Hase, Yoichi, Yokoyama, Shinichiro, Muto, Akira, Himeno, Hyouta
RsgA is a unique GTP hydrolytic protein in which GTPase activity is significantly enhanced by the small ribosomal subunit. Deletion of RsgA causes slow cell growth as well as defects in subunit...
tRNADB-CE: tRNA gene database curated manually by experts (2009)
Abe, Takashi, Ikemura, Toshimichi, Ohara, Yasuo, Uehara, Hiroshi, Kinouchi, Makoto, Kanaya, Shigehiko, ...
We constructed a new large-scale database of tRNA genes by analyzing 534 complete genomes of prokaryotes and 394 draft genomes in WGS (Whole Genome Shotgun) division in DDBJ/EMBL/GenBank and...
Ujiie, Hiromi, Matsutani, Tomoko, Tomatsu, Hisashi, Fujihara, Ai, Ushida, Chisato, Miwa, Yasuhiko, ...
TreP [trehalose-permease (phosphotransferase system (PTS) trehalose-specific enzyme IIBC component)] is one of the target proteins of tmRNA-mediated trans-translation in Bacillus subtilis [Fujihara...
Physiological role of RsgA in ribosome biosynthesis (2009)
Hase, Yoichi, Yokoyama, Shinichiro, Kimura, Takatugu, Goto, Shimon, Muto, Akira, Himeno, Hyouta
RsgA is a unique GTP hydrolytic protein, in which the GTPase activity is significantly enhanced by the small ribosomal subunit. Depletion of RsgA causes slow cell growth as well as defects in the...
Trans-translation by tmRNA and SmpB (2009)
Une, Masataka, Kurita, Daisuke, Muto, Akira, Himeno, Hyouta
tmRNA has a dual function both as a tRNA and an mRNA to facilitate trans-translation, in which a ribosome can switch translation from a truncated or other problematic mRNA to the tmRNA's tag-encoding...
Konno, Takayuki, Kurita, Daisuke, Takada, Kazuma, Muto, Akira, Himeno, Hyouta
In trans-translation, transfer-messenger RNA (tmRNA), possessing a dual function as a tRNA and an mRNA, relieves a stalled translation on the ribosome with the help of SmpB. Here, we established an...
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Hanawa-Suetsugu, Kyoko, Lee, SungGa, ...
Transfer-messenger RNA (tmRNA) plays a dual role as a tRNA and an mRNA in trans-translation, during which the ribosome replaces mRNA with tmRNA encoding the tag-peptide. These processes have been...
ThermusthermophilustmRNA andtranstranslation (2007)
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Shirouzu, Mikako, Yokoyama, Shigeyuki, Muto, Akira, ...
In transtranslation, ribosome switches the template for protein synthesis from an mRNA to tmRNA. The molecular mechanism of transtranslation remains mysterious. In order to clarify how tmRNA move...
Interaction between RsgA and the ribosome (2007)
Kimura, Takatsugu, Takagi, Kuniaki, Kyoko, Hanawa-Suetsugu, Kalachnyuk, Liliya, Muto, Akira, Himeno, Hyouta
RsgA is a unique GTP hydrolytic protein that is widely found in bacteria and plants, and is activated by the small subunit of the ribosome. Disruption of the gene for RsgA from the genome affects the...
Molecular mechanism of trans-translation (2007)
Kurita, Daisuke, Konno, Takayuki, Takada, Kazuma, Muto, Akira, Himeno, Hyouta
tmRNA has a dual function as a tRNA and an mRNA to relieve the stalled ribosome. During this process, tmRNA enters the ribosomal A-site without a codonanticodon interaction, but with a protein factor...
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Hanawa-Suetsugu, Kyoko, Lee, SungGa, ...
Transfer-messenger RNA (tmRNA) plays a dual role as a tRNA and an mRNA in trans-translation, during which the ribosome replaces mRNA with tmRNA encoding the tag-peptide. These processes have been...
