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Caro-Astorga J, Meyerowitz JT, Stork DA, Nattermann U, Piszkiewicz S, Vimercati L, Schwendner P, Hocher A, Cockell C, DeBenedictis E. Polyextremophile engineering: a review of organisms that push the limits of life. Front Microbiol 2024; 15:1341701. [PMID: 38903795 PMCID: PMC11188471 DOI: 10.3389/fmicb.2024.1341701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/16/2024] [Indexed: 06/22/2024] Open
Abstract
Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not "find a way"? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biology's efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents.
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Affiliation(s)
| | | | - Devon A. Stork
- Pioneer Research Laboratories, San Francisco, CA, United States
| | - Una Nattermann
- Pioneer Research Laboratories, San Francisco, CA, United States
| | | | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | | | - Antoine Hocher
- London Institute of Medical Sciences, London, United Kingdom
| | - Charles Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Erika DeBenedictis
- The Francis Crick Institute, London, United Kingdom
- Pioneer Research Laboratories, San Francisco, CA, United States
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2
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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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3
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Kobayashi T, Sakamoto A, Hisano T, Kashiwagi K, Igarashi K, Takao K, Uemura T, Furuchi T, Sugita Y, Moriya T, Oshima T, Terui Y. Caldomycin, a new guanidopolyamine produced by a novel agmatine homocoupling enzyme involved in homospermidine biosynthesis. Sci Rep 2024; 14:7566. [PMID: 38555406 PMCID: PMC10981699 DOI: 10.1038/s41598-024-58296-0] [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: 12/06/2023] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
An extreme thermophilic bacterium, Thermus thermophilus produces more than 20 unusual polyamines, but their biosynthetic pathways, including homospermidine, are not yet fully understood. Two types of homospermidine synthases have been identified in plants and bacteria, which use spermidine and putrescine or two molecules of putrescine as substrates. However, homospermidine synthases with such substrate specificity have not been identified in T. thermophilus. Here we identified a novel agmatine homocoupling enzyme that is involved in homospermidine biosynthesis in T. thermophilus. The reaction mechanism is different from that of a previously described homospermidine synthase, and involves conjugation of two molecules of agmatine, which produces a diamidino derivative of homospermidine (caldomycin) as an immediate precursor of homospermidine. We conclude that there is a homospermidine biosynthetic pathway from agmatine via caldomycin synthase followed by ureohydrolase in T. thermophilus. Furthermore, it is shown that caldomycin is a novel compound existing in nature.
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Affiliation(s)
- Teruyuki Kobayashi
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Akihiko Sakamoto
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
- Department of Pathophysiology and Therapeutics, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Shinagawa, Tokyo, Japan
| | - Tamao Hisano
- RIKEN Center for Biosystems Dynamics Research (BDR), Tsurumi, Kanagawa, Japan
| | - Keiko Kashiwagi
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan
| | - Kazuei Igarashi
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba, Japan
| | - Koichi Takao
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Takeshi Uemura
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Takemitsu Furuchi
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Yoshiaki Sugita
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, Japan
| | - Toshiyuki Moriya
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | - Tairo Oshima
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba, 288-0025, Japan.
- School of Pharmacy, International University of Health and Welfare, Otawara, Tochigi, Japan.
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4
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Takemata N. How Do Thermophiles Organize Their Genomes? Microbes Environ 2024; 39:n/a. [PMID: 38839371 DOI: 10.1264/jsme2.me23087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
All cells must maintain the structural and functional integrity of the genome under a wide range of environments. High temperatures pose a formidable challenge to cells by denaturing the DNA double helix, causing chemical damage to DNA, and increasing the random thermal motion of chromosomes. Thermophiles, predominantly classified as bacteria or archaea, exhibit an exceptional capacity to mitigate these detrimental effects and prosper under extreme thermal conditions, with some species tolerating temperatures higher than 100°C. Their genomes are mainly characterized by the presence of reverse gyrase, a unique topoisomerase that introduces positive supercoils into DNA. This enzyme has been suggested to maintain the genome integrity of thermophiles by limiting DNA melting and mediating DNA repair. Previous studies provided significant insights into the mechanisms by which NAPs, histones, SMC superfamily proteins, and polyamines affect the 3D genomes of thermophiles across different scales. Here, I discuss current knowledge of the genome organization in thermophiles and pertinent research questions for future investigations.
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Affiliation(s)
- Naomichi Takemata
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
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5
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Kim S, Chang JH. Structural Analysis of Spermidine Synthase from Kluyveromyces lactis. Molecules 2023; 28:molecules28083446. [PMID: 37110680 PMCID: PMC10146546 DOI: 10.3390/molecules28083446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Spermidine is a polyamine molecule that performs various cellular functions, such as DNA and RNA stabilization, autophagy modulation, and eIF5A formation, and is generated from putrescine by aminopropyltransferase spermidine synthase (SpdS). During synthesis, the aminopropyl moiety is donated from decarboxylated S-adenosylmethionine to form putrescine, with 5'-deoxy-5'-methylthioadenosine being produced as a byproduct. Although the molecular mechanism of SpdS function has been well-established, its structure-based evolutionary relationships remain to be fully understood. Moreover, only a few structural studies have been conducted on SpdS from fungal species. Here, we determined the crystal structure of an apo-form of SpdS from Kluyveromyces lactis (KlSpdS) at 1.9 Å resolution. Structural comparison with its homologs revealed a conformational change in the α6 helix linked to the gate-keeping loop, with approximately 40° outward rotation. This change caused the catalytic residue Asp170 to move outward, possibly due to the absence of a ligand in the active site. These findings improve our understanding of the structural diversity of SpdS and provide a missing link that expands our knowledge of the structural features of SpdS in fungal species.
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Affiliation(s)
- Seongjin Kim
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Department of Biomedical Convergence Science and Technology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Science Education Research Institute, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2023; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam
- Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
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7
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Alkaline Stress Causes Changes in Polyamine Biosynthesis in Thermus thermophilus. Int J Mol Sci 2022; 23:ijms232113523. [DOI: 10.3390/ijms232113523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022] Open
Abstract
An extreme thermophile, Thermus thermophilus, produces 16 different polyamines including long-chain and branched-chain polyamines. The composition and content of polyamines in the thermophile cells change not only with growth temperature but also with pH changes. In particular, cell growth decreased greatly at alkaline medium together with significant changes in the composition and content of polyamines. The amounts of tetraamines (spermine and its homologs) markedly decreased at alkaline pH. Thus, we knocked out the speE gene, which is involved in the biosynthesis of tetraamines, and changes of composition of polyamines with pH changes in the mutant cells were studied. Cell growth in the ΔspeE strain was decreased compared with that of the wild-type strain for all pHs, suggesting that tetraamines are important for cell proliferation. Interestingly, the amount of spermidine decreased and that of putrescine increased in wild-type cells at elevated pH, although T. thermophilus lacks a putrescine synthesizing pathway. In addition, polyamines possessing a diaminobutane moiety, such as spermine, decreased greatly at high pH. We assessed whether the speB gene encoding aminopropylagmatine ureohydrolase (TtSpeB) is directly involved in the synthesis of putrescine. The catalytic assay of the purified enzyme indicated that TtSpeB accepts agmatine as its substrate and produces putrescine due to the change in substrate specificity at high pH. These results suggest that pH stress was exacerbated upon intracellular depletion of polyamines possessing a diaminobutane moiety induced by unusual changes in polyamine biosynthesis under high pH conditions.
