Hiroji Aiba

Summary

Affiliation: Nagoya University
Country: Japan

Publications

  1. ncbi request reprint Bacterial SsrA system plays a role in coping with unwanted translational readthrough caused by suppressor tRNAs
    Koji Ueda
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Cells 7:509-19. 2002
  2. ncbi request reprint Mechanism of RNA silencing by Hfq-binding small RNAs
    Hiroji Aiba
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Curr Opin Microbiol 10:134-9. 2007
  3. pmc RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Dev 19:2176-86. 2005
  4. pmc RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA
    Kimika Maki
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Proc Natl Acad Sci U S A 105:10332-7. 2008
  5. pmc Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli
    Hiroshi Kawamoto
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Dev 19:328-38. 2005
  6. ncbi request reprint Metabolic block at early stages of the glycolytic pathway activates the Rcs phosphorelay system via increased synthesis of dTDP-glucose in Escherichia coli
    Waleed El-Kazzaz
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 51:1117-28. 2004
  7. ncbi request reprint Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq
    Hiroshi Kawamoto
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 61:1013-22. 2006
  8. pmc Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA
    Takafumi Sunohara
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 10:378-86. 2004
  9. doi request reprint Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli
    Yoshiki Ikeda
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 79:419-32. 2011
  10. pmc The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail
    Hirokazu Ishikawa
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 18:1062-74. 2012

