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Kohno Y, Ito A, Okamoto A, Yamagami R, Hirata A, Hori H. Escherichia coli tRNA (Gm18) methyltransferase (TrmH) requires the correct localization of its methylation site (G18) in the D-loop for efficient methylation. J Biochem 2023; 175:43-56. [PMID: 37844264 DOI: 10.1093/jb/mvad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/08/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023] Open
Abstract
TrmH is a eubacterial tRNA methyltransferase responsible for formation of 2'-O-methylguaosine at position 18 (Gm18) in tRNA. In Escherichia coli cells, only 14 tRNA species possess the Gm18 modification. To investigate the substrate tRNA selection mechanism of E. coli TrmH, we performed biochemical and structural studies. Escherichia coli TrmH requires a high concentration of substrate tRNA for efficient methylation. Experiments using native tRNA SerCGA purified from a trmH gene disruptant strain showed that modified nucleosides do not affect the methylation. A gel mobility-shift assay reveals that TrmH captures tRNAs without distinguishing between relatively good and very poor substrates. Methylation assays using wild-type and mutant tRNA transcripts revealed that the location of G18 in the D-loop is very important for efficient methylation by E. coli TrmH. In the case of tRNASer, tRNATyrand tRNALeu, the D-loop structure formed by interaction with the long variable region is important. For tRNAGln, the short distance between G18 and A14 is important. Thus, our biochemical study explains all Gm18 modification patterns in E. coli tRNAs. The crystal structure of E. coli TrmH has also been solved, and the tRNA binding mode of E. coli TrmH is discussed based on the structure.
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Affiliation(s)
- Yoh Kohno
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Asako Ito
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Aya Okamoto
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Akira Hirata
- Department of Natural Science, Graduate School of Technology, Industrial and Social Science, Tokushima University, 2-1 Minamijosanjimacho, Tokushima, Tokushima 770-8506, Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate school of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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2
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Hori H. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Genes (Basel) 2023; 14:genes14020382. [PMID: 36833309 PMCID: PMC9957541 DOI: 10.3390/genes14020382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According to their enzymatic activity, THUMP-related tRNA modification enzymes can be classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase. In this review, I focus on the functions and structures of these tRNA modification enzymes and the modified nucleosides they produce. Biochemical, biophysical and structural studies of tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase have established the concept that the THUMP domain captures the 3'-end of RNA (in the case of tRNA, the CCA-terminus). However, in some cases, this concept is not simply applicable given the modification patterns observed in tRNA. Furthermore, THUMP-related proteins are involved in the maturation of other RNAs as well as tRNA. Moreover, the modified nucleosides, which are produced by the THUMP-related tRNA modification enzymes, are involved in numerous biological phenomena, and the defects of genes for human THUMP-related proteins are implicated in genetic diseases. In this review, these biological phenomena are also introduced.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
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3
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Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
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Fukuda W, Yamori Y, Hamakawa M, Osaki M, Fukuda M, Hidese R, Kanesaki Y, Okamoto-Kainuma A, Kato S, Fujiwara S. Genes regulated by branched-chain polyamine in the hyperthermophilic archaeon Thermococcus kodakarensis. Amino Acids 2019; 52:287-299. [DOI: 10.1007/s00726-019-02793-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/01/2019] [Indexed: 01/22/2023]
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Sánchez-Jiménez F, Medina MÁ, Villalobos-Rueda L, Urdiales JL. Polyamines in mammalian pathophysiology. Cell Mol Life Sci 2019; 76:3987-4008. [PMID: 31227845 PMCID: PMC11105599 DOI: 10.1007/s00018-019-03196-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 02/07/2023]
Abstract
Polyamines (PAs) are essential organic polycations for cell viability along the whole phylogenetic scale. In mammals, they are involved in the most important physiological processes: cell proliferation and viability, nutrition, fertility, as well as nervous and immune systems. Consequently, altered polyamine metabolism is involved in a series of pathologies. Due to their pathophysiological importance, PA metabolism has evolved to be a very robust metabolic module, interconnected with the other essential metabolic modules for gene expression and cell proliferation/differentiation. Two different PA sources exist for animals: PA coming from diet and endogenous synthesis. In the first section of this work, the molecular characteristics of PAs are presented as determinant of their roles in living organisms. In a second section, the metabolic specificities of mammalian PA metabolism are reviewed, as well as some obscure aspects on it. This second section includes information on mammalian cell/tissue-dependent PA-related gene expression and information on crosstalk with the other mammalian metabolic modules. The third section presents a synthesis of the physiological processes described as modulated by PAs in humans and/or experimental animal models, the molecular bases of these regulatory mechanisms known so far, as well as the most important gaps of information, which explain why knowledge around the specific roles of PAs in human physiology is still considered a "mysterious" subject. In spite of its robustness, PA metabolism can be altered under different exogenous and/or endogenous circumstances so leading to the loss of homeostasis and, therefore, to the promotion of a pathology. The available information will be summarized in the fourth section of this review. The different sections of this review also point out the lesser-known aspects of the topic. Finally, future prospects to advance on these still obscure gaps of knowledge on the roles on PAs on human physiopathology are discussed.
