Nomura N

References (20)

Title : Dechlorination of chloral hydrate is influenced by the biofilm adhesin protein LapA in Pseudomonas putida LF54 - Zhang_2013_Appl.Environ.Microbiol_79_4166
Author(s) : Zhang W , Huhe , Pan Y , Toyofuku M , Nomura N , Nakajima T , Uchiyama H
Ref : Applied Environmental Microbiology , 79 :4166 , 2013
Abstract : LapA is the largest surface adhesion protein of Pseudomonas putida that initiates biofilm formation. Here, by using transposon insertion mutagenesis and a conditional lapA mutant, we demonstrate for the first time that LapA influences chloral hydrate (CH) dechlorination in P. putida LF54.
ESTHER : Zhang_2013_Appl.Environ.Microbiol_79_4166
PubMedSearch : Zhang_2013_Appl.Environ.Microbiol_79_4166
PubMedID: 23603683
Gene_locus related to this paper: psepu-PIP , psepu-PP1500 , psepu-PP4249 , psepu-q9wwz4 , psepu-u2t3m5

Title : Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome - Mayumi_2008_Appl.Microbiol.Biotechnol_79_743
Author(s) : Mayumi D , Akutsu-Shigeno Y , Uchiyama H , Nomura N , Nakajima-kambe T
Ref : Applied Microbiology & Biotechnology , 79 :743 , 2008
Abstract : Many poly(lactic acid) (PLA)-degrading microorganisms have been isolated from the natural environment by culture-based methods, but there is no study about unculturable PLA-degrading microorganisms. In this study, we constructed a metagenomic library consisting of the DNA extracted from PLA disks buried in compost. We identified three PLA-degrading genes encoding lipase or hydrolase. The purified enzymes degraded not only PLA, but also various aliphatic polyesters, tributyrin, and p-nitrophenyl esters. From their substrate specificities, the PLA depolymerases were classified into an esterase rather than a lipase. Among the PLA depolymerases, PlaM4 exhibited thermophilic properties; that is, it showed the highest activity at 70 degrees C and was stable even after incubation for 1 h at 50 degrees C. PlaM4 had absorption and degradation activities for solid PLA at 60 degrees C, which indicates that the enzyme can effectively degrade PLA in a high-temperature environment. On the other hand, the enzyme classification based on amino acid sequences showed that the other PLA depolymerases, PlaM7 and PlaM9, were not classified into known lipases or esterases. This is the first report on the identification and characterization of PLA depolymerase from a metagenome.
ESTHER : Mayumi_2008_Appl.Microbiol.Biotechnol_79_743
PubMedSearch : Mayumi_2008_Appl.Microbiol.Biotechnol_79_743
PubMedID: 18461319
Gene_locus related to this paper: 9bact-a4uz11 , 9bact-a4uz12 , 9bact-a4uz10 , 9bact-a4uz14

Title : Isolation of a bacterium that degrades urethane compounds and characterization of its urethane hydrolase - Akutsu-Shigeno_2006_Appl.Microbiol.Biotechnol_70_422
Author(s) : Akutsu-Shigeno Y , Adachi Y , Yamada C , Toyoshima K , Nomura N , Uchiyama H , Nakajima-kambe T
Ref : Applied Microbiology & Biotechnology , 70 :422 , 2006
Abstract : A bacterium which degrades urethane compounds was isolated and identified as Rhodococcus equi strain TB-60. Strain TB-60 degraded toluene-2,4-dicarbamic acid dibutyl ester (TDCB) and accumulated toluene diamine as the degradation product. The enzyme which cleaves urethane bond in TDCB was strongly induced by acetanilide. The purified enzyme (urethane hydrolase) was found to be homogeneous on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The molecular weight was estimated to be 55 kDa. The optimal temperature and pH were 45 degrees C and 5.5, respectively. The enzyme hydrolyzed aliphatic urethane compound as well as aromatic ones. The activity was inhibited by HgCl(2), p-chrolomercuribenzoic acid, and phenylmethylsulfonyl fluoride, suggesting that cysteine and/or serine residues play an important role in the activity. The enzyme catalyzed the hydrolysis of anilides, amides, and esters as well as TDCB. It was characterized as a novel amidase/esterase, differing in some properties from other known amidases/esterases.
ESTHER : Akutsu-Shigeno_2006_Appl.Microbiol.Biotechnol_70_422
PubMedSearch : Akutsu-Shigeno_2006_Appl.Microbiol.Biotechnol_70_422
PubMedID: 16041575

