Sato S

References (48)

Title : Functional roles of CD26\/DPP4 in lipopolysaccharide-induced lung injury - Sato_2024_Am.J.Physiol.Lung.Cell.Mol.Physiol__
Author(s) : Sato S , Kawasaki T , Hatano R , Koyanagi Y , Takahashi Y , Ohnuma K , Morimoto C , Dudek SM , Tatsumi K , Suzuki T
Ref : American Journal of Physiology Lung Cell Mol Physiol , : , 2024
Abstract : Acute respiratory distress syndrome (ARDS) is characterized by dysregulated inflammation and increased permeability of lung microvascular cells. CD26/Dipeptidyl peptidase-4 (DPP4) is a type II membrane protein that is expressed in several cell types and mediates multiple pleiotropic effects. We previously reported that DPP4 inhibition by sitagliptin attenuates lipopolysaccharide (LPS)-induced lung injury in mice. The current study characterized the functional role of CD26/DPP4 expression in LPS-induced lung injury in mice, isolated alveolar macrophages, and cultured lung endothelial cells. In LPS-induced lung injury, inflammatory responses (bronchoalveolar lavage fluid (BALF) neutrophil numbers and several pro-inflammatory cytokine levels) were attenuated in Dpp4 knockout (Dpp4 KO) mice. However, multiple assays of alveolar capillary permeability were similar between the Dpp4 KO and wild-type mice. TNF-alpha and IL-6 production was suppressed in alveolar macrophages isolated from Dpp4 KO mice. In contrast, in cultured mouse lung microvascular endothelial cells (MLMVECs), reduction in CD26/DPP4 expression by siRNA resulted in greater ICAM-1 and IL-6 expression after LPS stimulation. Moreover, the LPS-induced vascular monolayer permeability in vitro was higher in MLMVECs treated with Dpp4 siRNA, suggesting that CD26/DPP4 plays a protective role in endothelial barrier function. In summary, this study demonstrated that genetic deficiency of Dpp4 attenuates inflammatory responses but not permeability in LPS-induced lung injury in mice, potentially through differential functional roles of CD26/DPP4 expression in resident cellular components of the lung. CD26/DPP4 may be a potential therapeutic target for ARDS and warrants further exploration to precisely identify the multiple functional effects of CD26/DPP4 in ARDS pathophysiology.
ESTHER : Sato_2024_Am.J.Physiol.Lung.Cell.Mol.Physiol__
PubMedSearch : Sato_2024_Am.J.Physiol.Lung.Cell.Mol.Physiol__
PubMedID: 38469626

Title : Hormone-sensitive lipase protects adipose triglyceride lipase-deficient mice from lethal lipotoxic cardiomyopathy - Yamada_2022_J.Lipid.Res__100194
Author(s) : Yamada M , Suzuki J , Sato S , Zenimaru Y , Saito R , Konoshita T , Kraemer FB , Ishizuka T
Ref : J Lipid Res , :100194 , 2022
Abstract : Lipid droplets (LDs) are multifunctional organelles that regulate energy storage and cellular homeostasis. The first step of triacylglycerol (TAG) hydrolysis in LDs is catalyzed by adipose triglyceride lipase (ATGL), deficiency of which results in lethal cardiac steatosis. Although hormone-sensitive lipase (HSL) functions as a diacylglycerol (DAG) lipase in the heart, we hypothesized that activation of HSL might compensate for ATGL deficiency. To test this hypothesis, we crossed ATGL-knockout (KO) mice and cardiac-specific HSL-overexpressing mice (cHSL) to establish homozygous ATGL-KO (AKO) mice and AKO mice with cardiac-specific HSL overexpression (AKO+cHSL). We found that cardiac TAG content was 160-fold higher in AKO relative to wild type (Wt) mice, while that of AKO+cHSL mice was comparable to the latter. In addition, AKO cardiac tissues exhibited reduced mRNA expression of PPARalpha-regulated genes, and upregulation of genes involved in inflammation, fibrosis, and cardiac stress. In contrast, AKO+cHSL cardiac tissues exhibited expression levels similar to those observed in Wt mice. AKO cardiac tissues also exhibited macrophage infiltration, apoptosis, interstitial fibrosis, impaired systolic function, and marked increases in ceramide and DAG contents, while no such pathological alterations were observed in AKO+cHSL tissues. Furthermore, electron microscopy revealed considerable LDs, damaged mitochondria, and disrupted intercalated discs in AKO cardiomyocytes, none of which were noted in AKO+cHSL cardiomyocytes. Importantly, the lifespan of AKO+cHSL mice was comparable to that of Wt mice. We conclude cardiac HSL overexpression normalizes lipotoxic cardiomyopathy in AKO mice. These findings highlight the applicability of cardiac HSL activation as a therapeutic strategy for ATGL deficiency-associated lipotoxic cardiomyopathies.
ESTHER : Yamada_2022_J.Lipid.Res__100194
PubMedSearch : Yamada_2022_J.Lipid.Res__100194
PubMedID: 35283217

Title : The association between sarcopenia and endotoxin in patients with alcoholic cirrhosis - Sato_2021_Medicine.(Baltimore)_100_e27212
Author(s) : Sato S , Namisaki T , Murata K , Fujimoto Y , Takeda S , Enomoto M , Shibamoto A , Ishida K , Ogawa H , Takagi H , Tsuji Y , Kaya D , Fujinaga Y , Furukawa M , Inoue T , Sawada Y , Nishimura N , Kitagawa K , Ozutsumi T , Takaya H , Kaji K , Shimozato N , Kawaratani H , Moriya K , Akahane T , Mitoro A , Yoshiji H
Ref : Medicine (Baltimore) , 100 :e27212 , 2021
Abstract : We aimed to prospectively identify the risk factors of sarcopenia in patients with cirrhosis.Patients (n=193) included in a discovery cohort (January 2011 and December 2014) were categorized into alcoholic (A1; n=55) and non-alcoholic cirrhosis (NA; n=138) groups, and those (n=235) in a validation cohort (January 2015 to December 2019) were categorized into alcoholic (n=92), non-alcoholic steatohepatitis-related (n=27), and hepatitis C virus-related cirrhosis groups (n=116). Skeletal muscle mass index (SMI) was determined using computed tomography (SMI-CT) and bioelectrical impedance analysis (SMI-BIA). Endotoxin activity (EA) was measured with an EA assay.SMI-CT correlated with grip strength in all the groups but significantly correlated with SMI-BIA of the men in group A1 (R=0.64, P<.0001) and both sexes in group NA (male: R=0.44, P=.0001; female: R=0.35, P=.003). SMI-CT inversely correlated with the EA levels of the men in group A1 (R=-0.67, P<.0001) and myostatin levels in group NA (R=-0.53, P<.0001). Lower extremity SMI had a strong negative correlation with the EA levels of the men in group A1 (R=-0.58, P<.001), whereas upper extremity SMI showed an inverse trend with EA levels (R=-0.28, P=.08). SMI-CT also inversely correlated with the EA levels in groups A2 (R=-0.52, P=.003) and N (R=-0.67, P<.0001) and myostatin levels in group C (R=-0.65, P<.0001). Moreover, SMI-CT correlated with nutritional factors, including cholinesterase (R=0.50, P=.005), zinc (R=0.45, P=.01), branched amino acid-to-tyrosine ratio (R=0.39, P=.02), and triglyceride (R=0.33, P=.03) in group N.Sarcopenia risk factors differ among cirrhosis etiologies. Alcohol-induced, intestine-mediated peripheral endotoxemia could participate in sarcopenia development in patients with alcoholic cirrhosis.
ESTHER : Sato_2021_Medicine.(Baltimore)_100_e27212
PubMedSearch : Sato_2021_Medicine.(Baltimore)_100_e27212
PubMedID: 34516526

