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Oberbauer V, Schaefer MR. tRNA-Derived Small RNAs: Biogenesis, Modification, Function and Potential Impact on Human Disease Development. Genes (Basel) 2018; 9:genes9120607. [PMID: 30563140 PMCID: PMC6315542 DOI: 10.3390/genes9120607] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundant small non-coding RNAs that are crucially important for decoding genetic information. Besides fulfilling canonical roles as adaptor molecules during protein synthesis, tRNAs are also the source of a heterogeneous class of small RNAs, tRNA-derived small RNAs (tsRNAs). Occurrence and the relatively high abundance of tsRNAs has been noted in many high-throughput sequencing data sets, leading to largely correlative assumptions about their potential as biologically active entities. tRNAs are also the most modified RNAs in any cell type. Mutations in tRNA biogenesis factors including tRNA modification enzymes correlate with a variety of human disease syndromes. However, whether it is the lack of tRNAs or the activity of functionally relevant tsRNAs that are causative for human disease development remains to be elucidated. Here, we review the current knowledge in regard to tsRNAs biogenesis, including the impact of RNA modifications on tRNA stability and discuss the existing experimental evidence in support for the seemingly large functional spectrum being proposed for tsRNAs. We also argue that improved methodology allowing exact quantification and specific manipulation of tsRNAs will be necessary before developing these small RNAs into diagnostic biomarkers and when aiming to harness them for therapeutic purposes.
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Affiliation(s)
- Vera Oberbauer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
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2
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Ogawa T. tRNA-targeting ribonucleases: molecular mechanisms and insights into their physiological roles. Biosci Biotechnol Biochem 2016; 80:1037-45. [PMID: 26967967 DOI: 10.1080/09168451.2016.1148579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Most bacteria produce antibacterial proteins known as bacteriocins, which aid bacterial defence systems to provide a physiological advantage. To date, many kinds of bacteriocins have been characterized. Colicin has long been known as a plasmidborne bacteriocin that kills other Escherichia coli cells lacking the same plasmid. To defeat other cells, colicins exert specific activities such as ion-channel, DNase, and RNase activity. Colicin E5 and colicin D impair protein synthesis in sensitive E. coli cells; however, their physiological targets have not long been identified. This review describes our finding that colicins E5 and D are novel RNases targeting specific E. coli tRNAs and elucidates their enzymatic properties based on biochemical analyses and X-ray crystal structures. Moreover, tRNA cleavage mediates bacteriostasis, which depends on trans-translation. Based on these results and others, cell growth regulation depending on tRNA cleavage is also discussed.
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Affiliation(s)
- Tetsuhiro Ogawa
- a Department of Biotechnology , The University of Tokyo , Tokyo , Japan
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3
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Sakai F, Sugita R, Chang JW, Ogawa T, Tsumadori N, Takahashi K, Hidaka M, Masaki H. Transfer-messenger RNA and SmpB mediate bacteriostasis in Escherichia coli cells against tRNA cleavage. MICROBIOLOGY-SGM 2015. [PMID: 26199088 DOI: 10.1099/mic.0.000144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
RNAs, such as mRNA, rRNA and tRNA, are essential macromolecules for cell survival and maintenance. Any perturbation of these molecules, such as by degradation or mutation, can be toxic to cells and may occasionally induce cell death. Therefore, cells have mechanisms known as quality control systems to eliminate abnormal RNAs. Although tRNA is a stable molecule, the anticodon loop is quite susceptible to tRNA-targeting RNases such as colicin E5 and colicin D. However, the mechanism underlying cellular reaction to tRNA cleavage remains unclear. It had long been believed that tRNA cleavage by colicins E5 and D promptly induces cell death because colony formation of the sensitive cells is severely reduced; this indicates that cells do not resist the tRNA cleavage. Here, we show that Escherichia coli cells enter a bacteriostatic state against the tRNA cleavage of colicins D and E5. The bacteriostasis requires small protein B (SmpB) and transfer-messenger RNA (tmRNA), which are known to mediate trans-translation. Furthermore, another type of colicin, colicin E3 cleaving rRNA, immediately reduces the viability of sensitive cells. Moreover, nascent peptide degradation has an additive effect on bacteriostasis. Considering the recent observation that tRNA cleavage may be used as a means of cell-to-cell communication, tRNA cleavage could be used by bacteria not only to dominate other bacteria living in the same niche, but also to regulate growth of their own or other cells.
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Affiliation(s)
- Fusako Sakai
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Risa Sugita
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jung-Wei Chang
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tetsuhiro Ogawa
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Natsuko Tsumadori
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kazutoshi Takahashi
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Hidaka
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Haruhiko Masaki
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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4
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Shigematsu M, Ogawa T, Kitamoto HK, Hidaka M, Masaki H. Specific phase arrest of cell cycle restores cell viability against tRNA cleavage by killer toxin. Biochem Biophys Res Commun 2012; 420:750-4. [PMID: 22450321 DOI: 10.1016/j.bbrc.2012.03.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 03/12/2012] [Indexed: 11/17/2022]
Abstract
Zymocin and PaT are killer toxins that induce cell cycle arrest of sensitive yeast cells in G1 and S phase, respectively. Recent studies have revealed that these two toxins cleave specific tRNAs, indicating that the cell growth impairment is due to the tRNA cleavage. Additionally, we have previously shown that the active domain of colicin D (D-CRD), which also cleaves specific Escherichia coli tRNAs, statically impairs growth when expressed in yeast cells. To verify that phase-specific cell cycle arrest is also induced by the expression of D-CRD, D-CRD and the subunits of zymocin and PaT that have tRNA cleaving activity were expressed in yeast cells and cell cycle status was analyzed. Our results indicate that phase-specific arrest does not commonly occur by tRNA cleavage, and it saves the cell viability. Furthermore, the extent of protein synthesis impairment may determine the phase specificity of cell cycle arrest.