Title : Complete sequencing and characterization of 21,243 full-length human cDNAs - Ota_2004_Nat.Genet_36_40
Author(s) : Ota T , Suzuki Y , Nishikawa T , Otsuki T , Sugiyama T , Irie R , Wakamatsu A , Hayashi K , Sato H , Nagai K , Kimura K , Makita H , Sekine M , Obayashi M , Nishi T , Shibahara T , Tanaka T , Ishii S , Yamamoto J , Saito K , Kawai Y , Isono Y , Nakamura Y , Nagahari K , Murakami K , Yasuda T , Iwayanagi T , Wagatsuma M , Shiratori A , Sudo H , Hosoiri T , Kaku Y , Kodaira H , Kondo H , Sugawara M , Takahashi M , Kanda K , Yokoi T , Furuya T , Kikkawa E , Omura Y , Abe K , Kamihara K , Katsuta N , Sato K , Tanikawa M , Yamazaki M , Ninomiya K , Ishibashi T , Yamashita H , Murakawa K , Fujimori K , Tanai H , Kimata M , Watanabe M , Hiraoka S , Chiba Y , Ishida S , Ono Y , Takiguchi S , Watanabe S , Yosida M , Hotuta T , Kusano J , Kanehori K , Takahashi-Fujii A , Hara H , Tanase TO , Nomura Y , Togiya S , Komai F , Hara R , Takeuchi K , Arita M , Imose N , Musashino K , Yuuki H , Oshima A , Sasaki N , Aotsuka S , Yoshikawa Y , Matsunawa H , Ichihara T , Shiohata N , Sano S , Moriya S , Momiyama H , Satoh N , Takami S , Terashima Y , Suzuki O , Nakagawa S , Senoh A , Mizoguchi H , Goto Y , Shimizu F , Wakebe H , Hishigaki H , Watanabe T , Sugiyama A , Takemoto M , Kawakami B , Watanabe K , Kumagai A , Itakura S , Fukuzumi Y , Fujimori Y , Komiyama M , Tashiro H , Tanigami A , Fujiwara T , Ono T , Yamada K , Fujii Y , Ozaki K , Hirao M , Ohmori Y , Kawabata A , Hikiji T , Kobatake N , Inagaki H , Ikema Y , Okamoto S , Okitani R , Kawakami T , Noguchi S , Itoh T , Shigeta K , Senba T , Matsumura K , Nakajima Y , Mizuno T , Morinaga M , Sasaki M , Togashi T , Oyama M , Hata H , Komatsu T , Mizushima-Sugano J , Satoh T , Shirai Y , Takahashi Y , Nakagawa K , Okumura K , Nagase T , Nomura N , Kikuchi H , Masuho Y , Yamashita R , Nakai K , Yada T , Ohara O , Isogai T , Sugano S
Ref : Nat Genet , 36 :40 , 2004
Abstract : As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs.
ESTHER : Ota_2004_Nat.Genet_36_40
PubMedSearch : Ota_2004_Nat.Genet_36_40
PubMedID: 14702039
Gene_locus related to this paper: human-ABHD1 , human-ABHD4 , human-ABHD12 , human-ABHD16A , human-ACOT1 , human-LDAH , human-ABHD18 , human-CES1 , human-CES4A , human-CES5A , human-CPVL , human-DAGLB , human-EPHX2 , human-KANSL3 , human-LIPA , human-LPL , human-MEST , human-NDRG1 , human-NLGN1 , human-NLGN4X , human-PRCP , human-PRSS16 , human-SERAC1 , human-TMEM53

