1
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Noda S, Akanuma G, Keyamura K, Hishida T. RecN spatially and temporally controls RecA-mediated repair of DNA double-strand breaks. J Biol Chem 2023; 299:105466. [PMID: 37979912 PMCID: PMC10714372 DOI: 10.1016/j.jbc.2023.105466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
RecN, a bacterial structural maintenance of chromosomes-like protein, plays an important role in maintaining genomic integrity by facilitating the repair of DNA double-strand breaks (DSBs). However, how RecN-dependent chromosome dynamics are integrated with DSB repair remains unclear. Here, we investigated the dynamics of RecN in response to DNA damage by inducing RecN from the PBAD promoter at different time points. We found that mitomycin C (MMC)-treated ΔrecN cells exhibited nucleoid fragmentation and reduced cell survival; however, when RecN was induced with arabinose in MMC-exposed ΔrecN cells, it increased a level of cell viability to similar extent as WT cells. Furthermore, in MMC-treated ΔrecN cells, arabinose-induced RecN colocalized with RecA in nucleoid gaps between fragmented nucleoids and restored normal nucleoid structures. These results suggest that the aberrant nucleoid structures observed in MMC-treated ΔrecN cells do not represent catastrophic chromosome disruption but rather an interruption of the RecA-mediated process. Thus, RecN can resume DSB repair by stimulating RecA-mediated homologous recombination, even when chromosome integrity is compromised. Our data demonstrate that RecA-mediated presynapsis and synapsis are spatiotemporally separable, wherein RecN is involved in facilitating both processes presumably by orchestrating the dynamics of both RecA and chromosomes, highlighting the essential role of RecN in the repair of DSBs.
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Affiliation(s)
- Shunsuke Noda
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Genki Akanuma
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo, Japan.
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2
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Sugaya N, Tanaka S, Keyamura K, Noda S, Akanuma G, Hishida T. N-terminal acetyltransferase NatB regulates Rad51-dependent repair of double-strand breaks in Saccharomyces cerevisiae. Genes Genet Syst 2023; 98:61-72. [PMID: 37331807 DOI: 10.1266/ggs.23-00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023] Open
Abstract
Homologous recombination (HR) is a highly accurate mechanism for repairing DNA double-strand breaks (DSBs) that arise from various genotoxic insults and blocked replication forks. Defects in HR and unscheduled HR can interfere with other cellular processes such as DNA replication and chromosome segregation, leading to genome instability and cell death. Therefore, the HR process has to be tightly controlled. Protein N-terminal acetylation is one of the most common modifications in eukaryotic organisms. Studies in budding yeast implicate a role for NatB acetyltransferase in HR repair, but precisely how this modification regulates HR repair and genome integrity is unknown. In this study, we show that cells lacking NatB, a dimeric complex composed of Nat3 and Mdm2, are sensitive to the DNA alkylating agent methyl methanesulfonate (MMS), and that overexpression of Rad51 suppresses the MMS sensitivity of nat3Δ cells. Nat3-deficient cells have increased levels of Rad52-yellow fluorescent protein foci and fail to repair DSBs after release from MMS exposure. We also found that Nat3 is required for HR-dependent gene conversion and gene targeting. Importantly, we observed that nat3Δ mutation partially suppressed MMS sensitivity in srs2Δ cells and the synthetic sickness of srs2Δ sgs1Δ cells. Altogether, our results indicate that NatB functions upstream of Srs2 to activate the Rad51-dependent HR pathway for DSB repair.
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Affiliation(s)
- Natsuki Sugaya
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Shion Tanaka
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Shunsuke Noda
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Genki Akanuma
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University
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3
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Shibata M, Keyamura K, Shioiri T, Noda S, Akanuma G, Hishida T. Diploid-associated adaptation to chronic low-dose UV irradiation requires homologous recombination in Saccharomyces cerevisiae. Genetics 2022; 222:iyac115. [PMID: 35946552 PMCID: PMC9434230 DOI: 10.1093/genetics/iyac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/25/2022] [Indexed: 11/14/2022] Open
Abstract
Ultraviolet-induced DNA lesions impede DNA replication and transcription and are therefore a potential source of genome instability. Here, we performed serial transfer experiments on nucleotide excision repair-deficient (rad14Δ) yeast cells in the presence of chronic low-dose ultraviolet irradiation, focusing on the mechanisms underlying adaptive responses to chronic low-dose ultraviolet irradiation. Our results show that the entire haploid rad14Δ population rapidly becomes diploid during chronic low-dose ultraviolet exposure, and the evolved diploid rad14Δ cells were more chronic low-dose ultraviolet-resistant than haploid cells. Strikingly, single-stranded DNA, but not pyrimidine dimer, accumulation is associated with diploid-dependent fitness in response to chronic low-dose ultraviolet stress, suggesting that efficient repair of single-stranded DNA tracts is beneficial for chronic low-dose ultraviolet tolerance. Consistent with this hypothesis, homologous recombination is essential for the rapid evolutionary adaptation of diploidy, and rad14Δ cells lacking Rad51 recombinase, a key player in homologous recombination, exhibited abnormal cell morphology characterized by multiple RPA-yellow fluorescent protein foci after chronic low-dose ultraviolet exposure. Furthermore, interhomolog recombination is increased in chronic low-dose ultraviolet-exposed rad14Δ diploids, which causes frequent loss of heterozygosity. Thus, our results highlight the importance of homologous recombination in the survival and genomic stability of cells with unrepaired lesions.