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Bacterial SsrA system plays a role in coping with unwanted translational readthrough caused by suppressor tRNAs
    Koji Ueda
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Cells 7:509-19. 2002
    ..The aim of the present study is to examine how translational readthrough by suppressor tRNAs affects trans-translation in Escherichia coli...
  2. ncbi request reprint Mechanism of RNA silencing by Hfq-binding small RNAs
    Hiroji Aiba
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Curr Opin Microbiol 10:134-9. 2007
    ..Hfq accelerates the rate of duplex formation between SgrS and the target mRNA. Membrane localization of target mRNA contributes to efficient SgrS action by competing with ribosome loading...
  3. pmc RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Dev 19:2176-86. 2005
    ..The formation of ribonucleoprotein complexes containing RNases could be a general way by which small RNAs destabilize target mRNAs in both prokaryotes and eukaryotes...
  4. pmc RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA
    Kimika Maki
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Proc Natl Acad Sci U S A 105:10332-7. 2008
    ..This simple mechanism is in striking contrast to miRNA action in eukaryote in which the RNA is believed to act only as a guide of protein partners...
  5. pmc Implication of membrane localization of target mRNA in the action of a small RNA: mechanism of post-transcriptional regulation of glucose transporter in Escherichia coli
    Hiroshi Kawamoto
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Dev 19:328-38. 2005
    ....
  6. ncbi request reprint Metabolic block at early stages of the glycolytic pathway activates the Rcs phosphorelay system via increased synthesis of dTDP-glucose in Escherichia coli
    Waleed El-Kazzaz
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 51:1117-28. 2004
    ..Taken together, we conclude that an increased synthesis of dTDP-glucose activates the Rcs phosphorelay system, presumably by affecting the synthesis of oligosaccharides for enterobacterial common antigen and O-antigen...
  7. ncbi request reprint Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq
    Hiroshi Kawamoto
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 61:1013-22. 2006
    ..We also showed in vitro that SgrS forms a stable duplex with the ptsG mRNA, and that Hfq markedly facilitates the rate of duplex formation...
  8. pmc Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA
    Takafumi Sunohara
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 10:378-86. 2004
    ....
  9. doi request reprint Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli
    Yoshiki Ikeda
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 79:419-32. 2011
    ..Finally, we demonstrate that overexpression of RhlB partially inhibits the Hfq binding to RNase E and the rapid degradation of ptsG mRNA...
  10. pmc The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail
    Hirokazu Ishikawa
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 18:1062-74. 2012
    ..We also demonstrate that increasing the spacing between the base-pairing region and the Hfq-binding module reduces or impairs the silencing ability. These findings allowed us to design synthetic Hfq-binding sRNAs to target desired mRNAs...
  11. pmc Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Proc Natl Acad Sci U S A 103:4858-63. 2006
    ..One possible physiological role of mRNA degradation mediated by sRNP is to rid the cell of translationally inactive mRNAs, making gene silencing irreversible...
  12. doi request reprint Cleavage of mRNAs and role of tmRNA system under amino acid starvation in Escherichia coli
    Xia Li
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 68:462-73. 2008
    ..The ribosome-mediated mRNA cleavage along with the tmRNA system is an important mechanism that enables cells to adapt to amino acid starvation conditions...
  13. doi request reprint A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA
    Kimika Maki
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 76:782-92. 2010
    ..Interestingly, the 14 nt oligo efficiently inhibited ptsG translation without the high-temperature pre-treatment, suggesting that remodelling of structured SgrS is an important mechanism by which Hfq promotes the base pairing...
  14. ncbi request reprint Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli
    Takafumi Sunohara
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    J Biol Chem 279:15368-75. 2004
    ..We propose that the mRNA cleavage induced by ribosome stalling acts in concert with the tmRNA system as a way to ensure quality control of protein synthesis and possibly to regulate the expression of certain genes...
  15. doi request reprint Analyses of mRNA destabilization and translational inhibition mediated by Hfq-binding small RNAs
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
    Methods Enzymol 447:359-78. 2008
    ..Here, we describe major experimental methods and results used to study functions of Hfq-binding small RNAs in our laboratory. These are illustrated using the regulation of ptsG mRNA by SgrS is used as an example...
  16. ncbi request reprint Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 54:1063-75. 2004
    ..In addition, we show that PNPase and RhlB within the degradosome cooperate to eliminate short degradation intermediates of ptsG mRNA...
  17. pmc Protein tagging at rare codons is caused by tmRNA action at the 3' end of nonstop mRNA generated in response to ribosome stalling
    Xia Li
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 12:248-55. 2006
    ..We conclude that a ribosome stalled by the rare codon induces mRNA cleavage, resulting in nonstop mRNAs that are recognized by tmRNA...
  18. ncbi request reprint Membrane localization itself but not binding to IICB is directly responsible for the inactivation of the global repressor Mlc in Escherichia coli
    Yuya Tanaka
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 53:941-51. 2004
    ..We conclude that the IICBGlc-Mlc interaction is dispensable for the inactivation of Mlc, and that membrane localization is directly responsible for the inactivation of Mlc...
  19. pmc SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs
    Yasufumi Yamamoto
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 9:408-18. 2003
    ..We conclude that the SsrA system not only promotes the degradation of incomplete polypeptides but also minimizes the synthesis of incomplete polypeptides by facilitating the degradation of truncated mRNAs that are produced in cells...
  20. ncbi request reprint Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli
    Xia Li
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 63:116-26. 2007
    ....
  21. pmc The C-terminal amino acid sequence of nascent peptide is a major determinant of SsrA tagging at all three stop codons
    Takafumi Sunohara
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 8:1416-27. 2002
    ..We conclude that the amino acid sequence of nascent polypeptide prior to stop codons is a major determinant for the SsrA tagging at all three stop codons...
  22. doi request reprint Analysis of nonstop mRNA translation in the absence of tmRNA in Escherichia coli
    Kazushige Kuroha
    Department of Molecular Biology, Graduate School of Science, Nagoya University, Chikusa ku, Nagoya 464 8602, Japan
    Genes Cells 14:739-49. 2009
    ..Possible factors involved in the hydrolysis of the peptidyl-tRNAs of nonstop mRNAs are discussed...
  23. pmc PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action
    Hironori Otaka
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Proc Natl Acad Sci U S A 108:13059-64. 2011
    ..We conclude that the polyU tail of sRNAs is essential for Hfq action in general. The data also indicate that the terminator polyU tail plays a role in Hfq-dependent stabilization of sRNAs...
  24. ncbi request reprint SsrA-mediated protein tagging in the presence of miscoding drugs and its physiological role in Escherichia coli
    Tatsuhiko Abo
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Genes Cells 7:629-38. 2002
    ..The aim of the present study was to address how miscoding antibiotics affect the read-through of stop codons and SsrA-mediated protein tagging...
  25. pmc Small RNAs making a small protein
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Proc Natl Acad Sci U S A 104:20149-50. 2007
  26. pmc Photo-induced regulation of the chromatic adaptive gene expression by Anabaena sensory rhodopsin
    Hiroki Irieda
    Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464 8602, Japan
    J Biol Chem 287:32485-93. 2012
    ..In the future, the ASR activity could be utilized as a tool for arbitrary protein expression in vivo regulated by visible light...
  27. pmc Translation of aberrant mRNAs lacking a termination codon or with a shortened 3'-UTR is repressed after initiation in yeast
    Toshifumi Inada
    Department of Molecular Biology, Graduate School of Science, Nagoya University, Nagoya, Japan
    EMBO J 24:1584-95. 2005
    ..We also found that translation of aberrant mRNAs with a shortened 3'-UTR was repressed, suggesting that an improper spatial distance between the termination codon and the 3' end of mRNA results in translation repression...
  28. ncbi request reprint [RNA silencing mediated by small RNAs in Escherichia coli]
    Teppei Morita
    Tanpakushitsu Kakusan Koso 51:2478-83. 2006
  29. ncbi request reprint Accumulation of glucose 6-phosphate or fructose 6-phosphate is responsible for destabilization of glucose transporter mRNA in Escherichia coli
    Teppei Morita
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    J Biol Chem 278:15608-14. 2003
    ..We conclude that the RNase E-dependent destabilization of ptsG mRNA occurs in response to accumulation of glucose-6-P or fructose-6-P...
  30. pmc An oncoprotein from the plant pathogen agrobacterium has histone chaperone-like activity
    Shinji Terakura
    Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
    Plant Cell 19:2855-65. 2007
    ..Our results suggest a relationship between alterations in nucleosome structure and the expression of growth-regulating genes on the one hand and the induction of aberrant cell proliferation on the other...
  31. ncbi request reprint [When trans-translation occurs?]
    Tatsuhiko Abo
    Tanpakushitsu Kakusan Koso 49:1067-8. 2004
  32. pmc YeeI, a novel protein involved in modulation of the activity of the glucose-phosphotransferase system in Escherichia coli K-12
    Ann Katrin Becker
    Department of Biology and Chemistry, University of Osnabruck, D 49069 Osnabruck, Germany
    J Bacteriol 188:5439-49. 2006
    ..By measuring the surface plasmon resonance, we found that YeeI (proposed gene designation, mtfA) directly interacts with Mlc with high affinity...