Title : Cloning and sequencing of a poly(DL-lactic acid) depolymerase gene from Paenibacillus amylolyticus strain TB-13 and its functional expression in Escherichia coli - Akutsu-Shigeno_2003_Appl.Environ.Microbiol_69_2498
Author(s) : Akutsu-Shigeno Y , Teeraphatpornchai T , Teamtisong K , Nomura N , Uchiyama H , Nakahara T , Nakajima-kambe T
Ref : Applied Environmental Microbiology , 69 :2498 , 2003
Abstract : The gene encoding a poly(DL-lactic acid) (PLA) depolymerase from Paenibacillus amylolyticus strain TB-13 was cloned and overexpressed in Escherichia coli. The purified recombinant PLA depolymerase, PlaA, exhibited degradation activities toward various biodegradable polyesters, such as poly(butylene succinate), poly(butylene succinate-co-adipate), poly(ethylene succinate), and poly(epsilon-caprolactone), as well as PLA. The monomeric lactic acid was detected as the degradation product of PLA. The substrate specificity toward triglycerides and p-nitrophenyl esters indicated that PlaA is a type of lipase. The gene encoded 201 amino acid residues, including the conserved pentapeptide Ala-His-Ser-Met-Gly, present in the lipases of mesophilic Bacillus species. The identity of the amino acid sequence of PlaA with Bacillus lipases was no more than 45 to 50%, and some of its properties were different from those of these lipases.
ESTHER : Akutsu-Shigeno_2003_Appl.Environ.Microbiol_69_2498
PubMedSearch : Akutsu-Shigeno_2003_Appl.Environ.Microbiol_69_2498
PubMedID: 12732514
Gene_locus related to this paper: paeam-PLAA

Title : Isolation and characterization of a bacterium that degrades various polyester-based biodegradable plastics - Teeraphatpornchai_2003_Biotechnol.Lett_25_23
Author(s) : Teeraphatpornchai T , Nakajima-kambe T , Shigeno-Akutsu Y , Nakayama M , Nomura N , Nakahara T , Uchiyama H
Ref : Biotechnol Lett , 25 :23 , 2003
Abstract : Microorganisms isolated from soil samples were screened for their ability to degrade various biodegradable polyester-based plastics. The most active strain, designated as strain TB-13, was selected as the best strain for degrading these plastics. From its phenotypic and genetic characteristics, strain TB-13 was closely related to Paenibacillus amyloyticus. It could degrade poly(lactic acid), poly(butylene succinate), poly(butylene succinate-co-adipate), poly(caprolactone) and poly(ethylene succinate) but not poly(hydroxybutylate-co-valerate). However, it could not utilize these plastics as sole carbon sources. Both protease and esterase activities, which may be involved in the degradation of plastic, were constitutively detected in the culture broth.
ESTHER : Teeraphatpornchai_2003_Biotechnol.Lett_25_23
PubMedSearch : Teeraphatpornchai_2003_Biotechnol.Lett_25_23
PubMedID: 12882301

Title : Cloning and sequence analysis of poly(tetramethylene succinate) depolymerase from Acidovorax delafieldii strain BS-3 - Uchida_2002_J.Biosci.Bioeng_93_245
Author(s) : Uchida H , Shigeno-Akutsu Y , Nomura N , Nakahara T , Nakajima-kambe T
Ref : J Biosci Bioeng , 93 :245 , 2002
Abstract : A gene encoding poly(tetramethylene succinate), PBS, depolymerase, pbsA, has been cloned from Acidovorax delafieldii strain BS-3 chromosomal DNA. The clone expressed in Escherichia coli showed the ability to degrade both PBS and poly[(tetramethylene succinate)-co-adipate] that are kinds of biodegradable plastics. PBS depolymerase was considered to be a kind of lipase, since it also degrades olive oil. It had no apparent hydrophobic-amino-acid-rich region which exists in other known plastic-degrading enzymes. From the result of amino acid homology search, PbsA was found to have some similarities with lipases of Streptomyces sp. and Mollaxella sp. In the motif surrounding the active site Ser residue (Gly-X1-Ser-X2-Gly), PbsA was revealed to have a Trp residue in the X1 position instead of His which is most likely found in other bacterial lipases.
ESTHER : Uchida_2002_J.Biosci.Bioeng_93_245
PubMedSearch : Uchida_2002_J.Biosci.Bioeng_93_245
PubMedID: 16233195
Gene_locus related to this paper: acide-PBSA