Interaction of SmpB with ribosome from directed hydroxyl radical probing (2007)
Kurita, Daisuke, Sasaki, Rumi, Muto, Akira, Himeno, Hyouta
To add a tag-peptide for degradation to the nascent polypeptide in a stalled ribosome, an unusual translation called trans-translation is facilitated by transfer-messenger RNA (tmRNA) having an upper...
Forward genetic analysis of visual behavior in zebrafish (2005)
Muto, Akira, Orger, Michael B, Wehman, Ann M, Smear, Matthew C, Kay, Jeremy N, Page-McCaw, Patrick S, ...
The visual system converts the distribution and wavelengths of photons entering the eye into patterns of neuronal activity, which then drive motor and endocrine behavioral responses. The gene...
Forward Genetic Analysis of Visual Behavior in Zebrafish (2005)
Akira Muto, Michael B. Orger, Ann M. Wehman, Matthew C. Smear, Jeremy N. Kay, ...
The visual system converts the distribution and wavelengths of photons entering the eye into patterns of neuronal activity, which then drive motor and endocrine behavioral responses. The gene...
Functional analysis of factors involved in trans-translation (2005)
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Matsuta, Noriko, Kurita, Daisuke, ...
trans-translation is a rescue system for stalled ribosomes to terminate the translation for recycling of ribosome and lead the incomplete protein on the stalled ribosome to degradation. In...
Competition between trans-translation and termination or elongation of translation (2005)
Asano, Krisana, Kurita, Daisuke, Takada, Kazuma, Konno, Takayuki, Muto, Akira, Himeno, Hyouta
The effects of tRNA, RF1 and RRF on trans-translation by tmRNA were examined using a stalled complex of ribosome prepared using a synthetic mRNA and pure Escherichia coli translation factors. No...
Interaction Analysis between tmRNA and SmpB from Thermus thermophilus (2005)
Nameki, Nobukazu, Someya, Tatsuhiko, Okano, Satoshi, Suemasa, Reiko, Kimoto, Michiko, Hanawa-Suetsugu, Kyoko, ...
Small protein B, SmpB, is a tmRNA-specific binding protein essential for trans-translation. We examined the interaction between SmpB and tmRNA from Thermus thermophilus, using biochemical and NMR...
Initiation-shift of trans-translation by aminoglycosides (2004)
Konno, Takayuki, Kurita, Daisuke, Takahashi, Toshiharu, Muto, Akira, Himeno, Hyouta
Trans-translation is an unusual translation in which tmRNA plays a dual function as a tRNA and an mRNA to relieve the stalled translation on the ribosome. In this study, we examined the effects of...
A novel GTPase activated by the small subunit of ribosome (2004)
Himeno, Hyouta, Hanawa-Suetsugu, Kyoko, Kimura, Takatsugu, Takagi, Kuniaki, Sugiyama, Wakana, Shirata, Shinobu, ...
The GTPase activity of Escherichia coli YjeQ, here named RsgA (ribosome small subunit-dependent GTPase A), has been shown to be significantly enhanced by ribosome or its small subunit. The...
Various effects of paromomycin on tmRNA-mediated trans-translation (2003)
Konno, Takayuki, Takahashi, Toshiharu, Muto, Akira, Himeno, Hyouta
Trans-translation is an unusual translation in which tmRNA plays a dual function as a tRNA and an mRNA to relieve the stalled translation on the ribosome. In this study, we examined the effects of an...
In vitro analysis of the initial steps of trans-translation (2003)
Takada, Kazuma, Hori-Takemoto, Chie, Kawazoe, Masahito, Lee, SungGa, Shirouzu, Mikako, Yokoyama, Shigeyuki, ...
tmRNA has a dual function both as tRNA and mRNA and facilitates trans-translation. We observed the tagging derived from tmRNA from Bacillus subtilis in vivo and in vitro. Our studies give progressive...
Various effects of paromomycin on tmRNA-mediated trans-translation (2003)
Konno, Takayuki, Takahashi, Toshiharu, Muto, Akira, Himeno, Hyouta
In vitro analysis of the initial steps of trans-translation (2003)
Takada, Kazuma, Hori-Takemoto, Chie, Kawazoe, Masahito, Lee, SungGa, Shirouzu, Mikako, Yokoyama, Shigeyuki, ...