Title : Identification and characterization of a novel extracellular polyhydroxyalkanoate depolymerase in the complete genome sequence of Undibacterium sp. KW1 and YM2 strains - Morohoshi_2020_PLoS.One_15_e0232698
Author(s) : Morohoshi T , Oi T , Suzuki T , Sato S
Ref : PLoS ONE , 15 :e0232698 , 2020
Abstract : Polyhydroxyalkanoate (PHA) is a biodegradable polymer that is synthesized by a wide range of microorganisms. One of the derivatives of PHA, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH) has flexible material properties and low melting temperature. We have previously demonstrated that PHBH is degradable in a freshwater environment via the formation of biofilm on the surface of the PHBH film. Undibacterium sp. KW1 and YM2, which were isolated from the biofilm present on the PHBH film in the freshwater sample, were shown to have PHBH-degrading activity. In this study, the complete genome sequence of KW1 and YM2 revealed that the extracellular PHA depolymerase gene, designated as phaZUD, was present in their chromosomes. Sequence analysis revealed that PhaZUD contained four domains: a signal peptide, catalytic domain, linker domain, and substrate-binding domain. Escherichia coli harboring a PhaZUD-expressing plasmid showed PHBH-degrading activity in LB medium containing 1 wt% PHBH powder. The recombinant His-tagged PhaZUD from KW1 and YM2 was purified from the culture supernatant and shown to have PHBH-degrading activity at the optimum temperature of 35 and 40 degreesC, respectively. When the degradation product in the PHBH solution was treated with PhaZUD and assayed by LC-TOF-MS, we detected various oligomer structures, but no more than pentamers, which consist of 3-hydroxybutyrate and 3-hydroxyhexanoate. These results demonstrated that PhaZUD may have an endo-type extracellular PHA depolymerase activity.
ESTHER : Morohoshi_2020_PLoS.One_15_e0232698
PubMedSearch : Morohoshi_2020_PLoS.One_15_e0232698
PubMedID: 32369496

Title : Cardiac overexpression of perilipin 2 induces dynamic steatosis: Prevention by hormone-sensitive lipase - Ueno_2017_Am.J.Physiol.Endocrinol.Metab__ajpendo 00098 2017
Author(s) : Ueno M , Suzuki J , Hirose M , Sato S , Imagawa M , Zenimaru Y , Takahashi S , Ikuyama S , Koizumi T , Konoshita T , Kraemer FB , Ishizuka T
Ref : American Journal of Physiology Endocrinol Metab , :ajpendo 00098 2017 , 2017
Abstract : Cardiac intracellular lipid accumulation (steatosis) is a pathophysiological phenomenon observed in starvation and diabetes mellitus. Perilipin 2 (PLIN2) is a lipid droplet (LD)-associated protein expressed in non-adipose tissues, including the heart. To explore the pathophysiological function of myocardial PLIN2, we generated transgenic (Tg) mice by cardiac-specific overexpression of PLIN2. Tg hearts showed accumulation of numerous small LDs associated with mitochondrial chains, and high cardiac triacylglycerol (TAG) content (8-fold greater than wild-type (Wt) mice). Despite massive steatosis, cardiac uptake of glucose, fatty acids and VLDL, systolic function, and expression of metabolic genes were comparable in the two genotypes, and no morphological changes were observed by electron microscopy in the Tg hearts. Twenty-four hours fasting markedly reduced steatosis in Tg hearts, while Wt mice showed accumulation of LDs. Although activity of adipose triglyceride lipase in heart homogenate was comparable between Wt and Tg mice, activity of hormone-sensitive lipase (HSL) was 40-50% less in Tg than Wt mice, under both feeding and fasting conditions, suggesting interference of PLIN2 with HSL. Mice generated through crossing of PLIN2-Tg mice and HSL-Tg mice showed cardiac-specific HSL overexpression and complete lack of steatosis. The results suggest that cardiac PLIN2 plays an important pathophysiological role in the development of dynamic steatosis, and that the latter was prevented by upregulation of intracellular lipases, including HSL.
ESTHER : Ueno_2017_Am.J.Physiol.Endocrinol.Metab__ajpendo 00098 2017
PubMedSearch : Ueno_2017_Am.J.Physiol.Endocrinol.Metab__ajpendo 00098 2017
PubMedID: 28851734

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

Title : Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation - Hori_2014_Nat.Commun_5_3978
Author(s) : Hori K , Maruyama F , Fujisawa T , Togashi T , Yamamoto N , Seo M , Sato S , Yamada T , Mori H , Tajima N , Moriyama T , Ikeuchi M , Watanabe M , Wada H , Kobayashi K , Saito M , Masuda T , Sasaki-Sekimoto Y , Mashiguchi K , Awai K , Shimojima M , Masuda S , Iwai M , Nobusawa T , Narise T , Kondo S , Saito H , Sato R , Murakawa M , Ihara Y , Oshima-Yamada Y , Ohtaka K , Satoh M , Sonobe K , Ishii M , Ohtani R , Kanamori-Sato M , Honoki R , Miyazaki D , Mochizuki H , Umetsu J , Higashi K , Shibata D , Kamiya Y , Sato N , Nakamura Y , Tabata S , Ida S , Kurokawa K , Ohta H
Ref : Nat Commun , 5 :3978 , 2014
Abstract : The colonization of land by plants was a key event in the evolution of life. Here we report the draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum (Division Charophyta, Order Klebsormidiales) to elucidate the early transition step from aquatic algae to land plants. Comparison of the genome sequence with that of other algae and land plants demonstrate that K. flaccidum acquired many genes specific to land plants. We demonstrate that K. flaccidum indeed produces several plant hormones and homologues of some of the signalling intermediates required for hormone actions in higher plants. The K. flaccidum genome also encodes a primitive system to protect against the harmful effects of high-intensity light. The presence of these plant-related systems in K. flaccidum suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments.
ESTHER : Hori_2014_Nat.Commun_5_3978
PubMedSearch : Hori_2014_Nat.Commun_5_3978
PubMedID: 24865297
Gene_locus related to this paper: kleni-a0a1y1i5c5 , kleni-a0a1y1i3f9 , kleni-a0a1y1hnk2 , kleni-a0a1y1hsz2 , kleni-a0a1y1hva2 , kleni-a0a1y1i2g3 , kleni-a0a1y1i4h5 , kleni-a0a1y1i9h9