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Affiliation(s)
- Francisca Sánchez-Jiménez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain
- UNIT 741, CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain
| | - Miguel Ángel Medina
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain
- UNIT 741, CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain
| | - Lorena Villalobos-Rueda
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain
| | - José Luis Urdiales
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Andalucía Tech, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain.
- UNIT 741, CIBER de Enfermedades Raras (CIBERER), 29071, Málaga, Spain.
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Hidese R, Toyoda M, Yoshino KI, Fukuda W, Wihardja GA, Kimura S, Fujita J, Niitsu M, Oshima T, Imanaka T, Mizohata E, Fujiwara S. The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis. FEBS J 2019; 286:3926-3940. [PMID: 31162806 DOI: 10.1111/febs.14949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/03/2019] [Accepted: 06/01/2019] [Indexed: 01/26/2023]
Abstract
Branched-chain polyamine synthase (BpsA) catalyzes sequential aminopropyl transfer from the donor, decarboxylated S-adenosylmethionine (dcSAM), to the acceptor, linear-chain polyamine, resulting in the production of a quaternary-branched polyamine via tertiary branched polyamine intermediates. Here, we analyzed the catalytic properties and X-ray crystal structure of Tth-BpsA from Thermus thermophilus and compared them with those of Tk-BpsA from Thermococcus kodakarensis, which revealed differences in acceptor substrate specificity and C-terminal structure between these two enzymes. To investigate the role of the C-terminal flexible region in acceptor recognition, a region (QDEEATTY) in Tth-BpsA was replaced with that in Tk-BpsA (YDDEESSTT) to create chimeric Tth-BpsA C9, which showed a severe reduction in catalytic efficiency toward N4 -aminopropylnorspermidine, but not toward N4 -aminopropylspermidine, mimicking Tk-BpsA substrate specificity. Tth-BpsA C9 Tyr346 and Thr354 contributed to discrimination between tertiary branched-chain polyamine substrates, suggesting that the C-terminal region of BpsA recognizes acceptor substrates. Liquid chromatography-tandem mass spectrometry analysis on a Tk-BpsA reaction mixture with dcSAM revealed two aminopropyl groups bound to two of five aspartate/glutamate residues (Glu339 , Asp342 , Asp343 , Glu344 , and Glu345 ) in the C-terminal flexible region. Mutating each of these five amino acid residues to asparagine/glutamine resulted in a slight decrease in activity. The quadruple mutant D342N/D343N/E344Q/E345Q exhibited a severe reduction in catalytic efficiency, suggesting that these aspartate/glutamate residues function to receive aminopropyl chains. In addition, the X-ray crystal structure of the Tk-BpsA ternary complex bound to N4 -bis(aminopropyl)spermidine revealed that Asp126 and Glu259 interacted with the aminopropyl moiety in N4 -aminopropylspermidine.
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Affiliation(s)
- Ryota Hidese
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Japan
| | - Masataka Toyoda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan
| | | | - Wakao Fukuda
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Japan
| | - Gita Adhirani Wihardja
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Japan
| | - Seigo Kimura
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Japan
| | - Junso Fujita
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Masaru Niitsu
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Japan
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa-kako Co., Ltd, Machida, Japan
| | - Tadayuki Imanaka
- The Research Organization of Science & Technology, Ritsumeikan University, Kusatsu, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Japan
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7
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Hori H. Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus. Front Genet 2019; 10:204. [PMID: 30906314 PMCID: PMC6418473 DOI: 10.3389/fgene.2019.00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023] Open
Abstract
Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50-83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Sciences and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
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8
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RNA Modifications Modulate Activation of Innate Toll-Like Receptors. Genes (Basel) 2019; 10:genes10020092. [PMID: 30699960 PMCID: PMC6410116 DOI: 10.3390/genes10020092] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
Self/foreign discrimination by the innate immune system depends on receptors that identify molecular patterns as associated to pathogens. Among others, this group includes endosomal Toll-like receptors, among which Toll-like receptors (TLR) 3, 7, 8, and 13 recognize and discriminate mammalian from microbial, potentially pathogen-associated, RNA. One of the discriminatory principles is the recognition of endogenous RNA modifications. Previous work has identified a couple of RNA modifications that impede activation of TLR signaling when incorporated in synthetic RNA molecules. Of note, work that is more recent has now shown that RNA modifications in their naturally occurring context can have immune-modulatory functions: Gm, a naturally occurring ribose-methylation within tRNA resulted in a lack of TLR7 stimulation and within a defined sequence context acted as antagonist. Additional RNA modifications with immune-modulatory functions have now been identified and recent work also indicates that RNA modifications within the context of whole prokaryotic or eukaryotic cells are indeed used for immune-modulation. This review will discuss new findings and developments in the field of immune-modulatory RNA modifications.