The structure and function of tmRNA (2002)
Takada, Kazuma, Hanawa, Kyoko, Lee, Sung Ga, Himeno, Hyouta, Muto, Akira
The structure and function of tmRNA (2002)
Takada, Kazuma, Hanawa, Kyoko, Lee, Sung Ga, Himeno, Hyouta, Muto, Akira
tmRNA has a dual function both as tRNA and mRNA and facilitates trans-translation. We made various mutation in tRNA domain of tmRNA. Our mutation studies give progressive suggestions on the structure...
SmpB functions in various steps of trans-translation (2002)
Hanawa-Suetsugu, Kyoko, Takagi, Mitsuru, Inokuchi, Hachiro, Himeno, Hyouta, Muto, Akira
tmRNA has a dual function as a tRNA and an mRNA to facilitate trans-translation, in which a ribosome can switch between translation of a truncated mRNA and the tmRNA’s tag sequence. SmpB is a tmRNA...
Hanawa-Suetsugu, Kyoko, Bordeau, Valérie, Himeno, Hyouta, Muto, Akira, Felden, Brice
A bacterial RNA functioning as both tRNA and mRNA, transfer-messenger RNA (tmRNA) rescues stalled ribosomes and clears the cell of incomplete polypeptides. For function, Escherichia coli tmRNA...
The structure and function of tRNA-like domain in E. coli tmRNA (2000)
Hanawa, Kyoko, Lee, SungGa, Himeno, Hyouta, Muto, Akira
tmRNA has a dual function both as a tRNA and as an mRNA in trans-translation. tmRNA possesses structural elements similar to canonical tRNAs. Our mutation studies show that the tRNA-like structure is...
Probing the Secondary Structure of MCS4 RNA of Mycoplasma capricolum (1997)
Ushida, Chisato, Sasamura, Shinpei, Muto, Akira
MCS4 RNA is one of the small stable RNAs found in Mycoplasma capricolum. Its function is unknown. The conformation of MCS4 RNA (125 nucleotides in length) in solution was investigated using chemical...
tRNA-like structures in 10Sa RNAs of Mycoplasma capricolum and Bacillus subtilis (1994)
Ushida, Chisato, Himeno, Hyouta, Watanabe, Tsuneaki, Muto, Akira
The stable RNAs, whose sequences are homologous to 10Sa RNA of Escherichia coli, have been isolated from Mycoplasma capricolum and Bacillus subtilis, both belonging to the Gram-positive bacterial...
A small RNA of Mycoplasma capricolum that resembles eukaryotic U6 small nuclear RNA (1993)
Mycoplasma capricolum, a parasitic prokaryote, contains several small stable RNAs, besides rRNAs and tRNAs. One of them, designated MCS4 RNA (125 nucleotides in length), has been isolated and...
Levels of tRNAs in bacterial cells as affected by amino acid usage in proteins (1991)
Yamao, Fumiaki, Andachi, Yoshiki, Muto, Akira, Ikemura, Toshimichi, Osawa, Syozo
Transfer RNAs of Mycoplasma capricolum were separated by two-dimensional polyacrylamide gel electrophoresis, and the relative abundance of each of the 28 known tRNA species was measured. There...
Evolution of tRNAs and tRNA enes in Acholeplasma laidlawii (1991)
Tanaka, Reiji, Andachi, Yoshiki, Muto, Akira
The genes for 22 tRNA species from Acholeplasma laidlawil, belonging to the class Mollicutes (RAycoplasmas), have been cloned and sequenced. Sixteen genes are organized in 3 clusters consisting of...
The organization and evolution of transfer RNA genes in Mycoplasma capricolum (1990)
Muto, Akira, Andachi, Yoshiki, Yuzawa, Harumi, Yamao, Fumiaki, Osawa, Syozo
The genes for presumably all the tRNA species in Mycoplasma capricolum, a derivative of Gram-positive eubacteria, have been cloned and sequenced. There are 30 genes encoding 29 tRNA species. This...
