Genomes and Genes
Experts and Doctors on amino acid sequence in Mishima, Shizuoka, Japan
Locale: Mishima, Shizuoka, Japan
Topic: amino acid sequence
- Ito Y, Chujo A, Eiguchi M, Kurata N. Radial axis differentiation in a globular embryo is marked by HAZ1, a PHD-finger homeobox gene of rice. Gene. 2004;331:9-15 pubmed..Radial axis differentiation marked by HAZ1 is then collapsed dynamically along with embryo morphogenesis, and HAZ1 later marks the ventral surface of the embryo. ..
- Ito Y, Takaya K, Kurata N. Expression of SERK family receptor-like protein kinase genes in rice. Biochim Biophys Acta. 2005;1730:253-8 pubmed publisher..This promoter activity suggests that OsSERK1 may have roles in non-embryonic tissues rather than in the embryo...
- Saze H, Kakutani T. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J. 2007;26:3641-52 pubmed..We discuss possible molecular mechanisms and the evolutionary implications of transposon-mediated epigenetic changes in the BNS locus. ..
- Sadaie Y, Takamatsu H, Nakamura K, Yamane K. Sequencing reveals similarity of the wild-type div+ gene of Bacillus subtilis to the Escherichia coli secA gene. Gene. 1991;98:101-5 pubmed..subtilis. Since both genes are similar in their functions and deduced aa sequences, we propose that the div+ gene is the counterpart of the secA gene of E. coli. ..
- Ogawa Y, Ono T, Wakata Y, Okawa K, Tagami H, Shibahara K. Histone variant macroH2A1.2 is mono-ubiquitinated at its histone domain. Biochem Biophys Res Commun. 2005;336:204-9 pubmed..2 and histone H2A has similar or synergistic implications, but that the multiple ubiquitination sites in macroH2A1.2 might confer a variety of functions upon macroH2A1.2 to modulate chromatin states. ..
- Takayama Y, Kamimura Y, Okawa M, Muramatsu S, Sugino A, Araki H. GINS, a novel multiprotein complex required for chromosomal DNA replication in budding yeast. Genes Dev. 2003;17:1153-65 pubmed..Moreover, genetic and two-hybrid interactions suggest that GINS interacts with Sld3 and Dpb11. Therefore, Dpb11, Sld3, Cdc45, and GINS assemble in a mutually dependent manner on replication origins to initiate DNA synthesis. ..
- Kimura M, Suzuki H, Ishihama A. Formation of a carboxy-terminal domain phosphatase (Fcp1)/TFIIF/RNA polymerase II (pol II) complex in Schizosaccharomyces pombe involves direct interaction between Fcp1 and the Rpb4 subunit of pol II. Mol Cell Biol. 2002;22:1577-88 pubmed..This result indicates the importance of Fcp1-Rpb4 interaction for formation of the Fcp1/TFIIF/pol II complex in vivo. ..
- Goto S, Taniguchi M, Muraoka M, Toyoda H, Sado Y, Kawakita M, et al. UDP-sugar transporter implicated in glycosylation and processing of Notch. Nat Cell Biol. 2001;3:816-22 pubmed..The results suggest that changes in nucleotide-sugar levels can differently affect Wingless and two distinct aspects of Notch signalling. ..
- Nonomura K, Miyoshi K, Eiguchi M, Suzuki T, Miyao A, Hirochika H, et al. The MSP1 gene is necessary to restrict the number of cells entering into male and female sporogenesis and to initiate anther wall formation in rice. Plant Cell. 2003;15:1728-39 pubmed..These results suggest that the MSP1 product plays crucial roles in restricting the number of cells entering into male and female sporogenesis and in initiating anther wall formation in rice. ..
- Ohta T, Kobayashi M, Hirose S. Cloning of a cDNA for DNA supercoiling factor reveals a distinctive Ca(2+)-binding protein. J Biol Chem. 1995;270:15571-5 pubmed..The factor contains three other potential EF-hand domains and actually binds Ca2+. Moreover, the supercoiling reaction has been shown to be activated by Ca2+. These results implicate Ca2+ in the control of the superhelical state of DNA. ..