Title : Mannosylerythritol lipid induces characteristics of neuronal differentiation in PC12 cells through an ERK-related signal cascade - Wakamatsu_2001_Eur.J.Biochem_268_374
Author(s) : Wakamatsu Y , Zhao X , Jin C , Day N , Shibahara M , Nomura N , Nakahara T , Murata T , Yokoyama KK
Ref : European Journal of Biochemistry , 268 :374 , 2001
Abstract : Rat pheochromocytoma PC12 cells undergo neuronal differentiation in response to nerve growth factor (NGF). The differentiation involves protein kinase cascades that include the kinases MEK and ERK, as well as activation of the transcription factors c-Jun and c-Fos. We show here, that exposure of PC12 cells to mannosylerythritol lipid (MEL), a yeast extracellular glycolipid, enhances the activity of acetylcholinesterase and interrupts the cell cycle at the G1 phase, with resulting outgrowth of neurites and partial cellular differentiation. Treatment with MEL stimulates the phosphorylation of ERK to a similar extent as treatment with NGF, although, the appearance of phosphorylated ERK is somewhat delayed. Both the MEL-induced outgrowth of neurites and the increase in the activity of acetylcholinesterase are prevented by PD98059, a specific inhibitor of MEK. Northern blotting analysis of c-jun transcripts and analysis of transcription in PC12 cells of a c-jun/CAT reporter construct demonstrated a significant increase in the rate of transcription of the c-jun gene upon treatment with MEL. The sequence elements required for the MEL-mediated activation of transcription of the c-jun gene are located between nucleotides -126 and -79 in the 5' flanking region. Our results suggest that MEL induces characteristics of neuronal differentiation in PC12 cells, with transactivation of the c-jun gene, via an ERK-related signal cascade that is partially overlapping the pathways activated in response to NGF. These results might provide the groundwork for the use of microbial extracellular glycolipids as novel reagents for the treatment of cancer cells.
ESTHER : Wakamatsu_2001_Eur.J.Biochem_268_374
PubMedSearch : Wakamatsu_2001_Eur.J.Biochem_268_374
PubMedID: 11168372

Title : Mannosylerythritol lipid increases levels of galactoceramide in and neurite outgrowth from PC12 pheochromocytoma cells - Shibahara_2000_Cytotech_33_247
Author(s) : Shibahara M , Zhao X , Wakamatsu Y , Nomura N , Nakahara T , Jin C , Nagaso H , Murata T , Yokoyama KK
Ref : Cytotechnology , 33 :247 , 2000
Abstract : We report here that a microbial extracellular glycolipid,mannosylerythritol lipid (MEL), induces the outgrowth ofneurites from and enhances the activity of acetylcholinesterase(AChE) in PC12 pheochromocytoma cells. Furthermore, treatment ofPC12 cells with MEL increased levels of galactosylceramide(Galbeta1-1'Cer; GalCer). Exposure of PC12 cells to exogenous GalCer caused the dose-dependent outgrowth ofneurites. By contrast, treatment of PC12 cells with nerve growthfactor (NGF) did not increase the level of GalCer in the cells. The neurite-related morphological changes induced by GalCerdifferend from those induced by NGF, indicating differencesbetween the signal transduction pathways triggered by NGF and by GalCer.
ESTHER : Shibahara_2000_Cytotech_33_247
PubMedSearch : Shibahara_2000_Cytotech_33_247
PubMedID: 19002832