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Immobilization of a Broad Range of Polypeptides on the Frustule of the Diatom Thalassiosira pseudonana. Appl Environ Microbiol 2022; 88:e0115322. [PMID: 36226967 PMCID: PMC9642022 DOI: 10.1128/aem.01153-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. One recently developed technique, living diatom silica immobilization (LiDSI), has made it possible to immobilize proteins, including multimeric and redox enzymes, via a cellular excretion system onto the silica frustule of the marine diatom Thalassiosira pseudonana. However, the number of application examples so far is limited, and the type of proteins appropriate for the technique is still enigmatic. Here, we applied LiDSI to six industrially relevant polypeptides, including protamine, metallothionein, phosphotriesterase, choline oxidase, laccase, and polyamine synthase. Protamine and metallothionein were successfully immobilized on the frustule as protein fusions with green fluorescent protein (GFP) at the N terminus, indicating that LiDSI can be used for polypeptides which are rich in arginine and cysteine. In contrast, we obtained mutants for the latter four enzymes in forms without green fluorescent protein. Immobilized phosphotriesterase, choline oxidase, and laccase showed enzyme activities even after the purification of frustule in the presence of 1% (wt/vol) octylphenoxy poly(ethyleneoxy)ethanol. An immobilized branched-chain polyamine synthase changed the intracellular polyamine composition and silica nanomorphology. These results illustrate the possibility of LiDSI for industrial applications. IMPORTANCE Proteins immobilized on biosilica which have superior reactivity and specificity and are innocuous to natural environments could be useful biological materials in industrial processes. Living diatom silica immobilization (LiDSI) is a recently developed technique for in vivo protein immobilization on the diatom frustule. We aimed to explore the possibility of using LiDSI for industrial applications by successfully immobilizing six polypeptides: (i) protamine (Oncorhynchus keta), a stable antibacterial agent; (ii) metallothionein (Saccharomyces cerevisiae), a metal adsorption molecule useful for bioremediation; (iii) phosphotriesterase (Sulfolobus solfataricus), a scavenger for toxic organic phosphates; (iv) choline oxidase (Arthrobacter globiformis), an enhancer for photosynthetic activity and yield of plants; (v) laccase (Bacillus subtilis), a phenol oxidase utilized for delignification of lignocellulosic materials; and (vi) branched-chain polyamine synthase (Thermococcus kodakarensis), which produces branched-chain polyamines important for DNA and RNA stabilization at high temperatures. This study provides new insights into the field of applied biological materials.
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9
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Sakamoto A, Tamakoshi M, Moriya T, Oshima T, Takao K, Sugita Y, Furuchi T, Niitsu M, Uemura T, Igarashi K, Kashiwagi K, Terui Y. Polyamines produced by an extreme thermophile are essential for cell growth at high temperature. J Biochem 2022; 172:109-115. [PMID: 35639548 DOI: 10.1093/jb/mvac048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
An extreme thermophile, Thermus thermophilus grows at an optimum temperature of around 70 oC and produces 16 different polyamines including long-chain and branched-chain polyamines. We found that the composition of polyamines in the thermophile cells changes with culture temperature. Long-chain and branched-chain polyamines (unusual polyamines) were increased in the cells grown at high temperature such as 80 oC, but they were minor components in the cells grown at relatively lower temperature such as 60 oC. The effects of polyamines on cell growth were studied using T. thermophilus HB8 ΔspeA deficient in arginine decarboxylase. Cell growth of this mutant strain was significantly decreased at 70 oC. This mutant strain cannot produce polyamines and grows poorly at 75 oC. It was also determined whether polyamines are directly involved in protecting DNA from DNA double-strand breaks induced by heat. Polyamines protected DNA against double-strand breaks. Therefore, polyamines play essential roles in cell growth at extremely high temperature through maintaining a functional conformation of DNA against DNA double-strand breaks and depurination.
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Affiliation(s)
- Akihiko Sakamoto
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba 288-0025, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0302, Japan
| | - Toshiyuki Moriya
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo 194-0035, Japan
| | - Tairo Oshima
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo 194-0035, Japan
| | - Koichi Takao
- Department of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0295, Japan
| | - Yoshiaki Sugita
- Department of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0295, Japan
| | - Takemitsu Furuchi
- Department of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0295, Japan
| | - Masaru Niitsu
- Department of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0295, Japan
| | - Takeshi Uemura
- Department of Pharmaceutical Sciences, Josai University, Sakado, Saitama 350-0295, Japan
| | - Kazuei Igarashi
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba 260-0856, Japan.,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Keiko Kashiwagi
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba 288-0025, Japan
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba 288-0025, Japan
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10
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Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis. Catalysts 2022. [DOI: 10.3390/catal12050567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The facultative anaerobic hyperthermophilic crenarchaeon Pyrobaculum calidifontis possesses norspermine (333), norspermidine (33), and spermidine (34) as intracellular polyamines (where the number in parentheses represents the number of methylene CH2 chain units between NH2, or NH). In this study, the polyamine biosynthesis pathway of P. calidifontis was predicted on the basis of the enzymatic properties and crystal structures of an aminopropyltransferase from P. calidifontis (Pc-SpeE). Pc-SpeE shared 75% amino acid identity with the thermospermine synthase from Pyrobaculum aerophilum, and recombinant Pc-SpeE could synthesize both thermospermine (334) and spermine (343) from spermidine and decarboxylated S-adenosyl methionine (dcSAM). Recombinant Pc-SpeE showed high enzymatic activity when aminopropylagmatine and norspermidine were used as substrates. By comparison, Pc-SpeE showed low affinity toward putrescine, and putrescine was not stably bound in its active site. Norspermidine was produced from thermospermine by oxidative degradation using a cell-free extract of P. calidifontis, whereas 1,3-diaminopropane (3) formation was not detected. These results suggest that thermospermine was mainly produced from arginine via agmatine, aminopropylagmatine, and spermidine. Norspermidine was produced from thermospermine by an unknown polyamine oxidase/dehydrogenase followed by norspermine formation by Pc-SpeE.
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11
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Ma C, Zeng W, Meng Q, Wang C, Peng Y. Identification of partial denitrification granulation enhanced by low C/N ratio in the aspect of metabolomics and quorum sensing. CHEMOSPHERE 2022; 286:131895. [PMID: 34435576 DOI: 10.1016/j.chemosphere.2021.131895] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/18/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Partial denitrification granular sludge (PDGS) and denitrification granular sludge (DGS) play an important role in nitrogen removal from wastewater. However, the inherent cause of aggregation capacity related to the ratio of COD to nitrogen (COD/N) is still unclear. In this study, metabolomics analysis was combined with microbiological analyses, granular performance and extracellular polymeric substances (EPS) structure to explore the granulation mechanism at different influent COD/N ratios. The results showed that the higher COD/N ratio selectively enhanced the gluconeogenesis pathway, purine and pyrimidine metabolism pathway, resulting in more extracellular polysaccharide (PS) excretion and floc sludge. The absence of carbon source weakened tricarboxylic acid cycle (TCA) reaction, resulting in NAD+ and ADP decrease, nitrite accumulation and change of microbial community structure. The amino acids biosynthesis pathway was enhanced under low COD/N ratio, which promoted the hydrophobicity of EPS. PDGS had stronger Acyl-homoserine lactones (AHLs)-based quorum sensing (QS) than DGS during the operational period. CO8-HSL, C8-HSL and C6-HSL, as the main form of AHLs, played a dominating role in DGS and PDGS. Batch tests illustrated that adding AHLs obviously improved the synthesis of the amino acids, threonine (Thr), tryptophan (Trp), methionine (Met) and glycine (Gly). Dosing AHLs regulated PS synthesis only at a high COD/N ratio. The glucose-6P, glycerate-3p and UDP-Glc were up-regulated only in DSG, which increased the hydrophilic groups in EPS. The results not only provided the new insights into the metabolism of denitrifying granular sludge, but also indicated the application potential of the technologies regarding start-up and operation of granule sludge.
