Papers - NIIMURA Yoshihito
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Evolution of olfactory receptor genes in the human genome. Reviewed
Niimura Y, Nei M
Proceedings of the National Academy of Sciences of the United States of America 100 ( 21 ) 12235 - 40 2003.10
Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES
Olfactory receptor (OR) genes form the largest known multigene family in the human genome. To obtain some insight into their evolutionary history, we have identified the complete set of OR genes and their chromosomal locations from the latest human genome sequences. We detected 388 potentially functional genes that have intact ORFs and 414 apparent pseudogenes. The number and the fraction (48%) of functional genes are considerably larger than the ones previously reported. The human OR genes can clearly be divided into class I and class II genes, as was previously noted. Our phylogenetic analysis has shown that the class II OR genes can further be classified into 19 phylogenetic clades supported by high bootstrap values. We have also found that there are many tandem arrays of OR genes that are phylogenetically closely related. These genes appear to have been generated by tandem gene duplication. However, the relationships between genomic clusters and phylogenetic clades are very complicated. There are a substantial number of cases in which the genes in the same phylogenetic clade are located on different chromosomal regions. In addition, OR genes belonging to distantly related phylogenetic clades are sometimes located very closely in a chromosomal region and form a tight genomic cluster. These observations can be explained by the assumption that several chromosomal rearrangements have occurred at the regions of OR gene clusters and the OR genes contained in different genomic clusters are shuffled.
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Comparative analysis of the base biases at the gene terminal portions in seven eukaryote genomes. Reviewed
Niimura Y, Terabe M, Gojobori T, Miura K
Nucleic acids research 31 ( 17 ) 5195 - 201 2003.9
Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS
Adenine nucleotides have been found to appear preferentially in the regions after the initiation codons or before the termination codons of bacterial genes. Our previous experiments showed that AAA and AAT, the two most frequent second codons in Escherichia coli, significantly enhance translation efficiency. To determine whether such a characteristic feature of base frequencies exists in eukaryote genes, we performed a comparative analysis of the base biases at the gene terminal portions using the proteomes of seven eukaryotes. Here we show that the base appearance at the codon third positions of gene terminal regions is highly biased in eukaryote genomes, although the codon third positions are almost free from amino acid preference. The bias changes depending on its position in a gene, and is characteristic of each species. We also found that bias is most outstanding at the second codon, the codon after the initiation codon. NCN is preferred in every genome; in particular, GCG is strongly favored in human and plant genes. The presence of the bias implies that the base sequences at the second codon affect translation efficiency in eukaryotes as well as bacteria.
DOI： 10.1093/nar/gkg701
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The genome sequence and structure of rice chromosome 1. Reviewed
Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T
Nature 420 ( 6913 ) 312 - 6 2002.11
Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP
The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.
DOI： 10.1038/nature01184
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In silico chromosome staining: reconstruction of Giemsa bands from the whole human genome sequence. Reviewed
Niimura Y, Gojobori T
Proceedings of the National Academy of Sciences of the United States of America 99 ( 2 ) 797 - 802 2002.1
Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES
Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several experiments showed that the correspondence is quite poor. To elucidate the precise relationship between GC content and Giemsa banding patterns, we developed an "in silico chromosome staining" method for reconstructing Giemsa bands computationally from the whole human genome sequence. Here we show that 850-level Giemsa bands are best correlated with the difference in GC content between a local window of 2.5 megabases and a regional window of 9.3 megabases along a chromosome. The correlations are of strong statistical significance for almost all 43 chromosomal arms. Our results clearly show that Giemsa-dark bands are locally GC-poor regions compared with the flanking regions. These findings are consistent with the model that matrix-associated regions, which are known to be AT-rich, are present more densely in Giemsa-dark bands than in -light bands.
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Real-time fluorescence analysis on molecular mechanisms for regulation of cytochrome P450scc activity upon steroidogenic stimulation in adrenocortical cells Reviewed
Ryota Homma, Tetsuya Kimoto, Yoshihito Niimura, Alexander Krivosheev, Takayuki Hara, Yoshihiro Ohta, Suguru Kawato
Journal of Inorganic Biochemistry 82 ( 1-4 ) 171 - 180 2000
Language：English Publishing type：Research paper (scientific journal)
Real-time fluorescence analysis revealed that the activity of cytochrome P450scc was related to Ca2+ signals arising from extracellular NADPH, ACTH and ATP stimulation in adrenocortical fasciculata cells. The side-chain cleavage reaction by cytochrome P450scc was measured with 3β-hydroxy-22,23-bisnor-5-cholenyl ether (cholesterol-resorufin) by observing the distinct increase in fluorescence upon conversion of cholesterol-resorufin to resorufin and pregnenolone. Adrenocorticotropic hormone (ACTH) induced a relatively small stimulation of the P450scc activity. A significant production of resorufin was revealed after stimulation of cell cultures with 100 pM, 1 nM of ACTH for 3 h. On the other hand, extracellular NADPH was found to rapidly and greatly stimulate the resorufin production in intact cells immediately after the addition of 50-500 μM NADPH. The extracellular NADPH stimulation was prevented by the addition of thapsigargin and EGTA which abolished Ca2+ oscillations induced by NADPH. Suramin, a specific antagonist of the P(2y) type ATP receptor, also completely abolished the NADPH-induced cholesterol-resorufin conversion. These results imply that extracellular NADPH (membrane impermeable) produced Ca2+ oscillations through its binding to ATP receptor thereby stimulating the activity of P450scc. The application of 45-500 μM extracellular ATP to cells did not, however, significantly increase the resorufin production. These three stimulators produced very different types of Ca2+ signals. ACTH induced mainly a series of Ca2+ spikes superimposed on a long-lasting basal Ca2+ elevation. The Ca2+ signals induced by NADPH showed predominantly a series of Ca2+ spikes without elevation of the basal Ca2+ concentration. Only long-lasting Ca2+ elevation was induced by extracellular ATP. The stimulation of cytochrome P450scc may thus be correlated with the different patterns of Ca2+ signals. Copyright (C) 2000 Elsevier Science B.V.