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Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A. Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA. Microorganisms 2018; 6:E110. [PMID: 30347855 PMCID: PMC6313347 DOI: 10.3390/microorganisms6040110] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022] Open
Abstract
To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takuya Kawamura
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Takako Awai
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
| | - Akira Hirata
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan.
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10
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Terui Y, Yoshida T, Sakamoto A, Saito D, Oshima T, Kawazoe M, Yokoyama S, Igarashi K, Kashiwagi K. Polyamines protect nucleic acids against depurination. Int J Biochem Cell Biol 2018; 99:147-153. [PMID: 29649565 DOI: 10.1016/j.biocel.2018.04.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/21/2018] [Accepted: 04/06/2018] [Indexed: 11/20/2022]
Abstract
Depurination is accelerated by heat and reactive oxygen species under physiological conditions. We previously reported that polyamines are involved in mitigation of heat shock and oxidative stresses through stimulation of the synthesis of heat shock and antioxidant proteins. This time, we investigated whether polyamines are directly involved in protecting nucleic acids from thermal depurination induced by high temperature. The suppressing efficiencies of depurination of DNA by spermine, caldopentamine and caldohexamine in the presence of 1 mM Mg2+, were approximately 50%, 60% and 80%, respectively. Mg2+ also protected nucleic acids against depurination but to a lesser degree than polyamines. Longer unusual polyamines were more effective at protecting DNA against depurination compared to standard polyamines. The tRNA depurination suppressing efficiencies of spermine, caldopentamine and caldohexamine in the presence of 1 mM Mg2+, were approximately 60%, 70% and 80%, respectively. Standard polyamines protected tRNA and ribosomes more effectively than DNA against thermal depurination. Branched polyamines such as mitsubishine and tetrakis(3-aminopropyl)ammonium also protected RNA more effectively than DNA against depurination. These results suggest that the suppressing effect of depurination of nucleic acids (DNA and RNA) depends on the types of polyamines: i.e. to maintain functional conformation of nucleic acids at high temperature, longer and branched polyamines play important roles in protecting nucleic acids from depurination compared to standard polyamines and Mg2+.
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Affiliation(s)
- Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan.
| | - Taketo Yoshida
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan
| | - Akihiko Sakamoto
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan
| | | | - Tairo Oshima
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | | | | | - Kazuei Igarashi
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Keiko Kashiwagi
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan.
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11
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Hidese R, Tse KM, Kimura S, Mizohata E, Fujita J, Horai Y, Umezawa N, Higuchi T, Niitsu M, Oshima T, Imanaka T, Inoue T, Fujiwara S. Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine. FEBS J 2017; 284:3684-3701. [DOI: 10.1111/febs.14262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Ryota Hidese
- Department of Bioscience; Graduate School of Science and Technology; Kwansei-Gakuin University; Sanda Japan
| | - Ka Man Tse
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita Japan
| | - Seigo Kimura
- Department of Bioscience; Graduate School of Science and Technology; Kwansei-Gakuin University; Sanda Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita Japan
| | - Junso Fujita
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita Japan
| | - Yuhei Horai
- Department of Bioorganic-inorganic Chemistry; Graduate School of Pharmaceutical Sciences; Nagoya City University; Japan
| | - Naoki Umezawa
- Department of Bioorganic-inorganic Chemistry; Graduate School of Pharmaceutical Sciences; Nagoya City University; Japan
| | - Tsunehiko Higuchi
- Department of Bioorganic-inorganic Chemistry; Graduate School of Pharmaceutical Sciences; Nagoya City University; Japan
| | - Masaru Niitsu
- Faculty of Pharmacy and Pharmaceutical Sciences; Josai University; Sakado Japan
| | - Tairo Oshima
- Institute of Environmental Microbiology; Kyowa-kako Co. Ltd.; Machida Japan
| | - Tadayuki Imanaka
- The Research Organization of Science & Technology; Ritsumeikan University; Kusatsu Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry; Graduate School of Engineering; Osaka University; Suita Japan
| | - Shinsuke Fujiwara
- Department of Bioscience; Graduate School of Science and Technology; Kwansei-Gakuin University; Sanda Japan