Title : Left frontal lobe hypoperfusion and depressive symptoms in Alzheimers disease patients taking cholinesterase inhibitors - Oshima_2014_Psychiatry.Res_224_319
Author(s) : Oshima E , Terada S , Sato S , Ikeda C , Oda K , Inoue S , Kawada K , Yokota O , Uchitomi Y
Ref : Psychiatry Res , 224 :319 , 2014
Abstract : Depressive symptoms are common in patients with Alzheimers disease (AD) and increase the caregiver burden. Many studies have reported dorsolateral prefrontal hypometabolism or hypoperfusion in AD patients with depressive symptoms, most of whom did not take acetylcholinesterase inhibitors (AChEI). It is not clear, however, whether a similar condition is present in patients taking AChEI medication. Fifty-seven consecutive AD patients taking AChEI were recruited at a memory clinic. Objective depressive symptoms were evaluated using the depression domain of the Neuropsychiatric Inventory (NPI-dep). All patients underwent brain single photon emission computed tomography (SPECT) with 99mTc-ethylcysteinate dimer, and the SPECT images were analyzed using the Statistical Parametric Mapping 8 program. No significant differences between groups with positive and negative NPI-dep scores were found with respect to age, sex, years of education, and cognitive function. Compared with patients with negative NPI-dep scores, patients with NPI-dep scores >/=1 showed significant hypoperfusion in the left middle frontal region. Our results indicate that the dorsolateral prefrontal area is significantly involved in the pathogenesis of depressive symptoms in AD patients being treated with AChEI. The area on the left side especially may be closely related to the depressive symptoms evaluated using the NPI.
ESTHER : Oshima_2014_Psychiatry.Res_224_319
PubMedSearch : Oshima_2014_Psychiatry.Res_224_319
PubMedID: 25453992

Title : Draft Genome Sequence of Gluconobacter frateurii NBRC 103465, a Glyceric Acid-Producing Strain - Sato_2013_Genome.Announc_1_e00369
Author(s) : Sato S , Umemura M , Koike H , Habe H
Ref : Genome Announc , 1 : , 2013
Abstract : Gluconobacter frateurii strain NBRC 103465 can efficiently produce glyceric acid (GA) from raw glycerol feedstock derived from biodiesel fuel production processes. Here, we report the 3.4-Mb draft genome sequence of G. frateurii NBRC 103465. The draft genome sequence can be applied to examine the enzymes and electron transport system involved in GA production.
ESTHER : Sato_2013_Genome.Announc_1_e00369
PubMedSearch : Sato_2013_Genome.Announc_1_e00369
PubMedID: 23887908
Gene_locus related to this paper: 9prot-a0a0s6tgj4

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

Title : The tomato genome sequence provides insights into fleshy fruit evolution - Sato_2012_Nature_485_635
Author(s) : Sato S , Tomato Genome Consortium
Ref : Nature , 485 :635 , 2012
Abstract : Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.
ESTHER : Sato_2012_Nature_485_635
PubMedSearch : Sato_2012_Nature_485_635
PubMedID: 22660326
Gene_locus related to this paper: lyces-Q9ZWF3 , lyces-q56r03 , sollc-k4bm34 , sollc-k4ctq1 , soltu-m1a5u0 , sollc-a0a3q7i5e0 , soltu-m1baq1 , sollc-a0a3q7j0r2 , sollc-a0a3q7ehh5 , sollc-a0a3q7f7t8 , sollc-a0a3q7iqx6

Title : Hair shaft abnormalities in localized autosomal recessive hypotrichosis 2 and a review of other non-syndromic human alopecias -
Author(s) : Suga H , Tsunemi Y , Sugaya M , Shinkuma S , Akiyama M , Shimizu H , Sato S
Ref : Acta Derm Venereol , 91 :486 , 2011
PubMedID: 21537821

Title : Genomic structure of the cyanobacterium Synechocystis sp. PCC 6803 strain GT-S - Tajima_2011_DNA.Res_18_393
Author(s) : Tajima N , Sato S , Maruyama F , Kaneko T , Sasaki NV , Kurokawa K , Ohta H , Kanesaki Y , Yoshikawa H , Tabata S , Ikeuchi M , Sato N
Ref : DNA Research , 18 :393 , 2011
Abstract : Synechocystis sp. PCC 6803 is the most popular cyanobacterial strain, serving as a standard in the research fields of photosynthesis, stress response, metabolism and so on. A glucose-tolerant (GT) derivative of this strain was used for genome sequencing at Kazusa DNA Research Institute in 1996, which established a hallmark in the study of cyanobacteria. However, apparent differences in sequences deviating from the database have been noticed among different strain stocks. For this reason, we analysed the genomic sequence of another GT strain (GT-S) by 454 and partial Sanger sequencing. We found 22 putative single nucleotide polymorphisms (SNPs) in comparison to the published sequence of the Kazusa strain. However, Sanger sequencing of 36 direct PCR products of the Kazusa strains stored in small aliquots resulted in their identity with the GT-S sequence at 21 of the 22 sites, excluding the possibility of their being SNPs. In addition, we were able to combine five split open reading frames present in the database sequence, and to remove the C-terminus of an ORF. Aside from these, two of the Insertion Sequence elements were not present in the GT-S strain. We have thus become able to provide an accurate genomic sequence of Synechocystis sp. PCC 6803 for future studies on this important cyanobacterial strain.
ESTHER : Tajima_2011_DNA.Res_18_393
PubMedSearch : Tajima_2011_DNA.Res_18_393
PubMedID: 21803841
Gene_locus related to this paper: synsp-ester

Title : Prevention of scopolamine-induced memory deficits by schisandrin B, an antioxidant lignan from Schisandra chinensis in mice - Giridharan_2011_Free.Radic.Res_45_950
Author(s) : Giridharan VV , Thandavarayan RA , Sato S , Ko KM , Konishi T
Ref : Free Radical Research , 45 :950 , 2011
Abstract : The preventive effect of schisandrin B (Sch B), an antioxidant ingredient of Schisandra chinensis, was studied on scopolamine-induced dementia in mouse. Scopolamine developed oxidative stress in the brain with the decreased levels of antioxidant enzymes and increased nitrite level. At the same time, a significant impairment of learning and memory occurred when evaluated by passive avoidance task (PAT) and Morris water maze (MWM) with concomitant increase of acetylcholinesterase (AChE) activity and decreased acetylcholine levels. Pre-treatment by Sch B (10, 25, 50 mg/kg) effectively prevented scopolamine-induced oxidative stress and improved behavioural tasks. Further, the scopolamine-induced increase in AChE activity was significantly suppressed and the level of acetylcholine was maintained as normal by Sch B treatment. These results suggest that Sch B have protective function against cerebral functional defects such as dementia not only by antioxidant prevention but also exerting its potent cognitive-enhancing activity through modulation of acetylcholine level.
ESTHER : Giridharan_2011_Free.Radic.Res_45_950
PubMedSearch : Giridharan_2011_Free.Radic.Res_45_950
PubMedID: 21615274

