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Kato H, Onai K, Abe A, Shimizu M, Takagi H, Tateda C, Utsushi H, Singkarabanit-Ogawa S, Kitakura S, Ono E, Zipfel C, Takano Y, Ishiura M, Terauchi R. Lumi-Map, a Real-Time Luciferase Bioluminescence Screen of Mutants Combined with MutMap, Reveals Arabidopsis Genes Involved in PAMP-Triggered Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1366-1380. [PMID: 32876529 DOI: 10.1094/mpmi-05-20-0118-ta] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plants recognize pathogen-associated molecular patterns (PAMPs) to activate PAMP-triggered immunity (PTI). However, our knowledge of PTI signaling remains limited. In this report, we introduce Lumi-Map, a high-throughput platform for identifying causative single-nucleotide polymorphisms (SNPs) for studying PTI signaling components. In Lumi-Map, a transgenic reporter plant line is produced that contains a firefly luciferase (LUC) gene driven by a defense gene promoter, which generates luminescence upon PAMP treatment. The line is mutagenized and the mutants with altered luminescence patterns are screened by a high-throughput real-time bioluminescence monitoring system. Selected mutants are subjected to MutMap analysis, a whole-genome sequencing-based method of rapid mutation identification, to identify the causative SNP responsible for the luminescence pattern change. We generated nine transgenic Arabidopsis reporter lines expressing the LUC gene fused to multiple promoter sequences of defense-related genes. These lines generate luminescence upon activation of FLAGELLIN-SENSING 2 (FLS2) by flg22, a PAMP derived from bacterial flagellin. We selected the WRKY29-promoter reporter line to identify mutants in the signaling pathway downstream of FLS2. After screening 24,000 ethylmethanesulfonate-induced mutants of the reporter line, we isolated 22 mutants with altered WRKY29 expression upon flg22 treatment (abbreviated as awf mutants). Although five flg22-insensitive awf mutants harbored mutations in FLS2 itself, Lumi-Map revealed three genes not previously associated with PTI. Lumi-Map has the potential to identify novel PAMPs and their receptors as well as signaling components downstream of the receptors.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Hiroaki Kato
- Iwate Biotechnology Research Center, Kitakami, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kiyoshi Onai
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Chika Tateda
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | - Saeko Kitakura
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Erika Ono
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, U.K
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Yoshitaka Takano
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Fustin JM, Ye S, Rakers C, Kaneko K, Fukumoto K, Yamano M, Versteven M, Grünewald E, Cargill SJ, Tamai TK, Xu Y, Jabbur ML, Kojima R, Lamberti ML, Yoshioka-Kobayashi K, Whitmore D, Tammam S, Howell PL, Kageyama R, Matsuo T, Stanewsky R, Golombek DA, Johnson CH, Kakeya H, van Ooijen G, Okamura H. Methylation deficiency disrupts biological rhythms from bacteria to humans. Commun Biol 2020; 3:211. [PMID: 32376902 PMCID: PMC7203018 DOI: 10.1038/s42003-020-0942-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
The methyl cycle is a universal metabolic pathway providing methyl groups for the methylation of nuclei acids and proteins, regulating all aspects of cellular physiology. We have previously shown that methyl cycle inhibition in mammals strongly affects circadian rhythms. Since the methyl cycle and circadian clocks have evolved early during evolution and operate in organisms across the tree of life, we sought to determine whether the link between the two is also conserved. Here, we show that methyl cycle inhibition affects biological rhythms in species ranging from unicellular algae to humans, separated by more than 1 billion years of evolution. In contrast, the cyanobacterial clock is resistant to methyl cycle inhibition, although we demonstrate that methylations themselves regulate circadian rhythms in this organism. Mammalian cells with a rewired bacteria-like methyl cycle are protected, like cyanobacteria, from methyl cycle inhibition, providing interesting new possibilities for the treatment of methylation deficiencies. Fustin et al. reveal the evolutionarily conserved link between methyl metabolism and biological clocks. This study suggests the possibility of translating fundamental understanding of methylation deficiencies to clinical applications.