Title : Purification and properties of culture-broth-secreted esterase from the polyurethane degrader Comamonas acidovorans TB-35 - Shigeno-Akutsu_1999_J.Biosci.Bioeng_88_484
Author(s) : Shigeno-Akutsu Y , Nakajima-kambe T , Nomura N , Nakahara T
Ref : J Biosci Bioeng , 88 :484 , 1999
Abstract : The polyester-polyurethane (PUR)-degrading bacterium Comamonas acidovorans TB-35 produces two kinds of esterases, one cell-bound esterase (PUR esterase) and the other secreted in the culture broth (CBS esterase). In this study, the CBS esterase and the two recombinant esterases were purified. Identification of the physical and biochemical properties of the CBS and PUR esterases revealed that they have the same polypeptide from one gene. This finding was supported by the observation that Escherichia coli harboring the PUR esterase gene also produced two kinds of esterases. Though the PUR esterase degraded PUR and poly(diethylene glycol adipate), the soft segment of the PUR, the CBS esterase degraded only poly(diethylene glycol adipate). Furthermore, the hydrophobicity of the CBS esterase was lower than that of the PUR esterase. As the PUR esterase has been previously indicated to possess a PUR-binding domain, it was assumed that structural change around the PUR-binding domain of the CBS esterase was responsible for its inability to degrade PUR.
ESTHER : Shigeno-Akutsu_1999_J.Biosci.Bioeng_88_484
PubMedSearch : Shigeno-Akutsu_1999_J.Biosci.Bioeng_88_484
PubMedID: 16232649
Gene_locus related to this paper: comac-polest

Title : Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro - Nagase_1999_DNA.Res_6_337
Author(s) : Nagase T , Ishikawa K , Kikuno R , Hirosawa M , Nomura N , Ohara O
Ref : DNA Research , 6 :337 , 1999
Abstract : In order to obtain information on the coding sequences of unidentified human genes, we newly determined the sequences of 100 cDNA clones of unknown human genes, which we named KIAA1193 to KIAA1292, from two sets of size-fractionated human adult and fetal brain cDNA libraries. The results of our particular strategy to select cDNA clones which have the potentiality of coding for large proteins in vitro revealed that the average sizes of the inserts and the corresponding open reading frames reached 5.2 kb and 2.8 kb (933 amino acid residues), respectively. By the computational analysis of the predicted amino acid sequences against the OWL and Pfam databases, 58 predicted gene products were classified into the following five functional categories: cell signaling/communication, cell structure/motility, nucleic acid management, protein management and metabolism. It was also found that 30 gene products had homologues in the public databases which were similar in sequence throughout almost their entire regions to the newly identified genes. The chromosomal loci of the genes were assigned by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of the genes were studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.
ESTHER : Nagase_1999_DNA.Res_6_337
PubMedSearch : Nagase_1999_DNA.Res_6_337
PubMedID: 10574462
Gene_locus related to this paper: human-NDRG2 , human-NLGN4X

Title : Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1 - Kawarabayasi_1999_DNA.Res_6_83
Author(s) : Kawarabayasi Y , Hino Y , Horikawa H , Yamazaki S , Haikawa Y , Jin-no K , Takahashi M , Sekine M , Baba S , Ankai A , Kosugi H , Hosoyama A , Fukui S , Nagai Y , Nishijima K , Nakazawa H , Takamiya M , Masuda S , Funahashi T , Tanaka T , Kudoh Y , Yamazaki J , Kushida N , Oguchi A , Aoki KI , Kubota K , Nakamura Y , Nomura N , Sako Y , Kikuchi H
Ref : DNA Research , 6 :83 , 1999
Abstract : The complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1, which optimally grows at 95 degrees C, has been determined by the whole genome shotgun method with some modifications. The entire length of the genome was 1,669,695 bp. The authenticity of the entire sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2,694 open reading frames (ORFs) were assigned. By similarity search against public databases, 633 (23.5%) of the ORFs were related to genes with putative function and 523 (19.4%) to the sequences registered but with unknown function. All the genes in the TCA cycle except for that of alpha-ketoglutarate dehydrogenase were included, and instead of the alpha-ketoglutarate dehydrogenase gene, the genes coding for the two subunits of 2-oxoacid:ferredoxin oxidoreductase were identified. The remaining 1,538 ORFs (57.1%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs suggested that a considerable member of ORFs were generated by sequence duplication. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 47 tRNA genes including 14 genes with intron structures. All the assigned ORFs and RNA coding regions occupied 89.12% of the whole genome. The data presented in this paper are available on the internet homepage (http:\/\/www.mild.nite.go.jp).
ESTHER : Kawarabayasi_1999_DNA.Res_6_83
PubMedSearch : Kawarabayasi_1999_DNA.Res_6_83
PubMedID: 10382966
Gene_locus related to this paper: aerpe-APE1244 , aerpe-APE1547 , aerpe-APE1832 , aerpe-APE2290 , aerpe-APE2361 , aerpe-APE2441

