Author Report for: Seki MNo contact information in database for Seki M
Li W, Nguyen KH, Chu HD, Ha CV, Watanabe Y, Osakabe Y, Leyva-Gonzalez MA, Sato M, Toyooka K and Tran LP <9 more author(s)> Li W, Nguyen KH, Chu HD, Ha CV, Watanabe Y, Osakabe Y, Leyva-Gonzalez MA, Sato M, Toyooka K, Voges L, Tanaka M, Mostofa MG, Seki M, Seo M, Yamaguchi S, Nelson DC, Tian C, Herrera-Estrella L, Tran LP (- 9) Ref: PLoS Genet, 13:e1007076, 2017 : PubMed ESTHER: Li_2017_PLoS.Genet_13_e1007076 PubMedSearch: Li 2017 PLoS.Genet 13 e1007076 PubMedID: 29131815 Gene_locus related to this paper: arath-KAI2.D14L Abstract Drought causes substantial reductions in crop yields worldwide. Therefore, we set out to identify new chemical and genetic factors that regulate drought resistance in Arabidopsis thaliana. Karrikins (KARs) are a class of butenolide compounds found in smoke that promote seed germination, and have been reported to improve seedling vigor under stressful growth conditions. Here, we discovered that mutations in KARRIKIN INSENSITIVE2 (KAI2), encoding the proposed karrikin receptor, result in hypersensitivity to water deprivation. We performed transcriptomic, physiological and biochemical analyses of kai2 plants to understand the basis for KAI2-regulated drought resistance. We found that kai2 mutants have increased rates of water loss and drought-induced cell membrane damage, enlarged stomatal apertures, and higher cuticular permeability. In addition, kai2 plants have reduced anthocyanin biosynthesis during drought, and are hyposensitive to abscisic acid (ABA) in stomatal closure and cotyledon opening assays. We identified genes that are likely associated with the observed physiological and biochemical changes through a genome-wide transcriptome analysis of kai2 under both well-watered and dehydration conditions. These data provide evidence for crosstalk between ABA- and KAI2-dependent signaling pathways in regulating plant responses to drought. A comparison of the strigolactone receptor mutant d14 (DWARF14) to kai2 indicated that strigolactones also contributes to plant drought adaptation, although not by affecting cuticle development. Our findings suggest that chemical or genetic manipulation of KAI2 and D14 signaling may provide novel ways to improve drought resistance. Title: Expression of adrenergic and cholinergic receptors in murine renal intercalated cells Jun JG, Maeda S, Kuwahara-Otani S, Tanaka K, Hayakawa T, Seki M Ref: J Vet Med Sci, 76:1493, 2014 : PubMed ESTHER: Jun_2014_J.Vet.Med.Sci_76_1493 PubMedSearch: Jun 2014 J.Vet.Med.Sci 76 1493 PubMedID: 25069412 Abstract Neurons influence renal function and help to regulate fluid homeostasis, blood pressure and ion excretion. Intercalated cells (ICCs) are distributed throughout the renal collecting ducts and help regulate acid/base equilibration. Because ICCs are located among principal cells, it has been difficult to determine the effects that efferent nerve fibers have on this cell population. In this study, we examined the expression of neurotransmitter receptors on the murine renal epithelial M-1 cell line. We found that M-1 cells express a2 and b2 adrenergic receptor mRNA and the b2 receptor protein. Further, b2 receptor-positive cells in the murine cortical collecting ducts also express AQP6, indicating that these cells are ICCs. M-1 cells were found to express m1, m4 and m5 muscarinic receptor mRNAs and the m1 receptor protein. Cells in the collecting ducts also express the m1 receptor protein, and some m1-positive cells express AQP6. Acetylcholinesterase was detected in cortical collecting duct cells. Interestingly, acetylcholinesterase-positive cells neighbored AQP6-positive cells, suggesting that principal cells may regulate the availability of acetylcholine. In conclusion, our data suggest that ICCs in murine renal collecting ducts may be regulated by the adrenergic and cholinergic systems. Title: Comparative genomic analysis of 1047 completely sequenced cDNAs from an Arabidopsis-related model halophyte, Thellungiella halophila Taji T, Komatsu K, Katori T, Kawasaki Y, Sakata Y, Tanaka S, Kobayashi M, Toyoda A, Seki M, Shinozaki K Ref: BMC Plant Biol, 10:261, 2010 : PubMed ESTHER: Taji_2010_BMC.Plant.Biol_10_261 PubMedSearch: Taji 2010 BMC.Plant.Biol 10 261 PubMedID: 21106055 Gene_locus related to this paper: theha-e4mwi7, theha-e4mwx5, theha-e4mxu0, eutsa-v4kvd3 Abstract BACKGROUND: Thellungiella halophila (also known as T. salsuginea) is a model halophyte with a small size, short life cycle, and small genome. Thellungiella genes exhibit a high degree of sequence identity with Arabidopsis genes (90% at the cDNA level). We previously generated a full-length enriched cDNA library of T. halophila from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes. Title: Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs Iida K, Fukami-Kobayashi K, Toyoda A, Sakaki Y, Kobayashi M, Seki M, Shinozaki K Ref: DNA Research, 16:155, 2009 : PubMed ESTHER: Iida_2009_DNA.Res_16_155 PubMedSearch: Iida 2009 DNA.Res 16 155 PubMedID: 19423640 Gene_locus related to this paper: arath-AT2G42690, arath-AT5G20060, arath-eds1, arath-MES2, arath-o65713, arath-pip, arath-Q8LFB7, arath-q66gm8, arath-B9DFR3 Abstract Alternative splicing (AS) is a mechanism by which multiple types of mature mRNAs are generated from a single pre-mature mRNA. In this study, we completely sequenced 1800 full-length cDNAs from Arabidopsis thaliana, which had 5' and/or 3' sequences that were previously found to have AS events or alternative transcription start sites. Unexpectedly, these sequences gave us further evidence of AS, as 601 out of 1800 transcripts showed novel AS events. We focused on the combination patterns of multiple AS events within individual genes. Interestingly, some specific AS event combination patterns tended to appear more frequently than expected. The two most common patterns were: (i) alternative donor-0 approximately 12 times of exon skips-alternative acceptor and (ii) several times ( approximately 8) of retained introns. We also found that multiple AS events in a transcript tend to have the same effects concerning the length of the mature mRNA. Our current results are consistent with our previous observations, which showed changes in AS profiles under different conditions, and suggest the involvement of hypothetical cis- and trans-acting factors in the regulation of AS events. Title: Whole genome sequence analysis of Mycobacterium bovis bacillus Calmette-Guerin (BCG) Tokyo 172: a comparative study of BCG vaccine substrains Seki M, Honda I, Fujita I, Yano I, Yamamoto S, Koyama A Ref: Vaccine, 27:1710, 2009 : PubMed ESTHER: Seki_2009_Vaccine_27_1710 PubMedSearch: Seki 2009 Vaccine 27 1710 PubMedID: 19200449 Gene_locus related to this paper: myctu-a85a, myctu-a85b, myctu-a85c, myctu-bpoC, myctu-cut3, myctu-cutas1, myctu-cutas2, myctu-d5yk66, myctu-ephB, myctu-ephc, myctu-ephd, myctu-ephE, myctu-hpx, myctu-linb, myctu-lipG, myctu-lipJ, myctu-LIPS, myctu-lipv, myctu-LPQC, myctu-LPQP, myctu-MBTB, myctu-metx, myctu-mpt51, myctu-MT1628, myctu-MT3441, myctu-p71654, myctu-p95011, myctu-PKS6, myctu-PKS13, myctu-ppe42, myctu-ppe63, myctu-Rv1430, myctu-RV0045C, myctu-Rv0077c, myctu-Rv0151c, myctu-Rv0152c, myctu-Rv0159c, myctu-Rv0160c, myctu-rv0183, myctu-Rv0217c, myctu-Rv0220, myctu-Rv0272c, myctu-RV0293C, myctu-RV0457C, myctu-RV0519C, myctu-RV0774C, myctu-RV0782, myctu-RV0840C, myctu-Rv1069c, myctu-Rv1076, myctu-RV1123C, myctu-Rv1184c, myctu-Rv1190, myctu-Rv1191, myctu-RV1192, myctu-RV1215C, myctu-Rv1399c, myctu-Rv1400c, myctu-Rv1426c, myctu-RV1639C, myctu-RV1683, myctu-RV1758, myctu-Rv1800, myctu-Rv1833c, myctu-Rv2045c, myctu-RV2054, myctu-RV2296, myctu-Rv2385, myctu-RV2627C, myctu-RV2672, myctu-RV2695, myctu-RV2765, myctu-RV2800, myctu-RV2854, myctu-Rv2970c, myctu-Rv3084, myctu-Rv3097c, myctu-rv3177, myctu-Rv3312c, myctu-RV3452, myctu-RV3473C, myctu-Rv3487c, myctu-Rv3569c, myctu-Rv3591c, myctu-RV3724, myctu-Rv3802c, myctu-Rv3822, myctu-y0571, myctu-y963, myctu-Y1834, myctu-y1835, myctu-y2079, myctu-yc88, myctu-ym23, myctu-ym24, myctu-YR15, myctu-yt28 