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Affiliation(s)
- Mana Shibata
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Kenji Keyamura
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Takuya Shioiri
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Shunsuke Noda
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Genki Akanuma
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
| | - Takashi Hishida
- Department of Molecular Biology, Graduate School of Science, Gakushuin University, Tokyo 1718588, Japan
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4
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Ohtsuka H, Kobayashi M, Shimasaki T, Sato T, Akanuma G, Kitaura Y, Otsubo Y, Yamashita A, Aiba H. Magnesium depletion extends fission yeast lifespan via general amino acid control activation. Microbiologyopen 2021; 10:e1176. [PMID: 33970532 PMCID: PMC8088111 DOI: 10.1002/mbo3.1176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022] Open
Abstract
Nutrients including glucose, nitrogen, sulfur, zinc, and iron are involved in the regulation of chronological lifespan (CLS) of yeast, which serves as a model of the lifespan of differentiated cells of higher organisms. Herein, we show that magnesium (Mg2+) depletion extends CLS of the fission yeast Schizosaccharomyces pombe through a mechanism involving the Ecl1 gene family. We discovered that ecl1+ expression, which extends CLS, responds to Mg2+ depletion. Therefore, we investigated the underlying intracellular responses. In amino acid auxotrophic strains, Mg2+ depletion robustly induces ecl1+ expression through the activation of the general amino acid control (GAAC) pathway—the equivalent of the amino acid response of mammals. Polysome analysis indicated that the expression of Ecl1 family genes was required for regulating ribosome amount when cells were starved, suggesting that Ecl1 family gene products control the abundance of ribosomes, which contributes to longevity through the activation of the evolutionarily conserved GAAC pathway. The present study extends our understanding of the cellular response to Mg2+ depletion and its influence on the mechanism controlling longevity.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Mikuto Kobayashi
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Teppei Sato
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Genki Akanuma
- Department of Life Science, College of Sciences, Rikkyo University, Tokyo, Japan.,Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Yasuyuki Kitaura
- Laboratory of Nutritional Biochemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoko Otsubo
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,National Institute for Fusion Science, Toki, Japan.,Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Japan
| | - Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Okazaki, Japan.,Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies, Okazaki, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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Abstract
The ribosome requires metal ions for structural stability and translational activity. These metal ions are important for stabilizing the secondary structure of ribosomal RNA, binding of ribosomal proteins to the ribosome, and for interaction of ribosomal subunits. In this review, various relationships between ribosomes and metal ions, especially Mg2+ and Zn2+, are presented. Mg2+ regulates gene expression by modulating the translational stability and synthesis of ribosomes, which in turn contribute to the cellular homeostasis of Mg2+. In addition, Mg2+ can partly complement the function of ribosomal proteins. Conversely, a reduction in the cellular concentration of Zn2+ induces replacement of ribosomal proteins, which mobilizes free-Zn2+ in the cell and represses translation activity. Evolutional relationships between these metal ions and the ribosome are also discussed.
