CES2 gene, which encodes hCE-2, in a Japanese population was conducted. Using 21 single nucleotide polymorphisms (SNPs), including 4 nonsynonymous SNPs, 100C>T (Arg(34)Trp, *2), 424G>A (Val(142)Met, *3), 1A>T (Met(1)Leu, *5), and 617G>A (Arg(206)His, *6), and a SNP at the splice acceptor site of intron 8 (IVS8-2A>G, *4), 20 haplotypes were identified in 262 Japanese subjects. In 176 Japanese cancer patients who received irinotecan, associations of CES2 haplotypes and changes in a pharmacokinetic parameter, (SN-38 + SN-38G)/CPT-11 area under the plasma concentration curve (AUC) ratio, were analyzed. No significant association was found among the major haplotypes of the *1 group lacking nonsynonymous or defective SNPs. However, patients with nonsynonymous SNPs, 100C>T (Arg(34)Trp) or 1A>T (Met(1)Leu), showed substantially reduced AUC ratios. In vitro functional characterization of the SNPs was conducted and showed that the 1A>T SNP affected translational but not transcriptional efficiency. These findings are useful for further pharmacogenetic studies on CES2-activated prodrugs.
ESTHER : Kim_2007_Drug.Metab.Dispos_35_1865
PubMedSearch : Kim_2007_Drug.Metab.Dispos_35_1865
PubMedID: 17640957
Gene_locus related to this paper: human-CES2

Title : Localization of diacylglycerol lipase-alpha around postsynaptic spine suggests close proximity between production site of an endocannabinoid, 2-arachidonoyl-glycerol, and presynaptic cannabinoid CB1 receptor - Yoshida_2006_J.Neurosci_26_4740
Author(s) : Yoshida T , Fukaya M , Uchigashima M , Miura E , Kamiya H , Kano M , Watanabe M
Ref : Journal of Neuroscience , 26 :4740 , 2006
Abstract : 2-arachidonoyl-glycerol (2-AG) is an endocannabinoid that is released from postsynaptic neurons, acts retrogradely on presynaptic cannabinoid receptor CB1, and induces short- and long-term suppression of transmitter release. To understand the mechanisms of the 2-AG-mediated retrograde modulation, we investigated subcellular localization of a major 2-AG biosynthetic enzyme, diacylglycerol lipase-alpha (DAGLalpha), by using immunofluorescence and immunoelectron microscopy in the mouse brain. In the cerebellum, DAGLalpha was predominantly expressed in Purkinje cells. DAGLalpha was detected on the dendritic surface and occasionally on the somatic surface, with a distal-to-proximal gradient from spiny branchlets toward somata. DAGLalpha was highly concentrated at the base of spine neck and also accumulated with much lower density on somatodendritic membrane around the spine neck. However, DAGLalpha was excluded from the main body of spine neck and head. In hippocampal pyramidal cells, DAGLalpha was also accumulated in spines. In contrast to the distribution in Purkinje cells, DAGLalpha was distributed in the spine head, neck, or both, whereas somatodendritic membrane was labeled very weakly. These results indicate that DAGLalpha is essentially targeted to postsynaptic spines in cerebellar and hippocampal neurons, but its fine distribution within and around spines is differently regulated between the two neurons. The preferential spine targeting should enable efficient 2-AG production on excitatory synaptic activity and its swift retrograde modulation onto nearby presynaptic terminals expressing CB1. Furthermore, different fine localization within and around spines suggests that the distance between postsynaptic 2-AG production site and presynaptic CB1 is differentially controlled depending on neuron types.
ESTHER : Yoshida_2006_J.Neurosci_26_4740
PubMedSearch : Yoshida_2006_J.Neurosci_26_4740
PubMedID: 16672646

Title : Comparative analysis of binding energy of chymostatin with human cathepsin A and its homologous proteins by molecular orbital calculation - Yoshida_2006_J.Chem.Inf.Model_46_2093
Author(s) : Yoshida T , Lepp Z , Kadota Y , Satoh Y , Itoh K , Chuman H
Ref : J Chem Inf Model , 46 :2093 , 2006
Abstract : Cathepsin A is a mammalian lysosomal enzyme that catalyzes the hydrolysis of the carboxy-terminal amino acids of polypeptides and also regulates beta-galactosidase and neuraminidase-1 activities through the formation of a multienzymic complex in lysosomes. Human cathepsin A (hCathA), yeast carboxypeptidase (CPY), and wheat carboxypeptidase II (CPW) belong to the alpha/beta-hydrolase fold family. They have structurally similar active-site clefts, but there are small differences in the amino acid residues comprising their active sites that might determine the substrate specificity and sensitivity to microbial inhibitors including chymostatin. To examine the selectivity and binding mechanism of chymostatin as to hCathA, CPY, and CPW at the atomic level, we analyzed the interaction energy between chymostatin and each protein quantitatively by semiempirical molecular orbital calculation AM1 with the continuum solvent model. We predicted the electrostatic repulsion between the P3 cyclic arginine residue of the inhibitor and the Arg344 in the S3 active subsite of hCathA. Genetic conversion of Arg344 of the wild-type hCathA to Ile also caused an increase in its sensitivity to chymostatin, which was correlated with the decrease in the interaction energy calculated with the molecular orbital method. The present results suggest that such molecular calculation should be useful for evaluating the interactions between ligands, including inhibitors and homologous enzymes, in their docking models.
ESTHER : Yoshida_2006_J.Chem.Inf.Model_46_2093
PubMedSearch : Yoshida_2006_J.Chem.Inf.Model_46_2093
PubMedID: 16995740

Title : Biological function of the pld gene product that degrades epsilon-poly-L-lysine in Streptomyces albulus - Hamano_2006_Appl.Microbiol.Biotechnol_72_173
Author(s) : Hamano Y , Yoshida T , Kito M , Nakamori S , Nagasawa T , Takagi H
Ref : Applied Microbiology & Biotechnology , 72 :173 , 2006
Abstract : Epsilon-poly-L-lysine (epsilon-PL) is one of the few naturally occurring biopolymers and is characterized by a peptide bond between the alpha-carboxyl and epsilon-amino groups. Previously, we purified and characterized the epsilon-PL-degrading enzyme (Pld) from Streptomyces albulus, which is an epsilon-PL producer, and this enzyme was expected to confer self-resistance to the epsilon-PL produced by the organism itself. The gene encoding Pld was cloned based on the N-terminal amino acid sequence determined in this study, and a sequencing analysis revealed eight open reading frames (ORFs), i.e., ORF1 to ORF8 in the flanking region surrounding the pld gene (present in ORF5). To investigate the biological function of Pld, we constructed a knockout mutant in which the pld gene is inactivated. Studies on epsilon-PL susceptibility, epsilon-PL-degrading activity, and epsilon-PL productivity demonstrated that the pld gene does play a partial role in self-resistance and that S. albulus was found to produce other epsilon-PL-degrading enzyme(s) in addition to Pld. To the best of our knowledge, this is the first report on a self-resistance gene for a biopolymer possessing antibacterial activity.
ESTHER : Hamano_2006_Appl.Microbiol.Biotechnol_72_173
PubMedSearch : Hamano_2006_Appl.Microbiol.Biotechnol_72_173
PubMedID: 16568315
Gene_locus related to this paper: 9acto-q2wfe0