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

Title : The genome of the mesopolyploid crop species Brassica rapa - Wang_2011_Nat.Genet_43_1035
Author(s) : Wang X , Wang H , Wang J , Sun R , Wu J , Liu S , Bai Y , Mun JH , Bancroft I , Cheng F , Huang S , Li X , Hua W , Freeling M , Pires JC , Paterson AH , Chalhoub B , Wang B , Hayward A , Sharpe AG , Park BS , Weisshaar B , Liu B , Li B , Tong C , Song C , Duran C , Peng C , Geng C , Koh C , Lin C , Edwards D , Mu D , Shen D , Soumpourou E , Li F , Fraser F , Conant G , Lassalle G , King GJ , Bonnema G , Tang H , Belcram H , Zhou H , Hirakawa H , Abe H , Guo H , Jin H , Parkin IA , Batley J , Kim JS , Just J , Li J , Xu J , Deng J , Kim JA , Yu J , Meng J , Min J , Poulain J , Hatakeyama K , Wu K , Wang L , Fang L , Trick M , Links MG , Zhao M , Jin M , Ramchiary N , Drou N , Berkman PJ , Cai Q , Huang Q , Li R , Tabata S , Cheng S , Zhang S , Sato S , Sun S , Kwon SJ , Choi SR , Lee TH , Fan W , Zhao X , Tan X , Xu X , Wang Y , Qiu Y , Yin Y , Li Y , Du Y , Liao Y , Lim Y , Narusaka Y , Wang Z , Li Z , Xiong Z , Zhang Z
Ref : Nat Genet , 43 :1035 , 2011
Abstract : We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
ESTHER : Wang_2011_Nat.Genet_43_1035
PubMedSearch : Wang_2011_Nat.Genet_43_1035
PubMedID: 21873998
Gene_locus related to this paper: braol-Q8GTM3 , braol-Q8GTM4 , brarp-m4ei94 , brarp-m4c988 , brana-a0a078j4a9 , brana-a0a078e1m0 , brana-a0a078cd75 , brarp-m4dwa6 , brana-a0a078j4f0 , brana-a0a078cus4 , brana-a0a078f8c2 , brana-a0a078jql1 , brana-a0a078dgj3 , brana-a0a078hw50 , brana-a0a078cuu0 , brana-a0a078dfa9 , brana-a0a078ic91 , brarp-m4ctw3 , brana-a0a078ca65 , brana-a0a078ctc8 , brana-a0a078h021 , brana-a0a078jx23 , brarp-m4da84 , brarp-m4dwr7 , brana-a0a078dh94 , brana-a0a078h612 , brana-a0a078j2t3 , braol-a0a0d3dpb2 , braol-a0a0d3dx76 , brana-a0a078jxa8 , brana-a0a078i2k3 , brarp-m4cwq4 , brarp-m4dcj8 , brarp-m4eh17 , brarp-m4eey4 , brarp-m4dnj8 , brarp-m4ey83 , brarp-m4ey84

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

Title : Molecular cloning and expression of a novel cholinephosphotransferase involved in glycoglycerophospholipid biosynthesis of Mycoplasma fermentans - Ishida_2009_Curr.Microbiol_58_535
Author(s) : Ishida N , Irikura D , Matsuda K , Sato S , Sone T , Tanaka M , Asano K
Ref : Curr Microbiol , 58 :535 , 2009
Abstract : A gene, mf1, encoding a novel cholinephosphotransferase in glycoglycerophospholipid (GGPL) biosynthesis of Mycoplasma fermentans PG18 was identified by genomic analysis, cloned, and expressed in Escherichia coli. The mf1 gene comprises an open reading frame of 777 bp encoding 258 amino acids. The mf1 gene product, Mf1, has 23% amino acid homology with LicD of Haemophilus influenzae but no homology with genes of other Mycoplasma species in the GenBank database. The reaction product of Mf1 using alpha-glucopyranosyl-1,2-dipalmitoilglycerol and cytidine 5'-diphosphocholine (CDP-choline) as substrates showed the specific protonated molecule at m/z 896, which corresponded to GGPL-I as determined by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Furthermore, the product ions of choline, phosphocholine, and hexose-bound phosphocholine were detected by tandem mass spectrometry (MS) analysis of protonated molecules at m/z 896. These results identified mf1 as a novel cholinephosphotransferase and showed that the phosphocholine transfer step is involved in the GGPL biosynthesis pathway of M. fermentans. This is the first report of a GGPL biosynthesis enzyme.
ESTHER : Ishida_2009_Curr.Microbiol_58_535
PubMedSearch : Ishida_2009_Curr.Microbiol_58_535
PubMedID: 19219498
Gene_locus related to this paper: mycfe-c4xfi7 , mycfe-c4xfu4 , mycfp-c4xfg3

Title : Lipid peroxidation is enhanced in Yusho victims 35 years after accidental poisoning with polychlorinated biphenyls in Nagasaki, Japan - Shimizu_2007_J.Appl.Toxicol_27_195
Author(s) : Shimizu K , Ogawa F , Thiele JJ , Bae S , Sato S
Ref : J Appl Toxicol , 27 :195 , 2007
Abstract : Thirty-five years have passed since the accidental poisoning with polychlorinated biphenyls (PCB) in Japan and yet high concentrations of PCB are still detected in the serum of the victims. PCB produces superoxide and thus victims are considered to be in a persistent state of oxidative stress. Urinary concentrations of 8-isoprostane (8IP) in the victims and age-matched controls were measured to assess this hypothesis. The mean urinary concentration of 8IP was significantly higher than that in the controls. There was a positive correlation between urinary 8IP and serum concentrations of cholinesterase. It was considered that Yusho is an oxidative stress and 8IP is a useful tool for checking the oxidative condition in Yusho victims.
ESTHER : Shimizu_2007_J.Appl.Toxicol_27_195
PubMedSearch : Shimizu_2007_J.Appl.Toxicol_27_195
PubMedID: 17186569

Title : Alterations in cognitive function in prepubertal mice with protein malnutrition: relationship to changes in choline acetyltransferase - Nakagawasai_2006_Behav.Brain.Res_167_111
Author(s) : Nakagawasai O , Yamadera F , Sato S , Taniguchi R , Hiraga H , Arai Y , Murakami H , Mawatari K , Niijima F , Tan-No K , Tadano T
Ref : Behavioural Brain Research , 167 :111 , 2006
Abstract : We have found that protein malnutrition (PM) causes a significant impairment of memory-related behavior on the 15th and 20th day after the start of PM (5% casein) feeding in prepubertal mice but not in postpubertal mice, as measured by a passive-avoidance task. This impairment was almost completely reversed by merely switching to a standard protein (20% casein) diet on the 10th day after the start of PM. However, the reversal was not observed when the switching to a standard protein regimen was done on the 15th day of the PM diet. Interestingly, the impairment of memory-related behavior on the 20th day was improved by the chronic administration of physostigmine (0.1 mg/kg/day x last 10 days, i.p.), a cholinesterase inhibitor. To correlate brain cholinergic neuron function with the memory-related behavior impairment induced by PM, microphotometry was used to determine the histological distribution of the imunofluorescence intensity for choline acetyltransferase (ChAT), a functional marker of presynapse in cholinergic neurons. The change in the intensity of fluorescence indicated that ChAT protein was decreased in the hippocampus (CA1, CA3 and dentate gyrus) on the 20th day after PM feeding in comparison with controls. These results suggest the possibility that the memory-related behavior deficits observed in prepubertal mice with PM are caused by a dysfunction of the cholinergic neurons in the hippocampus.
ESTHER : Nakagawasai_2006_Behav.Brain.Res_167_111
PubMedSearch : Nakagawasai_2006_Behav.Brain.Res_167_111
PubMedID: 16242790

Title : A pregnant woman with genetic variants of butyrylcholinesterase and inflammatory bowel disease -
Author(s) : Futagami M , Sakamoto T , Sakamoto A , Shigetou T , Taniguchi R , Sato S , Tutaya S , Kojima K , Yasujima M , Mizunuma H
Ref : J Obstet Gynaecol , 26 :562 , 2006
PubMedID: 17000508