Abstract To investigate the molecular characteristics of bacillus Calmette-Guerin (BCG) vaccines, the complete genomic sequence of Mycobacterium bovis BCG Tokyo 172 was determined, and the results were compared with those for BCG Pasteur and other M. tuberculosis complex. The genome of BCG Tokyo had a length of 4,371,711bp and contained 4033 genes, including 3950 genes coding for proteins (CDS). There were 18 regions of difference (showing differences of more than 20bp), 20 insertion or deletion (ins/del) mutations of less than 20bp, and 68 SNPs between the two BCG substrains. These findings are useful for better understanding of the genetic differences in BCG substrains due to in vitro evolution of BCG. Title: Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila Taji T, Sakurai T, Mochida K, Ishiwata A, Kurotani A, Totoki Y, Toyoda A, Sakaki Y, Seki M and Shinozaki K <3 more author(s)> Taji T, Sakurai T, Mochida K, Ishiwata A, Kurotani A, Totoki Y, Toyoda A, Sakaki Y, Seki M, Ono H, Sakata Y, Tanaka S, Shinozaki K (- 3) Ref: BMC Plant Biol, 8:115, 2008 : PubMed ESTHER: Taji_2008_BMC.Plant.Biol_8_115 PubMedSearch: Taji 2008 BMC.Plant.Biol 8 115 PubMedID: 19014467 Gene_locus related to this paper: theha-e4mwi7, theha-e4mwx5, theha-e4mxu0, eutsa-v4kvd3 Abstract BACKGROUND: Thellungiella halophila (also known as Thellungiella salsuginea) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic transformation by the floral dipping method used with its close relative, Arabidopsis thaliana. Thellungiella genes exhibit high sequence identity (approximately 90% at the cDNA level) with Arabidopsis genes. Furthermore, Thellungiella not only shows tolerance to extreme salinity stress, but also to chilling, freezing, and ozone stress, supporting the use of Thellungiella as a good genomic resource in studies of abiotic stress tolerance. RESULTS: We constructed a full-length enriched Thellungiella (Shan Dong ecotype) cDNA library from various tissues and whole plants subjected to environmental stresses, including high salinity, chilling, freezing, and abscisic acid treatment. We randomly selected about 20,000 clones and sequenced them from both ends to obtain a total of 35 171 sequences. CAP3 software was used to assemble the sequences and cluster them into 9569 nonredundant cDNA groups. We named these cDNAs "RTFL" (RIKEN Thellungiella Full-Length) cDNAs. Information on functional domains and Gene Ontology (GO) terms for the RTFL cDNAs were obtained using InterPro. The 8289 genes assigned to InterPro IDs were classified according to the GO terms using Plant GO Slim. Categorical comparison between the whole Arabidopsis genome and Thellungiella genes showing low identity to Arabidopsis genes revealed that the population of Thellungiella transport genes is approximately 1.5 times the size of the corresponding Arabidopsis genes. This suggests that these genes regulate a unique ion transportation system in Thellungiella. CONCLUSION: As the number of Thellungiella halophila (Thellungiella salsuginea) expressed sequence tags (ESTs) was 9388 in July 2008, the number of ESTs has increased to approximately four times the original value as a result of this effort. Our sequences will thus contribute to correct future annotation of the Thellungiella genome sequence. The full-length enriched cDNA clones will enable the construction of overexpressing mutant plants by introduction of the cDNAs driven by a constitutive promoter, the complementation of Thellungiella mutants, and the determination of promoter regions in the Thellungiella genome. Title: Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R and Sasaki T <85 more