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Affiliation(s)
- Jean-Michel Fustin
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan. .,The University of Manchester, Faculty of Biology, Medicine and Health, Oxford Road, Manchester, M13 9PL, UK.
| | - Shiqi Ye
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan
| | - Christin Rakers
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kensuke Kaneko
- Graduate School of Pharmaceutical Sciences, Department of System Chemotherapy and Molecular Sciences, Kyoto University, Kyoto, Japan
| | - Kazuki Fukumoto
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan
| | - Mayu Yamano
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Metabology, Kyoto University, Kyoto, Japan
| | - Marijke Versteven
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Ellen Grünewald
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - T Katherine Tamai
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yao Xu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maria Luísa Jabbur
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Melisa L Lamberti
- Department of Science and Technology, National University of Quilmes/CONICET, Buenos Aires, Argentina
| | | | - David Whitmore
- Centre for Cell and Molecular Dynamics, Department of Cell and Developmental Biology, University College London, London, UK
| | - Stephanie Tammam
- Molecular Medicine, Peter Gilgan Centre for Research and Learning (PGCRL), The Hospital for Sick Children, Toronto, ON, Canada
| | - P Lynne Howell
- Molecular Medicine, Peter Gilgan Centre for Research and Learning (PGCRL), The Hospital for Sick Children, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takuya Matsuo
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany
| | - Diego A Golombek
- Department of Science and Technology, National University of Quilmes/CONICET, Buenos Aires, Argentina
| | | | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Department of System Chemotherapy and Molecular Sciences, Kyoto University, Kyoto, Japan
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Hitoshi Okamura
- Graduate School of Pharmaceutical Sciences, Laboratory of Molecular Brain Science, Kyoto University, Kyoto, Japan. .,Kyoto University, Graduate School of Medicine, Department of Neuroscience, Division of Physiology and Neurobiology, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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Aoki S, Okada R, Satbhai SB. Transformation and measurement of bioluminescence rhythms in the moss Physcomitrella patens. Methods Mol Biol 2014; 1158:325-36. [PMID: 24792062 DOI: 10.1007/978-1-4939-0700-7_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Gene targeting is a highly effective and straightforward technique for the functional analysis of a gene of interest. However, its efficiency is not satisfactorily high in many model plants including Arabidopsis thaliana. In the moss Physcomitrella patens, a model species of basal plants, the efficiency of gene targeting is as high as in yeasts, and this moss is becoming widely recognized as an experimental model of choice in various areas of plant biology. Here we focus on the transformation of protoplast cells and on the measurement of bioluminescence rhythms from protonema tissues of luciferase reporter strains in P. patens, both of which are important for mechanistic studies of the circadian clock.
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Affiliation(s)
- Setsuyuki Aoki
- Graduate School of Information Science, Nagoya University Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan,
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Matsuo T, Ishiura M. Chlamydomonas reinhardtiias a new model system for studying the molecular basis of the circadian clock. FEBS Lett 2011; 585:1495-502. [DOI: 10.1016/j.febslet.2011.02.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Revised: 01/31/2011] [Accepted: 02/21/2011] [Indexed: 12/31/2022]
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Okamoto K, Ishiura M, Torii T, Aoki S. A compact multi-channel apparatus for automated real-time monitoring of bioluminescence. ACTA ACUST UNITED AC 2007; 70:535-8. [PMID: 17300843 DOI: 10.1016/j.jbbm.2007.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 01/05/2007] [Accepted: 01/05/2007] [Indexed: 11/17/2022]
Abstract
We have developed a multi-channel apparatus for automated monitoring of bioluminescence in real time. We designed this apparatus to be compact (230 mm wide, 600 mm deep, and 227.5 mm high) so that it can be operated in a relatively small commercially-available incubator. The apparatus can process 20 samples at maximum in a single run, providing enough processibility in small-scale experiments. We verified the reliability and sensitivity of the apparatus by observing circadian bioluminescence rhythms over one week from a bioluminescent reporter strain (E9) of the cyanobacterium Synechococcus sp. strain PCC 7942 [Ishiura, M., Kutsuna, S., Aoki, S., Iwasaki, H., Andersson, C.R., Tanabe, A., Golden, S.S., Johnson, C.H., Kondo, T., Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria, Science, 281 (1998) 1519-1523]. Our apparatus allows flexible experimental designs and will be effectively used for the studies of gene expression in various purposes.