Title : Anti-lipoprotein lipase antibody in systemic sclerosis: association with elevated serum triglyceride concentrations - Kodera_2005_J.Rheumatol_32_629
Author(s) : Kodera M , Hayakawa I , Komura K , Yanaba K , Hasegawa M , Takehara K , Sato S
Ref : J Rheumatol , 32 :629 , 2005
Abstract : OBJECTIVE: The vascular damage systemic sclerosis (SSc) consists mainly of microvascular changes, but recently macrovascular changes with dyslipidemia were recognized. In systemic lupus erythematosus (SLE), autoantibody to lipoprotein lipase (LPL), a key enzyme that hydrolyzes triglycerides, suggested a role of autoimmunity for elevated serum triglyceride levels and atherosclerosis. We investigated the prevalence and levels of anti-LPL antibodies, their clinical correlation, and their functional significance in patients with SSc.
METHODS: Serum samples from patients with diffuse cutaneous SSc (dSSc; n = 55), limited cutaneous SSc (lSSc; n = 75), SLE (n = 21), and dermatomyositis (DM; n = 21) and healthy controls (n = 41) were examined by ELISA. The presence of anti-LPL antibody was evaluated by immunoblotting analysis using purified LPL. To determine the functional relevance of anti-LPL antibody in vivo, we assessed whether anti-LPL autoantibody was able to inhibit LPL activity using the LPL activity kit.
RESULTS: ELISA revealed that IgG or IgM anti-LPL antibodies were detected in 35% of SSc patients, while they were also positive in 67% of SLE patients and 43% of DM patients. The presence of IgG anti-LPL antibody was associated with elevated serum triglyceride levels, greater extent of skin fibrosis, and more frequent presence of lung fibrosis, heart involvement, and anti-topoisomerase I antibodies. The presence of anti-LPL autoantibody was confirmed by immunoblotting analysis. LPL activity was inhibited by IgG anti-LPL antibodies in sera from SSc patients with elevated serum triglyceride levels. CONCLUSION: Our results suggest that anti-LPL autoantibody contributes to elevated serum triglyceride levels by inhibiting LPL enzyme activity in patients with SSc.
ESTHER : Kodera_2005_J.Rheumatol_32_629
PubMedSearch : Kodera_2005_J.Rheumatol_32_629
PubMedID: 15801017

Title : Changes in serum lipid concentrations in patients with chronic hepatitis C virus positive hepatitis responsive or non-responsive to interferon therapy - Hamamoto_2005_J.Gastroenterol.Hepatol_20_204
Author(s) : Hamamoto S , Uchida Y , Wada T , Moritani M , Sato S , Hamamoto N , Ishihara S , Watanabe M , Kinoshita Y
Ref : J Gastroenterol Hepatol , 20 :204 , 2005
Abstract : BACKGROUND: Changes in serum lipid concentrations during the administration of interferon to patients with chronic hepatitis C virus (HCV) infection have not been fully investigated. The present study was designed to compare changes in serum lipid concentrations before, during and after interferon therapy in responders and non-responders to treatment.
METHODS: In total, 101 patients with chronic HCV positive hepatitis were enrolled in this study. High dose interferon alpha was given on alternate days for 6 months. Six months after the end of treatment patients were assessed for the presence or absence of HCV RNA to determine the results of interferon treatment. The time courses of changes in serum lipid concentrations were measured in all patients.
RESULTS: The total cholesterol level increased gradually during and after interferon therapy, and its pattern of change coincided with that of serum cholinesterase activity. Pretreatment serum cholesterol concentrations did not differ between responders and non-responders to interferon therapy. The serum triglyceride concentration, conversely, showed a sharp increase during interferon administration and returned to its basal level after the end of treatment. Responders to interferon therapy tended to have higher pretreatment triglyceride concentrations than did non-responders.
CONCLUSIONS: We clarified that serum cholesterol and triglyceride levels showed different patterns of change during interferon therapy.
ESTHER : Hamamoto_2005_J.Gastroenterol.Hepatol_20_204
PubMedSearch : Hamamoto_2005_J.Gastroenterol.Hepatol_20_204
PubMedID: 15683422

Title : Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes - Gardner_2005_Science_309_134
Author(s) : Gardner MJ , Bishop R , Shah T , de Villiers EP , Carlton JM , Hall N , Ren Q , Paulsen IT , Pain A , Berriman M , Wilson RJ , Sato S , Ralph SA , Mann DJ , Xiong Z , Shallom SJ , Weidman J , Jiang L , Lynn J , Weaver B , Shoaibi A , Domingo AR , Wasawo D , Crabtree J , Wortman JR , Haas B , Angiuoli SV , Creasy TH , Lu C , Suh B , Silva JC , Utterback TR , Feldblyum TV , Pertea M , Allen J , Nierman WC , Taracha EL , Salzberg SL , White OR , Fitzhugh HA , Morzaria S , Venter JC , Fraser CM , Nene V
Ref : Science , 309 :134 , 2005
Abstract : We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated.
ESTHER : Gardner_2005_Science_309_134
PubMedSearch : Gardner_2005_Science_309_134
PubMedID: 15994558
Gene_locus related to this paper: thepa-q4mzr2 , thepa-q4n0b4 , thepa-q4n2i4 , thepa-q4n4i8 , thepa-q4n5d6 , thepa-q4n5m4 , thepa-q4n006 , thepa-q4n9g7 , thepa-q4n315 , thepa-q4n349 , thepa-q4n803