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Affiliation(s)
- Chenyang Ma
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Wei Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing, 100124, China.
| | - Qingan Meng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Chunyan Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing, 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing, 100124, China
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12
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Freudenberg RA, Baier T, Einhaus A, Wobbe L, Kruse O. High cell density cultivation enables efficient and sustainable recombinant polyamine production in the microalga Chlamydomonas reinhardtii. BIORESOURCE TECHNOLOGY 2021; 323:124542. [PMID: 33385626 DOI: 10.1016/j.biortech.2020.124542] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 05/27/2023]
Abstract
Modern chemical industry calls for new resource-efficient and sustainable value chains for production of key base chemicals such as polyamines. The green microalga Chlamydomonas reinhardtii offers great potential as an innovative green-cell factory by combining fast and inexpensive, phototrophic growth with mature genetic engineering. Here, overexpression of recombinant lysine decarboxylases in C. reinhardtii enabled the robust accumulation of the non-native polyamine cadaverine, which serves as building block for bio-polyamides. The issue of low cell densities, limiting most microalgal cultivation processes was resolved by systematically optimizing cultivation parameters. A new, easy-to-apply and fully phototrophic medium enables high cell density cultivations of C. reinhardtii with a 6-fold increase in biomass and cell count (20 g/L biomass dry weight, ~2·108 cells/mL). Application of high cell density cultivations in established photobioreactors resulted in a 10-fold increase of cadaverine yields, with up to 0.24 g/L after 9 days and maximal productivity of 0.1 g/L/d.
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Affiliation(s)
- Robert A Freudenberg
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Alexander Einhaus
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Lutz Wobbe
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany.
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13
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Kitagawa T, Nishio T, Yoshikawa Y, Umezawa N, Higuchi T, Shew CY, Kenmotsu T, Yoshikawa K. Effects of Structural Isomers of Spermine on the Higher-Order Structure of DNA and Gene Expression. Int J Mol Sci 2021; 22:ijms22052355. [PMID: 33652986 PMCID: PMC7956460 DOI: 10.3390/ijms22052355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers on the activity of gene expression by adapting a cell-free luciferase assay. Interestingly, the potency of their effects on the DNA conformation and also on the inhibition of gene expression activity indicates the highest for TSPM among spermine isomers. A numerical evaluation of the strength of the interaction of these polyamines with negatively charged double-strand DNA revealed that this ordering of the potency corresponds to the order of the strength of the attractive interaction between phosphate groups of DNA and positively charged amino groups of the polyamines.
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Affiliation(s)
- Tomoki Kitagawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Takashi Nishio
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Yuko Yoshikawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan; (N.U.); (T.H.)
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan; (N.U.); (T.H.)
| | - Chwen-Yang Shew
- Doctoral Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA;
- Department of Chemistry, College of Staten Island, Staten Island, New York, NY 10314, USA
| | - Takahiro Kenmotsu
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
- Correspondence: (T.K.); (K.Y.)
| | - Kenichi Yoshikawa
- Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan; (T.K.); (T.N.); (Y.Y.)
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (T.K.); (K.Y.)
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14
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Ito D, Ge D, Kogure N, Manaka H, Terui Y, Takayama H, Linhardt RJ, Toida T, Higashi K. Poly-ion complex (PIC) formation of heparin and polyamines: PIC with tetrakis (3-aminopropyl) ammonium allows sustained release of heparin. Heliyon 2020; 6:e05168. [PMID: 33043161 PMCID: PMC7538075 DOI: 10.1016/j.heliyon.2020.e05168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/04/2020] [Accepted: 10/01/2020] [Indexed: 01/29/2023] Open
Abstract
Physical mixtures of cationic polymers and heparin have been developed to overcome the limitations of unfractionated heparin. In this study, we found that heparin associates with natural polyamines in water, resulting in the generation of a poly-ion complex (PIC). PIC formation (or stability) was influenced by the concentration and ratio of heparin and polyamines, molecular weight of heparin, nature of polyamines, and pH conditions. Interestingly, the PIC obtained when heparin and tetrakis (3-aminopropyl) ammonium (Taa) were mixed exhibited stability and was sticky in nature. PIC formation was due to an electrostatic interaction between heparin and Taa. Heparin-Taa PIC was administered subcutaneously to mice, and the time to maximum heparin concentration within the therapeutic range of heparin was markedly increased compared to that after a single dose of heparin. These results suggest that the quaternary ammonium structure of Taa is critical for the preparation of a stable PIC, thereby allowing the sustained release of heparin into the blood.
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Affiliation(s)
- Daichi Ito
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Dan Ge
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Noriyuki Kogure
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Hitomi Manaka
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba 288-0025, Japan
| | - Hiromitsu Takayama
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Robert J. Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 121806, United States
| | - Toshihiko Toida
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kyohei Higashi
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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15
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Golbedaghi R, Tabanez AM, Esmaeili S, Fausto R. Biological Applications of Macrocyclic Schiff Base Ligands and Their Metal Complexes: A Survey of the Literature (2005–2019). Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5884] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reza Golbedaghi
- Chemistry Department Payame Noor University Tehran 19395‐4697 Iran
- University of Coimbra CQC, Department of Chemistry Coimbra P‐3004‐535 Portugal
| | - Andreia M. Tabanez
- University of Coimbra CQC, Department of Chemistry Coimbra P‐3004‐535 Portugal
| | - Somayeh Esmaeili
- Internal Medicine Department Shahid Beheshti University of Medical Sciences Tehran Iran
| | - Rui Fausto
- University of Coimbra CQC, Department of Chemistry Coimbra P‐3004‐535 Portugal
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16
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Keller C, Chattopadhyay M, Tabor H. Absolute requirement for polyamines for growth of Escherichia coli mutants (mnmE/G) defective in modification of the wobble anticodon of transfer-RNA. FEMS Microbiol Lett 2020; 366:5511269. [PMID: 31162608 DOI: 10.1093/femsle/fnz110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/29/2019] [Indexed: 01/31/2023] Open
Abstract
The genes mnmE and mnmG are responsible for the modification of uridine 34, 'the wobble position' of many aminoacyl-tRNAs. Deletion of these genes affects the strength of the codon-anticodon interactions of the aminoacyl-tRNAs with the mRNAs and the ribosomes. However, deletion of these genes does not usually have a significant effect on the growth rate of the standard Escherichia coli strains. In contrast, we have found that if the host E. coli strain is deficient in the synthesis of polyamines, deletion of the mnmE or mnmG gene results in complete inhibition of growth unless the medium contains polyamines. The finding of an absolute requirement for polyamines in our current work will be significant in studies on polyamine function, in studies on the function of the mnmE/G genes, and in studies on the role of aminoacyl-tRNAs in protein biosynthesis.