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Affiliation(s)
- Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Toshima-ku, Tokyo, Japan.,Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
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6
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Takada H, Roghanian M, Caballero-Montes J, Van Nerom K, Jimmy S, Kudrin P, Trebini F, Murayama R, Akanuma G, Garcia-Pino A, Hauryliuk V. Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis. Nucleic Acids Res 2021; 49:444-457. [PMID: 33330919 PMCID: PMC7797070 DOI: 10.1093/nar/gkaa1187] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
In the Gram-positive Firmicute bacterium Bacillus subtilis, amino acid starvation induces synthesis of the alarmone (p)ppGpp by the RelA/SpoT Homolog factor Rel. This bifunctional enzyme is capable of both synthesizing and hydrolysing (p)ppGpp. To detect amino acid deficiency, Rel monitors the aminoacylation status of the ribosomal A-site tRNA by directly inspecting the tRNA’s CCA end. Here we dissect the molecular mechanism of B. subtilis Rel. Off the ribosome, Rel predominantly assumes a ‘closed’ conformation with dominant (p)ppGpp hydrolysis activity. This state does not specifically select deacylated tRNA since the interaction is only moderately affected by tRNA aminoacylation. Once bound to the vacant ribosomal A-site, Rel assumes an ‘open’ conformation, which primes its TGS and Helical domains for specific recognition and stabilization of cognate deacylated tRNA on the ribosome. The tRNA locks Rel on the ribosome in a hyperactivated state that processively synthesises (p)ppGpp while the hydrolysis is suppressed. In stark contrast to non-specific tRNA interactions off the ribosome, tRNA-dependent Rel locking on the ribosome and activation of (p)ppGpp synthesis are highly specific and completely abrogated by tRNA aminoacylation. Binding pppGpp to a dedicated allosteric site located in the N-terminal catalytic domain region of the enzyme further enhances its synthetase activity.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Steffi Jimmy
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Pavel Kudrin
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Fabio Trebini
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu-Kubotamachi, Akita, 010-0874, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium.,WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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7
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Takada H, Roghanian M, Murina V, Dzhygyr I, Murayama R, Akanuma G, Atkinson GC, Garcia-Pino A, Hauryliuk V. The C-Terminal RRM/ACT Domain Is Crucial for Fine-Tuning the Activation of 'Long' RelA-SpoT Homolog Enzymes by Ribosomal Complexes. Front Microbiol 2020; 11:277. [PMID: 32184768 PMCID: PMC7058999 DOI: 10.3389/fmicb.2020.00277] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/19/2022] Open
Abstract
The (p)ppGpp-mediated stringent response is a bacterial stress response implicated in virulence and antibiotic tolerance. Both synthesis and degradation of the (p)ppGpp alarmone nucleotide are mediated by RelA-SpoT Homolog (RSH) enzymes which can be broadly divided in two classes: single-domain 'short' and multi-domain 'long' RSH. The regulatory ACT (Aspartokinase, Chorismate mutase and TyrA)/RRM (RNA Recognition Motif) domain is a near-universal C-terminal domain of long RSHs. Deletion of RRM in both monofunctional (synthesis-only) RelA as well as bifunctional (i.e., capable of both degrading and synthesizing the alarmone) Rel renders the long RSH cytotoxic due to overproduction of (p)ppGpp. To probe the molecular mechanism underlying this effect we characterized Escherichia coli RelA and Bacillus subtilis Rel RSHs lacking RRM. We demonstrate that, first, the cytotoxicity caused by the removal of RRM is counteracted by secondary mutations that disrupt the interaction of the RSH with the starved ribosomal complex - the ultimate inducer of (p)ppGpp production by RelA and Rel - and, second, that the hydrolytic activity of Rel is not abrogated in the truncated mutant. Therefore, we conclude that the overproduction of (p)ppGpp by RSHs lacking the RRM domain is not explained by a lack of auto-inhibition in the absence of RRM or/and a defect in (p)ppGpp hydrolysis. Instead, we argue that it is driven by misregulation of the RSH activation by the ribosome.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Ievgen Dzhygyr
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | | | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- WELBIO, Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
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8
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Nguyen HTM, Akanuma G, Hoa TTM, Nakai Y, Kimura K, Yamamoto K, Inaoka T. Ribosome Reconstruction during Recovery from High-Hydrostatic-Pressure-Induced Injury in Bacillus subtilis. Appl Environ Microbiol 2019; 86:e01640-19. [PMID: 31604775 PMCID: PMC6912085 DOI: 10.1128/aem.01640-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Vegetative cells of Bacillus subtilis can recover from injury after high-hydrostatic-pressure (HHP) treatment at 250 MPa. DNA microarray analysis revealed that substantial numbers of ribosomal genes and translation-related genes (e.g., translation initiation factors) were upregulated during the growth arrest phase after HHP treatment. The transcript levels of cold shock-responsive genes, whose products play key roles in efficient translation, and heat shock-responsive genes, whose products mediate correct protein folding or degrade misfolded proteins, were also upregulated. In contrast, the transcript level of hpf, whose product (Hpf) is involved in ribosome inactivation through the dimerization of 70S ribosomes, was downregulated during the growth arrest phase. Sucrose density gradient sedimentation analysis revealed that ribosomes were dissociated in a pressure-dependent manner and then reconstructed. We also found that cell growth after HHP-induced injury was apparently inhibited by the addition of Mn2+ or Zn2+ to the recovery medium. Ribosome reconstruction in the HHP-injured cells was also significantly delayed in the presence of Mn2+ or Zn2+ Moreover, Zn2+, but not Mn2+, promoted dimer formation of 70S ribosomes in the HHP-injured cells. Disruption of the hpf gene suppressed the Zn2+-dependent accumulation of ribosome dimers, partially relieving the inhibitory effect of Zn2+ on the growth recovery of HHP-treated cells. In contrast, it was likely that Mn2+ prevented ribosome reconstruction without stimulating ribosome dimerization. Our results suggested that both Mn2+ and Zn2+ can prevent ribosome reconstruction, thereby delaying the growth recovery of HHP-injured B. subtilis cells.IMPORTANCE HHP treatment is used as a nonthermal processing technology in the food industry to inactivate bacteria while retaining high quality of foods under suppressed chemical reactions. However, some populations of bacterial cells may survive the inactivation. Although the survivors are in a transient nongrowing state due to HHP-induced injury, they can recover from the injury and then start growing, depending on the postprocessing conditions. The recovery process in terms of cellular components after the injury remains unclear. Transcriptome analysis using vegetative cells of Bacillus subtilis revealed that the translational machinery can preferentially be reconstructed after HHP treatment. We found that both Mn2+ and Zn2+ prolonged the growth-arrested stage of HHP-injured cells by delaying ribosome reconstruction. It is likely that ribosome reconstruction is crucial for the recovery of growth ability in HHP-injured cells. This study provides further understanding of the recovery process in HHP-injured B. subtilis cells.