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

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

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

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

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

Title : The sequence of the human genome - Venter_2001_Science_291_1304
Author(s) : Venter JC , Adams MD , Myers EW , Li PW , Mural RJ , Sutton GG , Smith HO , Yandell M , Evans CA , Holt RA , Gocayne JD , Amanatides P , Ballew RM , Huson DH , Wortman JR , Zhang Q , Kodira CD , Zheng XH , Chen L , Skupski M , Subramanian G , Thomas PD , Zhang J , Gabor Miklos GL , Nelson C , Broder S , Clark AG , Nadeau J , McKusick VA , Zinder N , Levine AJ , Roberts RJ , Simon M , Slayman C , Hunkapiller M , Bolanos R , Delcher A , Dew I , Fasulo D , Flanigan M , Florea L , Halpern A , Hannenhalli S , Kravitz S , Levy S , Mobarry C , Reinert K , Remington K , Abu-Threideh J , Beasley E , Biddick K , Bonazzi V , Brandon R , Cargill M , Chandramouliswaran I , Charlab R , Chaturvedi K , Deng Z , Di Francesco V , Dunn P , Eilbeck K , Evangelista C , Gabrielian AE , Gan W , Ge W , Gong F , Gu Z , Guan P , Heiman TJ , Higgins ME , Ji RR , Ke Z , Ketchum KA , Lai Z , Lei Y , Li Z , Li J , Liang Y , Lin X , Lu F , Merkulov GV , Milshina N , Moore HM , Naik AK , Narayan VA , Neelam B , Nusskern D , Rusch DB , Salzberg S , Shao W , Shue B , Sun J , Wang Z , Wang A , Wang X , Wang J , Wei M , Wides R , Xiao C , Yan C , Yao A , Ye J , Zhan M , Zhang W , Zhang H , Zhao Q , Zheng L , Zhong F , Zhong W , Zhu S , Zhao S , Gilbert D , Baumhueter S , Spier G , Carter C , Cravchik A , Woodage T , Ali F , An H , Awe A , Baldwin D , Baden H , Barnstead M , Barrow I , Beeson K , Busam D , Carver A , Center A , Cheng ML , Curry L , Danaher S , Davenport L , Desilets R , Dietz S , Dodson K , Doup L , Ferriera S , Garg N , Gluecksmann A , Hart B , Haynes J , Haynes C , Heiner C , Hladun S , Hostin D , Houck J , Howland T , Ibegwam C , Johnson J , Kalush F , Kline L , Koduru S , Love A , Mann F , May D , McCawley S , McIntosh T , McMullen I , Moy M , Moy L , Murphy B , Nelson K , Pfannkoch C , Pratts E , Puri V , Qureshi H , Reardon M , Rodriguez R , Rogers YH , Romblad D , Ruhfel B , Scott R , Sitter C , Smallwood M , Stewart E , Strong R , Suh E , Thomas R , Tint NN , Tse S , Vech C , Wang G , Wetter J , Williams S , Williams M , Windsor S , Winn-Deen E , Wolfe K , Zaveri J , Zaveri K , Abril JF , Guigo R , Campbell MJ , Sjolander KV , Karlak B , Kejariwal A , Mi H , Lazareva B , Hatton T , Narechania A , Diemer K , Muruganujan A , Guo N , Sato S , Bafna V , Istrail S , Lippert R , Schwartz R , Walenz B , Yooseph S , Allen D , Basu A , Baxendale J , Blick L , Caminha M , Carnes-Stine J , Caulk P , Chiang YH , Coyne M , Dahlke C , Mays A , Dombroski M , Donnelly M , Ely D , Esparham S , Fosler C , Gire H , Glanowski S , Glasser K , Glodek A , Gorokhov M , Graham K , Gropman B , Harris M , Heil J , Henderson S , Hoover J , Jennings D , Jordan C , Jordan J , Kasha J , Kagan L , Kraft C , Levitsky A , Lewis M , Liu X , Lopez J , Ma D , Majoros W , McDaniel J , Murphy S , Newman M , Nguyen T , Nguyen N , Nodell M , Pan S , Peck J , Peterson M , Rowe W , Sanders R , Scott J , Simpson M , Smith T , Sprague A , Stockwell T , Turner R , Venter E , Wang M , Wen M , Wu D , Wu M , Xia A , Zandieh A , Zhu X
Ref : Science , 291 :1304 , 2001
Abstract : A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
ESTHER : Venter_2001_Science_291_1304
PubMedSearch : Venter_2001_Science_291_1304
PubMedID: 11181995
Gene_locus related to this paper: human-AADAC , human-ABHD1 , human-ABHD10 , human-ABHD11 , human-ACHE , human-BCHE , human-LDAH , human-ABHD18 , human-CMBL , human-ABHD17A , human-KANSL3 , human-LIPA , human-LYPLAL1 , human-NDRG2 , human-NLGN3 , human-NLGN4X , human-NLGN4Y , human-PAFAH2 , human-PREPL , human-RBBP9 , human-SPG21

Title : Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones - Sato_2000_DNA.Res_7_131
Author(s) : Sato S , Nakamura Y , Kaneko T , Katoh T , Asamizu E , Tabata S
Ref : DNA Research , 7 :131 , 2000
Abstract : Based on the physical map of Arabidopsis thaliana chromosome 3 previously constructed with CIC YAC, TAC, P1 and BAC clones (Sato, S. et al., DNA Res., 5, 163-168, 1998), a total of 60 P1 and TAC clones were sequenced, and the sequence features of the resulting 4,504,864 bp regions were analyzed by applying various computer programs for similarity search and gene modeling. As a result, a total of 1054 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4066 bp. Introns were observed in 77% of the genes, and the average number per gene and the average length of the introns were 3.9 and 156 bp, respectively. These sequence features are essentially identical to those of chromosome 5 in our previous reports, but the gene density was slightly higher than that observed for chromosomes 2 and 4. The regions also contained 10 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Sato_2000_DNA.Res_7_131
PubMedSearch : Sato_2000_DNA.Res_7_131
PubMedID: 10819329
Gene_locus related to this paper: arath-At3g14360 , arath-At3g27325 , arath-Y3684 , arath-Q9LI62 , arath-Q9LUG8 , arath-Q9LUH1 , arath-Q6NKN2 , arath-Q9LW14 , arath-Q9LW28 , arath-SCP21 , arath-SCP33

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

Title : Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC clones - Kaneko_2000_DNA.Res_7_217
Author(s) : Kaneko T , Katoh T , Sato S , Nakamura A , Asamizu E , Tabata S
Ref : DNA Research , 7 :217 , 2000
Abstract : To deduce the entire sequence of the top arm of the Arabidopsis thaliana chromosome 3, the sequence determination was performed on a total of 90 P1, TAC and BAC clones chosen according to our sequencing strategy. Sequence features of the resulting 4,251,695 bp regions were analyzed with various computer programs for similarity search and gene modeling. As a result, a total of 941 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4210 bp. Introns were observed in 73% of the genes, and the average number per gene and the average length of the introns were 3.6 and 159 bp, respectively. These sequence features are essentially identical to those of chromosomes 3 and 5 in our previous reports. The regions also contained 14 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Kaneko_2000_DNA.Res_7_217
PubMedSearch : Kaneko_2000_DNA.Res_7_217
PubMedID: 10907853
Gene_locus related to this paper: arath-SCP16 , arath-CXE11 , arath-q9lhe8 , arath-Q9LJI1 , arath-Q9LK01 , arath-SCP15

Title : Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones - Sato_2000_DNA.Res_7_31
Author(s) : Sato S , Nakamura Y , Kaneko T , Katoh T , Asamizu E , Kotani H , Tabata S
Ref : DNA Research , 7 :31 , 2000
Abstract : In our ongoing project to deduce the nucleotide sequence of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced on the basis of the fine physical map, and as of January, 2000, the sequences of 16.6 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. Along with the sequence determination, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and we already predicted a total of 2697 potential protein coding genes in the 11,166,130 bp regions, which are covered by 159 P1 and TAC clones. In this paper, we describe the structural features of the 3,076,755 bp regions covered by newly analyzed 60 P1 and TAC clones. A total of 715 potential protein coding genes were identified, giving an average density of the genes identified of 1 gene per 4001 bp. Introns were observed in 80% of the genes, and the average number per gene and the average length of the introns were 4.5 and 147 bp, respectively. These sequence features are nearly identical to those in our latest report in which the data were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 12 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/kaos/.
ESTHER : Sato_2000_DNA.Res_7_31
PubMedSearch : Sato_2000_DNA.Res_7_31
PubMedID: 10718197
Gene_locus related to this paper: arath-At5g47330 , arath-AT5G51180 , arath-AT5G62180 , arath-At5g67050 , arath-MES18 , arath-CXE18 , arath-Q9LTX5 , arath-Q9LVS4 , arath-Q9LVS5 , arath-Q9LVU7 , arath-Q9LVX9 , arath-SCP41 , arath-SCP42

