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Minazzato G, Gasparrini M, Heroux A, Sernova NV, Rodionov DA, Cianci M, Sorci L, Raffaelli N. Bacterial NadQ (COG4111) is a Nudix-like, ATP-responsive regulator of NAD biosynthesis. J Struct Biol 2022; 214:107917. [PMID: 36332744 DOI: 10.1016/j.jsb.2022.107917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/13/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Nicotinamide-adenine dinucleotide (NAD) is centrally important to metabolic reactions that involve redox chemistry. In bacteria, NAD biosynthesis is controlled by different transcription factors, depending on the species. Among the four regulators identified so far, the protein NadQ is reported to act as a repressor of the de novo NAD biosynthetic pathway in proteobacteria. Using comparative genomics, a systematic reconstruction of NadQ regulons in thousands of fully sequenced bacterial genomes has been performed, confirming that NadQ is present in α-proteobacteria and some β- and γ-proteobacteria, including pathogens like Bordetella pertussis and Neisseria meningitidis, where it likely controls de novo NAD biosynthesis. Through mobility shift assay and mutagenesis, the DNA binding activity of NadQ from Agrobacterium tumefaciens was experimentally validated and determined to be suppressed by ATP. The crystal structures of NadQ in native form and in complex with ATP were determined, indicating that NadQ is a dimer, with each monomer composed of an N-terminal Nudix domain hosting the effector binding site and a C-terminal winged helix-turn-helix domain that binds DNA. Within the dimer, we found one ATP molecule bound, at saturating concentration of the ligand, in keeping with an intrinsic asymmetry of the quaternary structure. Overall, this study provided the basis for depicting a working model of NadQ regulation mechanism.
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Affiliation(s)
- Gabriele Minazzato
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Massimiliano Gasparrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Annie Heroux
- Elettra - Sincrotrone Trieste S.C.P.A., Basovizza, Italy
| | - Natalia V Sernova
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Leonardo Sorci
- Department of Materials, Environmental Sciences and Urban Planning, Division of Bioinformatics and Biochemistry, Polytechnic University of Marche, Ancona, Italy.
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
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2
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Gao R, Wei W, Hassan BH, Li J, Deng J, Feng Y. A single regulator NrtR controls bacterial NAD + homeostasis via its acetylation. eLife 2019; 8:51603. [PMID: 31596237 PMCID: PMC6800001 DOI: 10.7554/elife.51603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/04/2019] [Indexed: 12/27/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an indispensable cofactor in all domains of life, and its homeostasis must be regulated tightly. Here we report that a Nudix-related transcriptional factor, designated MsNrtR (MSMEG_3198), controls the de novo pathway of NAD+biosynthesis in M. smegmatis, a non-tuberculosis Mycobacterium. The integrated evidence in vitro and in vivo confirms that MsNrtR is an auto-repressor, which negatively controls the de novo NAD+biosynthetic pathway. Binding of MsNrtR cognate DNA is finely mapped, and can be disrupted by an ADP-ribose intermediate. Unexpectedly, we discover that the acetylation of MsNrtR at Lysine 134 participates in the homeostasis of intra-cellular NAD+ level in M. smegmatis. Furthermore, we demonstrate that NrtR acetylation proceeds via the non-enzymatic acetyl-phosphate (AcP) route rather than by the enzymatic Pat/CobB pathway. In addition, the acetylation also occurs on the paralogs of NrtR in the Gram-positive bacterium Streptococcus and the Gram-negative bacterium Vibrio, suggesting that these proteins have a common mechanism of post-translational modification in the context of NAD+ homeostasis. Together, these findings provide a first paradigm for the recruitment of acetylated NrtR to regulate bacterial central NAD+ metabolism.
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Affiliation(s)
- Rongsui Gao
- Department of Pathogen Biology & Microbiology, and Department General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenhui Wei
- Department of Pathogen Biology & Microbiology, and Department General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | - Jun Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Jiaoyu Deng
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology, and Department General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,College of Animal Sciences, Zhejiang University, Hangzhou, China
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3
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Wang Q, Hassan BH, Lou N, Merritt J, Feng Y. Functional definition of NrtR, a remnant regulator of NAD + homeostasis in the zoonotic pathogen Streptococcus suis. FASEB J 2019; 33:6055-6068. [PMID: 30759348 PMCID: PMC8793812 DOI: 10.1096/fj.201802179rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/15/2019] [Indexed: 12/16/2022]
Abstract
NAD+ is an enzyme cofactor required for the 3 domains of life. However, little is known about the NAD+ biosynthesis and salvage pathways in the opportunistic pathogen Streptococcus suis. A genome-wide search allows us to identify the NAD+ salvage pathway encoded by an operon of nadR-pnuC-nrtR (from SSU05_1973 to SSU05_1971 on the reverse strand) in the S. suis 05ZYH33 that causes streptococcal toxin shock-like syndrome. The regulator of this pathway is Nudix-related transcriptional regulator (NrtR), a transcription regulator of the Nudix family comprising an N-terminal Nudix-like effector domain, and a C-terminal DNA-binding winged helix-turn-helix-like domain. Intriguingly, the S. suis NrtR naturally contains a single amino acid substitution (K92E) in the catalytic site of its Nudix domain that renders it catalytically inactive but does not influence its ability to bind DNA. Despite its lack of enzymatic activity, DNA-binding activity of NrtR is antagonized by the effector ADP-ribose. Furthermore, nrtR knockout in S. suis serotype 2 reduces its capacity to form biofilms and attenuates its virulence in a mouse infection model. Genome mining indicates that nrtR appears in a strain-specific manner whose occupancy is correlated to bacterial infectivity. Unlike the paradigmatic member of NrtR family having 2 unrelated functions (Nudix hydrolase and DNA binding), S. suis 2 retains a single regulatory role in the modulation of NAD+ salvage. This control of NAD+ homeostasis contributes to S. suis virulence.-Wang, Q., Hassan, B. H., Lou, N., Merritt, J., Feng, Y. Functional definition of NrtR, a remnant regulator of NAD+ homeostasis in the zoonotic pathogen Streptococcus suis.