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Affiliation(s)
- Kazuhisa Okamoto
- Gene Research Center, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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Abstract
Recent work on the circadian clock of the unicellular green alga Chlamydomonas reinhardtii strengthens its standing as a convenient model system for circadian study. It was shown to be amenable to molecular engineering using a luciferase-based real-time reporter for circadian rhythms. Together with the completed draft genomic sequence, the new system opens the door for genome-scale forward and reverse genetic analysis.
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Affiliation(s)
- Ghislain Breton
- The Scripps Research Institute, Biochemistry Department, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Steve A Kay
- The Scripps Research Institute, Biochemistry Department, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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Matsuo T, Onai K, Okamoto K, Minagawa J, Ishiura M. Real-time monitoring of chloroplast gene expression by a luciferase reporter: evidence for nuclear regulation of chloroplast circadian period. Mol Cell Biol 2006; 26:863-70. [PMID: 16428442 PMCID: PMC1347041 DOI: 10.1128/mcb.26.3.863-870.2006] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2005] [Revised: 10/08/2005] [Accepted: 11/03/2005] [Indexed: 11/20/2022] Open
Abstract
Chloroplast-encoded genes, like nucleus-encoded genes, exhibit circadian expression. How the circadian clock exerts its control over chloroplast gene expression, however, is poorly understood. To facilitate the study of chloroplast circadian gene expression, we developed a codon-optimized firefly luciferase gene for the chloroplast of Chlamydomonas reinhardtii as a real-time bioluminescence reporter and introduced it into the chloroplast genome. The bioluminescence of the reporter strain correlated well with the circadian expression pattern of the introduced gene and satisfied all three criteria for circadian rhythms. Moreover, the period of the rhythm was lengthened in per mutants, which are phototactic rhythm mutants carrying a long-period gene in their nuclear genome. These results demonstrate that chloroplast gene expression rhythm is a bona fide circadian rhythm and that the nucleus-encoded circadian oscillator determines the period length of the chloroplast rhythm. Our reporter strains can serve as a powerful tool not only for analysis of the circadian regulation mechanisms of chloroplast gene expression but also for a genetic approach to the molecular oscillator of the algal circadian clock.
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Affiliation(s)
- Takuya Matsuo
- Center for Gene Research, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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Iwase R, Imada K, Hayashi F, Uzumaki T, Morishita M, Onai K, Furukawa Y, Namba K, Ishiura M. Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex. J Biol Chem 2005; 280:43141-9. [PMID: 16227211 DOI: 10.1074/jbc.m503360200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The KaiB crystal diffracts at a resolution of 2.6 A and includes four subunits organized as a dimer of dimers, each composed of two non-equivalent subunits. The overall shape of the tetramer is an elongated hexagonal plate, with a single positively charged cleft flanked by two negatively charged ridges whose surfaces includes several terminal chains. Site-directed mutagenesis of Synechococcus KaiB confirmed that alanine substitution of residues Lys-11 or Lys-43 in the cleft, or deletion of C-terminal residues 95-108, which forms part of the ridges, strongly weakens in vivo circadian rhythms. Characteristics of KaiB deduced from the x-ray crystal structure were also confirmed by physicochemical measurements of KaiB in solution. These data suggest that the positively charged cleft and flanking negatively charged ridges in KaiB are essential for the biological function of KaiB in the circadian molecular machinery in cyanobacteria.