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

Title : Comparative analysis of argK-tox clusters and their flanking regions in phaseolotoxin-producing Pseudomonas syringae pathovars - Genka_2006_J.Mol.Evol_63_401
Author(s) : Genka H , Baba T , Tsuda M , Kanaya S , Mori H , Yoshida T , Noguchi MT , Tsuchiya K , Sawada H
Ref : Journal of Molecular Evolution , 63 :401 , 2006
Abstract : DNA fragments containing argK-tox clusters and their flanking regions were cloned from the chromosomes of Pseudomonas syringae pathovar (pv.) actinidiae strain KW-11 (ACT) and P. syringae pv. phaseolicola strain MAFF 302282 (PHA), and then their sequences were determined. Comparative analysis of these sequences and the sequences of P. syringae pv. tomato DC3000 (TOM) (Buell et al., Proc Natl Acad Sci USA 100:10181-10186, 2003) and pv. syringae B728a (SYR) (Feil et al., Proc Natl Acad Sci USA 102:11064-11069, 2005) revealed that the chromosomal backbone regions of ACT and TOM shared a high similarity to each other but presented a low similarity to those of PHA and SYR. Nevertheless, almost-identical DNA regions of about 38 kb were confirmed to be present on the chromosomes of both ACT and PHA, which we named "tox islands." The facts that the GC content of such tox islands was 6% lower than that of the chromosomal backbone regions of P. syringae, and that argK-tox clusters, which are considered to be of exogenous origin based on our previous studies (Sawada et al., J Mol Evol 54:437-457, 2002), were confirmed to be contained within the tox islands, suggested that the tox islands were an exogenous, mobile genetic element inserted into the chromosomes of P. syringae strains. It was also predicted that the tox islands integrated site-specifically into the homologous sites of the chromosomes of ACT and PHA in the same direction, respectively, wherein 34 common gene coding sequences (CDSs) existed. Furthermore, at the left end of the tox islands were three CDSs, which encoded polypeptides and had similarities to the members of the tyrosine recombinase family, suggesting that these putative site-specific recombinases were involved in the recent horizontal transfer of tox islands.
ESTHER : Genka_2006_J.Mol.Evol_63_401
PubMedSearch : Genka_2006_J.Mol.Evol_63_401
PubMedID: 16927007
Gene_locus related to this paper: psesy-PSPTO4540

Title : Risk factors for hospital-acquired bacteremia - Yoshida_2005_Intern.Med_44_1157
Author(s) : Yoshida T , Tsushima K , Tsuchiya A , Nishikawa N , Shirahata K , Kaneko K , Ito K , Kawakami H , Nakagawa S , Suzuki T , Kubo K , Ikeda S
Ref : Intern Med , 44 :1157 , 2005
Abstract : OBJECTIVE: Bacteremia is one of the most serious health problems associated with high morbidity and mortality. The aim of this study was to identify risk factors for bacteremia in daily medical care to facilitate rapid and accurate clinical decisions about treatment. PATIENTS AND
METHODS: We studied 306 inpatients retrospectively. Age, peripheral neutrophil count, C-reactive protein (CRP), platelets, serum total cholesterol, total protein, albumin and cholinesterase were compared in patients with positive- and negative-blood cultures. The associations between blood culture positivity and glucose tolerance, bedridden state, presence of a central venous catheter (CVC) or urinary catheter were examined. On October 14, 2002, strategies for prevention of catheter-related infection were altered in our hospital. We studied the impact of these changes on the risk of bacteremia.
RESULTS: Sixty-seven patients had positive and 239 had negative blood cultures. Age, neutrophil, platelets, total protein, albumin, and cholinesterase were significantly different between the culture-positive patients and the culture-negative patients. Multivariate analysis showed albumin and platelets as independent predictors. The bedridden state and catheter-inserted states (central venous or urinary) conferred significantly higher positive blood culture rates. Multivariate analysis showed using urinary catheters and indwelling femoral CVCs as independent risk factors. There was no significant difference in the blood culture-positive rate before and after the change in prevention strategies; before the change, 6 of 9 catheter-inserted blood culture-positive cases yielded MRSA, while 4 of 12 cultures yielded Staphylococcus epidermidis after the change. CONCLUSION: Our study highlights the risk factors of bacteremia in vulnerable patients.
ESTHER : Yoshida_2005_Intern.Med_44_1157
PubMedSearch : Yoshida_2005_Intern.Med_44_1157
PubMedID: 16357453

Title : Functional characterization of three naturally occurring single nucleotide polymorphisms in the CES2 gene encoding carboxylesterase 2 (HCE-2) - Kubo_2005_Drug.Metab.Dispos_33_1482
Author(s) : Kubo T , Kim SR , Sai K , Saito Y , Nakajima T , Matsumoto K , Saito H , Shirao K , Yamamoto N , Minami H , Ohtsu A , Yoshida T , Saijo N , Ohno Y , Ozawa S , Sawada J
Ref : Drug Metabolism & Disposition: The Biological Fate of Chemicals , 33 :1482 , 2005
Abstract : Twelve single nucleotide polymorphisms (SNPs) in the human CES2 gene, which encodes a carboxylesterase, hCE-2 [human carboxylesterase 2 (EC], have been reported in the Japanese. In this report, we have examined functional alterations of three SNPs, a nonsynonymous SNP (100C>T, R34W), an SNP at the splice acceptor site in intron 8 (IVS8-2A>G), and one newly discovered nonsynonymous SNP (424G>A, V142M). For the two nonsynonymous SNPs, the corresponding variant cDNAs were expressed in COS-1 cells. Both the R34W and V142M variants showed little esterase activities toward the anticancer agent irinotecan and two typical carboxylesterase substrates, p-nitrophenol acetate and 4-methylumbelliferyl acetate, although increased levels of cDNA-mediated protein expression were observed by Western blotting as compared with the wild type. To investigate a possible splicing aberration in IVS8-2A>G, an in vitro splicing assay was utilized and transcripts derived from CES2 gene fragments of the wild type and IVS8-2A>G were compared. Sequence analysis of the cloned transcripts revealed that IVS8-2A>G yielded mostly aberrantly spliced transcripts, including a deleted exon or a 32-bp deletion proximal to the 5' end of exon 9, which resulted in truncated hCE-2 proteins. These results suggested that 100C>T (R34W), 424G>A (V142M), and IVS8-2A>G are functionally deficient SNPs.
ESTHER : Kubo_2005_Drug.Metab.Dispos_33_1482
PubMedSearch : Kubo_2005_Drug.Metab.Dispos_33_1482
PubMedID: 16033949