- Ogino K, Ramsden S, Keib N, Schwarz G, Harvey R, Hirata H. Duplicated gephyrin genes showing distinct tissue distribution and alternative splicing patterns mediate molybdenum cofactor biosynthesis, glycine receptor clustering, and escape behavior in zebrafish. J Biol Chem. 2011;286:806-17 pubmed publisher..These data indicate that duplicated gephyrin genes mediate Moco biosynthesis and control postsynaptic clustering of GlyRs, thereby mediating key escape behaviors in zebrafish. ..
- Ohta T. Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc Natl Acad Sci U S A. 1993;90:4548-51 pubmed..These observations suggest that amino acid substitutions are facilitated by small population size. The result is in accord with the nearly neutral theory of molecular evolution...
- Li F, Takemaru K, Goto M, Ueda H, Handa H, Hirose S. Transcriptional activation through interaction of MBF2 with TFIIA. Genes Cells. 1997;2:143-53 pubmed..MBF2 activates transcription through its interaction with TFIIA. Selective transcriptional activation occurs when MBF2 is recruited to a promoter carrying the FTZ-F1 binding site by FTZ-F1 and MBF1. ..
- Torayama I, Ishihara T, Katsura I. Caenorhabditis elegans integrates the signals of butanone and food to enhance chemotaxis to butanone. J Neurosci. 2007;27:741-50 pubmed
- Subbarayan P, Sarkar M. Escherichia coli rpoS gene has an internal secondary translation initiation region. Biochem Biophys Res Commun. 2004;313:294-9 pubmed..coli rpoS, from where a truncated but nevertheless functional form of sigma(s) can be synthesized. ..
- Saze H, Shiraishi A, Miura A, Kakutani T. Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana. Science. 2008;319:462-5 pubmed publisher..Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes. ..
- Shimojima T, Okada M, Nakayama T, Ueda H, Okawa K, Iwamatsu A, et al. Drosophila FACT contributes to Hox gene expression through physical and functional interactions with GAGA factor. Genes Dev. 2003;17:1605-16 pubmed..These data illustrate a crucial role of FACT in the modulation of chromatin structure for the regulation of gene expression. ..
- Kagoshima H, Nimmo R, Saad N, Tanaka J, Miwa Y, Mitani S, et al. The C. elegans CBFbeta homologue BRO-1 interacts with the Runx factor, RNT-1, to promote stem cell proliferation and self-renewal. Development. 2007;134:3905-15 pubmed..These studies provide new insights into the function and regulation of this important cancer-associated DNA-binding complex in stem cells and support the view that Runx/CBFbeta factors have oncogenic potential. ..
- Hwang J, Takaku Y, Momose T, Adamczyk P, Ozbek S, Ikeo K, et al. Nematogalectin, a nematocyst protein with GlyXY and galectin domains, demonstrates nematocyte-specific alternative splicing in Hydra. Proc Natl Acad Sci U S A. 2010;107:18539-44 pubmed publisher..The emergence of nematogalectin A may have played a role in the morphological diversification of nematocysts in the medusozoan lineage. ..
- Yokomine T, Hata K, Tsudzuki M, Sasaki H. Evolution of the vertebrate DNMT3 gene family: a possible link between existence of DNMT3L and genomic imprinting. Cytogenet Genome Res. 2006;113:75-80 pubmed..The acquisition of DNMT3L by a common ancestor of eutherians and marsupials might have been closely related to the evolution of imprinting...
- Nishino T, Takeuchi K, Gascoigne K, Suzuki A, Hori T, Oyama T, et al. CENP-T-W-S-X forms a unique centromeric chromatin structure with a histone-like fold. Cell. 2012;148:487-501 pubmed publisher..These data suggest that the CENP-T-W-S-X complex forms a unique nucleosome-like structure to generate contacts with DNA, extending the "histone code" beyond canonical nucleosome proteins...