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Module-intron correlation and intron sliding in family F/10 xylanase genes Reviewed
Y Sato, Y Niimura, K Yura, M Go
GENE 238 ( 1 ) 93 - 101 1999.9
Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV
Xylanases are classified into two families, numbered F/10 and G/11 according to the similarity of amino acid sequences of their catalytic domain (Henrissat, B., Bairoch, A., 1993. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293, 781-788). Three-dimensional structure of the catalytic domain of the family F/10 xylanase was reported (White, A., Withers, S.G., Gilkes, N.R., Rose, D.R., 1994. Crystal structure of the catalytic domain of the beta-1,4-glycanase Cex from Cellulomonas fimi. Biochemistry 33, 12546-12552). The domain was decomposed into 22 modules by centripetal profiles (Gb, M., Nosaka, M., 1987. Protein architecture and the origin of introns. Cold Spring Harbor Symp. Quant. Biol. 52, 915-924; Noguti, T., Sakakibara, H., Gb, M., 1993. Localization of hydrogen-bonds within modules in barnase. Proteins 16, 357-363). A module is a contiguous polypeptide segment of amino acid residues having a compact conformation within a globular domain. Collected 31 intron sites of the family F/10 xylanase genes from fungus were found to be correlated to module boundaries with considerable statistical force (p values <0.001). The relationship between the intron locations and protein structures provides supporting evidence for the ancient origin of introns, because such a relationship cannot be expected by random insertion of introns into eukaryotic genes, but it rather suggests pre-existence of introns in the ancestral genes of prokaryotes and eukaryotes. A phylogenetic tree of the fungal and bacterial xylanase sequences made two clusters; one includes both the bacterial and fungal genes, but the other consists of only fungal genes. The mixed cluster of bacterial genes without introns and the fungal genes with introns further supports the ancient origin of introns. Comparison of the conserved base sequences of introns indicates that sliding of a splice site occurred in Aspergillus kawachii gene by one base from the ancestral position. Substrate-binding sites of xylanase are localized on eight modules, and introns are found at both termini of six out of these functional modules. This result suggests that introns might play a functional role in shuffling the exons encoding the substrate-binding modules. (C) 1999 Elsevier Science B.V. All rights reserved.
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Time-resolved study of effect of chlorpromazine on mobility of cytochrome P-450 and phospholipids in the inner membrane of adrenocortical mitochondria Reviewed
Ryota Homma, Tsutomu Kouyama, Makoto Yamada, Yoshihito Niimura, Alexander V. Krivosheev, Takayuki Hara, Suguru Kawato
Journal of Pharmaceutical and Biomedical Analysis 15 ( 9-10 ) 1215 - 1222 1997.6
Language：English Publishing type：Research paper (scientific journal)
The effects of chlorpromazine on the mobility of cytochrome P-450 and the fluidity of lipid membranes have been investigated in bovine adrenocortical submitochondrial particles (SMP). Rotational diffusion of the cytochrome was measured by observing the decay of absorption anisotropy, r(a)(t), after photolysis of the heme CO complex by a vertically polarized laser flash. Analysis of r(a)(t) was based on a 'rotation-about-membrane-normal' model. The anisotropy decayed within 2 ms to a time independent value r3. The presence of chlorpromazine decreased the mobile population of cytochrome P-450 from 28 to 23%. The rotational relaxation time Φ(a), of the mobile population (~ 1100 μs) was, however, not significantly changed by chlorpromazine. The lipid fluidity was examined by observing time-resolved fluorescence anisotropy, r(f)(t), of 1,6-diphenyl 1,3,5-hexatriene (DPH). The anisotropy r(f)(t) decayed within 70 ns to a time independent value r(∞). The motion of DPH was analyzed based on a 'wobbling-in-cone' model. The presence of chlorpromazine decreased the cone angle from 42°to 39°, while the rotational relaxation time Φ(f), (~ 2 ns) was not significantly changed by the presence of chlorpromazine. These results demonstrate that chlorpromazine decreased the mobility of not only lipids but also membrane proteins.