Title : Large plasmid pCAR2 and class II transposon Tn4676 are functional mobile genetic elements to distribute the carbazole\/dioxin-degradative car gene cluster in different bacteria - Shintani_2005_Appl.Microbiol.Biotechnol_67_370
Author(s) : Shintani M , Yoshida T , Habe H , Omori T , Nojiri H
Ref : Applied Microbiology & Biotechnology , 67 :370 , 2005
Abstract : The carbazole-catabolic plasmid pCAR1 isolated from Pseudomonas resinovorans strain CA10 was sequenced in its entirety; and it was found that pCAR1 carries the class II transposon Tn4676 containing carbazole-degradative genes. In this study, a new plasmid designated pCAR2 was isolated from P. putida strain HS01 that was a transconjugant from mating between the carbazole-degrader Pseudomonas sp. strain K23 and P. putida strain DS1. Southern hybridization and nucleotide sequence analysis of pCAR1 and pCAR2 revealed that the whole backbone structure was very similar in each. Plasmid pCAR2 was self-transmissible, because it was transferred from strain HS01 to P. fluorescens strain IAM12022 at the frequency of 2 x 10(-7) per recipient cell. After the serial transfer of strain HS01 on rich medium, we detected the transposition of Tn4676 from pCAR2 to the HS01 chromosome. The chromosome-located copy of Tn4676 was flanked by a 6-bp target duplication, 5'-AACATC-3'. These results experimentally demonstrated the transferability of pCAR2 and the functionality of Tn4676 on pCAR2. It was clearly shown that plasmid pCAR2 and transposon Tn4676 are active mobile genetic elements that can mediate the horizontal transfer of genes for the catabolism of carbazole.
ESTHER : Shintani_2005_Appl.Microbiol.Biotechnol_67_370
PubMedSearch : Shintani_2005_Appl.Microbiol.Biotechnol_67_370
PubMedID: 15856217
Gene_locus related to this paper: psest-bpdF

Title : Secretion of bacterial xenobiotic-degrading enzymes from transgenic plants by an apoplastic expressional system: an applicability for phytoremediation - Uchida_2005_Environ.Sci.Technol_39_7671
Author(s) : Uchida E , Ouchi T , Suzuki Y , Yoshida T , Habe H , Yamaguchi I , Omori T , Nojiri H
Ref : Environ Sci Technol , 39 :7671 , 2005
Abstract : In search of an effective method for phytoremediation of wastewater contaminated with organic compounds, we investigated the application of an apoplastic expressional system that secretes useful bacterial enzymes from transgenic plants into hydroponic media through the addition of a targeting signal. We constructed transgenic Arabidopsis expressing the aromatic-cleaving extradiol dioxygenase (DbfB), which degrades 2,3-dihydroxybiphenyl (2,3-DHB), and transgenic tobacco expressing haloalkane dehalogenase (DhaA), which catalyzes hydrolytic dechlorination of 1-chlorobutane (1-CB). Although crude leaf extracts of transgenic plants expressing cytoplasm-targeted degradative enzymes showed higher activity than did those from transgenic plants expressing apoplast-targeted enzymes, the hydroponic media of the latter showed 23.2 times (DbfB) and 76.4 times (DhaA) higher activity than plants containing the cytoplasm-targeted enzymes. Addition of crystalline 2,3-DHB to 100 mL of the hydroponic medium of transgenic or wild-type seedlings revealed that only medium from the transgenic Arabidopsis expressing apoplast-targeted DbfB showed rapid ring cleavage of 2,3-DHB. Transgenic tobacco expressing apoplast-targeted DhaA also resulted in the accumulation of the dehalogenation product 1-butanol in the hydroponic medium and showed a higher tolerance to 1-CB than wild-type or transgenic plants expressing cytoplasm-targeted DhaA. These results demonstrate the usefulness of the apoplastic expression of bacterial recombinant proteins in phytoremediation.
ESTHER : Uchida_2005_Environ.Sci.Technol_39_7671
PubMedSearch : Uchida_2005_Environ.Sci.Technol_39_7671
PubMedID: 16245843

Title : Characterization of [3Fe-4S] ferredoxin DbfA3, which functions in the angular dioxygenase system of Terrabacter sp. strain DBF63 - Takagi_2005_Appl.Microbiol.Biotechnol_68_336
Author(s) : Takagi T , Habe H , Yoshida T , Yamane H , Omori T , Nojiri H
Ref : Applied Microbiology & Biotechnology , 68 :336 , 2005
Abstract : Dibenzofuran 4,4a-dioxygenase (DFDO) from Terrabacter sp. strain DBF63 is comprised of three components, i.e., terminal oxygenase (DbfA1, DbfA2), putative [3Fe-4S] ferredoxin (ORF16b product), and unidentified ferredoxin reductase. We produced DbfA1 and DbfA2 using recombinant Escherichia coli BL21(DE3) cells as a native form and purified the complex to apparent homogeneity. We also produced and purified a putative [3Fe-4S] ferredoxin encoded by ORF16b, which is located 2.5 kb downstream of the dbfA1A2 genes, with E. coli as a histidine (His)-tagged form. The reconstructed DFDO system with three purified components, i.e., DbfA1A2, His-tagged ORF16b product, and His-tagged PhtA4 (which is a tentative reductase derived from the phthalate dioxygenase system of strain DBF63) could convert fluorene to 9-fluorenol (specific activity: 14.4 nmol min(-1) mg(-1)) and convert dibenzofuran to 2,2',3-trihydroxybiphenyl. This indicates that the ORF16b product can transport electrons to the DbfA1A2 complex; and therefore it was designated DbfA3. Based on spectroscopic UV-visible absorption characteristics and electron paramagnetic resonance spectra, DbfA3 was elucidated to contain a [3Fe-4S] cluster. Ferredoxin interchangeability analysis using several types of ferredoxins suggested that the redox partner of the DbfA1A2 complex may be rather specific to DbfA3.
ESTHER : Takagi_2005_Appl.Microbiol.Biotechnol_68_336
PubMedSearch : Takagi_2005_Appl.Microbiol.Biotechnol_68_336
PubMedID: 15717172
Gene_locus related to this paper: 9mico-q3mnp3