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Affiliation(s)
- Christopher Keller
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland, USA 20892-0830
| | - Manas Chattopadhyay
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland, USA 20892-0830
| | - Herbert Tabor
- Laboratory of Biochemistry and Genetics, NIDDK, National Institutes of Health, Bethesda, Maryland, USA 20892-0830
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17
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Mohammadi M, Shareghi B, Akbar Saboury A. Comparative studies on the interaction of spermidine with carboxypeptidase A using multispectroscopic and docking methods. Int J Biol Macromol 2020; 147:821-831. [PMID: 31751718 DOI: 10.1016/j.ijbiomac.2019.09.242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 10/25/2022]
Abstract
Carboxypeptidase A (CPA) (EC 3.4.17.1) is one of the main members of the M14 family that release one amino acid from the C-terminal region of the polypeptides at each time. The purpose of the present study was to study the effect of spermidine (NH2(CH2)3NH(CH2)4NH2) on the conformation, thermal stability, and activity of native CPA from bovine pancreas, by employing ultraviolet-visible (UV-Vis) spectroscopy, intrinsic fluorescence, thermal stability, circular dichroism (CD), kinetic techniques and molecular docking. It was found that the decrease in the CPA, UV-Vis absorption could be due to the formation of the CPA-spermidine complexes. The results of fluorescence spectroscopic measurements at the temperatures of 308 and 318 K also revealed that spermidine had the capability to quench the intrinsic fluorescence of CPA with the static mode. Further, the thermodynamic parameters, (Gibbs free-energy, enthalpy and entropy changes) showed that the binding process of spermidine to CPA was spontaneous and the main force in stabilizing the complex was the van der Waals and hydrogen interactions, along with the molecular docking results. In addition, CD spectra and fluorescence results revealed that spermidine had a partial effect on the CPA structure, leading to some changes in its secondary structure. The Tm studies of the CPA-spermidine complex also indicated that the Tm values were enhanced with increasing the spermidine concentration. Kinetic studies further showed that by spermidine binding, the Vmax value and activity of the enzyme were increased.
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Affiliation(s)
- Mozhgan Mohammadi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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18
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Agostinelli E. Biochemical and pathophysiological properties of polyamines. Amino Acids 2020; 52:111-117. [PMID: 32072296 DOI: 10.1007/s00726-020-02821-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Enzo Agostinelli
- Department of Biochemical Sciences, A. Rossi Fanelli', Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy. .,International Polyamines Foundation 'ETS-ONLUS', Via del Forte Tiburtino 98, 00159, Rome, Italy.
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19
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Esumi M, Sakurai S, Tanaka M. The effect of spermidine on guanine decomposition via photoinduced electron transfer in DNA. Org Biomol Chem 2020; 18:47-51. [DOI: 10.1039/c9ob01860c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of spermidine caused the attenuation of guanine decomposition via photoinduced electron transfer in pyrene-modified DNA, and higher added concentrations of spermidine resulted in the promotion of decomposition in condensed DNA.
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Affiliation(s)
- Mayu Esumi
- Department of Engineering Science
- Graduate School of Informatics and Engineering
- The University of Electro-Communications
- Chofu
- Japan
| | - Shunsuke Sakurai
- Department of Engineering Science
- Graduate School of Informatics and Engineering
- The University of Electro-Communications
- Chofu
- Japan
| | - Makiko Tanaka
- Department of Engineering Science
- Graduate School of Informatics and Engineering
- The University of Electro-Communications
- Chofu
- Japan
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20
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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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21
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Orita I, Futatsuishi R, Adachi K, Ohira T, Kaneko A, Minowa K, Suzuki M, Tamura T, Nakamura S, Imanaka T, Suzuki T, Fukui T. Random mutagenesis of a hyperthermophilic archaeon identified tRNA modifications associated with cellular hyperthermotolerance. Nucleic Acids Res 2019; 47:1964-1976. [PMID: 30605516 PMCID: PMC6393311 DOI: 10.1093/nar/gky1313] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 12/05/2018] [Accepted: 12/22/2018] [Indexed: 12/20/2022] Open
Abstract
Random mutagenesis for the hyperthermophilic archaeon Thermococcus kodakarensis was established by the insertion of an artificial transposon designed to allow easy identification of the transposon-inserted locus. The phenotypic screening was applied for the isolation of thermosensitive mutants of T. kodakarensis, which resulted in the isolation of 16 mutants showing defective growth at the supraoptimal temperature 93°C. The high occurrence of the mutants suggested that the high thermotolerance of hyperthermophiles was achieved by a combination of diverse gene functions. The transposon insertion sites in two-thirds of the mutants were identified in a group of genes responsible for tRNA modifications including 7-formamidino-7-deaza-guanosine (archaeosine), N1-methyladenosine/N1-methylinosine, N4-acetylcytidine, and N2-dimethylguanosine/N2,N2-dimethylguanosine. LC–MS/MS analyses of tRNA nucleosides and fragments exhibited disappearance of the corresponding modifications in the mutants. The melting temperature of total tRNA fraction isolated from the mutants lacking archaeosine or N1-methyladenosine/N1-methylinosine decreased significantly, suggesting that the thermosensitive phenotype of these mutants was attributed to low stability of the hypomodified tRNAs. Genes for metabolism, transporters, and hypothetical proteins were also identified in the thermosensitive mutants. The present results demonstrated the usefulness of random mutagenesis for the studies on the hyperthermophile, as well as crucial roles of tRNA modifications in cellular thermotolerance.
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Affiliation(s)
- Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Ryohei Futatsuishi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Kyoko Adachi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akira Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Keiichi Minowa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Miho Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Takeshi Tamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
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22
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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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23
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Branched-chain polyamine stabilizes RNA polymerase at elevated temperatures in hyperthermophiles. Amino Acids 2019; 52:275-285. [PMID: 31101997 DOI: 10.1007/s00726-019-02745-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 05/10/2019] [Indexed: 10/26/2022]
Abstract
Branched-chain polyamines (BCPAs) are unique polycations found in (hyper)thermophiles. Thermococcus kodakarensis grows optimally at 85 °C and produces the BCPA N4-bis(aminopropyl)spermidine by sequential addition of decarboxylated S-adenosylmethionine (dcSAM) aminopropyl groups to spermidine (SPD) by BCPA synthase A (BpsA). The T. kodakarensis bpsA deletion mutant (DBP1) did not grow at temperatures at or above 93 °C, and grew at 90 °C only after a long lag period following accumulation of excess cytoplasmic SPD. This suggests that BCPA plays an essential role in cell growth at higher temperatures and raises the possibility that BCPA is involved in controlling gene expression. To examine the effects of BCPA on transcription, the RNA polymerase (RNAP) core fraction was extracted from another bpsA deletion mutant, DBP4 (RNAPDBP4), which carried a His-tagged rpoL, and its enzymatic properties were compared with those of RNAP from wild-type (WT) cells (RNAPWT). LC-MS analysis revealed that nine ribosomal proteins were detected from RNAPWT but only one form RNAPDBP4. These results suggest that BCPA increases the linkage between RNAP and ribosomes to achieve efficient coupling of transcription and translation. Both RNAPs exhibited highest transcription activity in vitro at 80 °C, but the specific activity of RNAPDBP4 was lower than that of RNAPWT. Upon addition of SPD and BCPA, both increased the transcriptional activity of RNAPDBP4; however, elevation by BCPA was achieved at a tenfold lower concentration. Addition of BCPA also protected RNAPDBP4 against thermal inactivation at 90 °C. These results suggest that BCPA increases transcriptional activity in T. kodakarensis by stabilizing the RNAP complex at high temperatures.