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Affiliation(s)
- Qingjing Wang
- Department of Pathogen Biology and MicrobiologyDepartment of General Intensive Care Unit of Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Bachar H. Hassan
- Stony Brook Cancer CenterStony Brook UniversityStony BrookNew YorkUSA
| | - Ningjie Lou
- Department of Pathogen Biology and MicrobiologyDepartment of General Intensive Care Unit of Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Justin Merritt
- Department of Restorative DentistryOregon Health and Science UniversityPortlandOregonUSA
| | - Youjun Feng
- Department of Pathogen Biology and MicrobiologyDepartment of General Intensive Care Unit of Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
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4
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Brickman TJ, Suhadolc RJ, McKelvey PJ, Armstrong SK. Essential role of Bordetella NadC in a quinolinate salvage pathway for NAD biosynthesis. Mol Microbiol 2016; 103:423-438. [PMID: 27783449 DOI: 10.1111/mmi.13566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2016] [Indexed: 01/03/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) is produced via de novo biosynthesis pathways and by salvage or recycling routes. The classical Bordetella bacterial species are known to be auxotrophic for nicotinamide or nicotinic acid. This study confirmed that Bordetella bronchiseptica, Bordetella pertussis and Bordetella parapertussis have the recycling/salvage pathway genes pncA and pncB, for use of nicotinamide or nicotinic acid, respectively, for NAD synthesis. Although these Bordetellae lack the nadA and nadB genes needed for de novo NAD biosynthesis, remarkably, they have one de novo pathway gene, nadC, encoding quinolinate phosphoribosyltransferase. Genomic analyses of taxonomically related Bordetella and Achromobacter species also indicated the presence of an 'orphan' nadC and the absence of nadA and nadB. When supplied as the sole NAD precursor, quinolinate promoted B. bronchiseptica growth, and the ability to use it required nadC. Co-expression of Bordetella nadC with the nadB and nadA genes of Paraburkholderia phytofirmans allowed B. bronchiseptica to grow in the absence of supplied pyridines, indicative of de novo NAD synthesis and functional confirmation of Bordetella NadC activity. Expression of nadC in B. bronchiseptica was influenced by nicotinic acid and by a NadQ family transcriptional repressor, indicating that these organisms prioritize their use of pyridines for NAD biosynthesis.
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Affiliation(s)
- Timothy J Brickman
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
| | - Ryan J Suhadolc
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
| | - Pamela J McKelvey
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
| | - Sandra K Armstrong
- Department of Microbiology and Immunology, University of Minnesota Medical School, 3-117 Microbiology Research Facility, 689 23rd Ave. S.E, Minneapolis, MN, 55455-1507, USA
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Okon E, Dethlefsen S, Pelnikevich A, Barneveld AV, Munder A, Tümmler B. Key role of an ADP - ribose - dependent transcriptional regulator of NAD metabolism for fitness and virulence of Pseudomonas aeruginosa. Int J Med Microbiol 2016; 307:83-94. [PMID: 27865623 DOI: 10.1016/j.ijmm.2016.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 08/31/2016] [Accepted: 09/25/2016] [Indexed: 10/20/2022] Open
Abstract
NAD is an essential co-factor of redox reactions and metabolic conversions of NAD-dependent enzymes. NAD biosynthesis in the opportunistic pathogen Pseudomonas aeruginosa has yet not been experimentally explored. The in silico search for orthologs in the P. aeruginosa PAO1 genome identified the operon pncA - pncB1-nadE (PA4918-PA4920) to encode the nicotinamidase, nicotinate phosporibosyltransferase and Nad synthase of salvage pathway I. The functional role of the preceding genes PA4917 and PA4916 was resolved by the characterization of recombinant protein. PA4917 turned out to encode the nicotinate mononucleotide adenylyltransferase NadD2 and PA4916 was determined to encode the transcriptional repressor NrtR that binds to an intergenic sequence between nadD2 and pncA. Complex formation between the catalytically inactive Nudix protein NrtR and its DNA binding site was suppressed by the antirepressor ADP-ribose. NrtR plasposon mutagenesis abrogated virulence of P. aeruginosa TBCF10839 in a murine acute airway infection model and constrained its metabolite profile. When grown together with other isogenic plasposon mutants, the nrtR knock-out was most compromised in competitive fitness to persist in nutrient-rich medium in vitro or murine airways in vivo. This example demonstrates how tightly metabolism and virulence can be intertwined by key elements of metabolic control.