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

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

Title : Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAC clones - Kaneko_1999_DNA.Res_6_183
Author(s) : Kaneko T , Katoh T , Sato S , Nakamura Y , Asamizu E , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 6 :183 , 1999
Abstract : In this series of projects sequencing the entire genome of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced according to the fine physical map, and as of May 7, 1999, the sequences of 16.2 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. In parallel, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and to date we have predicted a total of 2380 potential protein-coding genes in the 10,154,580 bp regions, which are covered by 142 P1 and TAC clones. In this paper, we newly analyzed the structural features of the 1,011,550 bp regions covered by additional 17 P1 and TAC clones, and predicted 298 protein-coding genes. The average density of the genes identified was 1 gene per 3394 bp. Introns were observed in 67% of the genes, and the average number per gene and the average length of the introns were 3.2 and 159 bp, respectively. The gene density became higher than the value estimated in the previously analyzed regions (1 gene per 4,267 bp), as the data in this paper were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 8 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available on the database KAOS (Kazusa Arabidopsis data Opening Site) at http:\/\/www.kazusa.or.jp/arabi/.
ESTHER : Kaneko_1999_DNA.Res_6_183
PubMedSearch : Kaneko_1999_DNA.Res_6_183
PubMedID: 10470850
Gene_locus related to this paper: arath-At5g37710 , arath-SCP19 , arath-Q9FI59

Title : Effects of levosimendan on myocardial contractility and Ca2+ transients in aequorin-loaded right-ventricular papillary muscles and indo-1-loaded single ventricular cardiomyocytes of the rabbit - Sato_1998_J.Mol.Cell.Cardiol_30_1115
Author(s) : Sato S , Talukder MA , Sugawara H , Sawada H , Endoh M
Ref : Journal of Molecular & Cellular Cardiology , 30 :1115 , 1998
Abstract : Effects of levosimendan on myocardial contractility and Ca2+ transients were assessed in the ventricular myocardium of the rabbit. Levosimendan at and above 0.1 microM had a concentration-dependent positive inotropic effect (PIE) on isolated papillary muscles that had been loaded with aqeuorin. The maximum inotropic response to levosimendan at 3 microM was approximately 20% of the maximum response to isoproterenol (ISOmax), whereas the maximum increase in the amplitude of Ca2+ transients was approximately 11% of ISOmax. For a given PIE, levosimendan increased the amplitude of Ca2+ transients much less than an elevation of [Ca2+]o. Levosimendan did not prolong the relaxation time. Similar results were obtained in single ventricular cardiomyocytes that had been loaded with indo-1. In the presence of the muscarinic receptor agonist carbachol, both the PIE and the increase in the Ca2+ transient induced by levosimendan were markedly attenuated. During wash-out of both carbachol and levosimendan, the contractile force increased conspicuously with little change in the amplitude of Ca2+ transients, an indication that the increase in myofibrillar sensitivity to Ca2+ ions elicited by levosimendan was susceptible to carbachol. Levosimendan at and above 0.03 microM shifted the concentration-response curve for isoproterenol to the left. Levosimendan had a positive chronotropic effect at 0.01 microM and higher in the isolated right atrium of the rabbit. These findings indicate that, in addition to the increase by levosimendan of the sensitivity of contractile proteins to Ca2+ ions, the accumulation of cyclic AMP due to the phosphodiesterase-inhibitory action of levosimendan might contribute to the PIE of this drug.
ESTHER : Sato_1998_J.Mol.Cell.Cardiol_30_1115
PubMedSearch : Sato_1998_J.Mol.Cell.Cardiol_30_1115
PubMedID: 9689586

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence features of the regions of 1,081,958 bp covered by seventeen physically assigned P1 and TAC clones. -
Author(s) : Asamizu E , Sato S , Kaneko T , Nakamura Y , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 5 :379 , 1998
PubMedID: 10048488
Gene_locus related to this paper: arath-At5g14930 , arath-at5g18630 , arath-AT5G19050 , arath-At5g24180 , arath-AT5G24190 , arath-At5g24200 , arath-F2G14.100 , arath-F6H11.120 , arath-F9G14.280 , arath-F14F8.240 , arath-HNL , arath-At5g14310

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VII. Sequence features of the regions of 1,013,767 bp covered by sixteen physically assigned P1 and TAC clones - Nakamura_1998_DNA.Res_5_297
Author(s) : Nakamura Y , Sato S , Asamizu E , Kaneko T , Kotani H , Miyajima N , Tabata S
Ref : DNA Research , 5 :297 , 1998
Abstract : Sixteen P1 and TAC clones assigned to Arabidopsis thaliana chromosome 5 were sequenced, and their sequence features were analyzed using various computer programs. The total length of the sequences determined was 1,013,767 bp. Together with the nucleotide sequences of 109 clones previously reported, the regions of chromosome 5 sequenced so far now total 9,072,622 bp, which presumably covers approximately one-third of the chromosome. A similarity search against the reported gene sequences predicted the presence of a total of 225 protein-coding genes and/or gene segments in the newly sequenced regions, indicating an average gene density of one gene per 4.5 kb. Introns were identified in 72.4% of the potential protein genes for which the entire gene structure was predicted, and the average number per gene and the average length of the introns were 3.3 and 163 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Nakamura_1998_DNA.Res_5_297
PubMedSearch : Nakamura_1998_DNA.Res_5_297
PubMedID: 9872454
Gene_locus related to this paper: arath-At5g41900 , arath-Q9FJ29

Title : Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence features of the regions of 1,381,565 bp covered by twenty one physically assigned P1 and TAC clones - Kaneko_1998_DNA.Res_5_131
Author(s) : Kaneko T , Kotani H , Nakamura Y , Sato S , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 5 :131 , 1998
Abstract : The nucleotide sequences of 21 P1 and TAC clones which have been precisely localized to the fine physical map of the Arabidopsis thaliana chromosome 5, were determined, and their sequence features were analyzed. The total length of the regions sequenced in this study were 1,381,565 bp, bringing the total length of the chromosome 5 sequences determined so far to 6,691,670 bp together with the regions of the 69 clones previously reported. By computer-aided analyses including similarity search against protein and EST databases and gene modeling with computer programs, a total of 337 potential protein-coding genes and/or gene segments were identified on the basis of similarity to the reported gene sequences. An average density of the genes and/or gene segments thus assigned was 1 gene/4,100 bp. Introns were identified in 76.7% of the potential protein genes for which the entire gene structure were predicted, and the average number per gene and the average length of the introns were 3.9 and 176 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http:@www.kazusa.or.jp@arabi
ESTHER : Kaneko_1998_DNA.Res_5_131
PubMedSearch : Kaneko_1998_DNA.Res_5_131
PubMedID: 9679202
Gene_locus related to this paper: arath-AT5G39220 , arath-Q9FKP9

