Research Topics
Genomes and GenesSpecies | Naoki SatoSummaryAffiliation: University of Tokyo Country: Japan Publications
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Publications
[Diversity in molecular organization and function of plastid nucleoids--a hypothesis on the discontinuous evolution of plastid genomic machinery]Naoki Sato
Department of Biochemistry and Molecular Biology, Saitama University, 255 Shimo-Okubo, Saitama 338-8570
Seikagaku 74:27-37. 2002- Phylogenomic and structural modeling analyses of the PsbP superfamily reveal multiple small segment additions in the evolution of photosystem II-associated PsbP protein in green plantsNaoki Sato
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
Mol Phylogenet Evol 56:176-86. 2010..These results suggest that Family A-specific additions of short segments played a decisive role in the transition of PsbO/U/V to PsbO/P/Q complex in green plants... - Genomic and biochemical analysis of lipid biosynthesis in the unicellular rhodophyte Cyanidioschyzon merolae: lack of a plastidic desaturation pathway results in the coupled pathway of galactolipid synthesisNaoki Sato
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3 8 1 Komaba, Meguro ku, Tokyo 153 8902, Japan
Eukaryot Cell 6:1006-17. 2007..These results highlight essential differences in lipid biosynthetic pathways between the red algae and the green lineage, which includes plants and green algae... - Statistics of N-terminal alignment as a guide for refining prokaryotic gene annotationNaoki Sato
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro ku, Tokyo, Japan
Genomics 99:138-43. 2012.... - Gclust: trans-kingdom classification of proteins using automatic individual threshold settingNaoki Sato
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro ku, Tokyo, 153 8902, Japan
Bioinformatics 25:599-605. 2009..Here a method is described using two similarity measures and organism count... - Mass identification of chloroplast proteins of endosymbiont origin by phylogenetic profiling based on organism-optimized homologous protein groupsNaoki Sato
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3 8 1 Komaba, Tokyo 153 8902, Japan
Genome Inform 16:56-68. 2005..An initial minimal set of CPRENDOs was predicted without targeting prediction and experimentally validated... - [Structure, replication and dynamism of chloroplast nucleoids]Naoki Sato
Tanpakushitsu Kakusan Koso 50:1838-42. 2005 - Orthogenomics of photosynthetic organisms: bioinformatic and experimental analysis of chloroplast proteins of endosymbiont origin in Arabidopsis and their counterparts in SynechocystisMasayuki Ishikawa
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3 8 1 Komaba, Meguro ku, Tokyo 153 8902, Japan
Plant Cell Physiol 50:773-88. 2009..We conclude that phylogenetic profiling is useful in finding CPRENDOs, but the physiological functions of orthologous genes may be different in chloroplasts and cyanobacteria... - A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolaeHisayoshi Nozaki
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
BMC Biol 5:28. 2007..Therefore, we aimed to complete all previous gaps and sequence all remaining chromosomal ends, and now report the first nuclear-genome sequence for any eukaryote that is 100% complete... - Purification and characterization of organellar DNA polymerases in the red alga Cyanidioschyzon merolaeTakashi Moriyama
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Japan
FEBS J 275:2899-918. 2008..The expression of PolB was regulated by the cell cycle. The available results suggest that PolB is involved in the replication of plastids and mitochondria... - CyanoClust: comparative genome resources of cyanobacteria and plastidsNaobumi V Sasaki
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3 8 1 Komaba, Meguro ku, Tokyo, 153 8902, Japan
Database (Oxford) 2010:bap025. 2010..We have developed a web-server system for the protein homology database featuring cyanobacteria and plastids. Database URL: http://cyanoclust.c.u-tokyo.ac.jp/... - Genomic structure of the cyanobacterium Synechocystis sp. PCC 6803 strain GT-SNaoyuki Tajima
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3 8 1, Meguro ku, Tokyo 153 8902, Japan