Ohama, Takeshi, Muto, Akira, Osawa, Syozo
The GC (G+C, or G or C)-contents of codon silent positions in all two-codon sets and three codons AUY/A (lle), and in most of the family boxes of Micrococcus luteus (genomic GC-content: 74%) are 95%...
Muto, Akira, Kawauchi, Yasushi, Yamao, Fumiaki, Osawa, Syozo
The nucleotide sequence of the 1.3 kilobase-pair DNA segment, which contains the genes for ribosomal proteins S8 and L6, and a part of L18 of Mycoplasma capricolum, has been determined and compared...
Hanawa-Suetsugu, Kyoko, Bordeau, Valérie, Himeno, Hyouta, Muto, Akira, Felden, Brice
A bacterial RNA functioning as both tRNA and mRNA, transfer-messenger RNA (tmRNA) rescues stalled ribosomes and clears the cell of incomplete polypeptides. For function, Escherichia coli tmRNA...
SmpB functions in various steps of trans-translation
Hanawa-Suetsugu, Kyoko, Takagi, Mitsuru, Inokuchi, Hachiro, Himeno, Hyouta, Muto, Akira
tmRNA has a dual function as a tRNA and an mRNA to facilitate trans-translation, in which a ribosome can switch between translation of a truncated mRNA and the tmRNA’s tag sequence. SmpB is a tmRNA...
Location of Ribosomal Protein Binding Sites on 16S Ribosomal RNA
Zimmermann, Robert A., Muto, Akira, Fellner, Peter, Ehresmann, Chantal, Branlant, Christiane
The distribution of ribosomal protein binding sites on the 16S ribosomal RNA molecule has been analyzed by limited ribonuclease hydrolysis of RNA-protein complexes, as well as by the interaction of...
A minimum structure of aminoglycosides that causes an initiation shift of trans-translation
Konno, Takayuki, Takahashi, Toshiharu, Kurita, Daisuke, Muto, Akira, Himeno, Hyouta
Trans-translation is an unusual translation in which transfer-messenger RNA plays a dual function—as a tRNA and an mRNA—to relieve the stalled translation on the ribosome. It has been shown that...
A novel GTPase activated by the small subunit of ribosome
Himeno, Hyouta, Hanawa-Suetsugu, Kyoko, Kimura, Takatsugu, Takagi, Kuniaki, Sugiyama, Wakana, Shirata, Shinobu, ...
The GTPase activity of Escherichia coli YjeQ, here named RsgA (ribosome small subunit-dependent GTPase A), has been shown to be significantly enhanced by ribosome or its small subunit. The...
Participation of 3′-to-5′ Exoribonucleases in the Turnover of Bacillus subtilis mRNA
Oussenko, Irina A., Abe, Teppei, Ujiie, Hiromi, Muto, Akira, Bechhofer, David H.
Four 3′-to-5′ exoribonucleases have been identified in Bacillus subtilis: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Mutant strains were constructed that were lacking...
Competition between trans-translation and termination or elongation of translation
Asano, Krisana, Kurita, Daisuke, Takada, Kazuma, Konno, Takayuki, Muto, Akira, Himeno, Hyouta
The effects of tRNA, RF1 and RRF on trans-translation by tmRNA were examined using a stalled complex of ribosome prepared using a synthetic mRNA and pure Escherichia coli translation factors. No...
Forward Genetic Analysis of Visual Behavior in Zebrafish
Muto, Akira, Orger, Michael B, Wehman, Ann M, Smear, Matthew C, Kay, Jeremy N, Page-McCaw, Patrick S, ...
The visual system converts the distribution and wavelengths of photons entering the eye into patterns of neuronal activity, which then drive motor and endocrine behavioral responses. The gene...
Hanawa-Suetsugu, Kyoko, Bordeau, Valérie, Himeno, Hyouta, Muto, Akira, Felden, Brice
A bacterial RNA functioning as both tRNA and mRNA, transfer-messenger RNA (tmRNA) rescues stalled ribosomes and clears the cell of incomplete polypeptides. For function, Escherichia coli tmRNA...