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Affiliation(s)
- Megumi Shigematsu
- Department of Biotechnology, The University of Tokyo, Yayoi, Tokyo 113-8657, Japan
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5
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Meineke B, Shuman S. Determinants of the cytotoxicity of PrrC anticodon nuclease and its amelioration by tRNA repair. RNA (NEW YORK, N.Y.) 2012; 18:145-54. [PMID: 22101242 PMCID: PMC3261736 DOI: 10.1261/rna.030171.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/10/2011] [Indexed: 05/23/2023]
Abstract
Breakage of tRNA(Lys(UUU)) by the Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies a host antiviral response to phage T4 infection that is ultimately thwarted by a virus-encoded RNA repair system. PrrC homologs are prevalent in other bacteria, but their activities and substrates are not defined. We find that induced expression of EcoPrrC is toxic in Saccharomyces cerevisiae and E. coli, whereas the Neisseria meningitidis PrrC (NmePrrC) is not. PrrCs consist of an N-terminal NTPase module and a C-terminal nuclease module. Domain swaps identified the EcoPrrC nuclease domain as decisive for toxicity when linked to either the Eco or Nme NTPase. Indeed, a single arginine-to-tryptophan change in the NmePrrC nuclease domain (R316W) educed a gain-of-function and rendered NmePrrC toxic to yeast, with genetic evidence for tRNA(Lys(UUU)) being the relevant target. The reciprocal Trp-to-Arg change in EcoPrrC (W335R) abolished its toxicity. Further mutagenesis of the EcoPrrC nuclease domain highlighted an ensemble of 15 essential residues and distinguished between hypomorphic alleles and potential nuclease-nulls. We report that the RNA repair phase of the bacterial virus-host dynamic is also portable to yeast, where coexpression of the T4 enzymes Pnkp and Rnl1 ameliorated the toxicity of NmePrrC-R316W. Plant tRNA ligase AtRNL also countered NmePrrC-R316W toxicity, in a manner that depended on AtRNL's 5'-kinase and ligase functions.
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Affiliation(s)
- Birthe Meineke
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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6
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Meineke B, Schwer B, Schaffrath R, Shuman S. Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC. Nucleic Acids Res 2010; 39:687-700. [PMID: 20855293 PMCID: PMC3025547 DOI: 10.1093/nar/gkq831] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
tRNA damage inflicted by the Escherichia coli anticodon nuclease PrrC (EcoPrrC) underlies an antiviral response to phage T4 infection. PrrC homologs are present in many bacterial proteomes, though their biological activities are uncharted. PrrCs consist of two domains: an N-terminal NTPase module related to the ABC family and a distinctive C-terminal ribonuclease module. In this article, we report that the expression of EcoPrrC in budding yeast is fungicidal, signifying that PrrC is toxic in a eukaryon in the absence of other bacterial or viral proteins. Whereas Streptococcus PrrC is also toxic in yeast, Neisseria and Xanthomonas PrrCs are not. Via analysis of the effects of 118 mutations on EcoPrrC toxicity in yeast, we identified 22 essential residues in the NTPase domain and 11 in the nuclease domain. Overexpressing PrrCs with mutations in the NTPase active site ameliorated the toxicity of wild-type EcoPrrC. Our findings support a model in which EcoPrrC toxicity is contingent on head-to-tail dimerization of the NTPase domains to form two composite NTP phosphohydrolase sites. Comparisons of EcoPrrC activity in a variety of yeast genetic backgrounds, and the rescuing effects of tRNA overexpression, implicate tRNALys(UUU) as a target of EcoPrrC toxicity in yeast.
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Affiliation(s)
- Birthe Meineke
- Molecular Biology Program, Sloan-Kettering Institute, Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065 USA and Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Beate Schwer
- Molecular Biology Program, Sloan-Kettering Institute, Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065 USA and Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Raffael Schaffrath
- Molecular Biology Program, Sloan-Kettering Institute, Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065 USA and Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065 USA and Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
- *To whom correspondence should be addressed. Tel: +1 212 639 7145; Fax: +1 212 717 3623;
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7
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Shigematsu M, Ogawa T, Kido A, Kitamoto HK, Hidaka M, Masaki H. Cellular and transcriptional responses of yeast to the cleavage of cytosolic tRNAs induced by colicin D. Yeast 2009; 26:663-73. [PMID: 19877125 DOI: 10.1002/yea.1725] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
MESH Headings
- Base Sequence
- Cell Proliferation
- Cytosol/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Nucleic Acid Conformation
- Oligonucleotide Array Sequence Analysis
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/metabolism
- Pheromones/metabolism
- Plasmids/genetics
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
- Signal Transduction
- Transcription, Genetic
- Transformation, Genetic
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Affiliation(s)
- Megumi Shigematsu
- Department of Biotechnology, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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8
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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