Title : An attenuated LC16m8 smallpox vaccine: analysis of full-genome sequence and induction of immune protection - Morikawa_2005_J.Virol_79_11873
Author(s) : Morikawa S , Sakiyama T , Hasegawa H , Saijo M , Maeda A , Kurane I , Maeno G , Kimura J , Hirama C , Yoshida T , Asahi-Ozaki Y , Sata T , Kurata T , Kojima A
Ref : J Virol , 79 :11873 , 2005
Abstract : The potential threat of smallpox bioterrorism has made urgent the development of lower-virulence vaccinia virus vaccines. An attenuated LC16m8 (m8) vaccine was developed in 1975 from the Lister strain used in the World Health Organization smallpox eradication program but was not used against endemic smallpox. Today, no vaccines can be tested with variola virus for efficacy in humans, and the mechanisms of immune protection against the major intracellular mature virion (IMV) and minor extracellular enveloped virion (EEV) populations of poxviruses are poorly understood. Here, we determined the full-genome sequences of the m8, parental LC16mO (mO), and grandparental Lister (LO) strains and analyzed their evolutionary relationships. Sequence data and PCR analysis indicated that m8 was a progeny of LO and that m8 preserved almost all of the open reading frames of vaccinia virus except for the disrupted EEV envelope gene B5R. In accordance with this genomic background, m8 induced 100% protection against a highly pathogenic vaccinia WR virus in mice by a single vaccination, despite the lack of anti-B5R and anti-EEV antibodies. The immunogenicity and priming efficacy with the m8 vaccine consisting mainly of IMV were as high as those with the intact-EEV parental mO and grandparental LO vaccines. Thus, mice vaccinated with 10(7) PFU of m8 produced low levels of anti-B5R antibodies after WR challenge, probably because of quick clearance of B5R-expressing WR EEV by strong immunity induced by the vaccination. These results suggest that priming with m8 IMV provides efficient protection despite undetectable levels of immunity against EEV.
ESTHER : Morikawa_2005_J.Virol_79_11873
PubMedSearch : Morikawa_2005_J.Virol_79_11873
PubMedID: 16140764
Gene_locus related to this paper: cowvi-M5L

Title : Divergent structures of carbazole degradative car operons isolated from gram-negative bacteria - Inoue_2004_Biosci.Biotechnol.Biochem_68_1467
Author(s) : Inoue K , Widada J , Nakai S , Endoh T , Urata M , Ashikawa Y , Shintani M , Saiki Y , Yoshida T , Habe H , Omori T , Nojiri H
Ref : Biosci Biotechnol Biochem , 68 :1467 , 2004
Abstract : Southern hybridization analysis of the genomes from the newly-isolated 10 carbazole (CAR)-utilizing bacteria revealed that 8 of the isolates carried gene clusters homologous to the CAR-catabolic car operon of Pseudomonas resinovorans strain CA10. Sequencing analysis showed that two car operons and the neighboring regions of Pseudomonas sp. strain K23 are nearly identical to that of strain CA10. In contrast to strains CA10 and K23, carEF genes did not exist downstream of the car gene cluster of Janthinobacterium sp. strain J3. In the car gene clusters, strains CA10, K23 and J3 have Rieske-type ferredoxin as a component of carbazole dioxygenase, although Sphingomonas sp. strain KA1 possesses a putidaredoxin-type ferredoxin. We confirmed that this putidaredoxin-type ferredoxin CarAc can function as an electron mediator to CarAa of strain KA1. In the upstream regions of the carJ3 and carKA1 gene clusters, ORFs whose deduced amino acid sequences showed homology to GntR-family transcriptional regulators were identified.
ESTHER : Inoue_2004_Biosci.Biotechnol.Biochem_68_1467
PubMedSearch : Inoue_2004_Biosci.Biotechnol.Biochem_68_1467
PubMedID: 15277751
Gene_locus related to this paper: 9sphn-q0kj70 , 9sphn-q0kjk5 , 9sphn-q0kjm1 , 9sphn-q0kjt3 , 9sphn-q2pfa3

Title : Genetic characterization of the dibenzofuran-degrading Actinobacteria carrying the dbfA1A2 gene homologues isolated from activated sludge - Noumura_2004_FEMS.Microbiol.Lett_239_147
Author(s) : Noumura T , Habe H , Widada J , Chung JS , Yoshida T , Nojiri H , Omori T
Ref : FEMS Microbiology Letters , 239 :147 , 2004
Abstract : Thirteen dibenzofuran (DF)-utilizing bacteria carrying the DF terminal dioxygenase genes homologous to those of Terrabacter sp. strain DBF63 (dbfA1A2) were newly isolated from activated sludge samples. The amplified ribosomal DNA restriction analysis and the hybridization analyses showed that these strains were grouped into five genetically different types of bacteria. The sequence analyses of the 16S rRNA genes and the dbfA1A2 homologues from these five selected isolates revealed that the isolates belonged to the genus Rhodococcus, Terrabacter or Janibacter and that they shared 99-100% conserved dbfA1A2 homologues. We investigated the genetic organizations flanking the dbfA1A2 homologues and showed that the minimal conserved DNA region present in all five selected isolates consisted of an approximately 9.0-kb region and that their outer regions became abruptly non-homologous. Among them, Rhodococcus sp. strain DFA3 possessed not only the 9.0-kb region but also the 6.2-kb region containing dbfA1A2 homologues. Sequencing of their border regions suggested that some genetic rearrangement might have occurred with insertion sequence-like elements. Also, within their conserved regions, some insertions or deletions were observed.
ESTHER : Noumura_2004_FEMS.Microbiol.Lett_239_147
PubMedSearch : Noumura_2004_FEMS.Microbiol.Lett_239_147
PubMedID: 15451113
Gene_locus related to this paper: 9mico-q3mnp3 , rhosp-ORF4

Title : Characterization of the upper pathway genes for fluorene metabolism in Terrabacter sp. strain DBF63 - Habe_2004_J.Bacteriol_186_5938
Author(s) : Habe H , Chung JS , Kato H , Ayabe Y , Kasuga K , Yoshida T , Nojiri H , Yamane H , Omori T
Ref : Journal of Bacteriology , 186 :5938 , 2004
Abstract : Genes involved in the degradation of fluorene to phthalate were characterized in the fluorene degrader Terrabacter sp. strain DBF63. The initial attack on both fluorene and 9-fluorenone was catalyzed by DbfA to yield 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone, respectively. The FlnB protein exhibited activities against both 9-fluorenol and 1,1a-dihydroxy-1-hydro-9-fluorenone to produce 9-fluorenone and 2'-carboxy-2,3-dihydroxybiphenyl, respectively. FlnD is a heteromeric protein encoded by flnD1 and ORF16, being a member of the class III two-subunit extradiol dioxygenase. FlnE was identified as a serine hydrolase for the meta-cleavage products that yield phthalate.
ESTHER : Habe_2004_J.Bacteriol_186_5938
PubMedSearch : Habe_2004_J.Bacteriol_186_5938
PubMedID: 15317800
Gene_locus related to this paper: 9mico-q3mnp3