- Sumiyama K, Saitou N, Ueda S. Adaptive evolution of the IgA hinge region in primates. Mol Biol Evol. 2002;19:1093-9 pubmed
- Yamamoto K, Ogasawara H, Fujita N, Utsumi R, Ishihama A. Novel mode of transcription regulation of divergently overlapping promoters by PhoP, the regulator of two-component system sensing external magnesium availability. Mol Microbiol. 2002;45:423-38 pubmed..The PhoP box is located between -46 and -30 with respect to treRP3, and the alpha CTD is needed for this repression. ..
- Ito Y, Hirochika H, Kurata N. Organ-specific alternative transcripts of KNOX family class 2 homeobox genes of rice. Gene. 2002;288:41-7 pubmed..These results suggest that the expression of the alternative transcripts is organ-specific, and their products have different degrees of abilities for activation or repression of transcription. ..
- Fukagawa T, Mikami Y, Nishihashi A, Regnier V, Haraguchi T, Hiraoka Y, et al. CENP-H, a constitutive centromere component, is required for centromere targeting of CENP-C in vertebrate cells. EMBO J. 2001;20:4603-17 pubmed..These findings indicate that centromere assembly in vertebrate cells proceeds in a hierarchical manner in which localization of the centromere-specific histone CENP-A is an early event that occurs independently of CENP-C and CENP-H. ..
- Mochizuki K, Nishimiya Fujisawa C, Fujisawa T. Universal occurrence of the vasa-related genes among metazoans and their germline expression in Hydra. Dev Genes Evol. 2001;211:299-308 pubmed..These results suggest that the vas-related genes occur universally among metazoans and that their expression in germline cells was established at least before cnidarian evolution...
- Yamagishi M, Matsushima H, Wada A, Sakagami M, Fujita N, Ishihama A. Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. EMBO J. 1993;12:625-30 pubmed..The katF gene product, a stationary phase-specific sigma factor, was not required for the expression of rmf. Disruption of rmf resulted in loss of ribosome dimers and reduction of cell viability during stationary phase. ..
- Kitano T, Saitou N. Evolutionary history of the Rh blood group-related genes in vertebrates. Immunogenetics. 2000;51:856-62 pubmed..Both groups contain genes from three domains (bacteria, archaea, and eukaryota). The Rh blood group and related genes are separated from both amt alpha and beta groups. ..
- Imai N, Kaneda S, Nagai Y, Seno T, Ayusawa D, Hanaoka F, et al. Cloning and sequence of a functionally active cDNA encoding the mouse ubiquitin-activating enzyme E1. Gene. 1992;118:279-82 pubmed..The 3495-bp cDNA encodes 1058 amino acids (aa), and shares extensive homology with the human E1 enzyme at both the nucleotide and aa sequence levels. ..
- Hara H, Yamamoto Y, Higashitani A, Suzuki H, Nishimura Y. Cloning, mapping, and characterization of the Escherichia coli prc gene, which is involved in C-terminal processing of penicillin-binding protein 3. J Bacteriol. 1991;173:4799-813 pubmed..The mutation resulted in greatly reduced heat shock response at low osmolarity and in leakage of periplasmic proteins. ..
- Hishida R, Ishihara T, Kondo K, Katsura I. hch-1, a gene required for normal hatching and normal migration of a neuroblast in C. elegans, encodes a protein related to TOLLOID and BMP-1. EMBO J. 1996;15:4111-22 pubmed..Furthermore, in spite of its expression in embryogenesis, it is not required for the viability of embryos. These results show new functions of the tolloid/BMP-1 family proteins and give insight into their evolution. ..
- Hayakawa E, Takahashi T, Nishimiya Fujisawa C, Fujisawa T. A novel neuropeptide (FRamide) family identified by a peptidomic approach in Hydra magnipapillata. FEBS J. 2007;274:5438-48 pubmed publisher..In contrast, FRamide-2 evoked body column contraction. These results suggest that both of the neuropeptides directly act on epithelial cells as neurotransmitters and regulate body movement in an axial direction...