Title : Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain - Hirosawa_1999_DNA.Res_6_329
Author(s) : Hirosawa M , Nagase T , Ishikawa K-I , Kikuno R , Nomura N , Ohara O , Ishikawa K
Ref : DNA Research , 6 :329 , 1999
Abstract : We have conducted a sequencing project of human cDNAs which encode large proteins in brain. For selection of cDNA clones to be sequenced in this project, cDNA clones have been experimentally examined by in vitro transcription/translation prior to sequencing. In this study, we tested an alternative approach for picking up cDNA clones having a high probability of carrying protein coding region. This approach exploited 5'-end single-pass sequence data and the GeneMark program for assessing protein-coding potential, and allowed us to select 74 clones out of 14,804 redundant cDNA clones. The complete sequence data of these 74 clones revealed that 45% of them encoded proteins consisting of more than 500 amino acid residues while all the clones thus selected carried possible protein coding sequences as expected. The results indicated that the GeneMark analysis of 5'-end sequences of cDNAs offered us a simple and effective means to select cDNA clones with protein-coding potential although the sizes of the encoded proteins could not be predicted.
ESTHER : Hirosawa_1999_DNA.Res_6_329
PubMedSearch : Hirosawa_1999_DNA.Res_6_329
PubMedID: 10574461
Gene_locus related to this paper: human-NDRG4

Title : Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro - Kikuno_1999_DNA.Res_6_197
Author(s) : Kikuno R , Nagase T , Ishikawa K , Hirosawa M , Miyajima N , Tanaka A , Kotani H , Nomura N , Ohara O
Ref : DNA Research , 6 :197 , 1999
Abstract : To extend our cDNA project for accumulating basic information on unidentified human genes, we newly determined the sequences of 100 cDNA clones from a set of size-fractionated human adult and fetal brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA1019 to KIAA1118. The sequencing of these clones revealed that the average size of the inserts and corresponding open reading frames were 5.0 kb and 2.6 kb (880 amino acid residues), respectively. Database search of the predicted amino acid sequences classified 58 predicted gene products into the five functional categories, such as cell signaling/communication, cell structure/motility, nucleic acid management, protein management and cell division. It was also found that, for 34 gene products, homologues were detected in the databases, which were similar in sequence through almost the entire regions. The chromosomal locations of the genes were determined by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of all the genes among 10 human tissues, 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substania nigra, subthalamic nucleus, and thalamus), spinal cord, fetal brain and fetal liver were also examined by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.
ESTHER : Kikuno_1999_DNA.Res_6_197
PubMedSearch : Kikuno_1999_DNA.Res_6_197
PubMedID: 10470851
Gene_locus related to this paper: human-NLGN1

Title : Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro - Nagase_1999_DNA.Res_6_63
Author(s) : Nagase T , Ishikawa K , Suyama M , Kikuno R , Hirosawa M , Miyajima N , Tanaka A , Kotani H , Nomura N , Ohara O
Ref : DNA Research , 6 :63 , 1999
Abstract : As a part of our cDNA project for deducing the coding sequence of unidentified human genes, we newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0919 to KIAA1018. The sequencing of these clones revealed that the average sizes of the inserts and corresponding open reading frames were 4.9 kb and 2.6 kb (882 amino acid residues), respectively. A computer search of the sequences against the public databases indicated that predicted coding sequences of 87 genes contained sequences similar to known genes, 53% of which (46 genes) were categorized as proteins relating to cell signaling/communication, cell structure/motility and nucleic acid management. The chromosomal locations of the genes were determined by using human-rodent hybrid panels unless their mapping data were already available in the public databases. The expression profiles of all the genes among 10 human tissues, 8 brain regions (amygdala, corpus callosum, cerebellum, caudate nucleus, hippocampus, substania nigra, subthalamic nucleus, and thalamus), spinal cord, fetal brain and fetal liver were also examined by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.
ESTHER : Nagase_1999_DNA.Res_6_63
PubMedSearch : Nagase_1999_DNA.Res_6_63
PubMedID: 10231032
Gene_locus related to this paper: human-NLGN3 , human-NLGN4X , human-NLGN4Y