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24
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The therapeutic and nutraceutical potential of agmatine, and its enhanced production using Aspergillus oryzae. Amino Acids 2019; 52:181-197. [DOI: 10.1007/s00726-019-02720-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/05/2019] [Indexed: 12/30/2022]
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25
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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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26
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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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27
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Abstract
Most of the phylogenetic diversity of life is found in bacteria and archaea, and is reflected in the diverse metabolism and functions of bacterial and archaeal polyamines. The polyamine spermidine was probably present in the last universal common ancestor, and polyamines are known to be necessary for critical physiological functions in bacteria, such as growth, biofilm formation, and other surface behaviors, and production of natural products, such as siderophores. There is also phylogenetic diversity of function, indicated by the role of polyamines in planktonic growth of different species, ranging from absolutely essential to entirely dispensable. However, the cellular molecular mechanisms responsible for polyamine function in bacterial growth are almost entirely unknown. In contrast, the molecular mechanisms of essential polyamine functions in archaea are better understood: covalent modification by polyamines of translation factor aIF5A and the agmatine modification of tRNAIle As with bacterial hyperthermophiles, archaeal thermophiles require long-chain and branched polyamines for growth at high temperatures. For bacterial species in which polyamines are essential for growth, it is still unknown whether the molecular mechanisms underpinning polyamine function involve covalent or noncovalent interactions. Understanding the cellular molecular mechanisms of polyamine function in bacterial growth and physiology remains one of the great challenges for future polyamine research.
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Affiliation(s)
- Anthony J Michael
- From the Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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28
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Nishio T, Yoshikawa Y, Fukuda W, Umezawa N, Higuchi T, Fujiwara S, Imanaka T, Yoshikawa K. Branched-Chain Polyamine Found in Hyperthermophiles Induces Unique Temperature-Dependent Structural Changes in Genome-Size DNA. Chemphyschem 2018; 19:2299-2304. [PMID: 29931720 PMCID: PMC6175440 DOI: 10.1002/cphc.201800396] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/31/2022]
Abstract
A pentavalent branched‐chain polyamine, N4‐bis(aminopropyl)spermidine 3(3)(3)4, is a unique polycation found in the hyperthermophilic archaeon Thermococcus kodakarensis, which grows at temperatures between 60 and 100 °C. We studied the effects of this branched‐chain polyamine on DNA structure at different temperatures up to 80 °C. Atomic force microscopic observation revealed that 3(3)(3)4 induces a mesh‐like structure on a large DNA (166 kbp) at 24 °C. With an increase in temperature, DNA molecules tend to unwind, and multiple nano‐loops with a diameter of 10–50 nm are generated along the DNA strand at 80 °C. These results were compared to those obtained with linear‐chain polyamines, homocaldopentamine 3334 and spermidine, the former of which is a structural isomer of 3(3)(3)4. These specific effects are expected to neatly concern with its role on high‐temperature preference in hyperthermophiles.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Wakao Fukuda
- School of Science and Technology, Kwansei-gakuin University, Sanda, 669-1337, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shinsuke Fujiwara
- School of Science and Technology, Kwansei-gakuin University, Sanda, 669-1337, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
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29
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Sugiyama Y, Nara M, Sakanaka M, Kitakata A, Okuda S, Kurihara S. Analysis of polyamine biosynthetic- and transport ability of human indigenous Bifidobacterium. Biosci Biotechnol Biochem 2018; 82:1606-1614. [PMID: 29847302 DOI: 10.1080/09168451.2018.1475211] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bifidobacteria are members of the human intestinal microbiota, being numerically dominant in the colon of infants, and also being prevalent in the large intestine of adults. In this study, we measured the concentrations of major polyamines (putrescine, spermidine, and spermine) in cells and culture supernatant of 13 species of human indigenous Bifidobacterium at growing and stationary phase. Except for Bifidobacterium bifidum and Bifidobacterium gallicum, 11 species contained spermidine and/or spermine when grown in Gifu-anaerobic medium (GAM). However, Bifidobacterium scardovii and Bifidobacterium longum subsp. infantis, which contain spermidine when grown in GAM, did not contain spermidine when grown in polyamine-free 199 medium. Of the tested 13 Bifidobacterium species, 10 species showed polyamine transport ability. Combining polyamine concentration analysis in culture supernatant and in cells, with basic local alignment search tool analysis suggested that novel polyamine transporters are present in human indigenous Bifidobacterium. ABBREVIATIONS Put: putrescine; Spd: spermidine; Spm: spermine; GAM: Gifu anaerobic medium; BHI: brain-heart infusion.
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Affiliation(s)
- Yuta Sugiyama
- a Faculty of Bioresources and Environmental Sciences , Ishikawa Prefectural University , Nonoichi , Ishikawa , Japan
| | - Misaki Nara
- a Faculty of Bioresources and Environmental Sciences , Ishikawa Prefectural University , Nonoichi , Ishikawa , Japan
| | - Mikiyasu Sakanaka
- a Faculty of Bioresources and Environmental Sciences , Ishikawa Prefectural University , Nonoichi , Ishikawa , Japan
| | - Aya Kitakata
- a Faculty of Bioresources and Environmental Sciences , Ishikawa Prefectural University , Nonoichi , Ishikawa , Japan
| | - Shujiro Okuda
- b Graduate School of Medical and Dental Sciences , Niigata University , Niigata , Japan
| | - Shin Kurihara
- a Faculty of Bioresources and Environmental Sciences , Ishikawa Prefectural University , Nonoichi , Ishikawa , Japan
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30
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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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31
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Abstract
Themospermine is a structural isomer of spermine and is present in some bacteria and most of plants. An Arabidopsis mutant, acaulis5 (acl5), that is defective in the biosynthesis of thermospermine displays excessive proliferation of xylem vessels with dwarfed growth. Recent studies using acl5 and its suppressor mutants that recover the growth without thermospermine have revealed that thermospermine plays a key role in the negative control of the proliferation of xylem vessels through enhancing translation of specific mRNAs that contain a conserved upstream open-reading-frame (uORF) in the 5' leader region.
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Affiliation(s)
- Taku Takahashi
- Division of Earth, Life, and Molecular Sciences, Graduate School of Natural Science and Technology, Okayama University, Tsushimanaka 3-1-1, kita-ku, 700-8530, Okayama, Japan.
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32
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Feng Y, Zhao Y, Guo Y, Liu S. Microbial transcript and metabolome analysis uncover discrepant metabolic pathways in autotrophic and mixotrophic anammox consortia. WATER RESEARCH 2018; 128:402-411. [PMID: 29145079 DOI: 10.1016/j.watres.2017.10.069] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/12/2017] [Accepted: 10/29/2017] [Indexed: 06/07/2023]
Abstract
The ability of anammox bacteria to utilize organic matter has drawn extensive attention. However, the metabolic discrepancies between autotrophic and mixotrophic anammox consortia need to be further explored. Here, microbial transcript and metabolomic analysis were conducted for the samples harvested in the reactors and batch assays to investigate the phenotype discrepancies and intrinsic causes in autotrophic and mixotrophic anammox consortia. Results showed that metabolically active community structures did not show significant difference between autotrophic and mixotrophic anammox consortia (C/N = 0.3). Changes in the metabolic state were the main cause for those discrepancies in virtue of the added acetate oxidized via the acetyl-CoA pathway by mixotrophic anammox bacteria. At C/N ratio of 0.3, anammox activity was obviously promoted compared to that in the autotrophic condition, due to higher levels of NADH and NAD+, as well as ATP consumption. Mixotrophic anammox consortia were found to yield more biomass, resulting from enhanced purine, pyrimidine, and putrescine synthetic pathways for regulating bacterial growth. Up-regulated amino sugar and nucleotide sugar metabolism pathways participating in regulating more extracellular polysaccharides secreted by mixotrophic anammox consortia. In adverse environment with higher COD concentration, more extracellular proteins were produced by anammox consortia to protect themselves and amino acids also accumulated in the cell. This study provides useful information to catch the optimal metabolism way of anammox consortia and accelerate anammox bacterial cultivation or reactor startup for wastewater treatment.