Title : Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10 - Nojiri_2003_Biosci.Biotechnol.Biochem_67_36
Author(s) : Nojiri H , Taira H , Iwata K , Morii K , Nam JW , Yoshida T , Habe H , Nakamura S , Shimizu K , Yamane H , Omori T
Ref : Biosci Biotechnol Biochem , 67 :36 , 2003
Abstract : 2-Hydroxy-6-oxo-6-(2'-aminophenyl)-hexa-2,4dienoic acid [6-(2'-aminophenyl)-HODA] hydrolase, involved in carbazole degradation by Pseudomonas resinovorans strain CA10, was purified to near homogeneity from an overexpressing Escherichia coli strain. The enzyme was dimeric, and its optimum pH was 7.0-7.5. Phylogenetic analysis showed the close relationship of this enzyme to other hydrolases involved in the degradation of monocyclic aromatic compounds, and this enzyme was specific for 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (6-phenyl-HODA), having little activity toward 2-hydroxy-6-oxohepta-2,4-dienoic acid and 2-hydroxymuconic semialdehyde. The enzyme had a Km of 2.51 microM and k(cat) of 2.14 (s(-1)) for 6-phenyl-HODA (50 mM sodium phosphate, pH 7.5, 25 degrees C). The effect of the presence of an amino group or hydroxyl group at the 2'-position of phenyl moiety of 6-phenyl-HODA on the enzyme activity was found to be small; the activity decreased only in the order of 6-(2'-aminophenyl)-HODA (2.44 U/mg) > 6-phenyl-HODA (1.99 U / mg) > 2-hydroxy-6-oxo-6-(2'-hydroxyphenyl)-hexa-2,4-dienoic acid (1.05 U/mg). The effects of 2'-substitution on the activity were in accordance with the predicted reactivity based on the calculated lowest unoccupied molecular orbital energy for these substrates.
ESTHER : Nojiri_2003_Biosci.Biotechnol.Biochem_67_36
PubMedSearch : Nojiri_2003_Biosci.Biotechnol.Biochem_67_36
PubMedID: 12619671
Gene_locus related to this paper: psesp-Q9AQN6

Title : Crystal structure of a histidine-tagged serine hydrolase involved in the carbazole degradation (CarC enzyme) - Habe_2003_Biochem.Biophys.Res.Commun_303_631
Author(s) : Habe H , Morii K , Fushinobu S , Nam JW , Ayabe Y , Yoshida T , Wakagi T , Yamane H , Nojiri H , Omori T
Ref : Biochemical & Biophysical Research Communications , 303 :631 , 2003
Abstract : 2-Hydroxy-6-oxo-6-(2(')-aminophenyl)-hexa-2,4-dienoate hydrolases (CarC enzymes) from two carbazole-degrading bacteria were purified using recombinant Escherichia coli strains with the histidine (His)-tagged purification system. The His-tagged CarC (ht-CarC) enzymes from Pseudomonas resinovorans strain CA10 (ht-CarC(CA10)) and Janthinobacterium sp. strain J3 (ht-CarC(J3)) exhibited hydrolase activity toward 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate as the purified native CarC(CA10) did. ht-CarC(J3) was crystallized in the space group I422 with cell dimensions of a=b=130.3A, c=84.5A in the hexagonal setting, and the crystal structure of ht-CarC(J3) was determined at 1.86A resolution. The final refined model of ht-CarC(J3) yields an R-factor of 21.6%, although the electron-density corresponding to Ile146 to Asn155 was ambiguous in the final model. We compared the known structures of BphD from Rhodococcus sp. strain RHA1 and CumD from Pseudomonas fluorescens strain IP01. The backbone conformation of ht-CarC(J3) was better superimposed with CumD than with BphD(RHA1). The side-chain directions of Arg185 and Trp262 residues in the substrate binding pockets of these enzymes were different among these proteins, suggesting that these residues may take a conformational change during the catalytic cycles.
ESTHER : Habe_2003_Biochem.Biophys.Res.Commun_303_631
PubMedSearch : Habe_2003_Biochem.Biophys.Res.Commun_303_631
PubMedID: 12659866
Gene_locus related to this paper: jansp-Carc , psest-bpdF

Title : Twelve novel single nucleotide polymorphisms in the CES2 gene encoding human carboxylesterase 2 (hCE-2) - Kim_2003_Drug.Metab.Pharmacokinet_18_327
Author(s) : Kim SR , Nakamura T , Saito Y , Sai K , Nakajima T , Saito H , Shirao K , Minami H , Ohtsu A , Yoshida T , Saijo N , Ozawa S , Sawada J
Ref : Drug Metab Pharmacokinet , 18 :327 , 2003
Abstract : Twelve novel single nucleotide polymorphisms (SNPs) were found in the CES2 gene from 153 Japanese individuals, who were administered irinotecan or steroidal drugs. The detected SNPs were as follows:1) SNP, MPJ6_CS2001; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-CTGGAACAACTCG/CCTCCCCTCGGAA-3'. 2) SNP, MPJ6_CS2002; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-AACCACCACCGCT/CGATCCTAGCAGG-3'. 3) SNP, MPJ6_CS2003; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-AAATGTTTGTCAA/GGTGGATAAATGA-3'. 4) SNP, MPJ6_CS2004; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-CCTCCTATCGATC/GCCCCAGCGCGCT-3'. 5) SNP, MPJ6_CS2005; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-GCCAGTCCCATCC/TGGACCACACACA-3'. 6) SNP, MPJ6_CS2006; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-GCTGGGCAACCCG/AGGCTGAGCGGGG-3'. 7) SNP, MPJ6_CS2007; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-CAAGCACGCAACC/TGGCAACTGGGGC-3'. 8) SNP, MPJ6_CS2008; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-CATGGAGAGTGGC/TGTGGCCCTCCTG-3'. 9) SNP, MPJ6_CS2009; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-CCTGTTCTTGGCC/TAGGGCCTTGGGC-3'. 10) SNP, MPJ6_CS2010; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-CCCATCCCCAGCT/AACAGACTCTCTC-3'. 11) SNP, MPJ6_CS2011; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-TCCACCTGGGGTA/GGATGTTGCCTCC-3'. 12) SNP, MPJ6_CS2013; GENE NAME, CES2; ACCESSION NUMBER, NT_010498.13; LENGTH, 25 bases; 5'-GGACTGGGGACCG/AAGGTCTCGGGGG-3'The frequencies were 0.029 for MPJ6_CS2004 and CS2013, 0.026 for MPJ6_CS2009, 0.013 for MPJ6_CS2001, 0.007 for MPJ6_CS2003, and 0.003 for the other 7 SNPs. Among these SNPs, MPJ6_CS2005 (100C>T) resulted in an amino acid alteration (R34W), and MPJ6_CS2007 (579C>T) and MPJ6_CS2008 (765C>T) were synonymous (T193T and G255G, respectively). Furthermore, MPJ6_CS2011 (IVS8-2A>G) resulted in variation at ther 3' splice acceptor site.
ESTHER : Kim_2003_Drug.Metab.Pharmacokinet_18_327
PubMedSearch : Kim_2003_Drug.Metab.Pharmacokinet_18_327
PubMedID: 15618752
Gene_locus related to this paper: human-CES2

