Analysis of gene regulation network associated with the ribosomes in Bacillus subtilis

• Project/Area Number: 16570005
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Genetics/Genome dynamics
• Research Institution: Rikkyo University
• Principal Investigator: KAWAMURA Fujio Rikkyo University, College of Science, Professor, 理学部, 教授 (10126039)
• Project Period (FY): 2004 – 2006
• Project Status: Completed (Fiscal Year 2006)
• Budget Amount: ¥3,100,000 (Direct Cost: ¥3,100,000); Fiscal Year 2006: ¥800,000 (Direct Cost: ¥800,000); Fiscal Year 2005: ¥800,000 (Direct Cost: ¥800,000); Fiscal Year 2004: ¥1,500,000 (Direct Cost: ¥1,500,000)
• Keywords: ribosome / Bacillus subtilis / ribosomal protein / zinc binding protein / gene duplication / rRNA op eron / 翻訳制御 / tRNA

Research Abstract

Complete genome sequence of over 200 microorganisms has been done and paralogous pairs of ribosomal protein genes are found in many bacterial genomes. It has been reported that genes encoding ribosomal protein L31, L33, L36 and S14 are duplicated in several bacterial genomes, and each of them can be classified into two types: one type contains a zinc-binding motif, whereas another doses not. We have shown that two types of L31 protein can be detected in ribosomes prepared from cells at different growth phases in zinc-limiting minimal medium. The RpmE is stable when it contains a zinc ion bound to its CysXXCys motif, and the expression of ytiA, coding for the zinc-lacking form of L31 protein, is, repressed by Zur. We have also shown that when purified YtiA is added to an RpmE-containing ribosome solution in vitro, YtiA-containing ribosomes are detected, thus suggesting that newly synthesized YtiA can liberate RpmE from ribosomes. From these results, we proposed that the change between the two types of L31 proein in the ribosome is triggered by changes in the concentration of zinc in the environment.
We further analyzed another paralogous pair of ribosomal protein genes, rpsN and yhzA, and proposed that the switch between their products has a different significance. rpsN is indispensable for growth and depletion of RpsN results in defective 30S subunits. YhzA can functionally replace RpsN to allow continued ribosome assembly under zinc-limiting conditions. Unlike YtiA, YhzA appeared in the ribosome at a slower rate consistent with incorporation into newly synthesized, rather than pre-existing ribosomes. These results suggested that YhzA is involved in a fale-safe system for the denovo synthesis of ribosomes under zinc-limiting conditions.