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Affiliation(s)
- Elza Okon
- Klinische Forschergruppe, OE 6710, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Sarah Dethlefsen
- Klinische Forschergruppe, OE 6710, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Anna Pelnikevich
- Klinische Forschergruppe, OE 6710, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Andrea van Barneveld
- Klinische Forschergruppe, OE 6710, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Antje Munder
- Klinische Forschergruppe, OE 6710, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, Hannover, Germany
| | - Burkhard Tümmler
- Klinische Forschergruppe, OE 6710, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, Hannover, Germany.
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6
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Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A. A novel transcriptional regulator of L-arabinose utilization in human gut bacteria. Nucleic Acids Res 2015; 43:10546-59. [PMID: 26438537 PMCID: PMC4666351 DOI: 10.1093/nar/gkv1005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/23/2015] [Indexed: 01/08/2023] Open
Abstract
Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.
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Affiliation(s)
- Changsoo Chang
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Christine Tesar
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Xiaoqing Li
- Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Youngchang Kim
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Dmitry A Rodionov
- Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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7
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Platzen L, Koch-Koerfges A, Weil B, Brocker M, Bott M. Role of flavohaemoprotein Hmp and nitrate reductase NarGHJI ofCorynebacterium glutamicumfor coping with nitrite and nitrosative stress. FEMS Microbiol Lett 2013; 350:239-48. [DOI: 10.1111/1574-6968.12318] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 10/26/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Laura Platzen
- Institut für Bio- und Geowissenschaften; IBG-1: Biotechnologie; Forschungszentrum Jülich; Jülich Germany
| | - Abigail Koch-Koerfges
- Institut für Bio- und Geowissenschaften; IBG-1: Biotechnologie; Forschungszentrum Jülich; Jülich Germany
| | - Brita Weil
- Institut für Bio- und Geowissenschaften; IBG-1: Biotechnologie; Forschungszentrum Jülich; Jülich Germany
| | - Melanie Brocker
- Institut für Bio- und Geowissenschaften; IBG-1: Biotechnologie; Forschungszentrum Jülich; Jülich Germany
| | - Michael Bott
- Institut für Bio- und Geowissenschaften; IBG-1: Biotechnologie; Forschungszentrum Jülich; Jülich Germany
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Teramoto H, Inui M, Yukawa H. OxyR acts as a transcriptional repressor of hydrogen peroxide-inducible antioxidant genes in Corynebacterium glutamicum R. FEBS J 2013; 280:3298-312. [PMID: 23621709 DOI: 10.1111/febs.12312] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/02/2013] [Accepted: 04/24/2013] [Indexed: 12/13/2022]
Abstract
OxyR, a LysR-type transcriptional regulator, has been established as a redox-responsive activator of antioxidant genes in bacteria. This study shows that OxyR acts as a transcriptional repressor of katA, dps, ftn and cydA in Corynebacterium glutamicum R. katA encodes H2O2-detoxifing enzyme catalase, dps and ftn are implicated in iron homeostasis and cydA encodes a subunit of cytochrome bd oxidase. Quantitative RT-PCR analyses revealed that expression of katA and dps, but not of ftn and cydA, was induced by H2O2. Disruption of the oxyR gene encoding OxyR resulted in a marked increase in katA and dps mRNAs to a level higher than that induced by H2O2, and the oxyR-deficient mutant showed a H2O2-resistant phenotype. This is in contrast to the conventional OxyR-dependent regulatory model. ftn and cydA were also upregulated by oxyR disruption but to a smaller extent. Electrophoretic mobility shift assays revealed that the OxyR protein specifically binds to all four upstream regions of the respective genes under reducing conditions. We observed that the oxidized form of OxyR similarly bound to not only the target promoter regions, but also nonspecific DNA fragments. Based on these findings, we propose that the transcriptional repression by OxyR is alleviated under oxidative stress conditions in a titration mechanism due to the decreased specificity of its DNA-binding activity. DNase I footprinting analyses revealed that the OxyR-binding site in the four target promoters is ~ 50 bp in length and has multiple T-N11-A motifs, a feature of LysR-type transcriptional regulators, but no significant overall sequence conservation.
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Affiliation(s)
- Haruhiko Teramoto
- Research Institute of Innovative Technology for the Earth, Kyoto, Japan
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Teramoto H, Inui M, Yukawa H. Corynebacterium glutamicumZur acts as a zinc-sensing transcriptional repressor of both zinc-inducible and zinc-repressible genes involved in zinc homeostasis. FEBS J 2012; 279:4385-97. [DOI: 10.1111/febs.12028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/24/2012] [Accepted: 10/09/2012] [Indexed: 01/06/2023]
Affiliation(s)
- Haruhiko Teramoto
- Research Institute of Innovative Technology for the Earth; Kyoto; Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth; Kyoto; Japan
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth; Kyoto; Japan
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