Title : Identification of three novel salicylate 1-hydroxylases involved in the phenanthrene degradation of Sphingobium sp. strain P2 - Pinyakong_2003_Biochem.Biophys.Res.Commun_301_350
Author(s) : Pinyakong O , Habe H , Yoshida T , Nojiri H , Omori T
Ref : Biochemical & Biophysical Research Communications , 301 :350 , 2003
Abstract : Five sets of large and small subunits of terminal oxygenase (ahdA1[a-e] and ahdA2[a-e]) and a single gene set encoding ferredoxin (ahdA3) and ferredoxin reductase (ahdA4) were found to be scattered through 15.8- and 14-kb DNA fragments of phenanthrene-degrading Sphingobium sp. strain P2. RT-PCR analysis indicated the inducible and specific expression of ahdA3, ahdA4, and three sets of genes for terminal oxygenase (ahdA1[c-e] and ahdA2[c-e]) in this strain grown on phenanthrene. The biotransformation experiments with resting cells of Escherichia coli JM109 harboring recombinant ahd genes revealed that AhdA2cA1c, AhdA1dA2d, and AhdA1eA2e can all function as a salicylate 1-hydroxylase which converts salicylate, a metabolic intermediate of phenanthrene, to catechol in cooperation with the electron transport proteins AhdA3A4. The first two oxygenases exhibited a broad range of substrate specificities such that they also catalyzed the hydroxylation of methyl- and chloro-substituted salicylates to produce their corresponding substituted catechols.
ESTHER : Pinyakong_2003_Biochem.Biophys.Res.Commun_301_350
PubMedSearch : Pinyakong_2003_Biochem.Biophys.Res.Commun_301_350
PubMedID: 12565867
Gene_locus related to this paper: psepa-q6qhu7

Title : Complete nucleotide sequence of carbazole\/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676 - Maeda_2003_J.Mol.Biol_326_21
Author(s) : Maeda K , Nojiri H , Shintani M , Yoshida T , Habe H , Omori T
Ref : Journal of Molecular Biology , 326 :21 , 2003
Abstract : The car and ant operons originally isolated from Pseudomonas resinovorans strain CA10 contain the genes encoding the carbazole/dioxin-degrading enzymes and anthranilate 1,2-dioxygenase, respectively, and are located on the plasmid pCAR1. The entire nucleotide sequence of pCAR1 was determined to elucidate the mechanism by which the car operon may have been assembled and distributed in nature. pCAR1 is a 199,035-bp circular plasmid, and carries 190 open reading frames. Although the incompatibility group of pCAR1 is unclear, its potential origin for replication, OriP, and Rep and Par proteins appeared to be closely related to those of plasmid pL6.5 isolated from Pseudomonas fluorescens. The potential tellurite-resistance klaABC genes identified in the neighboring region of repA gene were also related to those in IncP plasmid originally identified from pseudomonads. On the other hand, we found genes encoding proteins that showed low but significant homology (20-45% identity) with Trh and Tra proteins from Enterobacteriaceae, which are potentially involved in conjugative transfer of plasmids or genomic island, suggesting that pCAR1 is also a conjugative plasmid. In pCAR1, we found tnpAcCST genes that encoded the proteins showing >70% length-wise identities with those are encoded by the toluene/xylene-degrading transposon Tn4651 of TOL plasmid pWW0. Both car and ant degradative operons were found within a 72.8-kb Tn4676 sequence defined by flanking tnpAcC and tnpST genes and bordered by a 46-bp inverted repeat (IR). Within Tn4676 and its flanking region, we found the remnants of numerous mobile genetic elements, such as the duplicated transposase genes that are highly homologous to tnpR of Tn4653 and the multiple candidates of IRs for Tn4676 and Tn4653-like element. We also found distinct regions with high and low G+C contents within Tn4676, which contain an ant operon and car operon, respectively. These results suggested that multiple step assembly could have taken place before the current structure of Tn4676 had been captured.
ESTHER : Maeda_2003_J.Mol.Biol_326_21
PubMedSearch : Maeda_2003_J.Mol.Biol_326_21
PubMedID: 12547188
Gene_locus related to this paper: psere-Q8GI31 , psest-bpdF

Title : Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63 - Habe_2003_Appl.Microbiol.Biotechnol_61_44
Author(s) : Habe H , Miyakoshi M , Chung J , Kasuga K , Yoshida T , Nojiri H , Omori T
Ref : Applied Microbiology & Biotechnology , 61 :44 , 2003
Abstract : Phthalate is a metabolic intermediate of the pathway of fluorene (FN) degradation via angular dioxygenation. A gene cluster responsible for the conversion of phthalate to protocatechuate was cloned from the dibenzofuran (DF)- and FN-degrading bacterium Terrabacter sp. strain DBF63 and sequenced. The genes encoding seven catabolic enzymes, oxygenase large subunit of phthalate 3,4-dioxygenase (phtA1), oxygenase small subunit of phthalate 3,4-dioxygenase (phtA2), cis-3,4-dihydroxy-3,4-dihydrophthalate dehydrogenase (phtB), [3Fe-4S] or [4Fe-4S] type of ferredoxin (phtA3), ferredoxin reductase (phtA4), 3,4-dihydroxyphthalate decarboxylase (phtC) and putative regulatory protein (phtR), were found in the upstream region of the angular dioxygenase gene (dbfA1A2), encoded in this order. Escherichia coli carrying phtA1A2BA3A4 genes converted phthalate to 3,4-dihydroxyphthalate, and the 3,4-dihydroxyphthalate decarboxylase activity by E. coli cells carrying phtC was finally detected with the introduction of a Shine-Dalgarno sequence in the upstream region of its initiation codon. Homology analysis on the upstream region of the pht gene cluster revealed that there was an insertion sequence (IS) (ISTesp2; ORF14 and its flanking region), part of which was almost 100% identical to the orf1 and its flanking region adjacent to the extradiol dioxygenase gene ( bphC1) involved in the DF degradation of Terrabacter sp. strain DPO360 [Schmid et al. (1997) J Bacteriol 179:53-62]. This suggests that ISTesp2 plays a role in the metabolism of aromatic compounds in Terrabacter sp. strains DBF63 and DPO360.
ESTHER : Habe_2003_Appl.Microbiol.Biotechnol_61_44
PubMedSearch : Habe_2003_Appl.Microbiol.Biotechnol_61_44
PubMedID: 12658514
Gene_locus related to this paper: 9mico-q3mnp3