- Higashitani A, Ishii Y, Kato Y, Koriuchi K. Functional dissection of a cell-division inhibitor, SulA, of Escherichia coli and its negative regulation by Lon. Mol Gen Genet. 1997;254:351-7 pubmed..These results indicate that the C-terminal 20 residues of SulA permit recognition by, and complex formation with, Lon, and are necessary, but not sufficient, for degradation by Lon...
- Tamura M, Tanaka S, Fujii T, Aoki A, Komiyama H, Ezawa K, et al. Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner. Genomics. 2007;89:618-29 pubmed..Further database searching revealed the presence of other related genes with a similar N-terminal motif. These results suggest that the Gsdm family and related genes have evolved divergent epithelial expression profiles. ..
- Shirayoshi Y, Yuasa Y, Suzuki T, Sugaya K, Kawase E, Ikemura T, et al. Proto-oncogene of int-3, a mouse Notch homologue, is expressed in endothelial cells during early embryogenesis. Genes Cells. 1997;2:213-24 pubmed
- Minoshima Y, Hori T, Okada M, Kimura H, Haraguchi T, Hiraoka Y, et al. The constitutive centromere component CENP-50 is required for recovery from spindle damage. Mol Cell Biol. 2005;25:10315-28 pubmed..We also observed severe mitotic defects in CENP-50-deficient cells with apparent premature sister chromatid separation when the mitotic checkpoint was activated, indicating that CENP-50 is required for recovery from spindle damage. ..
- Shiina N, Shinkura K, Tokunaga M. A novel RNA-binding protein in neuronal RNA granules: regulatory machinery for local translation. J Neurosci. 2005;25:4420-34 pubmed..These findings suggest that RNG105 is a translational repressor in the RNA granules and provide insight into the link between RNG105 dynamics and local translational regulation. ..
- Take uchi M, Kobayashi Y, Kimura K, Ishihara T, Katsura I. FLR-4, a novel serine/threonine protein kinase, regulates defecation rhythm in Caenorhabditis elegans. Mol Biol Cell. 2005;16:1355-65 pubmed..Thus, a novel protein kinase with a unique structural feature acts in the intestine to increase the length of defecation cycle periods. ..
- Nonomura K, Nakano M, Murata K, Miyoshi K, Eiguchi M, Miyao A, et al. An insertional mutation in the rice PAIR2 gene, the ortholog of Arabidopsis ASY1, results in a defect in homologous chromosome pairing during meiosis. Mol Genet Genomics. 2004;271:121-9 pubmed publisher..The study also suggested the possibility that a highly homologous copy of the PAIR2 gene located on a different chromosome is in fact a pseudogene...
- Ishiguro A, Nogi Y, Hisatake K, Muramatsu M, Ishihama A. The Rpb6 subunit of fission yeast RNA polymerase II is a contact target of the transcription elongation factor TFIIS. Mol Cell Biol. 2000;20:1263-70 pubmed..Taken together, the results lead us to propose that Rpb6 plays a role in the interaction between RNA polymerase II and the transcription elongation factor TFIIS. ..
- Yum S, Takahashi T, Hatta M, Fujisawa T. The structure and expression of a preprohormone of a neuropeptide, Hym-176 in Hydra magnipapillata. FEBS Lett. 1998;439:31-4 pubmed..No signals were detected in the two extremities of the body, tentacles and basal disk. The expression pattern is correlated with the distribution of Hym-176 and its myoactive function. ..
- Seino H, Kishi T, Nishitani H, Yamao F. Two ubiquitin-conjugating enzymes, UbcP1/Ubc4 and UbcP4/Ubc11, have distinct functions for ubiquitination of mitotic cyclin. Mol Cell Biol. 2003;23:3497-505 pubmed
- Furuya K, Miyabe I, Tsutsui Y, Paderi F, Kakusho N, Masai H, et al. DDK phosphorylates checkpoint clamp component Rad9 and promotes its release from damaged chromatin. Mol Cell. 2010;40:606-18 pubmed publisher..We propose that Rad9 phosphorylation by DDK releases Rad9 from DNA damage sites to facilitate DNA repair. ..