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Affiliation(s)
- Ryo Iwase
- Center for Gene Research, Nagoya University, Furo, Chikusa, Nagoya, Japan
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Kucho KI, Aoki K, Itoh S, Ishiura M. Improvement of the bioluminescence reporter system for real-time monitoring of circadian rhythms in the cyanobacterium Synechocystis sp. strain PCC 6803. Genes Genet Syst 2005; 80:19-23. [PMID: 15824452 DOI: 10.1266/ggs.80.19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Circadian rhythm is a self-sustaining oscillation whose period length coincides with the 24-hour day-night cycle. A powerful tool for circadian clock research is the real-time automated bioluminescence monitoring system in which a promoter region of a clock-controlled gene is fused to a luciferase reporter gene and rhythmic regulation of the promoter activity is monitored as bioluminescence. In the present study, we greatly improved the bioluminescence reporter system in the cyanobacterium Synechocystis sp. strain PCC 6803. We fused an 805-bp promoter region of the dnaK gene seamlessly to the luxA coding sequence and integrated the P(dnaK)::luxAB fusion gene into a specific intergenic region of the Synechocystis genome (targeting site 1). The resulting new reporter strain, PdnaK::luxAB(-), showed 12 times the bioluminescence intensity of the standard reporter strain, CFC2. Furthermore, we generated strain PdnaK::luxAB(+), in which the P(dnaK)::luxAB fusion gene and the selection-marker spectinomycin resistance gene are transcribed in opposite directions. The PdnaK::luxAB(+) strain showed 19 times the bioluminescence intensity of strain CFC2. The procedures used to increase the bioluminescence intensity are especially useful for bioluminescence monitoring of genes with low promoter activity. In addition, these reporter constructs facilitate bioluminescence monitoring of any gene because the promoter fragments they contain can easily be replaced by digestion with unique restriction enzymes. They would therefore contribute to a genome-wide analysis of gene expression in Synechocystis.
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Okamoto K, Onai K, Ishiura M. RAP, an integrated program for monitoring bioluminescence and analyzing circadian rhythms in real time. Anal Biochem 2005; 340:193-200. [PMID: 15840491 DOI: 10.1016/j.ab.2004.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2004] [Indexed: 10/26/2022]
Abstract
To process the large number of circadian rhythmic bioluminescence data that we generated with specially developed, high-throughput monitoring apparatuses, we developed an integrated rhythm-analyzing program (RAP) with a user-friendly graphical interface. RAP does all of the following in real time: (i) displays the bioluminescence time course, (ii) records time-series data, (iii) analyzes the data, (iv) displays the analyzed results, (v) statistically evaluates the analyzed results, and (vi) provides printouts. Because RAP can import files, it can analyze not only bioluminescence data but also other data such as those obtained by DNA array experiments and by Northern and Western blot analyses. The program is a powerful tool for large-scale investigations of biological rhythmic phenomena in general.
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Affiliation(s)
- Kazuhisa Okamoto
- Center for Gene Research, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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Onai K, Ishiura M. PHYTOCLOCK 1 encoding a novel GARP protein essential for the Arabidopsis circadian clock. Genes Cells 2005; 10:963-72. [PMID: 16164597 DOI: 10.1111/j.1365-2443.2005.00892.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Previously, we screened 50 000 seedlings of Arabidopsis thaliana carrying a P(GI)::LUC+ bioluminescence reporter gene mutagenized with ethylmethanesulfonate for mutants with phenotypes of extensively altered circadian rhythms, and identified three loci, PHYTOCLOCK 1 (PCL1), PCL2 and PCL3, whose mutations cause arrhythmia. Here we succeeded to clone the PCL1 gene and show that the PCL1 gene encodes a novel DNA binding protein belonging to the GARP protein family and is essential for a functional clock oscillator in A. thaliana. The PCL1 gene satisfies the requirements for the clock oscillator gene: (i) pcl1 null mutations caused arrhythmia in multiple circadian outputs, including expression of potential clock genes TOC1, CCA1 and LHY, and flowering lacked a photoperiodic response; (ii) PCL1 expression showed circadian rhythm in both constant light and constant dark; (iii) over-expression of the PCL1 gene gradually caused arrhythmicity in all the multiple circadian outputs examined; and (iv) the PCL1 gene controlled its own expression via negative feedback. Therefore, the PCL1 gene is the clock oscillator gene essential to the generation of clock oscillation in the higher plant.
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Affiliation(s)
- Kiyoshi Onai
- Center for Gene Research, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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