Research Products

• [Journal Article] Isolation and characterization of sporulation-initiation mutation in the Bacillus sublilis prfB gene. (2007)
  • Author(s): Asai, K., Inaoka, T., Nanamiya, H., Sadaie, Y., Ochi, K., Kawamura, F.
  • Journal Title: Biosci. Biotechnol. Biochem. 71 Pages: 379-406
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A fail-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis. (2007)
  • Author(s): Natori, Y., Nanamiya, H., Akanuma, G., Kosono, S., Kudo, T., Ochi, K., Kawamura, F.
  • Journal Title: Mol. Micrbiol. 63 Pages: 294-307
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] F. Isolation and characterization of sporulation-initiation mutation in the Bacillus subtilis prfB gene. (2007)
  • Author(s): Asai, K., Inaoka, T., Nanamiya, H., Sadaie, Y., Ochi, K., Kawamura
  • Journal Title: Biosci. Biotechnol. Biochem. 71 Pages: 397-406
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Ochi, K., and Kawamura, F. A fale-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis. (2007)
  • Author(s): Natori, Y., Nanamiya, H., Akanuma, G., Kosono, S., Kudo, T.
  • Journal Title: Mol. Microbiol. 63 Pages: 294-307
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A fail-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis (2007)
  • Author(s): Natori, Y., Nanamiya, H., Akanuma, G., Kosono, S., Kudo, T., Ochi, K., Kawamura, F.
  • Journal Title: Mol. Micrbiol. 63 Pages: 294-307
• [Journal Article] Proteomics study of the Bacillus subtilis ribosome : Finding of zinc-dependent replacement of ribosomal protein L31 paralogs. (2006)
  • Author(s): Nanamiya, H., Kawamura, F., Kosono, S.
  • Journal Title: J. Gen. Appl. Microbiol. 52 Pages: 249-258
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Isolated chloroplast division machinery can actively constrict after stretching. (2006)
  • Author(s): Yoshida, Y., Kuroiwa, Misumi, O., Nishida, K., Yagisawa, F., Fujiwara, T., Nanamiya, H., Kawamura, F., Kuroiwa, T.
  • Journal Title: Science 313 Pages: 1435-1438
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Construction and characterization of Bacillus subtilis deletion mutants lacking the prophase 2-trnS region. (2006)
  • Author(s): Akanuma, G., Habu, C., Natori, Y., Murayama, R., Nanamiya, H., Kawamura, F.
  • Journal Title: FEMS Microbiol. Lett. Pages: 220-226
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Construction of Bacillus subtilis strains carrying the transcriptional bgaB fusion with the promoter region of each rrn operon and their differential transcription during spore development. (2006)
  • Author(s): Koga, K., Ikegami, A., Nakasone, K., Murayama, R., Akanuma, G., Natori, Y., Nanamiya, H., Kawamura, F.
  • Journal Title: J. Gen. Appl. Microbiol. 52 Pages: 119-124
  • NAID: 130004449184
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Functional myo-inositol catabolic genes of Bacillus subtilis natto are involved in depletion of pinitol in natto (fermented soybean). (2006)
  • Author(s): Morinaga, T., Yamaguchi, M., Makino, Y., Nanamiya, H., Takahashi, K., Yoshikawa, H., Kawamura, F., Ashida, H., Yoshida, K.
  • Journal Title: Biosci. Biotechnol. Biochem. 70 Pages: 1913-1920
  • NAID: 10018528182
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Liberation of zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis. (2006)
  • Author(s): Akanuma, G., Nanamiya, H., Natori, Y., Nomura N., Kawamura, F.
  • Journal Title: J. Bacteriol 188 Pages: 2715-2720
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Nanamiya, H.,Kawamura, F., and Kuroiwa, Isolated chloroplast division machinery can actively constrict after stretching. (2006)
  • Author(s): Yoshida, Y., Kuroiwa, H., Misumi, Nishida, K., Yagisawa, F., Fujiwara, T.
  • Journal Title: Science 313 Pages: 1435-8
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Functional myo-Inositol Catabolic Genes of Bacillus subtilis Natto Are Involved in Depletion of Pinitol in Natto (Fermented Soybean). (2006)
  • Author(s): Morinaga, T., Yamaguchi, M., Makino, Y., Nanamiya, H., Takahashi, K., Yoshikawa, H., Kawamura, F., Ashida, H., Yoshida, K.
  • Journal Title: Biosci. Biotechnol. Biochem. 70 Pages: 1913-20
  • NAID: 10018528182
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Construction and characterization of Bacillus subtilis deletion mutants lacking the prophage 2-trnS region. (2006)
  • Author(s): Akanuma, G., Habu, C., Natori, Y., Murayama, R., Nanamiya, H., Kawamura, F.
  • Journal Title: FEMS Microbiol. Lett. 258 Pages: 220-6
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Liberation of zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis. (2006)
  • Author(s): Akanuma, G., Nanamiya, H., Natori, Y., Nomura, N., Kawamura, F.
  • Journal Title: J. Bacteriol. 188 Pages: 2715-20
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Construction and characterization of Bacillus subtills deletion mutants lacking the prophage 2-trnS region (2006)
  • Author(s): Akanuma, G., Habu, C., Natori, Y., Murayama, R., Nanamiya, H., Kawamura, F.
  • Journal Title: FEMS Microbiol., Lett. 258 Pages: 220-226
• [Journal Article] Construction of Bacillus subtills strains carrying the transcriptional bgaB fusion with the promoter region of each rrn operon and their differential transcription during spore development (2006)
  • Author(s): Koga, K., Ikegami, A., Nakasone, K., Murayama, R., Akanuma, G., Natori, Y., Nanamiya, H., Kawamura, F.
  • Journal Title: J. Gen. Appl. Microbiol. 52 Pages: 119-124
• [Journal Article] Functional myo-inositol catabolic genes of Bacillus subtills natto are involved in depletion of pinitol in natto (fermented soybean) (2006)
  • Author(s): Morinaga, T., Yamaguchi, M., Makino, Y., Nanamiya, H., Takahashi, K., Yoshikawa, H., Kawamura, F., Ashida, H., Yoshida, K.