Title : Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence features of the regions of 1,456,315 bp covered by nineteen physically assigned P1 and TAC clones - Sato_1998_DNA.Res_5_41
Author(s) : Sato S , Kaneko T , Kotani H , Nakamura Y , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 5 :41 , 1998
Abstract : Nineteen P1 and TAC clones, which have been precisely localized to the fine physical map of Arabidopsis thaliana chromosome 5, were newly sequenced, and their sequence features were analysed. The total length of the clones sequenced was 1,456,315 bp. Together with the previously reported sequences, the regions of chromosome 5 that have been sequenced to date is now 5,310,105 bp. When the sequences determined in this study were subjected to similarity search against protein and expressed sequence tag (EST) databases and analysis with computer programs for gene modeling, a total of 354 potential protein-coding genes and/or gene segments were identified. The average density of the assigned genes and/or gene segments was one gene per 4,114 bp. Introns were identified in 75% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 194 bp, respectively. These sequence features are essentially identical to those in the previously reported sequences. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (the Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Sato_1998_DNA.Res_5_41
PubMedSearch : Sato_1998_DNA.Res_5_41
PubMedID: 9628582
Gene_locus related to this paper: arath-AT5G41120 , arath-At5g41130 , arath-F6H11.120

Title : Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones. -
Author(s) : Kotani H , Nakamura Y , Sato S , Asamizu E , Kaneko T , Miyajima N , Tabata S
Ref : DNA Research , 5 :203 , 1998
PubMedID: 9734815
Gene_locus related to this paper: arath-At5g56750

Title : Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of the regions of 1,044,062 bp covered by thirteen physically assigned P1 clones - Kotani_1997_DNA.Res_4_291
Author(s) : Kotani H , Nakamura Y , Sato S , Kaneko T , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 4 :291 , 1997
Abstract : A total of 13 P1 clones, each containing a marker(s) specifically mapped on chromosome 5, were isolated from a P1 library of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun based strategy and precisely located on the physical map of chromosome 5. The total length of the sequenced regions was 1,044,062 bp. Since we have previously reported the sequence of 1,621,245 bp by analysis of 20 non-redundant P1 clones, the total length of the sequences of chromosome 5 determined so far reached 2,665,307 bp. The regions sequenced in this study were analysed by comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling; a total of 225 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit similarity to known genes were also predicted by computer-aided analysis. An average density of the genes and/or gene was 1 gene/4,640 bp. Introns were identified in approximately 84% of the potential genes, and the average number and length of the introns per gene were 5.3 and 184 bp, respectively. These sequence features are essentially identical to those for the previously sequenced regions. The transcription level of the predicted genes has been roughly monitored by counting the numbers of matched Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at https://www.kazusa.or.jp/kaos/.
ESTHER : Kotani_1997_DNA.Res_4_291
PubMedSearch : Kotani_1997_DNA.Res_4_291
PubMedID: 9405937
Gene_locus related to this paper: arath-At5g13640 , arath-AT5G24210 , arath-At5g24220 , arath-AT5G24230 , arath-At5g17670 , arath-Q9FN74 , arath-Q9FN79 , arath-Q9FNF6

Title : Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence features of the regions of 1,191,918 bp covered by seventeen physically assigned P1 clones - Nakamura_1997_DNA.Res_4_401
Author(s) : Nakamura Y , Sato S , Kaneko T , Kotani H , Asamizu E , Miyajima N , Tabata S
Ref : DNA Research , 4 :401 , 1997
Abstract : A total of 17 P1 and TAC clones each containing a marker(s) specifically mapped on chromosome 5 were isolated from P1 and TAC libraries of the Arabidopsis thaliana Columbia genome, and their nucleotide sequences were determined according to the shot gun-based strategy and precisely located on the physical map of chromosome 5. The total length of the clones sequenced in this study was 1,191,918 bp. As we have previously reported the sequence of 2,662,078 bp by analysis of 33 P1 clones, the total length of the sequences of chromosome 5 determined so far is now 3,853,996 bp. The sequences determined in this study were subjected to similarity search against protein and EST databases and analysis with computer programs for gene modeling, and a total of 310 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not show apparent similarity to known genes were also predicted by computer-aided analysis. An average density of the assigned genes and/or gene segments was 1 gene/3,845 bp. Introns were identified in 78% of the potential protein genes, and the average number per gene and the average length of the introns were 3.7 and 185 bp, respectively. The numbers of the Arabidopsis ESTs matched to each of the predicted genes have been counted to monitor the transcription level. The sequence data and gene information are available on the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.
ESTHER : Nakamura_1997_DNA.Res_4_401
PubMedSearch : Nakamura_1997_DNA.Res_4_401
PubMedID: 9501997
Gene_locus related to this paper: arath-AT5G22460 , arath-At5g42930 , arath-LIP2 , arath-SCPL34

Title : Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones - Sato_1997_DNA.Res_4_215
Author(s) : Sato S , Kotani H , Nakamura Y , Kaneko T , Asamizu E , Fukami M , Miyajima N , Tabata S
Ref : DNA Research , 4 :215 , 1997
Abstract : A total of 20 P1 clones with an average insert size of 80 kb and each containing a marker(s) specifically mapped on chromosome 5 were isolated from a P1 library of the Arabidopsis thaliana genome, and their nucleotide sequences were determined according to a shotgun-based strategy and precisely located on the physical map of chromosome 5 separately constructed. The total length of the sequenced regions were summed up to 1,621,245 bp. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 347 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit any similarity to known genes were also predicted. An average density of the genes and/or gene segments assigned so far as 1 gene/4,672 bp. Introns were identified in approximately 78% of the potential genes, and the average number and length of the introns per gene were 3.7 and 161 bp. The transcription level of the predicted genes was roughly monitored by counting the numbers of identified Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at http:/(/)www.kazusa.or.jp/arabi/.
ESTHER : Sato_1997_DNA.Res_4_215
PubMedSearch : Sato_1997_DNA.Res_4_215
PubMedID: 9330910
Gene_locus related to this paper: arath-AT5G38220 , arath-At5g38520 , arath-Q8LFB7 , arath-Q9FF27 , arath-q9ffg7 , arath-Q9FFZ1 , arath-SCP47 , arath-B9DFR3

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

Title : Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64\% to 92\% of the genome - Kaneko_1995_DNA.Res_2_153
Author(s) : Kaneko T , Tanaka A , Sato S , Kotani H , Sazuka T , Miyajima N , Sugiura M , Tabata S
Ref : DNA Research , 2 :153 , 1995
Abstract : The contiguous sequence of 1,003,450 bp spanning map positions 64% to 92% of the genome of Synechocystis sp. strain PCC6803 has been deduced. Computer analysis of the sequence predicts that this region contains at least 818 potential ORFs, in which 255 (31%) were either genes that had already been identified or their homologues, 84 (10%) were homologues to registered hypothetical genes, and 149 (18%) showed weak similarities to reported genes. The remaining 330 ORFs showed no apparent similarity to any reported genes or carried no significant protein motifs. The potential ORFs as a whole occupied 86% of the sequenced region, implying compact arrangement of genes in the genome. As to the structural RNA genes, one rRNA operon consisting of 5,028 bp and at least 11 species of tRNA genes were identified. It is noteworthy that 10 out of the 11 tRNA species showed significant sequence similarities to tRNAs reported in plant chloroplasts. As other notable unique sequences, three classes of IS-like elements each with characteristics typical of IS elements were identified, and a typical unit of WD(Trp-Asp)-repeats which have only been detected in the regulatory proteins of eukaryotes was identified within the large 5,079-bp ORF located at map position 69%.
ESTHER : Kaneko_1995_DNA.Res_2_153
PubMedSearch : Kaneko_1995_DNA.Res_2_153
PubMedID: 8590279
Gene_locus related to this paper: synsp-prxc , synsp-Q55130 , synsp-SLL0482 , synsp-sll0553 , synsp-SLR0825