author(s)> Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T (- 85) Ref: Genome Res, 17:175, 2007 : PubMed ESTHER: Itoh_2007_Genome.Res_17_175 PubMedSearch: Itoh 2007 Genome.Res 17 175 PubMedID: 17210932 Gene_locus related to this paper: orysa-Q7XTC5, orysa-Q852M6, orysa-Q8GSE8, orysa-Q9FYP7, orysa-Q5ZA26, orysa-Q5JLP6, orysa-Q8H5P5, orysa-Q7F1Y5, orysa-cbp3, orysa-cbpx, orysa-Q6YSZ8, orysa-Q9FW17, orysa-Q84QZ6, orysa-Q0JK71, orysa-B9EWJ8, orysa-Q6ZDG6, orysa-Q6ZDG5, orysa-Q658B2, orysa-Q5N7L1, orysa-Q8RYV9, orysa-Q8H3R3, orysa-Q5SNH3, orysa-pir7a, orysa-q2qnj4, orysa-q2qyj1, orysa-q2r077, orysa-Q4VWY7, orysa-q5smv5, orysa-q5z901, orysa-Q5ZBI5, orysa-q6atz0, orysa-q6i5q3, orysa-q6j657, orysa-q6k4q2, orysj-q6yse8, orysa-q6yy42, orysa-q6yzk1, orysa-q6z8b1, orysa-q6z995, orysa-q6zjq6, orysa-q7x7y5, orysa-Q7XC50, orysa-q7xr62, orysa-q7xr63, orysa-q7xsg1, orysa-q7xsq2, orysa-q7xts6, orysa-q7xv53, orysa-Q8LQS5, orysa-Q8RZ79, orysa-Q8S0U8, orysa-Q8W3C6, orysa-Q9LHX5, orysa-q53m20, orysa-q53nd8, orysa-q60e79, orysa-q67iz2, orysa-q67iz3, orysa-q67iz7, orysa-q67iz8, orysa-q67j02, orysa-q67j05, orysa-q67j09, orysa-q67j10, orysa-q67tr6, orysa-q67tv0, orysa-q69j38, orysa-q69y21, orysa-q75hy1, orysa-q75hy2, orysa-Q0J0A4, orysa-q651a8, orysa-q652g4, orysa-q688m8, orysa-Q6H8G1, orysi-a2z179, orysi-a2zef2, orysi-b8a7e6, orysi-b8a7e7, orysi-b8bfe5, orysi-b8bhp9, orysj-b9fi05, orysj-q0djj0, orysj-q0jaf0, orysj-q0jga1, orysj-q0jhi5, orysj-q5jl22, orysj-q5jlw7, orysj-q6h7q9, orysj-q6yvk6, orysj-q7f8x1, orysj-q7xcx3, orysj-q9fwm6, orysj-q10j20, orysj-q10ss2, orysj-q69uw6, orysj-q94d71, orysj-q0iq98, orysj-b9gbs4, orysj-b9gbs1 Abstract We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene. Title: A plant locus essential for phylloquinone (vitamin K1) biosynthesis originated from a fusion of four eubacterial genes Gross J, Cho WK, Lezhneva L, Falk J, Krupinska K, Shinozaki K, Seki M, Herrmann RG, Meurer J Ref: Journal of Biological Chemistry, 281:17189, 2006 : PubMed ESTHER: Gross_2006_J.Biol.Chem_281_17189 PubMedSearch: Gross 2006 J.Biol.Chem 281 17189 PubMedID: 16617180 Gene_locus related to this paper: arath-T6L1.8 Abstract Phylloquinone is a compound present in all photosynthetic plants serving as cofactor for Photosystem I-mediated electron transport. Newly identified seedling-lethal Arabidopsis thaliana mutants impaired in the biosynthesis of phylloquinone possess reduced Photosystem I activity. The affected gene, called PHYLLO, consists of a fusion of four previously individual eubacterial genes, menF, menD, menC, and menH, required for the biosynthesis of phylloquinone in photosynthetic cyanobacteria and the respiratory menaquinone in eubacteria. The fact that homologous men genes reside as polycistronic units in eubacterial chromosomes and in plastomes of red algae strongly suggests that PHYLLO derived from a plastid operon during endosymbiosis. The principle architecture of the fused PHYLLO locus is conserved in the nuclear genomes of plants, green algae, and the diatom alga Thalassiosira pseudonana. The latter arose from secondary endosymbiosis of a red algae and a eukaryotic host indicating selective driving forces for maintenance and/or independent generation of the composite gene cluster within the nuclear genomes. Besides, individual menF genes, encoding active isochorismate synthases (ICS), have been established followed by splitting of the essential 3' region of the menF module of PHYLLO only in genomes of higher plants. This resulted in inactivation of the ICS activity encoded by PHYLLO and enabled a metabolic branch from the phylloquinone biosynthetic route to independently regulate the synthesis of salicylic acid required for plant defense. Therefore, gene fusion, duplication, and fission events adapted a eubacterial multienzymatic system to the metabolic requirements of plants. Title: Evolutional study on acetylcholine expression Horiuchi Y, Kimura R, Kato