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Affiliation(s)
- Huyen Thi Minh Nguyen
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | | | - Tu Thi Minh Hoa
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Ha Noi, Viet Nam
| | - Yuji Nakai
- Institute of Regional Innovation, Hirosaki University, Aomori, Japan
| | - Keitarou Kimura
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Kazutaka Yamamoto
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Takashi Inaoka
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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9
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Akanuma G, Tagana T, Sawada M, Suzuki S, Shimada T, Tanaka K, Kawamura F, Kato-Yamada Y. C-terminal regulatory domain of the ε subunit of F o F 1 ATP synthase enhances the ATP-dependent H + pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis. Microbiologyopen 2019; 8:e00815. [PMID: 30809948 PMCID: PMC6692558 DOI: 10.1002/mbo3.815] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023] Open
Abstract
The ε subunit of FoF1‐ATPase/synthase (FoF1) plays a crucial role in regulating FoF1 activity. To understand the physiological significance of the ε subunit‐mediated regulation of FoF1 in Bacillus subtilis, we constructed and characterized a mutant harboring a deletion in the C‐terminal regulatory domain of the ε subunit (ε∆C). Analyses using inverted membrane vesicles revealed that the ε∆C mutation decreased ATPase activity and the ATP‐dependent H+‐pumping activity of FoF1. To enhance the effects of ε∆C mutation, this mutation was introduced into a ∆rrn8 strain harboring only two of the 10 rrn (rRNA) operons (∆rrn8 ε∆C mutant strain). Interestingly, growth of the ∆rrn8 ε∆C mutant stalled at late‐exponential phase. During the stalled growth phase, the membrane potential of the ∆rrn8 ε∆C mutant cells was significantly reduced, which led to a decrease in the cellular level of 70S ribosomes. The growth stalling was suppressed by adding glucose into the culture medium. Our findings suggest that the C‐terminal region of the ε subunit is important for alleviating the temporal reduction in the membrane potential, by enhancing the ATP‐dependent H+‐pumping activity of FoF1.
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Affiliation(s)
- Genki Akanuma
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Tomoaki Tagana
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Maho Sawada
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Shota Suzuki
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Tomohiro Shimada
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Yokohama, Midori-ku, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Yokohama, Midori-ku, Japan
| | - Fujio Kawamura
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Yasuyuki Kato-Yamada
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
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10
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Ishigaki Y, Akanuma G, Yoshida M, Horinouchi S, Kosono S, Ohnishi Y. Protein acetylation involved in streptomycin biosynthesis in Streptomyces griseus. J Proteomics 2016; 155:63-72. [PMID: 28034645 DOI: 10.1016/j.jprot.2016.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/03/2016] [Accepted: 12/16/2016] [Indexed: 12/25/2022]
Abstract
Protein acetylation, the reversible addition of an acetyl group to lysine residues, is a protein post-translational modification ubiquitous in living cells. Although the involvement of protein acetylation in the regulation of primary metabolism has been revealed, the function of protein acetylation is largely unknown in secondary metabolism. Here, we characterized protein acetylation in Streptomyces griseus, a streptomycin producer. Protein acetylation was induced in the stationary and sporulation phases in liquid and solid cultures, respectively, in S. griseus. By comprehensive acetylome analysis, we identified 134 acetylated proteins with 162 specific acetylated sites. Acetylation was found in proteins related to primary metabolism and translation, as in other bacteria. However, StrM, a deoxysugar epimerase involved in streptomycin biosynthesis, was identified as a highly acetylated protein by 2-DE-based proteomic analysis. The Lys70 residue, which is critical for the enzymatic activity of StrM, was the major acetylation site. Thus, acetylation of Lys70 was presumed to abolish enzymatic activity of StrM. In accordance with this notion, an S. griseus mutant producing the acetylation-mimic K70Q StrM hardly produced streptomycin, though the K70Q mutation apparently decreased the stability of StrM. A putative lysine acetyltransferase (KAT) SGR1683 in S. griseus, as well as the Escherichia coli KAT YfiQ, acetylated Lys70 of StrM in vitro. Furthermore, absolute quantification analysis estimated that 13% of StrM molecules were acetylated in mycelium grown in solid culture for 3days. These results indicate that StrM acetylation is of biological significance. We propose that StrM acetylation functions as a limiter of streptomycin biosynthesis in S. griseus. BIOLOGICAL SIGNIFICANCE Protein acetylation has been extensively studied not only in eukaryotes, but also in prokaryotes. The acetylome has been analyzed in more than 14 bacterial species. Here, by comprehensive acetylome analysis, we showed that acetylation was found in proteins related to primary metabolism and translation in Streptomyces griseus, similarly to other bacteria. However, five proteins involved in secondary metabolism were also identified as acetylated proteins; these proteins are enzymes in the biosynthesis of streptomycin (StrB1 and StrS), grixazone (GriF), a nonribosomal peptide (NRPS1-2), and a siderophore (AlcC). Additionally, StrM in streptomycin biosynthesis was identified as a highly acetylated protein by 2-DE-based proteomic analysis; approximately 13% of StrM molecules were acetylated. The acetylation occurs at Lys70 to abolish the enzymatic activity of StrM, suggesting that StrM acetylation functions as a limiter of streptomycin biosynthesis in S. griseus. This is the first detailed analysis of protein acetylation of an enzyme involved in secondary metabolism.