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Affiliation(s)
- Ying Feng
- Department of Environmental Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yunpeng Zhao
- Department of Environmental Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Yongzhao Guo
- Department of Environmental Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China
| | - Sitong Liu
- Department of Environmental Engineering, Peking University, Beijing 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing 100871, China.
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33
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Hidese R, Fukuda W, Niitsu M, Fujiwara S. Identification of Branched-Chain Polyamines in Hyperthermophiles. Methods Mol Biol 2018; 1694:81-94. [PMID: 29080158 DOI: 10.1007/978-1-4939-7398-9_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thermophiles are organisms that grow optimally at temperatures higher than 55 °C. They contain two types of unusual longer/branched-chain polyamines in addition to common polyamines such as spermidine and putrescine. These unusual polyamines contribute to the survival of hyperthermophiles at high temperatures. Recently, the novel aminopropyltransferase BpsA was found to be responsible for the biosynthesis of branched-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis, which contains N 4-bis(aminopropyl)spermidine as the major polyamine. This compound is synthesized by the sequential addition of decarboxylated S-adenosylmethionine (dcSAM) aminopropyl groups to spermidine via the bifunctional catalytic action of BpsA. In this chapter, methods for the extraction and identification of branched-chain polyamines are presented, along with methods for the production and characterization of recombinant T. kodakarensis BpsA as a model aminopropyltransferase.
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Affiliation(s)
- Ryota Hidese
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan
| | - Wakao Fukuda
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Masaru Niitsu
- Faculty of Pharmacy and Pharmaceutical Sciences, Josai University, Sakado, Saitama, 350-0295, Japan
| | - Shinsuke Fujiwara
- Department of Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan.
- Research Center for Intelligent, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan.
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34
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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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35
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Muramatsu A, Shimizu Y, Yoshikawa Y, Fukuda W, Umezawa N, Horai Y, Higuchi T, Fujiwara S, Imanaka T, Yoshikawa K. Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA. J Chem Phys 2017; 145:235103. [PMID: 28010109 DOI: 10.1063/1.4972066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We studied the effect of branched-chain polyamines on the folding transition of genome-sized DNA molecules in aqueous solution by the use of single-molecule observation with fluorescence microcopy. Detailed morphological features of polyamine/DNA complexes were characterized by atomic force microscopy (AFM). The AFM observations indicated that branched-chain polyamines tend to induce a characteristic change in the higher-order structure of DNA by forming bridges or crosslinks between the segments of a DNA molecule. In contrast, natural linear-chain polyamines cause a parallel alignment between DNA segments. Circular dichroism measurements revealed that branched-chain polyamines induce the A-form in the secondary structure of DNA, while linear-chain polyamines have only a minimum effect. This large difference in the effects of branched- and linear-chain polyamines is discussed in relation to the difference in the manner of binding of these polyamines to negatively charged double-stranded DNA.
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Affiliation(s)
- Akira Muramatsu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Yuta Shimizu
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
| | - Wakao Fukuda
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Yuhei Horai
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Shinsuke Fujiwara
- School of Science and Technology, Kwansei-Gakuin University, Sanda 669-1337, Japan
| | - Tadayuki Imanaka
- College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan
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36
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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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37
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Hamana K, Furuchi T, Hayashi H, Itoh T, Ohkuma M, Niitsu M. Occurrence of two novel linear penta-amines, pyropentamine and homopyropentamine, in extremely thermophilic Thermus composti. J GEN APPL MICROBIOL 2017; 62:334-339. [PMID: 27885192 DOI: 10.2323/jgam.2016.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Koei Hamana
- Faculty of Engineering, Maebashi Institute of Technology
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38
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Ge D, Higashi K, Ito D, Nagano K, Ishikawa R, Terui Y, Higashi K, Moribe K, Linhardt RJ, Toida T. Poly-ion Complex of Chondroitin Sulfate and Spermine and Its Effect on Oral Chondroitin Sulfate Bioavailability. Chem Pharm Bull (Tokyo) 2017; 64:390-8. [PMID: 27150471 DOI: 10.1248/cpb.c15-00940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chondroitin sulfate (CS) has been accepted as an ingredient in health foods for the treatment of symptoms related to arthritis and cartilage repair. However, CS is poorly absorbed through the gastrointestinal tract because of its high negative electric charges and molecular weight (MW). In this study, poly-ion complex (PIC) formation was found in aqueous solutions through electrostatic interaction between CS and polyamines-organic molecules having two or more primary amino groups ubiquitously distributed in natural products at high concentrations. Characteristic properties of various PICs generated by mixing CS and natural polyamines, including unusual polyamines, were studied based on the turbidity for PIC formation, the dynamic light scattering for the size of PIC particles, and ζ-potential measurements for the surface charges of PIC particles. The efficiency of PIC formation between CS and spermine increased in a CS MW-dependent manner, with 15 kDa CS being critical for the formation of PIC (particle size: 3.41 µm) having nearly neutral surface charge (ζ-potential: -0.80 mV). Comparatively, mixing tetrakis(3-aminopropyl)ammonium and 15 kDa of CS afforded significant levels of PIC (particle size: 0.42±0.16 µm) despite a strongly negative surface charge (-34.67±1.15 mV). Interestingly, the oral absorption efficiency of CS was greatly improved only when PIC possessing neutral surface charges was administered to mice. High formation efficiency and electrically neutral surface charge of PIC particles are important factors for oral CS bioavailability.
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Affiliation(s)
- Dan Ge
- Graduate School of Pharmaceutical Sciences, Chiba University
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39
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Zhang Y, Yin J, Zhang L, Qi CC, Ma ZL, Gao LP, Wang DG, Jing YH. Spermidine preconditioning ameliorates laurate-induced brain injury by maintaining mitochondrial stability. Neurol Res 2017; 39:248-258. [DOI: 10.1080/01616412.2017.1283830] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yi Zhang
- Department of Neurology, People Hospital of Gansu Province, Lanzhou, P.R. China
| | - Jie Yin
- School of Basic Medical Sciences, Institute of Anatomy and Histology & Embryology, Neuroscience, Lanzhou University, Lanzhou, P.R. China
| | - Lang Zhang
- School of Basic Medical Sciences, Institute of Anatomy and Histology & Embryology, Neuroscience, Lanzhou University, Lanzhou, P.R. China
| | - Chu-Chu Qi
- School of Basic Medical Sciences, Institute of Anatomy and Histology & Embryology, Neuroscience, Lanzhou University, Lanzhou, P.R. China
| | - Ze-Lin Ma
- School of Basic Medical Sciences, Institute of Biochemistry and Molecular Biology, Lanzhou University, Lanzhou, P.R. China
| | - Li-Ping Gao
- School of Basic Medical Sciences, Institute of Biochemistry and Molecular Biology, Lanzhou University, Lanzhou, P.R. China
| | - De-Gui Wang
- School of Basic Medical Sciences, Institute of Anatomy and Histology & Embryology, Neuroscience, Lanzhou University, Lanzhou, P.R. China
| | - Yu-Hong Jing
- School of Basic Medical Sciences, Institute of Anatomy and Histology & Embryology, Neuroscience, Lanzhou University, Lanzhou, P.R. China
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou, P.R. China
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40
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Kabir A, Dutta D, Mandal C, Suresh Kumar G. Molecular Recognition of tRNA with 1-Naphthyl Acetyl Spermine, Spermine, and Spermidine: A Thermodynamic, Biophysical, and Molecular Docking Investigative Approach. J Phys Chem B 2016; 120:10871-10884. [PMID: 27690446 DOI: 10.1021/acs.jpcb.6b05391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of tRNA in protein translational machinery and the influence of polyamines on the interaction of acylated and deacylated tRNA with ribosomes make polyamine-tRNA interaction conspicuous. We studied the interaction of two biogenic polyamines, spermine (SPM) and spermidine (SPD), with tRNAPhe and compared the results to those of the analogue 1-naphthyl acetyl spermine (NASPM). The binding affinity of SPM was comparable to that of NASPM; both were higher than that of SPD. The interactions led to significant thermal stabilization of tRNAPhe and an increase in the enthalpy of transition. All the interactions were exothermic in nature and displayed prominent enthalpy-entropy compensation behavior. The entropy-driven nature of the interaction, the structural perturbations observed, and docking results proved that the polyamines were bound in the groove of the anticodon arm of tRNAPhe. The amine groups of polyamines were involved in extensive electrostatic, H-bonding, and van der Waals interactions with tRNAPhe. The naphthyl group of NASPM showed an additional stacking interaction with G24 and G26 of tRNAPhe, which was absent in others. The results demonstrate that 1-naphthyl acetyl spermine can target the same binding sites as the biogenic polyamines without substituting for the functions played by them, which may lead to exhibition of selective anticancer cytotoxicity.