Title : Sphingomonas sp. strain KA1, carrying a carbazole dioxygenase gene homologue, degrades chlorinated dibenzo-p-dioxins in soil - Habe_2002_FEMS.Microbiol.Lett_211_43
Author(s) : Habe H , Ashikawa Y , Saiki Y , Yoshida T , Nojiri H , Omori T
Ref : FEMS Microbiology Letters , 211 :43 , 2002
Abstract : Hybridization analysis showed that a newly isolated carbazole (CAR)-degrading bacterium Sphingomonas sp. strain KA1 did not possess the gene encoding the terminal oxygenase component (carAa) of CAR 1,9a-dioxygenase at high homology (more than 90% identity) to that of another CAR-degrader, Pseudomonas resinovorans strain CA10. However, PCR experiments using the primers for amplifying the internal fragment of the carAa gene (810 bp for strain CA10) showed that a PCR product of unexpected size (1100 bp) was amplified. Sequence analysis revealed that this DNA region contained the portion of two possible ORFs, which showed moderate homology to CarAa and CarBa from strain CA10 (61% and 40% identities at the amino acid level, respectively). Inoculation of strain KA1 into dioxin-contaminated model soil resulted in 96% and 70% degradation of 2-mono- and 2,3-dichlorinated dibenzo-p-dioxin, respectively, after 7-day incubation.
ESTHER : Habe_2002_FEMS.Microbiol.Lett_211_43
PubMedSearch : Habe_2002_FEMS.Microbiol.Lett_211_43
PubMedID: 12052549
Gene_locus related to this paper: 9sphn-q0kj70 , 9sphn-q0kjk5 , 9sphn-q0kjm1 , 9sphn-q0kjt3 , 9sphn-q2pfa3

Title : Organization and transcriptional characterization of catechol degradation genes involved in carbazole degradation by Pseudomonas resinovorans strain CA10 - Nojiri_2002_Biosci.Biotechnol.Biochem_66_897
Author(s) : Nojiri H , Maeda K , Sekiguchi H , Urata M , Shintani M , Yoshida T , Habe H , Omori T
Ref : Biosci Biotechnol Biochem , 66 :897 , 2002
Abstract : Pseudomonas resinovorans strain CA10 assimilates catechol, which is an intermediate of carbazole degradation, by ortho cleavage pathway enzymes encoded by the catR, catBCA operon. Cat proteins of strain CA10 were very similar to those of P. putida, although the relatedness in non-coding regions was not high. It was found that catBCA genes were induced in carbazole-grown cells as a single transcriptional unit.
ESTHER : Nojiri_2002_Biosci.Biotechnol.Biochem_66_897
PubMedSearch : Nojiri_2002_Biosci.Biotechnol.Biochem_66_897
PubMedID: 12036072
Gene_locus related to this paper: psesp-Q9AQQ0

Title : Enhanced degradation of carbazole and 2,3-dichlorodibenzo-p-dioxin in soils by Pseudomonas resinovorans strain CA10 - Widada_2002_Chemosphere_49_485
Author(s) : Widada J , Nojiri H , Yoshida T , Habe H , Omori T
Ref : Chemosphere , 49 :485 , 2002
Abstract : We studied the degradation of carbazole (CAR) and 2,3-dichlorodibenzo-p-dioxin (2,3-DCDD) in soils inoculated with carbazole- and dioxin-degrader Pseudomonas resinovorans strain CA10. By using Tn5-based transposon delivery systems, this bacterium was chromosomally marked with a tandem green fluorescent protein (gfp) gene. Real-time competitive PCR and direct counting using the (gfp) marker were employed to monitor the total number of carbazole 1,9a-dioxygenase gene (carAa) and survival of CA10 cells in the soil and soil slurry microcosms. Bioaugmentation studies indicated that the survival of the marked CA10 cells in soil microcosms was strongly influenced by pH and organic matter. While the number of the marked CA10 cells decreased rapidly in pH 6 with low organic matter, a high cell density was maintained in pH 7.3 with 2.5% organic matters up to 21 days after inoculation. In pH 7.3 soil, the period needed for complete degradation of CAR (100 microg kg(-1)) was markedly shortened from 21 to 7 days by the inoculation with the CA10 cells. Single inoculation of CA10 cells into the soil slurry system of 2,3-DCDD-contaminated soil enhanced the degradation of 2,3-DCDD from 25.0% to 37.0%. In this system, the population density of CA10 cells and the total number of carAa gene were maintained up to 14 days after inoculation. By repeated inoculation (every 2 days) with CA10 cells each at a density of 10(9) CFU g(-1) of soil, almost all of the 2,3-DCDD (1 microg kg(-1)) was degraded within 14 days. Results of these experiments suggest that P. resinovorans strain CA10 may be an important resource for bioremediation of CAR and chlorinated dibenzo-p-dioxin in contaminated soils.
ESTHER : Widada_2002_Chemosphere_49_485
PubMedSearch : Widada_2002_Chemosphere_49_485
PubMedID: 12363321

Title : Genetic characterization and evolutionary implications of a car gene cluster in the carbazole degrader Pseudomonas sp. strain CA10 - Nojiri_2001_J.Bacteriol_183_3663
Author(s) : Nojiri H , Sekiguchi H , Maeda K , Urata M , Nakai S , Yoshida T , Habe H , Omori T
Ref : Journal of Bacteriology , 183 :3663 , 2001
Abstract : The nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of the carAaAaBaBbCAc(ORF7)Ad genes of carbazole-degrading Pseudomonas sp. strain CA10 were determined. Thirty-two open reading frames (ORFs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (carAaAaBaBbCAcAdDFE) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. The high identities (68 to 83%) with the enzymes involved in 3-(3-hydroxyphenyl)propionic acid degradation were observed only for CarFE. This observation, together with the fact that two ORFs are inserted between carD and carFE, makes it quite likely that the carFE genes were recruited from another locus. In the 21-kb region upstream from carAa, aromatic-ring-hydroxylating dioxygenase genes (ORF26, ORF27, and ORF28) were found. Inductive expression in carbazole-grown cells and the results of homology searching indicate that these genes encode the anthranilate 1,2-dioxygenase involved in carbazole degradation. Therefore, these ORFs were designated antABC. Four homologous insertion sequences, IS5car1 to IS5car4, were identified in the neighboring regions of car and ant genes. IS5car2 and IS5car3 constituted the putative composite transposon containing antABC. One-ended transposition of IS5car2 together with the 5' portion of antA into the region immediately upstream of carAa had resulted in the formation of IS5car1 and ORF9. In addition to the insertion sequence-dependent recombination, gene duplications and presumed gene fusion were observed. In conclusion, through the above gene rearrangement, the novel genetic structure of the car gene cluster has been constructed. In addition, it was also revealed that the car and ant gene clusters are located on the megaplasmid pCAR1.
ESTHER : Nojiri_2001_J.Bacteriol_183_3663
PubMedSearch : Nojiri_2001_J.Bacteriol_183_3663
PubMedID: 11371531
Gene_locus related to this paper: psesp-Q9AQN6 , psest-bpdF