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Affiliation(s)
- Yuji Ishigaki
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Genki Akanuma
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Minoru Yoshida
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Sueharu Horinouchi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Saori Kosono
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Biological Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
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11
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Akanuma G, Kazo Y, Tagami K, Hiraoka H, Yano K, Suzuki S, Hanai R, Nanamiya H, Kato-Yamada Y, Kawamura F. Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis. Microbiology (Reading) 2016; 162:448-458. [PMID: 26743942 DOI: 10.1099/mic.0.000234] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ribosome dimers are a translationally inactive form of ribosomes found in Escherichia coli and many other bacterial cells. In this study, we found that the 70S ribosomes of Bacillus subtilis dimerized during the early stationary phase and these dimers remained in the cytoplasm until regrowth was initiated. Ribosome dimerization during the stationary phase required the hpf gene, which encodes a homologue of the E. coli hibernation-promoting factor (Hpf). The expression of hpf was induced at an early stationary phase and its expression was observed throughout the rest of the experimental period, including the entire 6 h of the stationary phase. Ribosome dimerization followed the induction of hpf in WT cells, but the dimerization was impaired in cells harbouring a deletion in the hpf gene. Although the absence of ribosome dimerization in these Hpf-deficient cells did not affect their viability in the stationary phase, their ability to regrow from the stationary phase decreased. Thus, following the transfer of stationary-phase cells to fresh LB medium, Δhpf mutant cells grew slower than WT cells. This observed lag in growth of Δhpf cells was probably due to a delay in restoring their translational activity. During regrowth, the abundance of ribosome dimers in WT cells decreased with a concomitant increase in the abundance of 70S ribosomes and growth rate. These results suggest that the ribosome dimers, by providing 70S ribosomes to the cells, play an important role in facilitating rapid and efficient regrowth of cells under nutrient-rich conditions.
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Affiliation(s)
- Genki Akanuma
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuka Kazo
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Kazumi Tagami
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Hirona Hiraoka
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Koichi Yano
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan.,Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Shota Suzuki
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan.,Department of Biotechnology, Graduate School of Agriculture and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryo Hanai
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Hideaki Nanamiya
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan.,Fukushima Medical University, Hiragaoka 1, Fukushima 960-1295, Japan
| | - Yasuyuki Kato-Yamada
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Fujio Kawamura
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 155-8502, Japan.,Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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12
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Yano K, Masuda K, Akanuma G, Wada T, Matsumoto T, Shiwa Y, Ishige T, Yoshikawa H, Niki H, Inaoka T, Kawamura F. Growth and sporulation defects in Bacillus subtilis mutants with a single rrn operon can be suppressed by amplification of the rrn operon. Microbiology (Reading) 2016; 162:35-45. [DOI: 10.1099/mic.0.000207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Koichi Yano
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Kenta Masuda
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Genki Akanuma
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Tetsuya Wada
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Takashi Matsumoto
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Taichiro Ishige
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Hironori Niki
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies, Sokendai, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Takashi Inaoka
- Microbial Function Laboratory, National Food Research Institute, National Agriculture Research Organization, Tsukuba-shi Kannondai 2-1-12, Ibaraki 305-8642, Japan
| | - Fujio Kawamura
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
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13
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Akanuma G, Yoshizawa R, Nagakura M, Shiwa Y, Watanabe S, Yoshikawa H, Ushio K, Ishizuka M. EliA is required for inducing the stearyl alcohol-mediated expression of secretory proteins and production of polyester in Ralstonia sp. NT80. Microbiology (Reading) 2015; 162:408-419. [PMID: 26673629 DOI: 10.1099/mic.0.000225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Addition of stearyl alcohol to the culture medium of Ralstonia sp. NT80 induced expression of a significant amount of secretory lipase. Comparative proteomic analysis of extracellular proteins from NT80 cells grown in the presence or absence of stearyl alcohol revealed that stearyl alcohol induced expression of several secretory proteins including lipase, haemolysin-coregulated protein and nucleoside diphosphate kinase. Expression of these secreted proteins was upregulated at the transcriptional level. Stearyl alcohol also induced the synthesis of polyhydroxyalkanoate. Secretory protein EliA was required for all these responses of NT80 cells to stearyl alcohol. Accordingly, the effects of stearyl alcohol were significantly reduced in the eliA deletion mutant cells of NT80 (ΔeliA). The remaining concentration of stearyl alcohol in the culture supernatant of the wild-type cells, but not that in the culture supernatant of the ΔeliA cells, clearly decreased during the course of growth. These observed phenotypes of the ΔeliA mutant were rescued by gene complementation. The results suggested that EliA is essential for these cells to respond to stearyl alcohol, and that it plays an important role in the recognition and assimilation of stearyl alcohol by NT80 cells.