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Affiliation(s)
| | | | - Chhabinath Mandal
- National Institute of Pharmaceutical and Educational Research , Kolkata 700032, India
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41
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Abstract
The content of spermidine and spermine in mammalian cells has important roles in protein and nucleic acid synthesis and structure, protection from oxidative damage, activity of ion channels, cell proliferation, differentiation, and apoptosis. Spermidine is essential for viability and acts as the precursor of hypusine, a post-translational addition to eIF5A allowing the translation of mRNAs encoding proteins containing polyproline tracts. Studies with Gy mice and human patients with the very rare X-linked genetic condition Snyder-Robinson syndrome that both lack spermine synthase show clearly that the correct spermine:spermidine ratio is critical for normal growth and development.
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Affiliation(s)
- Anthony E Pegg
- From the Department of Cellular and Molecular Physiology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
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42
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Hori H, Terui Y, Nakamoto C, Iwashita C, Ochi A, Watanabe K, Oshima T. Effects of polyamines from Thermus thermophilus, an extreme-thermophilic eubacterium, on tRNA methylation by tRNA (Gm18) methyltransferase (TrmH). J Biochem 2015; 159:509-17. [PMID: 26721905 DOI: 10.1093/jb/mvv130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 12/13/2022] Open
Abstract
Thermus thermophilus is an extreme-thermophilic eubacterium, which grows at a wide range of temperatures (50-83°C). This thermophile produces various polyamines including long and branched polyamines. In tRNAs from T. thermophilus, three distinct modifications, 2'-O-methylguanosine at position 18 (Gm18), 5-methyl-2-thiouridine at position 54 and N(1)-methyladenosine at position 58, are assembled at the elbow region to stabilize the L-shaped tRNA structure. However, the structures of unmodified tRNA precursors are disrupted at high temperatures. We hypothesize that polyamine(s) might have a positive effect on the modification process of unmodified tRNA transcript. We investigated the effects of eight polyamines on Gm18 formation in the yeast tRNA(Phe) transcript by tRNA (Gm18) methyltransferase (TrmH). Higher concentrations of linear polyamines inhibited TrmH activity at 55°C, while optimum concentration increased TrmH activity at 45-75°C. Exceptionally, caldohexamine, a long polyamine, did not show any positive effect on the TrmH activity at 55°C. However, temperature-dependent experiments revealed that 1 mM caldohexamine increased TrmH activity at 60-80°C. Furthermore, 0.25 mM tetrakis(3-aminopropy)ammonium, a branched polyamine, increased TrmH activity at a broad range of temperatures (40-85°C). Thus, caldohexamine and tetrakis(3-aminopropy)ammonium were found to enhance the TrmH activity at high temperatures.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577;
| | - Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, 15-8 Shiomi-cho, Choshi, Chiba; and
| | - Chisato Nakamoto
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Chikako Iwashita
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Anna Ochi
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Kazunori Watanabe
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co. Ltd., Tadao 2-15-5, Machida 194-0035, Japan
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Abstract
Deciphering AUA codons is a difficult task for organisms, because AUA and AUG specify isoleucine (Ile) and methionine (Met), separately. Each of the other purine-ending sense co-don sets (NNR) specifies a single amino acid in the universal genetic code. In bacteria and archaea, the cytidine derivatives, 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm(2)C or agmatidine), respectively, are found at the first letter of the anticodon of tRNA(Ile) responsible for AUA codons. These modifications prevent base pairing with G of the third letter of AUG codon, and enable tRNA(Ile) to decipher AUA codon specifically. In addition, these modifications confer a charging ability of tRNA(Ile) with Ile. Despite their similar chemical structures, L and agm(2)C are synthesized by distinctive mechanisms and catalyzed by different classes of enzymes, implying that the analogous decoding systems for AUA codons were established by convergent evolution after the phylogenic split between bacteria and archaea-eukaryotes lineages following divergence from the last universal common ancestor (LUCA).
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Affiliation(s)
- Tsutomu Suzuki
- a Department of Chemistry and Biotechnology; Graduate School of Engineering ; University of Tokyo ; Hongo , Bunkyo-ku , Tokyo , Japan
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44
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Liu J, Zeng C, Hogan V, Zhou S, Monwar MM, Hines JV. Identification of Spermidine Binding Site in T-box Riboswitch Antiterminator RNA. Chem Biol Drug Des 2015; 87:182-9. [PMID: 26348362 DOI: 10.1111/cbdd.12660] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/24/2015] [Accepted: 08/14/2015] [Indexed: 01/08/2023]
Abstract
The T-box transcription antitermination riboswitch controls bacterial gene expression by structurally responding to uncharged, cognate tRNA. Previous studies indicated that cofactors, such as the polyamine spermidine, might serve a specific functional role in enhancing riboswitch efficacy. As riboswitch function depends on key RNA structural changes involving the antiterminator element, the interaction of spermidine with the T-box riboswitch antiterminator element was investigated. Spermidine binds antiterminator model RNA with high affinity (micromolar Kd ) based on isothermal titration calorimetry and fluorescence-monitored binding assays. NMR titration studies, molecular modeling, and inline and enzymatic probing studies indicate that spermidine binds at the 3' portion of the highly conserved seven-nucleotide bulge in the antiterminator. Together, these results support the conclusion that spermidine binds the T-box antiterminator RNA preferentially in a location important for antiterminator function. The implications of these findings are significant both for better understanding of the T-box riboswitch mechanism and for antiterminator-targeted drug discovery efforts.
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Affiliation(s)
- Jia Liu
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Chunxi Zeng
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Vivian Hogan
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Shu Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Md Masud Monwar
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Jennifer V Hines
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
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45
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Martinez P, Vera M, Bobadilla-Fazzini RA. Omics on bioleaching: current and future impacts. Appl Microbiol Biotechnol 2015; 99:8337-50. [PMID: 26278538 PMCID: PMC4768214 DOI: 10.1007/s00253-015-6903-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
Abstract
Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.