Title : Microbial degradation of polyurethane, polyester polyurethanes and polyether polyurethanes - Nakajima-Kambe_1999_Appl.Microbiol.Biotechnol_51_134
Author(s) : Nakajima-kambe T , Shigeno-Akutsu Y , Nomura N , Onuma F , Nakahara T
Ref : Applied Microbiology & Biotechnology , 51 :134 , 1999
Abstract : Polyurethane (PUR) is a polymer derived from the condensation of polyisocyanate and polyol and it is widely used as a base material in various industries. PUR, in particular, polyester PUR, is known to be vulnerable to microbial attack. Recently, environmental pollution by plastic wastes has become a serious issue and polyester PUR had attracted attention because of its biodegradability. There are many reports on the degradation of polyester PUR by microorganisms, especially by fungi. Microbial degradation of polyester PUR is thought to be mainly due to the hydrolysis of ester bonds by esterases. Recently, polyester-PUR-degrading enzymes have been purified and their characteristics reported. Among them, a solid-polyester-PUR-degrading enzyme (PUR esterase) derived from Comamonas acidovorans TB-35 had unique characteristics. This enzyme has a hydrophobic PUR-surface-binding domain and a catalytic domain, and the surface-binding domain was considered as being essential for PUR degradation. This hydrophobic surface-binding domain is also observed in other solid-polyester-degrading enzymes such as poly(hydroxyalkanoate) (PHA) depolymerases. There was no significant homology between the amino acid sequence of PUR esterase and that of PHA depolymerases, except in the hydrophobic surface-binding region. Thus, PUR esterase and PHA depolymerase are probably different in terms of their evolutionary origin and it is possible that PUR esterases come to be classified as a new solid-polyester-degrading enzyme family.
ESTHER : Nakajima-Kambe_1999_Appl.Microbiol.Biotechnol_51_134
PubMedSearch : Nakajima-Kambe_1999_Appl.Microbiol.Biotechnol_51_134
PubMedID: 10091317

Title : Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro - Ishikawa_1998_DNA.Res_5_169
Author(s) : Ishikawa K , Nagase T , Suyama M , Miyajima N , Tanaka A , Kotani H , Nomura N , Ohara O
Ref : DNA Research , 5 :169 , 1998
Abstract : As an extension of our cDNA analysis for deducing the coding sequences of unidentified human genes, we have newly determined the sequences of 100 cDNA clones from a set of size-fractionated human brain cDNA libraries, and predicted the coding sequences of the corresponding genes, named KIAA0611 to KIAA0710. In vitro transcription-coupled translation assay was applied as the first screening to select cDNA clones which produce proteins with apparent molecular mass of 50 kDa and over. One hundred unidentified cDNA clones thus selected were then subjected to sequencing of entire inserts. The average size of the inserts and corresponding open reading frames was 4.9 kb and 2.8 kb (922 amino acid residues), respectively. Computer search of the sequences against the public databases indicated that predicted coding sequences of 87 genes were similar to those of known genes, 62% of which (54 genes) were categorized as proteins related to cell signaling/communication, cell structure/motility and nucleic acid management. The expression profiles in 10 human tissues of all the clones characterized in this study were examined by reverse transcription-coupled polymerase chain reaction and the chromosomal locations of the clones were determined by using human-rodent hybrid panels.
ESTHER : Ishikawa_1998_DNA.Res_5_169
PubMedSearch : Ishikawa_1998_DNA.Res_5_169
PubMedID: 9734811
Gene_locus related to this paper: human-DAGLA