- Mitobe J, Mitsuzawa H, Ishihama A. Functional analysis of RNA polymerase II Rpb3 mutants of the fission yeast Schizosaccharomyces pombe. Curr Genet. 2001;39:210-21 pubmed..We propose that both terminal regions (A and D) play important roles in RNA polymerase assembly, while the central portion (regions B and C) is involved in activated transcription. ..
- Mitsuzawa H, Seino H, Yamao F, Ishihama A. Two WD repeat-containing TATA-binding protein-associated factors in fission yeast that suppress defects in the anaphase-promoting complex. J Biol Chem. 2001;276:17117-24 pubmed..Our study thus provides evidence for a possible role of WD repeat-containing TAFs in the expression of genes involved in progression through the M phase of the cell cycle. ..
- Hwang J, Takaku Y, Chapman J, Ikeo K, David C, Gojobori T. Cilium evolution: identification of a novel protein, nematocilin, in the mechanosensory cilium of Hydra nematocytes. Mol Biol Evol. 2008;25:2009-17 pubmed publisher..Thus, the evolution of a novel ciliary structure, which provides mechanical rigidity to the sensory cilium during the process of mechanoreception, is associated with the evolution of a novel protein. ..
- Miyao T, Yasui K, Sakurai H, Yamagishi M, Ishihama A. Molecular assembly of RNA polymerase II from the fission yeast Schizosaccharomyces pombe: subunit-subunit contact network involving Rpb5. Genes Cells. 1996;1:843-54 pubmed..Rpb3 and Rpb5, the putative subunits of RNA polymerase II, associate each other to form binary complexes. These two subunits also bind to the two large subunits, Rpb1 and Rpb2, independently. ..
- Tanaka S, Miura I, Yoshiki A, Kato Y, Yokoyama H, Shinogi A, et al. Mutations in the helix termination motif of mouse type I IRS keratin genes impair the assembly of keratin intermediate filament. Genomics. 2007;90:703-11 pubmed..These results suggest that the helix termination motif is essential for the proper assembly of types I and II IRS keratin protein complexes and the formation of keratin intermediate filaments. ..
- Take uchi M, Kawakami M, Ishihara T, Amano T, Kondo K, Katsura I. An ion channel of the degenerin/epithelial sodium channel superfamily controls the defecation rhythm in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1998;95:11775-80 pubmed..These results suggest that FLR-1 may be a component of an intestinal regulatory system that controls the defecation rhythm as well as other functions. ..
- Kobayashi M, Aita N, Hayashi S, Okada K, Ohta T, Hirose S. DNA supercoiling factor localizes to puffs on polytene chromosomes in Drosophila melanogaster. Mol Cell Biol. 1998;18:6737-44 pubmed..Upon heat treatment of larvae, the staining on the endogenous puffs disappeared, and strong staining appeared on heat shock puffs. These results implicate SCF in gene expression. ..
- Jishage M, Ishihama A. A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase. Proc Natl Acad Sci U S A. 1998;95:4953-8 pubmed..The isolated Rsd inhibited transcription in vitro to various extents depending on the promoters used. We propose that Rsd is a stationary phase E. coli protein with regulatory activity of the sigma70 function...
- Kagoshima H, Sawa H, Mitani S, Burglin T, Shigesada K, Kohara Y. The C. elegans RUNX transcription factor RNT-1/MAB-2 is required for asymmetrical cell division of the T blast cell. Dev Biol. 2005;287:262-73 pubmed..All our data suggest that RNT-1/MAB-2 functions with POP-1 to control the asymmetry of the T cell division. ..
- Takemaru K, Harashima S, Ueda H, Hirose S. Yeast coactivator MBF1 mediates GCN4-dependent transcriptional activation. Mol Cell Biol. 1998;18:4971-6 pubmed..These findings indicate that the coactivator MBF1 functions by recruiting TBP to promoters where DNA-binding regulators are bound. ..