  • Journal Title: Biosci. Biotechnol. Biochem. 70 Pages: 1913-1920
• [Journal Article] Proteomic study of the Bacillus subtilis ribosome : finding of zinc-dependent replacement for ribosomal protein L31 paralogues (2006)
  • Author(s): Nanamiya, H., Kawamura, F., Kosono, S.
  • Journal Title: J. Gen. Appl. Microbiol. 52 Pages: 249-258
  • NAID: 130004802070
• [Journal Article] Liberation of Zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis (2006)
  • Author(s): Akanuma, G., Nanamiya, H., Natori, Y., Nomura, N., Kawamura, F.
  • Journal Title: J.Bacteriology 188 Pages: 2715-2720
• [Journal Article] Construction and characterization of Bacillus subtilis deletion mutants lacking the prophage 2-trnS region (2006)
  • Author(s): Akanuma, G., Habu, C., Natori, Y., Murayama, R., Nanamiya, H., Kawamura, F.
  • Journal Title: FEMS Microbiol.Lett.
• [Journal Article] Construction of B.subtilis strains carrying the transcriptional bgab fusion with the promoter region of each rrn operon and their differential transcription during spore development (2006)
  • Author(s): Koga, K., Ikegami, A., Nakasone, K., Murayama, R., Akanuma, G., Natori, Y., Nanamiya, H., Kawamura, F.
  • Journal Title: J.Gen.Appl.Microbiol.
• [Journal Article] Identification of the nonA and nonB loci of Bacillus subtilis Marburg permitting the growth of SP10 phase. (2004)
  • Author(s): Matsuoka, S., Arai, T., Murayama, R., Kawamura, F., Asai, K., Sadaie, Y.
  • Journal Title: Genes Genet. Syst. 79 Pages: 311-317
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Spontaneous transformation and its use for genetic mapping in Bacillus subtilis. (2004)
  • Author(s): Murayama, R., Akanuma, G., Makino, Y., Nanamiya, H., Kawamura, F.
  • Journal Title: Biosci. Biotechnol. Biochem. 68 Pages: 1672-1680
  • NAID: 10013520665
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Glr, a glutamate racemase, supplies D-glutamate to both peptideglycan synthesis and poly-gamma-glutamate production in gamma-PGA-producing Bacillus subtilis. (2004)
  • Author(s): Kada, S., Nanamiya, H., Kawamura, F., Horinouchi, S.
  • Journal Title: FEMS Microbiol. Lett. 236 Pages: 13-20
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Genetic analysis of an incomplete bio Operon in a biotin auxotrophic strain of Bacillus subtilis natto OK2. (2004)
  • Author(s): Sasaki, M., Kawamura, F., Kurusu, Y.
  • Journal Title: Biosci. Biotechnol. Biochem. 68 Pages: 739-742
  • NAID: 10013143398
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Zinc is a key factor in controlling alteration of two types of L31 protein in the Bacillus subtilis ribosome. (2004)
  • Author(s): Nanamiya, H., Akanuma, G., Natori, Y., Murayama, R., Kosono, S., Kudo, T., Kobayashi, K., Ogasawara, N., Park, SM., Ochi, K., Kawamura, F.
  • Journal Title: Mol. Microbiol. 52 Pages: 273-283
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Identification of the nonA and nonB loci of Bacillus subtilis Marburg permitting the growth of SP10 phage. (2004)
  • Author(s): Matsuoka, S., Arai, T., Murayama, R., Kawamura, F., Asai, K., Sadaie, Y.
  • Journal Title: Genes Genet. Syst. 79 Pages: 311-7
  • NAID: 10015427377
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Spontaneous transformation and its use for genetic mapping in Bacillus subtilis. (2004)
  • Author(s): Murayama, R., Akanuma, G., Makino, Y., Nanamiya, H., Kawamura.F.
  • Journal Title: Biosci Biotechnol Biochem. 68 Pages: 1672-80
  • NAID: 10013520665
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] a glutamate racemase, supplies D-glutamate to both peptidoglycan synthesis and poly-gamma-glutamate production in gamma-PGA-producing Bacillus subtilis. (2004)
  • Author(s): Kada, S., Nanamiya, H., Kawamura, F., Horinouchi, S.Glr
  • Journal Title: FEMS Microbiol. Lett. 236 Pages: 13-20
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Genetic analysis of an incomplete bio operon in a biotin auxotrophic strain of Bacillus subtilis natto OK2 (2004)
  • Author(s): Sasaki, M., Kawamura, F., Kurusu, Y.
  • Journal Title: Biosci. Biotechnol. Biochem. 68 Pages: 739-42
  • NAID: 10013143398
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. (2004)
  • Author(s): Nanamiya, H., Akanuma, G., Natori, Y., Murayama, R., Kosono, S., Kudo, T., Kobayashi, K., Ogasawara, N., Park, SM., Ochi, K., Kawamura, F.
  • Journal Title: Mol. Microbiol. 52 Pages: 273-83
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Zinc is a key factor in controlling alteration in the Bacillus subtilis ribosome. (2004)
  • Author(s): Nanamiya, H., Akanuma, G., Natori, Y., Murayama.R., 他7名(最後)
  • Journal Title: Mol.Microbiol. 52 Pages: 273-283
• [Journal Article] Genetic analysis of an incomplete bio operon in a biotin auxotrophic strain of Bacillus subtilis natto OK2. (2004)
  • Author(s): Sasaki, M., Kawamura, F., Kurusu.Y.
  • Journal Title: Biosci.Biotechnol.Biochem. 68 Pages: 739-742
  • NAID: 10013143398
• [Journal Article] Spontaneous transformation and its use for genetic mapping in Bacillus subtilis. (2004)
  • Author(s): Murayama, R., Akanuma, G., Makino, Y., 他2名(最後)
  • Journal Title: Biosci.Biotechnol.Biochem. 68 Pages: 1672-1680
• [Journal Article] Glr, a glutamate racemase, supplies D-glutamate to both peptide-glycan synthesis and poly-γ-glutamate(γ-PGA) production in γ-PGA-producing Bacillus subtilis. (2004)
  • Author(s): Kada, S., Nanamiya, H., Kawamura, F., Horinouchi, S.
  • Journal Title: FEMS Microbiol.Lett. 236 Pages: 13-20
• [Journal Article] Identification of the nonA and nonB loci of Bacillus subtilis Marburg permitting the growth of SP10 (2004)
  • Author(s): Matsuoka, S., Arai, T., Murayama, R., Kawamura, F.他2名
  • Journal Title: Genes Genet.Syst. 79 Pages: 311-317