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Affiliation(s)
- Genki Akanuma
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.,Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo, Japan
| | - Rie Yoshizawa
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan
| | - Mari Nagakura
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.,Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Kazutoshi Ushio
- Department of Applied Chemistry and Biotechnology, Niihama National College of Technology, Niihama, Ehime, Japan
| | - Morio Ishizuka
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan
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14
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15
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Murayama R, Akanuma G, Makino Y, Nanamiya H, Kawamura F. Spontaneous Transformation and Its Use for Genetic Mapping inBacillus subtilis. Biosci Biotechnol Biochem 2014; 68:1672-80. [PMID: 15322350 DOI: 10.1271/bbb.68.1672] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Using a simple semi-synthetic competence and sporulation medium (CSM), we found evidence that Bacillus subtilis cells transformed in the competence phase can sporulate, indicating that genetic information acquired during the competence phase is inherited by the next generation after germination of the transformed spores. Moreover, the results from mixed cell culture experiments suggest that spontaneous genetic transformation can occur between competent cells and DNA released from lysed cells in the natural environment. We also found evidence that the spontaneous transformation system can be used for genetic mapping in B. subtilis.
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Affiliation(s)
- Rikinori Murayama
- Laboratory of Molecular Genetics and Frontier Project Life's Adaptation Strategies to Environmental Changes, Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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16
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Yano K, Wada T, Suzuki S, Tagami K, Matsumoto T, Shiwa Y, Ishige T, Kawaguchi Y, Masuda K, Akanuma G, Nanamiya H, Niki H, Yoshikawa H, Kawamura F. Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis. Microbiology (Reading) 2013; 159:2225-2236. [DOI: 10.1099/mic.0.067025-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Koichi Yano
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Tetsuya Wada
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Shota Suzuki
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Kazumi Tagami
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Takashi Matsumoto
- Genome Research Center, Nodai Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Yuh Shiwa
- Genome Research Center, Nodai Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Taichiro Ishige
- Genome Research Center, Nodai Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Yasuhiro Kawaguchi
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Kenta Masuda
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Genki Akanuma
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Hideaki Nanamiya
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hironori Niki
- Department of Genetics, Graduate University for Advanced Studies, Sokendai, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
- Genome Research Center, Nodai Research Institute, Tokyo University of Agriculture, Setagaya-ku, Sakuragaoka 1-1-1, Tokyo 156-8502, Japan
| | - Fujio Kawamura
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
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17
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Akanuma G, Suzuki S, Yano K, Nanamiya H, Natori Y, Namba E, Watanabe K, Tagami K, Takeda T, Iizuka Y, Kobayashi A, Ishizuka M, Yoshikawa H, Kawamura F. Single mutations introduced in the essential ribosomal proteins L3 and S10 cause a sporulation defect in Bacillus subtilis. J GEN APPL MICROBIOL 2013; 59:105-17. [DOI: 10.2323/jgam.59.105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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Akanuma G, Ishibashi H, Miyagawa T, Yoshizawa R, Watanabe S, Shiwa Y, Yoshikawa H, Ushio K, Ishizuka M. EliA facilitates the induction of lipase expression by stearyl alcohol in Ralstonia sp. NT80. FEMS Microbiol Lett 2012; 339:48-56. [PMID: 23173706 DOI: 10.1111/1574-6968.12055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 11/13/2012] [Indexed: 11/28/2022] Open
Abstract
Extracellular lipase activity from Ralstonia sp. NT80 is induced significantly by fatty alcohols such as stearyl alcohol. We found that when lipase expression was induced by stearyl alcohol, a 14-kDa protein (designated EliA) was produced concomitantly and abundantly in the culture supernatant. Cloning and sequence analysis revealed that EliA shared 30% identity with the protein-like activator protein of Pseudomonas aeruginosa, which facilitates oxidation and assimilation of n-hexadecane. Inactivation of the eliA gene caused a significant reduction in the level of induction of lipase expression by stearyl alcohol. Furthermore, turbidity that was caused by the presence of emulsified stearyl alcohol, an insoluble material, remained in the culture supernatant of the ΔeliA mutant during the late stationary phase, whereas the culture supernatant of the wild type at 72 h was comparatively clear. In contrast, when lipase expression was induced by polyoxyethylene (20) oleyl ether, a soluble material, inactivation of eliA did not affect the extracellular lipase activity greatly. These results strongly indicate that EliA facilitates the induction of lipase expression, presumably by promoting the recognition and/or incorporation of the induction signal that is attributed to stearyl alcohol.