- Research Center for Intelligent Bio-Materials; Graduate School of Science and Technology; Kwansei-Gakuin University; Sanda Japan
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12
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Nakashima M, Yamagami R, Tomikawa C, Ochi Y, Moriya T, Asahara H, Fourmy D, Yoshizawa S, Oshima T, Hori H. Long and branched polyamines are required for maintenance of the ribosome, tRNAHisand tRNATyrinThermus thermophiluscells at high temperatures. Genes Cells 2017; 22:628-645. [DOI: 10.1111/gtc.12502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Misa Nakashima
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Ryota Yamagami
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Chie Tomikawa
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Yuki Ochi
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
| | - Toshiyuki Moriya
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 Japan
| | - Haruichi Asahara
- New England Biolabs, Inc; 240 County Road Ipswich Massachusetts 01938 USA
| | - Dominique Fourmy
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Satoko Yoshizawa
- Institute for Integrative Biology of the Cell (I2BC); CEA, CNRS; Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Tairo Oshima
- Institute of Environmental Microbiology; Kyowa Kako Co. Ltd.; Tadao 2-15-5 Machida 194-0035 Japan
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology; Graduate School of Science and Engineering; Ehime University; 3 Bunkyo-cho Matsuyama Ehime 790-8577 Japan
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13
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Acosta-Andrade C, Artetxe I, Lete MG, Monasterio BG, Ruiz-Mirazo K, Goñi FM, Sánchez-Jiménez F. Polyamine-RNA-membrane interactions: From the past to the future in biology. Colloids Surf B Biointerfaces 2017; 155:173-181. [PMID: 28456048 DOI: 10.1016/j.colsurfb.2017.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 03/12/2017] [Accepted: 04/04/2017] [Indexed: 01/06/2023]
Abstract
Biogenic polyamines (PAs), spermine, spermidine and putrescine are widely spread amino acid derivatives, present in living cells throughout the whole evolutionary scale. Their amino groups confer them a marked basic character at the cellular pH. We have tested the interaction of PAs with negatively-charged phospholipids in the absence and presence of nucleic acids (tRNA was mainly used for practical reasons). PAs induced aggregation of lipid vesicles containing acidic phospholipids. Aggregation was detected using both spectroscopic and fluorescence microscopy methods (the latter with giant unilamellar vesicles). PA-liposome complexes were partially disaggregated when nucleic acids were added to the mixture, indicating a competition between lipids and nucleic acids for PAs in a multiple equilibrium phenomenon. Equivalent observations could be made when vesicles composed of oleic acid and 1-decanol (1:1mol ratio) were used instead of phospholipid liposomes. The data could evoke putative primitive processes of proto-biotic evolution. At the other end of the time scale, this system may be at the basis of an interesting tool in the development of nanoscale drug delivery.
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Affiliation(s)
- Carlos Acosta-Andrade
- Department of Molecular Biology and Biochemistry, University of Malaga, and Unit 741 of CIBER de Enfermedades Raras, Málaga, Spain
| | - Ibai Artetxe
- Biofisika Institute (CSIC, UPV/EHU), and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
| | - Marta G Lete
- Biofisika Institute (CSIC, UPV/EHU), and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
| | - Bingen G Monasterio
- Biofisika Institute (CSIC, UPV/EHU), and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain; Department of Logic and Philosophy of Science, University of the Basque Country, Donostia, Spain
| | - Félix M Goñi
- Biofisika Institute (CSIC, UPV/EHU), and Department of Biochemistry, University of the Basque Country, 48940 Leioa, Spain
| | - Francisca Sánchez-Jiménez
- Department of Molecular Biology and Biochemistry, University of Malaga, and Unit 741 of CIBER de Enfermedades Raras, Málaga, Spain.
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Lorenz C, Lünse CE, Mörl M. tRNA Modifications: Impact on Structure and Thermal Adaptation. Biomolecules 2017; 7:E35. [PMID: 28375166 PMCID: PMC5485724 DOI: 10.3390/biom7020035] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/27/2022] Open
Abstract
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots-the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.
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Affiliation(s)
- Christian Lorenz
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Christina E Lünse
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Mario Mörl
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
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