DNA Res 18:393-9. 2011..We have thus become able to provide an accurate genomic sequence of Synechocystis sp. PCC 6803 for future studies on this important cyanobacterial strain... - Involvement of digalactosyldiacylglycerol in cellular thermotolerance in Synechocystis sp. PCC 6803Naoki Mizusawa
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3 8 1, Meguro ku, Tokyo 153 8902, Japan
Arch Microbiol 191:595-601. 2009..Analysis of photosynthesis in intact cells suggested that the inhibition of repair processes and accelerated photodamage resulted in growth retardation in dgdA mutant cells at high temperatures... - Lack of digalactosyldiacylglycerol increases the sensitivity of Synechocystis sp. PCC 6803 to high light stressNaoki Mizusawa
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba 3 8 1, Meguro ku, Tokyo 153 8902, Japan
FEBS Lett 583:718-22. 2009..Although both photodamage and repair processes of photosynthesis were affected, the repair process was more severely affected than the photodamage process, suggesting that DGDG plays an important role in the photosynthetic repair cycle... - Plastid localization of the PEND protein is mediated by a noncanonical transit peptideKimihiro Terasawa
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
FEBS J 276:1709-19. 2009..This raises the possibility of plastid-to-nuclear signal transduction by the relocalization of PEND... - Early candidacy for differentiation into heterocysts in the filamentous cyanobacterium Anabaena sp. PCC 7120Masakazu Toyoshima
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3 8 1 Komaba, Meguro ku, Tokyo, Japan
Arch Microbiol 192:23-31. 2010..Such early candidacy could be explained by different properties of the outer and inner cells of a quartet, but the molecular nature of candidacy remains to be uncovered... - The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plantsKimihiro Terasawa
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro ku, Tokyo, Japan
Mol Biol Evol 24:699-709. 2007..The phylogenetic analysis as well as the syntenic structure suggest that the mitochondrial genomes of Physcomitrella and Marchantia retain prototype features among land plant mitochondrial genomes... - Conservation of POPs, the plant organellar DNA polymerases, in eukaryotesTakashi Moriyama
Department of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305 8602, Japan Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3 8 1, Meguro ku, Tokyo 153 8902, Japan
Protist 162:177-87. 2011..Finally, we propose a model for the succession of organellar DNA polymerases... - Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10DMotomichi Matsuzaki
Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
Nature 428:653-7. 2004..These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells... - Digalactosyldiacylglycerol is required for stabilization of the oxygen-evolving complex in photosystem IIIsamu Sakurai
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro ku, Tokyo 153 8902, Japan
Plant Physiol 145:1361-70. 2007..These results demonstrate that DGDG plays important roles in PSII through the binding of extrinsic proteins required for stabilization of the oxygen-evolving complex... - A novel variant of ferredoxin-dependent sulfite reductase having preferred substrate specificity for nitrite in the unicellular red alga Cyanidioschyzon merolaeKohsuke Sekine
Center for Structuring Life Sciences, University of Tokyo, Meguro ku, Japan
Biochem J 423:91-8. 2009..These combined results indicate that CmSiRB has a significant nitrite-reducing activity and plays a physiological role in nitrate assimilation... - Elucidating Genome Structure Evolution by Analysis of Isoapostatic Gene Clusters using Statistics of Variance of Gene DistancesNaobumi V Sasaki
Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
Genome Biol Evol 2010:1-12. 2010..The stability and the robustness of the variance statistics are discussed. This method will also be useful in deciphering the structural organization of genomes in other groups of bacteria... - Identification and characterization of two phage-type RNA polymerase cDNAs in the moss Physcomitrella patens: implication of recent evolution of nuclear-encoded RNA polymerase of plastids in plantsYukihiro Kabeya
Department of Molecular Biology, Faculty of Science, Saitama University, Saitama Prefecture, 338-8570, Japan