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Affiliation(s)
- Genki Akanuma
- Department of Applied Chemistry, Chuo University, Bunkyo-ku, Tokyo, Japan
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19
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Akanuma G, Ueki M, Ishizuka M, Ohnishi Y, Horinouchi S. Control of aerial mycelium formation by the BldK oligopeptide ABC transporter in Streptomyces griseus. FEMS Microbiol Lett 2010; 315:54-62. [DOI: 10.1111/j.1574-6968.2010.02177.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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20
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Nanamiya H, Sato M, Masuda K, Sato M, Wada T, Suzuki S, Natori Y, Katano M, Akanuma G, Kawamura F. Bacillus subtilis mutants harbouring a single copy of the rRNA operon exhibit severe defects in growth and sporulation. Microbiology (Reading) 2010; 156:2944-2952. [DOI: 10.1099/mic.0.035295-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The number of copies of rRNA genes in bacterial genomes differs greatly among bacterial species. It is difficult to determine the functional significance of the heterogeneity of each rRNA operon fully due to the existence of multiple rRNA operons and because the sequence heterogeneity among the rRNA genes is extremely low. To overcome this problem, we sequentially deleted the ten rrn operons of Bacillus subtilis and constructed seven mutant strains that each harboured a single rrn operon (either rrnA, B, D, E, I, J or O) in their genome. The growth rates and sporulation frequencies of these mutants were reduced drastically compared with those of the wild-type strain, and this was probably due to decreased levels of ribosomes in the mutants. Interestingly, the ability to sporulate varied significantly among the mutant strains. These mutants have proved to be invaluable in our initial attempts to reveal the functional significance of the heterogeneity of each rRNA operon.
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Affiliation(s)
- Hideaki Nanamiya
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Makiko Sato
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Kenta Masuda
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Mikiko Sato
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Tetsuya Wada
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Shota Suzuki
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Yousuke Natori
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Masato Katano
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Genki Akanuma
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
| | - Fujio Kawamura
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
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21
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Akanuma G, Hara H, Ohnishi Y, Horinouchi S. Dynamic changes in the extracellular proteome caused by absence of a pleiotropic regulator AdpA in Streptomyces griseus. Mol Microbiol 2009; 73:898-912. [PMID: 19678896 DOI: 10.1111/j.1365-2958.2009.06814.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In Streptomyces griseus, A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) triggers morphological development and secondary metabolism by inducing a pleiotropic transcriptional regulator AdpA. Extracellular proteome analysis of the wild-type and DeltaadpA strains grown to the end of the exponential phase in liquid minimal medium revealed that 38 secreted proteins, including many catabolic enzymes, such as protease, glycosyl hydrolase and esterase, were produced in an AdpA-dependent manner. Transcriptome analysis showed that almost all of these AdpA-dependent secreted proteins were regulated at the transcriptional level. In vitro AdpA-binding assays and determination of transcriptional start sites led to identification of 11 promoters as novel targets of AdpA. Viability staining revealed that some hyphae lysed during the exponential growth phase, which could explain the detection of 3 and 23 cytoplasmic proteins in the culture media of the wild-type and DeltaadpA strains respectively. In the wild-type strain, due to high protease activity in the culture medium, cytoplasmic proteins that leaked from dead cells seemed to be degraded and reused for the further growth. The existence of many AdpA-dependent (i.e. A-factor-inducible) secreted catabolic enzymes, which are likely involved in the assimilation of material that leaked from dead cells, reemphasizes the importance of A-factor in the morphological differentiation of S. griseus.