Title : Isolation and characterization of the genes encoding a novel oxygenase component of angular dioxygenase from the gram-positive dibenzofuran-degrader Terrabacter sp. strain DBF63 - Kasuga_2001_Biochem.Biophys.Res.Commun_283_195
Author(s) : Kasuga K , Habe H , Chung JS , Yoshida T , Nojiri H , Yamane H , Omori T
Ref : Biochemical & Biophysical Research Communications , 283 :195 , 2001
Abstract : A gram-positive bacterium Terrabacter sp. strain DBF63 is able to degrade dibenzofuran (DF) via initial dioxygenation by a novel angular dioxygenase. The dbfA1 and dbfA2 genes, which encode the large and small subunits of the dibenzofuran 4,4a-dioxygenase (DFDO), respectively, were isolated by a polymerase chain reaction-based method. DbfA1 and DbfA2 showed moderate homology to the large and small subunits of other ring-hydroxylating dioxygenases (less than 40%), respectively, and some motifs such as the Fe(II) binding site and the [2Fe-2S] cluster ligands were conserved in DbfA1. DFDO activity was confirmed in Escherichia coli cells containing the cloned dbfA1 and dbfA2 genes with the complementation of nonspecific ferredoxin and ferredoxin reductase component of E. coli. Under this condition, these cells exhibited angular dioxygenation of DF and dibenzo-p-dioxin, and monooxygenation of fluorene, but not angular dioxygenation of carbazole, xanthene, and phenoxathiin. Phylogenetic analysis revealed that DbfA1 formed a branch with recently reported large subunits of polycyclic aromatic hydrocarbon (PAH) dioxygenase from gram-positive bacteria but did not cluster with that of other angular dioxygenases, i.e., DxnA1 from Sphingomonas sp. strain RW1 [Armengaud, J., Happe, B., and Timmis, K. N. J. Bacteriol. 180, 3954-3966, 1998] and CarAa from Pseudomonas sp. strain CA10 [Sato, S., Nam, J.-W., Kasuga, K., Nojiri, H., Yamane, H., and Omori, T. J. Bacteriol. 179, 4850-4858, 1997].
ESTHER : Kasuga_2001_Biochem.Biophys.Res.Commun_283_195
PubMedSearch : Kasuga_2001_Biochem.Biophys.Res.Commun_283_195
PubMedID: 11322788
Gene_locus related to this paper: 9mico-q3mnp3 , tersp-Q93UV1

Title : A Japanese patient with lipoprotein lipase deficiency homozygous for the Gly188Glu mutation prevalent worldwide - Yoshida_2000_J.Atheroscler.Thromb_7_45
Author(s) : Yoshida T , Gotoda T , Okubo M , Iizuka Y , Ishibashi S , Kojima T , Murakami T , Murase T , Yamada N
Ref : J Atheroscler Thromb , 7 :45 , 2000
Abstract : We studied the molecular basis of familial lipoprotein lipase (LPL) deficiency in a new Japanese kindred. The proband was a four-month-old infant with severe hyperchylomicronemia. In postheparin plasma, LPL activity was virtually absent, although LPL mass was detectable. Single strand conformational polymorphism (SSCP) analysis showed an abnormal band with exon 5 of the LPL gene that was amplified by PCR from the proband's genomic DNA. DNA sequence analysis of the amplified fragment demonstrated that the proband was homozygous for a G-to-A change at nucleotide position 818 resulting in the substitution of glutamic acid for glycine at codon 188. Although this is among the first Gly188Glu mutations identified in Japanese, the missense mutation has previously been reported as a prevalent cause of familial LPL deficiency worldwide and has been proposed to have a common origin. However, DNA haplotype analysis with either restriction fragment length polymorphism (RFLP) or microsatellite markers revealed that the DNA haplotype of the proband was not identical to the haplotype previously reported as common to the other patients with the Gly188Glu mutation. These results add the Gly188Glu mutation to the growing list of LPL gene mutations underlying familial LPL deficiency in Japanese and indicate that the origin of the Gly188Glu mutation is not necessarily common but would be multicentric at least in part.
ESTHER : Yoshida_2000_J.Atheroscler.Thromb_7_45
PubMedSearch : Yoshida_2000_J.Atheroscler.Thromb_7_45
PubMedID: 11425044
Gene_locus related to this paper: human-LPL

Title : Probucol prevents the progression of fatty liver in MSG obese mice - Yoshida_1995_Exp.Clin.Endocrinol.Diabetes_103_119
Author(s) : Yoshida T , Yoshioka K , Sakane N , Umekawa T , Kondo M
Ref : Experimental & Clinical Endocrinology & Diabetes , 103 :119 , 1995
Abstract : We investigated the effect of Probucol in preventing fatty liver in monosodium-L-glutamate (MSG) treated obese mice and control mice fed a high fat diet. MSG mice became significantly obese 9 weeks after birth with higher levels of serum blood glucose, total cholesterol, HDL-cholesterol, GPT, and cholinesterase, and had greater triglyceride contents in their livers relative to control mice. Morphologically, MSG obese mice also had a marked fatty liver. Administration of Probucol mixed with the high fat diet for 2 weeks significantly decreased the serum levels of total cholesterol and HDL-cholesterol, and liver triglyceride contents in both MSG and control mice. Morphologically, the livers were less fatty after Probucol treatment. These results suggest that Probucol prevents the development of fatty liver, and in addition reduces hypercholesterolemia.
ESTHER : Yoshida_1995_Exp.Clin.Endocrinol.Diabetes_103_119
PubMedSearch : Yoshida_1995_Exp.Clin.Endocrinol.Diabetes_103_119
PubMedID: 7553075

Title : Cloning, sequencing, and expression of the dipeptidyl peptidase IV gene from Flavobacterium meningosepticum in Escherichia coli - Kabashima_1995_Arch.Biochem.Biophys_320_123
Author(s) : Kabashima T , Yoshida T , Ito K , Yoshimoto T
Ref : Archives of Biochemistry & Biophysics , 320 :123 , 1995
Abstract : The dipeptidyl peptidase IV (DP IV, EC gene from Flavobacterium meningosepticum was cloned by Southern and colony hybridizations using probes amplified by PCR, and expressed in Escherichia coli DH1. E. coli DH1 harboring pFDP-H1, which was a subclone derived from the positive clone pFDP-1, showed 3.5-fold higher activity than F. meningosepticum. Nucleotide sequencing analysis revealed an open reading frame of 2133 bp, coding for a protein of 711 amino acids with a predicted molecular weight of 80,626. The expressed enzyme in E. coli DH1/pFDP-H1 was purified about 345-fold with an activity recovery of 12.3%. The molecular weight of the purified enzyme was estimated to be 75,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 160,000 by gel filtration, respectively, suggesting a dimeric form of the native enzyme. The deduced amino acid sequence of DP IV was homologous to those of the serine proteases of the "prolyl endopeptidase family." A sequence near the C-terminal region and the putative catalytic triad residues were well conserved among these enzymes.
ESTHER : Kabashima_1995_Arch.Biochem.Biophys_320_123
PubMedSearch : Kabashima_1995_Arch.Biochem.Biophys_320_123
PubMedID: 7793970
Gene_locus related to this paper: flame-Q47900