Plant Cell Physiol 43:245-55. 2002..We therefore suggest that the generation of nuclear-encoded RNA polymerase of chloroplast is a rather recent event during the evolution of land plants... - Organization, developmental dynamics, and evolution of plastid nucleoidsNaoki Sato
Department of Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
Int Rev Cytol 232:217-62. 2003.... - [Bioinformatics of evolution of metabolic system]Naoki Sato
Tanpakushitsu Kakusan Koso 48:2211-7. 2003 - Cloning and characterization of glycine-rich RNA-binding protein cDNAs in the moss Physcomitrella patensTsuyoshi Nomata
Department of Molecular Biology, Faculty of Science, Saitama University, Saitama, Saitama Prefecture, 338-8570 Japan
Plant Cell Physiol 45:48-56. 2004..Results of phylogenetic analysis suggest that the nuclear and mitochondrial forms of GRP have been established early during the evolution of green plants... - Visualization of plastid nucleoids in situ using the PEND-GFP fusion proteinKimihiro Terasawa
Department of Molecular Biology, Faculty of Science, Saitama University, Sakura-ku, Saitama, 338-8570 Japan
Plant Cell Physiol 46:649-60. 2005..During the division of plastid, nucleoids formed a network structure, which made possible equal partition of nucleoids... - Comparative analysis of the genomes of cyanobacteria and plantsNaoki Sato
Department of Molecular Biology, Saitama University, Shimo Ohkubo 255, Saitama 338 8570, Japan
Genome Inform 13:173-82. 2002..In addition, only 80 groups are identified as the gene groups that could not have been acquired by plants without cyanobacterial endosymbiosis. Further study is needed to identify plant genes of cyanobacterial origin... - Occurrence and characterization of PEND proteins in angiospermsKimihiro Terasawa
Department of Molecular Biology, Faculty of Science, Saitama University, Sakura-ku, Saitama, 338-8570, Japan
J Plant Res 118:111-9. 2005..These results suggest that PEND protein is present in angiosperms, and the homologs in crucifers are functionally analogous to the PEND protein in pea... - Molecular cloning, expression, and serological evaluation of an 8-kilodalton subunit of antigen B from Echinococcus multilocularisWulamu Mamuti
Department of Parasitology, Asahikawa Medical College, Asahikawa, Japan
J Clin Microbiol 42:1082-8. 2004..There was no cross-reaction with sera from patients with cysticercosis, which often cross-react when native antigens are used for serodiagnosis... - Active alveolar hydatidosis with sero-negativity for antibody to the 18 kDa antigenKimiaki Yamano
Department of Biological Science, Hokkaido Institute of Public Health, Sapporo 060-0819, Japan
Jpn J Infect Dis 58:122-4. 2005 - Reversible DNA compaction by sulfite reductase regulates transcriptional activity of chloroplast nucleoidsKohsuke Sekine
Department of Molecular Biology, Faculty of Science, Saitama University, 255 Shimo-ohkubo, Saitama, Saitama Prefecture, 338-8570, Japan
J Biol Chem 277:24399-404. 2002..These results suggest that SiR regulates the transcriptional activity of chloroplast nucleoids through changes in DNA compaction... - Signal transduction genes required for heterocyst maturation in Anabaena sp. strain PCC 7120Qing Fan
MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824-1312, USA
J Bacteriol 188:6688-93. 2006..One of these genes has a hitherto unreported mutant phenotype. Two previously identified regulatory genes were further characterized... - DNA binding and partial nucleoid localization of the chloroplast stromal enzyme ferredoxin:sulfite reductaseKohsuke Sekine
Department of Molecular Biology, Faculty of Science, Saitama University, Japan
FEBS J 274:2054-69. 2007..These results suggest that SiR plays an essential role in compacting nucleoids in plastids, but that the extent of association of SiR with nucleoids varies among plant species... - GenoMap, a circular genome data viewerNaoki Sato
Department of Molecular Biology, Faculty of Science, Saitama University, 255 Shimo ohkubo, Saitama, 338 8570 Japan
Bioinformatics 19:1583-4. 2003..An interactive interface facilitates easy identification of the expressed region. This software is also used for drawing genome-wide quantitative data... - The assembly of the FtsZ ring at the mid-chloroplast division site depends on a balance between the activities of AtMinE1 and ARC11/AtMinD1Makoto T Fujiwara
RIKEN, Hirosawa 2 1, Wako, Saitama 351 0198, Japan
Plant Cell Physiol 49:345-61. 2008....