Title : Cloning and sequence analysis of a polyurethane esterase of Comamonas acidovorans TB-35 - Nomura_1998_J.Ferment.Bioeng_86_339
Author(s) : Nomura N , Shigeno-Akutsu Y , Nakajima-kambe T , Nakahara T
Ref : J.Ferment.Bioeng , 86 :339 , 1998
Abstract : omamonas acidovorans strain TB-35 has an esterase that degrades solid polyester polyurethane (PUR). The structural gene, pudA, for the PUR esterase has now been cloned in Escherichia coli. When pudA was expressed in E. coli, the recombinant protein was able to degrade solid PUR. The predicted amino acid sequence contains the Gly-X1-Ser-X2-Gly motif characteristic of serine hydrolases. The highest degree of homology was detected with the Torpedo californica acetylcholinesterase (T AChE), possessing the Ser-His-Glu catalytic triad, with the glutamate residue replacing the usual aspartate residue. Similarity in the number and positions of cysteine and salt bonds was very apparent between PudA and T AChE, as were also identities of sequences and their positions in the alpha-helix and beta-strand regions between the two. In the neighborhood of the glutamate residue of the Ser199-His433-Glu324 catalytic domain of PudA, there were three hydrophobic domains, one of which constituted the surface-binding domain, which occurred in the C-terminus of most bacterial poly(hydroxyalkanoate)(PHA) depolymerases
ESTHER : Nomura_1998_J.Ferment.Bioeng_86_339
PubMedSearch : Nomura_1998_J.Ferment.Bioeng_86_339
PubMedID:
Gene_locus related to this paper: comac-polest

Title : Purification and Properties of a Polyester Polyurethane-Degrading Enzyme from Comamonas acidovorans TB-35 - Akutsu_1998_Appl.Environ.Microbiol_64_62
Author(s) : Akutsu Y , Nakajima-kambe T , Nomura N , Nakahara T
Ref : Applied Environmental Microbiology , 64 :62 , 1998
Abstract : A polyester polyurethane (PUR)-degrading enzyme, PUR esterase, derived from Comamonas acidovorans TB-35, a bacterium that utilizes polyester PUR as the sole carbon source, was purified until it showed a single band in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This enzyme was bound to the cell surface and was extracted by addition of 0.2% N,N-bis(3-d-gluconamidopropyl)deoxycholamide (deoxy-BIGCHAP). The results of gel filtration and SDS-PAGE showed that the PUR esterase was a monomer with a molecular mass of about 62,000 Da. This enzyme, which is a kind of esterase, degraded solid polyester PUR, with diethylene glycol and adipic acid released as the degradation products. The optimum pH for this enzyme was 6.5, and the optimum temperature was 45 degrees C. PUR degradation by the PUR esterase was strongly inhibited by the addition of 0.04% deoxy-BIGCHAP. On the other hand, deoxy-BIGCHAP did not inhibit the activity when p-nitrophenyl acetate, a water-soluble compound, was used as a substrate. These observations indicated that this enzyme degrades PUR in a two-step reaction: hydrophobic adsorption to the PUR surface and hydrolysis of the ester bond of PUR.
ESTHER : Akutsu_1998_Appl.Environ.Microbiol_64_62
PubMedSearch : Akutsu_1998_Appl.Environ.Microbiol_64_62
PubMedID: 16349494
Gene_locus related to this paper: comac-polest

Title : Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro - Ishikawa_1997_DNA.Res_4_307
Author(s) : Ishikawa K , Nagase T , Nakajima D , Seki N , Ohira M , Miyajima N , Tanaka A , Kotani H , Nomura N , Ohara O
Ref : DNA Research , 4 :307 , 1997
Abstract : As a part of our project for accumulating sequence information of the coding regions of unidentified human genes, we herein report the sequence features of 78 new cDNA clones isolated from human brain cDNA libraries as those which may code for large proteins. The sequence data showed that the average size of the cDNA inserts and their open reading frames was 6.0 kb and 2.8 kb (925 amino acid residues), respectively, and these clones produced the corresponding sizes of protein products in an in vitro transcription/translation system. Homology search against the public databases indicated that the predicted coding sequences of 68 genes contained sequences similar to known genes, 69% of which (47 genes) were related to cell signaling/communication, nucleic acid management, and cell structure/motility. The expression profiles of these genes in 14 different tissues have been analyzed by the reverse transcription-coupled polymerase chain reaction method, and 8 genes were found to be predominantly expressed in the brain.
ESTHER : Ishikawa_1997_DNA.Res_4_307
PubMedSearch : Ishikawa_1997_DNA.Res_4_307
PubMedID: 9455477
Gene_locus related to this paper: human-PREPL