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Affiliation(s)
- Patricio Martinez
- BioSigma 'S.A.', Parque Industrial Los Libertadores, Lote 106, Colina, Chile
| | - Mario Vera
- Biofilm Centre, Aquatische Biotechnologie, Universität Duisburg-Essen, Universitätstraße 5, 45141, Essen, Germany
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Pollo SM, Zhaxybayeva O, Nesbø CL. Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae. Can J Microbiol 2015. [DOI: 10.1139/cjm-2015-0073] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Thermophiles are extremophiles that grow optimally at temperatures >45 °C. To survive and maintain function of their biological molecules, they have a suite of characteristics not found in organisms that grow at moderate temperature (mesophiles). At the cellular level, thermophiles have mechanisms for maintaining their membranes, nucleic acids, and other cellular structures. At the protein level, each of their proteins remains stable and retains activity at temperatures that would denature their mesophilic homologs. Conversely, cellular structures and proteins from thermophiles may not function optimally at moderate temperatures. These differences between thermophiles and mesophiles presumably present a barrier for evolutionary transitioning between the 2 lifestyles. Therefore, studying closely related thermophiles and mesophiles can help us determine how such lifestyle transitions may happen. The bacterial phylum Thermotogae contains hyperthermophiles, thermophiles, mesophiles, and organisms with temperature ranges wide enough to span both thermophilic and mesophilic temperatures. Genomic, proteomic, and physiological differences noted between other bacterial thermophiles and mesophiles are evident within the Thermotogae. We argue that the Thermotogae is an ideal group of organisms for understanding of the response to fluctuating temperature and of long-term evolutionary adaptation to a different growth temperature range.
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Affiliation(s)
- Stephen M.J. Pollo
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences and Department of Computer Science, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
| | - Camilla L. Nesbø
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, 0316 Oslo, Norway
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47
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Umezawa N, Horai Y, Imamura Y, Kawakubo M, Nakahira M, Kato N, Muramatsu A, Yoshikawa Y, Yoshikawa K, Higuchi T. Structurally Diverse Polyamines: Solid-Phase Synthesis and Interaction with DNA. Chembiochem 2015; 16:1811-9. [DOI: 10.1002/cbic.201500121] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 12/17/2022]
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Identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles. J Bacteriol 2014; 196:1866-76. [PMID: 24610711 DOI: 10.1128/jb.01515-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Longer- and/or branched-chain polyamines are unique polycations found in thermophiles. N(4)-aminopropylspermine is considered a major polyamine in Thermococcus kodakarensis. To determine whether a quaternary branched penta-amine, N(4)-bis(aminopropyl)spermidine, an isomer of N(4)-aminopropylspermine, was also present, acid-extracted cytoplasmic polyamines were analyzed by high-pressure liquid chromatography, gas chromatography (HPLC), and gas chromatography-mass spectrometry. N(4)-bis(aminopropyl)spermidine was an abundant cytoplasmic polyamine in this species. To identify the enzyme that catalyzes N(4)-bis(aminopropyl)spermidine synthesis, the active fraction was concentrated from the cytoplasm and analyzed by linear ion trap-time of flight mass spectrometry with an electrospray ionization instrument after analysis by the MASCOT database. TK0545, TK0548, TK0967, and TK1691 were identified as candidate enzymes, and the corresponding genes were individually cloned and expressed in Escherichia coli. Recombinant forms were purified, and their N(4)-bis(aminopropyl)spermidine synthesis activity was measured. Of the four candidates, TK1691 (BpsA) was found to synthesize N(4)-bis(aminopropyl)spermidine from spermidine via N(4)-aminopropylspermidine. Compared to the wild type, the bpsA-disrupted strain DBP1 grew at 85°C with a slightly longer lag phase but was unable to grow at 93°C. HPLC analysis showed that both N(4)-aminopropylspermidine and N(4)-bis(aminopropyl)spermidine were absent from the DBP1 strain grown at 85°C, demonstrating that the branched-chain polyamine synthesized by BpsA is important for cell growth at 93°C. Sequence comparison to orthologs from various microorganisms indicated that BpsA differed from other known aminopropyltransferases that produce spermidine and spermine. BpsA orthologs were found only in thermophiles, both in archaea and bacteria, but were absent from mesophiles. These findings indicate that BpsA is a novel aminopropyltransferase essential for the synthesis of branched-chain polyamines, enabling thermophiles to grow in high-temperature environments.
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49
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Kurihara S, Sakai Y, Suzuki H, Muth A, Phanstiel O, Rather PN. Putrescine importer PlaP contributes to swarming motility and urothelial cell invasion in Proteus mirabilis. J Biol Chem 2013; 288:15668-76. [PMID: 23572531 DOI: 10.1074/jbc.m113.454090] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Previously, we reported that the speA gene, encoding arginine decarboxylase, is required for swarming in the urinary tract pathogen Proteus mirabilis. In addition, this previous study suggested that putrescine may act as a cell-to-cell signaling molecule (Sturgill, G., and Rather, P. N. (2004) Mol. Microbiol. 51, 437-446). In this new study, PlaP, a putative putrescine importer, was characterized in P. mirabilis. In a wild-type background, a plaP null mutation resulted in a modest swarming defect and slightly decreased levels of intracellular putrescine. In a P. mirabilis speA mutant with greatly reduced levels of intracellular putrescine, plaP was required for the putrescine-dependent rescue of swarming motility. When a speA/plaP double mutant was grown in the presence of extracellular putrescine, the intracellular levels of putrescine were greatly reduced compared with the speA mutant alone, indicating that PlaP functioned as the primary putrescine importer. In urothelial cell invasion assays, a speA mutant exhibited a 50% reduction in invasion when compared with wild type, and this defect could be restored by putrescine in a PlaP-dependent manner. The putrescine analog Triamide-44 partially inhibited the uptake of putrescine by PlaP and decreased both putrescine stimulated swarming and urothelial cell invasion in a speA mutant.
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Affiliation(s)
- Shin Kurihara
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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50
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Martínez P, Gálvez S, Ohtsuka N, Budinich M, Cortés MP, Serpell C, Nakahigashi K, Hirayama A, Tomita M, Soga T, Martínez S, Maass A, Parada P. Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay. Metabolomics 2013; 9:247-257. [PMID: 23335869 PMCID: PMC3548112 DOI: 10.1007/s11306-012-0443-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 06/29/2012] [Indexed: 12/20/2022]
Abstract
In this study, we present the first metabolic profiles for two bioleaching bacteria using capillary electrophoresis coupled with mass spectrometry. The bacteria, Acidithiobacillus ferrooxidans strain Wenelen (DSM 16786) and Acidithiobacillus thiooxidans strain Licanantay (DSM 17318), were sampled at different growth phases and on different substrates: the former was grown with iron and sulfur, and the latter with sulfur and chalcopyrite. Metabolic profiles were scored from planktonic and sessile states. Spermidine was detected in intra- and extracellular samples for both strains, suggesting it has an important role in biofilm formation in the presence of solid substrate. The canonical pathway for spermidine synthesis seems absent as its upstream precursor, putrescine, was not present in samples. Glutathione, a catalytic activator of elemental sulfur, was identified as one of the most abundant metabolites in the intracellular space in A. thiooxidans strain Licanantay, confirming its participation in the sulfur oxidation pathway. Amino acid profiles varied according to the growth conditions and bioleaching species. Glutamic and aspartic acid were highly abundant in intra- and extracellular extracts. Both are constituents of the extracellular matrix, and have a probable role in cell detoxification. This novel metabolomic information validates previous knowledge from in silico metabolic reconstructions based on genomic sequences, and reveals important biomining functions such as biofilm formation, energy management and stress responses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0443-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Marko Budinich
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - María Paz Cortés
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Cristián Serpell
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Servet Martínez
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
- Department of Mathematical Engineering and Center for Mathematical Modeling (UMI 2807, CNRS), Faculty of Mathematical and Physical Sciences, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
- Department of Mathematical Engineering and Center for Mathematical Modeling (UMI 2807, CNRS), Faculty of Mathematical and Physical Sciences, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
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