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Affiliation(s)
- Genki Akanuma
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
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22
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Natori Y, Nanamiya H, Akanuma G, Kosono S, Kudo T, Ochi K, Kawamura F. A fail-safe system for the ribosome under zinc-limiting conditions in Bacillus subtilis. Mol Microbiol 2006; 63:294-307. [PMID: 17163968 DOI: 10.1111/j.1365-2958.2006.05513.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
As zinc is an essential trace metal ion for all living cells, cells elaborate a variety of strategies to cope with zinc starvation. In Bacillus subtilis, genes encoding ribosomal proteins L31 and S14 are duplicated into two types: one type contains a zinc-binding motif (RpmE or RpsN), whereas the other does not (YtiA or YhzA). We have previously shown that displacement of RpmE (L31) by YtiA from already assembled ribosomes is controlled by zinc, and this replacement could contribute to zinc mobilization under zinc-limiting conditions. We propose here that the switch between the two types of S14 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 raise the possibility that YhzA is involved in a fail-safe system for the de novo synthesis of ribosomes under zinc-limiting conditions.
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Affiliation(s)
- Yousuke Natori
- Laboratory of Molecular Genetics and Research Information Center for Extremophile, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
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23
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Koga K, Ikegami A, Nakasone K, Murayama R, Akanuma G, Natori Y, Nanamiya H, Kawamura F. 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. J GEN APPL MICROBIOL 2006; 52:119-24. [PMID: 16778356 DOI: 10.2323/jgam.52.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Keiko Koga
- Laboratory of Molecular Genetics and Frontier Project 'Life's Adaptation Strategies to Environmental Changes', College of Science, Rikkyo University, Japan
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24
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Akanuma G, Habu C, Natori Y, Murayama R, Nanamiya H, Kawamura F. Construction and characterization ofBacillus subtilisdeletion mutants lacking theprophage 2-trnSregion. FEMS Microbiol Lett 2006; 258:220-6. [PMID: 16640577 DOI: 10.1111/j.1574-6968.2006.00234.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
During development of a novel method for constructing a series of deletions in Bacillus subtilis using an isogenic set of gene-disrupted mutants created by integration of pMutin, deletion of the trnS operon, consisting of seven tRNA genes, was found to affect cell growth, development of competence and spore formation. A suppressor (sts1) of the DeltatrnS mutant was isolated, sequenced and found to have undergone a single base change, CAG to GAG, in the first anticodon of tRNA(Leu), in the trnB operon.
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Affiliation(s)
- Genki Akanuma
- Laboratory of Molecular Genetics and Frontier Project Life's Adaptation Strategies to Environmental Changes, Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
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Akanuma G, Nanamiya H, Natori Y, Nomura N, Kawamura F. Liberation of zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis. J Bacteriol 2006; 188:2715-20. [PMID: 16547061 PMCID: PMC1428384 DOI: 10.1128/jb.188.7.2715-2720.2006] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have found that alternative localization of two types of L31 ribosomal protein, RpmE and YtiA, is controlled by the intracellular concentration of zinc in Bacillus subtilis. The detailed mechanisms for the alternation of L31 proteins under zinc-deficient conditions were previously unknown. To obtain further information about this regulatory mechanism, we have studied the stability of RpmE in vivo and the binding affinity of these proteins to ribosomes in vitro, and we have found that liberation of RpmE from ribosomes is triggered by the expression of ytiA, which is induced by the derepression of Zur under zinc-deficient conditions.
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Affiliation(s)
- Genki Akanuma
- College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
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Nanamiya H, Akanuma G, Natori Y, Murayama R, Kosono S, Kudo T, Kobayashi K, Ogasawara N, Park SM, Ochi K, Kawamura F. Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. Mol Microbiol 2004; 52:273-83. [PMID: 15049826 DOI: 10.1111/j.1365-2958.2003.03972.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have analysed changes in the composition of ribosomal proteins during cell growth in Bacillus subtilis. Ribosome fractions were prepared from B. subtilis cells at different phases of growth and were separated by radical-free and highly reducing (RFHR) two-dimensional polyacrylamide gel electrophoresis. We identified 50 ribosomal proteins, including two paralogues of L31 protein (RpmE and YtiA). Although the ribosome fraction extracted from exponentially growing cells contained RpmE protein, this protein disappeared during the stationary phase. In contrast, YtiA was detected in the ribosome fraction extracted after the end of exponential growth. Expression of the ytiA gene encoding YtiA was found to be negatively controlled by Zur, a zinc-specific transcriptional repressor that controls zinc transport operons. Analysis by inductively coupled plasma mass spectrometry (ICP-MS) indicated that RpmE contains one zinc ion per molecule of protein. In addition, mutagenesis of the rpmE gene encoding RpmE revealed that Cys-36 and Cys-39, located within a CxxC motif, are required not only for binding zinc but also for the accumulation of RpmE in the cell. Taken together, these results indicate that zinc plays an essential role in the alternation between two types of L31 protein in the ribosome of B. subtilis.
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Affiliation(s)
- Hideaki Nanamiya
- Laboratory of Molecular Genetics and Frontier Project Life's Adaptation Strategies to Environmental Changes, College of Science, Rikkyo University, Toshima-ku Nishi-ikebukuro 3-34-1, Tokyo 171-8501, Japan
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