SmpB functions in various steps of trans-translation
Hanawa-Suetsugu, Kyoko, Takagi, Mitsuru, Inokuchi, Hachiro, Himeno, Hyouta, Muto, Akira
tmRNA has a dual function as a tRNA and an mRNA to facilitate trans-translation, in which a ribosome can switch between translation of a truncated mRNA and the tmRNA’s tag sequence. SmpB is a tmRNA...
Location of Ribosomal Protein Binding Sites on 16S Ribosomal RNA
Zimmermann, Robert A., Muto, Akira, Fellner, Peter, Ehresmann, Chantal, Branlant, Christiane
The distribution of ribosomal protein binding sites on the 16S ribosomal RNA molecule has been analyzed by limited ribonuclease hydrolysis of RNA-protein complexes, as well as by the interaction of...
A minimum structure of aminoglycosides that causes an initiation shift of trans-translation
Konno, Takayuki, Takahashi, Toshiharu, Kurita, Daisuke, Muto, Akira, Himeno, Hyouta
Trans-translation is an unusual translation in which transfer-messenger RNA plays a dual function—as a tRNA and an mRNA—to relieve the stalled translation on the ribosome. It has been shown that...
A novel GTPase activated by the small subunit of ribosome
Himeno, Hyouta, Hanawa-Suetsugu, Kyoko, Kimura, Takatsugu, Takagi, Kuniaki, Sugiyama, Wakana, Shirata, Shinobu, ...
The GTPase activity of Escherichia coli YjeQ, here named RsgA (ribosome small subunit-dependent GTPase A), has been shown to be significantly enhanced by ribosome or its small subunit. The...
Participation of 3′-to-5′ Exoribonucleases in the Turnover of Bacillus subtilis mRNA
Oussenko, Irina A., Abe, Teppei, Ujiie, Hiromi, Muto, Akira, Bechhofer, David H.
Four 3′-to-5′ exoribonucleases have been identified in Bacillus subtilis: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Mutant strains were constructed that were lacking...
Competition between trans-translation and termination or elongation of translation
Asano, Krisana, Kurita, Daisuke, Takada, Kazuma, Konno, Takayuki, Muto, Akira, Himeno, Hyouta
The effects of tRNA, RF1 and RRF on trans-translation by tmRNA were examined using a stalled complex of ribosome prepared using a synthetic mRNA and pure Escherichia coli translation factors. No...
Forward Genetic Analysis of Visual Behavior in Zebrafish
Muto, Akira, Orger, Michael B, Wehman, Ann M, Smear, Matthew C, Kay, Jeremy N, Page-McCaw, Patrick S, ...
The visual system converts the distribution and wavelengths of photons entering the eye into patterns of neuronal activity, which then drive motor and endocrine behavioral responses. The gene...
Takada, Kazuma, Takemoto, Chie, Kawazoe, Masahito, Konno, Takayuki, Hanawa-Suetsugu, Kyoko, Lee, SungGa, ...
Transfer-messenger RNA (tmRNA) plays a dual role as a tRNA and an mRNA in trans-translation, during which the ribosome replaces mRNA with tmRNA encoding the tag-peptide. These processes have been...
Interaction of SmpB with ribosome from directed hydroxyl radical probing
Kurita, Daisuke, Sasaki, Rumi, Muto, Akira, Himeno, Hyouta
To add a tag-peptide for degradation to the nascent polypeptide in a stalled ribosome, an unusual translation called trans-translation is facilitated by transfer-messenger RNA (tmRNA) having an upper...
Konno, Takayuki, Kurita, Daisuke, Takada, Kazuma, Muto, Akira, Himeno, Hyouta
In trans-translation, transfer-messenger RNA (tmRNA), possessing a dual function as a tRNA and an mRNA, relieves a stalled translation on the ribosome with the help of SmpB. Here, we established an...
tRNADB-CE: tRNA gene database curated manually by experts
Abe, Takashi, Ikemura, Toshimichi, Ohara, Yasuo, Uehara, Hiroshi, Kinouchi, Makoto, Kanaya, Shigehiko, ...
We constructed a new large-scale database of tRNA genes by analyzing 534 complete genomes of prokaryotes and 394 draft genomes in WGS (Whole Genome Shotgun) division in DDBJ/EMBL/GenBank and...