N, Fujii T, Seki M, Endo T, Kato T, Kawashima K Ref: Life Sciences, 72:1745, 2003 : PubMed ESTHER: Horiuchi_2003_Life.Sci_72_1745 PubMedSearch: Horiuchi 2003 Life.Sci 72 1745 PubMedID: 12559395 Abstract Acetylcholine (ACh) is a well-known neurotransmitter in the cholinergic nervous systems of vertebrates and insects; however, there is only indirect evidence for its presence in lower invertebrates, such as plants and fungi. We therefore investigated the expression of ACh in invertebrates (sea squirt, sea urchin, trepang, squid, abalone, nereis, sea anemone, coral and sponge), plants (arabidopsis, eggplant, bamboo shoot, cedar, hinoki, pine, podcarp, fern, horsetail and moss), fungi (yeast and mushroom) and bacteria by assaying ACh content and synthesis, focusing on the presence of two synthetic enzymes, choline acetyltransferase (ChAT) and carnitine acetyltransferase (CarAT). Using a specific radioimmunoassay, ACh was detected in all samples tested. The levels varied considerably, however, with the upper portion of bamboo shoots having the highest content (2.9 micromol/g). ACh synthesis was also detected in all samples tested; moreover, the activity in most samples from the animal kingdom, as well as bamboo shoots and the stem of the shiitake mushroom, were sensitive to both ChAT and CarAT inhibitors. Levels of ACh synthesis were lower in samples from other plants, fungi and bacteria and were insensitive to ChAT and CarAT inhibitors. These findings demonstrate the presence of ACh and ACh-synthesizing activity in evolutionally primitive life as well as in more complex multicellular organisms. In the context of the recent discovery of non-neuronal ACh in various mammalian species, these findings suggest that ACh been expressed in organisms from the beginning of life, functioning as a local mediator as well as a neurotransmitter. Title: Estrogenic and Acetylcholinesterase-Enhancement Activity of a New Isoflavone, 7,2',4'-Trihydroxyisoflavone-4'-O-beta-D-Glucopyranoside from Crotalaria Sessililflora Mun'im A, Isoda H, Seki M, Negishi O, Ozawa T Ref: Cytotechnology, 43:127, 2003 : PubMed ESTHER: Mun'im_2003_Cytotech_43_127 PubMedSearch: Mun'im 2003 Cytotech 43 127 PubMedID: 19003217 Abstract A new isoflavone, 7,2',4'-trihydroxyisoflavone-4'-O-beta-D-glucopyranoside has been isolated from the aerial part of Crotalaria sessiliflora. The isoflavone glucoside enhanced the proliferation of the MCF-7 human breast cancer cell line, which possesses estrogen receptor (ER) and responds to estrogen in culture. The estrogenic property of the isoflavone glucoside was blocked by the known ER antagonist tamoxifen, indicating the involvement of the ER. Furthermore, the isoflavone glucoside was found to enhance the acetylcholinesterase (AChE) activity of the rat neuronal cell line PC12 at low concentrations of nerve growth factor (NGF). Title: Empirical analysis of transcriptional activity in the Arabidopsis genome Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C and Ecker JR <60 more author(s)> Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, Pham P, Cheuk R, Karlin-Newmann G, Liu SX, Lam B, Sakano H, Wu T, Yu G, Miranda M, Quach HL, Tripp M, Chang CH, Lee JM, Toriumi M, Chan MM, Tang CC, Onodera CS, Deng JM, Akiyama K, Ansari Y, Arakawa T, Banh J, Banno F, Bowser L, Brooks S, Carninci P, Chao Q, Choy N, Enju A, Goldsmith AD, Gurjal M, Hansen NF, Hayashizaki Y, Johnson-Hopson C, Hsuan VW, Iida K, Karnes M, Khan S, Koesema E, Ishida J, Jiang PX, Jones T, Kawai J, Kamiya A, Meyers C, Nakajima M, Narusaka M, Seki M, Sakurai T, Satou M, Tamse R, Vaysberg M, Wallender EK, Wong C, Yamamura Y, Yuan S, Shinozaki K, Davis RW, Theologis A, Ecker JR (- 60) Ref: Science, 302:842, 2003 : PubMed ESTHER: Yamada_2003_Science_302_842 PubMedSearch: Yamada 2003 Science 302 842 PubMedID: 14593172 Gene_locus related to this paper: arath-AT2G42690, arath-AT4g30610, arath-At5g13640, arath-AT5G20520, arath-AT5G27320, arath-CGEP, arath-clh1, arath-clh2, arath-CXE12, arath-CXE15, arath-SCP25, arath-F14F8.240, arath-MES6, arath-LCAT1, arath-PLA11, arath-PLA15, arath-PLA16, arath-PLA17, arath-SCP8, arath-SCP11, arath-SCP40, arath-MES14, arath-AXR4, arath-SFGH, arath-B9DFR3, arath-pae2 Abstract Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome. Title: A practical procedure for the large-scale preparation of methyl (2R,3S)-3-(4-methoxyphenyl)glycidate, a key intermediate for diltiazem Furutani T, Imashiro R, Hatsuda M, Seki M Ref: J Org Chem, 67:4599, 2002 : PubMed ESTHER: Furutani_2002_J.Org.Chem_67_4599 PubMedSearch: Furutani 2002 J.Org.Chem 67 4599 PubMedID: 12076164 Abstract A practical synthesis of methyl (2R,3S)-3-(4-methoxyphenyl)glycidate (-)-2, a key intermediate for diltiazem (1), was developed. Treatment of methyl (E)-4-methoxycinnamate 3 with chiral dioxirane, generated from chiral ketone 4, provided (-)-2 in 77% ee and 89% yield. The crude mixture of (-)-2 and 4 was efficiently separated by the use of novel and simple equipment performing a lipase-catalyzed transesterification and a continuous dissolution and crystallization to furnish the optically pure (-)-2 and recovery of 4 in 74% and 91% yield, respectively. Title: Functional annotation of a full-length Arabidopsis cDNA collection Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K and Shinozaki K <10 more author(s)> Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y, Muramatsu M, Hayashizaki Y, Kawai J, Carninci P, Itoh M, Ishii Y, Arakawa T, Shibata K, Shinagawa A, Shinozaki K (- 10) Ref: Science, 296:141, 2002 : PubMed ESTHER: Seki_2002_Science_296_141 PubMedSearch: Seki 2002 Science 296 141 PubMedID: 11910074 Gene_locus related to this paper: arath-CXE15 Abstract Full-length complementary DNAs (cDNAs) are essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products. We isolated 155,144 RIKEN Arabidopsis full-length (RAFL) cDNA clones. The 3'-end expressed sequence tags (ESTs) of 155,144 RAFL cDNAs were clustered into 14,668 nonredundant cDNA groups, about 60% of predicted genes. We also obtained 5' ESTs from 14,034 nonredundant cDNA groups and constructed a promoter database. The sequence database of the RAFL cDNAs is useful for promoter analysis and correct annotation of predicted transcription units and gene products. Furthermore, the full-length cDNAs are useful resources for analyses of the expression profiles, functions, and structures of plant proteins. Title: Effect of hydrocarbon-water interfaces on synthetic and hydrolytic activities of lipases Maruyama T, Nakajima M, Seki M Ref: J Biosci Bioeng, 92:242, 2001 : PubMed ESTHER: Maruyama_2001_J.Biosci.Bioeng_92_242 PubMedSearch: Maruyama 2001 J.Biosci.Bioeng 92 242 PubMedID: 16233091 Abstract We have developed a new method of lipase activation for interesterification, in which lipase, in contact with a hydrocarbon-water interface, has been found to have high interesterification activity in an anhydrous solvent. We have applied this activation method to various lipase and obtained high synthetic activity in n-hexane, and have investigated the effect of various hydrocarbon-water interfaces on the synthetic and hydrolytic activities of lipases. The esterification and/or interesterification activity of lipases tested was improved by this activation method, using an n-tetradecane-water interface. From the initial group of lipases, three representative lipases (from Rhizopus japonicus, Chromobacterium viscosum and porcine pancreas) were selected for further study. The effect of various hydrocarbon-water interfaces on synthetic (interesterification or esterification) activity was studied. We demonstrated that the resulting synthetic activity was affected by the choice of hydrocarbon-water interface and that there were differences in the effects of interfaces on the synthetic activity of these lipases. | |||||||
|
