Updated on 2023/10/28

写真a

 
MURANAKA Tomoaki
 
Organization
Graduate School of Bioagricultural Sciences Department of Applied Biosciences Assistant Professor
Graduate School
Graduate School of Bioagricultural Sciences
Undergraduate School
School of Agricultural Sciences Department of Applied Biosciences
Title
Assistant Professor
External link

Degree 1

  1. 博士(理学) ( 2015.9   京都大学 ) 

Research History 5

  1. 鹿児島大学農学部   農学部   学振特別研究員PD

    2020.4 - 2023.2

      More details

  2. Kyoto University   Center for Ecological Research

    2017.4 - 2020.3

      More details

  3. Nagoya University   Graduate School of Science

    2016.3 - 2017.3

      More details

  4. Kyoto University   Graduate School of Science

    2015.10 - 2016.2

      More details

  5. Japan Society for Promotion of Science

    2012.4 - 2015.3

      More details

Education 3

  1. 京都大学大学院理学研究科生物科学専攻博士後期課程

    2012.4 - 2015.9

      More details

  2. 京都大学大学院理学研究科生物科学専攻修士課程

    2010.4 - 2012.3

      More details

  3. 京都大学理学部理学科

    2006.4 - 2010.3

      More details

Professional Memberships 5

  1. 植物学会

    2020

      More details

  2. 生態学会

    2017

      More details

  3. 種生物学会

    2017

      More details

  4. 時間生物学会

    2010

      More details

  5. 植物生理学会

    2009

      More details

Awards 2

  1. 第30回学術奨励賞

    2023.10   日本時間生物学会  

     More details

  2. 第14回片岡奨励賞

    2020.12   種生物学会  

     More details

 

Papers 17

  1. A non-cell-autonomous circadian rhythm of bioluminescence reporter activities in individual duckweed cells. Reviewed International journal

    Emiri Watanabe, Tomoaki Muranaka, Shunji Nakamura, Minako Isoda, Yu Horikawa, Tsuyoshi Aiso, Shogo Ito, Tokitaka Oyama

    Plant physiology     2023.4

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    The circadian clock is responsible for the temporal regulation of various physiological processes in plants. Individual cells contain a circadian oscillator consisting of a clock gene circuit that coordinates physiological rhythms within the plant body in an orderly manner. The coordination of time information has been studied from the perspective of cell-cell local coupling and long-distance communication between tissues based on the view that the behavior of circadian oscillators represents physiological rhythms. Here, we report the cellular circadian rhythm of bioluminescence reporters that are not governed by the clock gene circuit in expressing cells. We detected cellular bioluminescence rhythms with different free-running periods in the same cells using a dual-color bioluminescence monitoring system in duckweed (Lemna minor) transfected with Arabidopsis CIRCADIAN CLOCK ASSOCIATED 1::luciferace + (AtCCA1::LUC+) and Cauliflower mosaic virus 35S::modified click-beetle red-color luciferase (CaMV35S::PtRLUC) reporters. Co-transfection experiments with the two reporters and a clock gene-overexpressing effector revealed that the AtCCA1::LUC + rhythm, but not the CaMV35S::PtRLUC rhythm, was altered in cells with a dysfunctional clock gene circuit. This indicated that the AtCCA1::LUC + rhythm is a direct output of the cellular circadian oscillator, whereas the CaMV35S::PtRLUC rhythm is not. After plasmolysis, the CaMV35S::PtRLUC rhythm disappeared, whereas the AtCCA1::LUC + rhythm persisted. This suggests that the CaMV35S::PtRLUC bioluminescence has a symplast/apoplast-mediated circadian rhythm generated at the organismal level. The CaMV35S::PtRLUC-type bioluminescence rhythm was also observed when other bioluminescence reporters were expressed. These results reveal that the plant circadian system consists of both cell-autonomous and non-cell-autonomous rhythms that are unaffected by cellular oscillators.

    DOI: 10.1093/plphys/kiad218

    PubMed

    researchmap

  2. Effects of fruit dimorphism on genetic structure and gene flow in the coastal shrub <i>Scaevola taccada</i> Reviewed International journal

    Naoko Emura, Tomoaki Muranaka, Takaya Iwasaki, Mie N Honjo, Atsushi J Nagano, Yuji Isagi, Hiroshi Kudoh

    Annals of Botany   Vol. 130 ( 7 ) page: 1029 - 1040   2022.12

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Background and Aims

    Plant propagules often possess specialized morphologies that facilitate dispersal across specific landscapes. In the fruit dimorphism of a coastal shrub, Scaevola taccada, individual plants produce either cork-morph or pulp-morph fruits. The former is buoyant and common on sandy beaches, whereas the latter does not float, is bird-dispersed, and is common on elevated sites such as slopes on sea cliffs and behind rocky shores. We hypothesized that beach populations bridge the heterogeneous landscapes by serving as a source of both fruit types, while dispersal is biased for the pulp morph on elevated sites within the islands and for the cork morph between beaches of different islands. Based on this hypothesis, we predicted that populations in elevated sites would diverge genetically over time due to isolation by distance, whereas beach populations would maintain high genetic similarity via current gene flow.

    Methods

    The genetic structure and gene flow in S. taccada were evaluated by investigating genome-wide single nucleotide polymorphisms in plants from 17 sampling sites on six islands (belonging to the Ryukyu, Daito and Ogasawara Islands) in Japan.

    Key Results

    Geographical isolation was detected among the three distant island groups. Analyses within the Ryukyu Islands suggested that sandy beach populations were characterized by genetic admixture, whereas populations in elevated sites were relatively isolated between the islands. Pairwise FST values between islands were lowest between sandy beaches, intermediate between sandy beaches and elevated sites, and highest between elevated sites.

    Conclusions

    Dispersal across the ocean by cork morphs is sufficiently frequent to prevent genetic divergence between beaches of different islands. Stronger genetic isolation of elevated sites between islands suggests that bird dispersal by pulp morphs is restricted mainly within islands. These contrasting patterns of gene flow realized by fruit dimorphism provide evidence that fruit characteristics can strongly mediate genetic structure.

    DOI: 10.1093/aob/mcac138

    PubMed

    researchmap

    Other Link: https://academic.oup.com/aob/article-pdf/130/7/1029/49857759/mcac138.pdf

  3. Multifunctional chemical inhibitors of the florigen activation complex discovered by structure‐based high‐throughput screening Reviewed International journal

    Ken‐ichiro Taoka, Ikumi Kawahara, Shoko Shinya, Ken‐ichi Harada, Eiki Yamashita, Zenpei Shimatani, Kyoko Furuita, Tomoaki Muranaka, Tokitaka Oyama, Rie Terada, Atsushi Nakagawa, Toshimichi Fujiwara, Hiroyuki Tsuji, Chojiro Kojima

    The Plant Journal   Vol. 112 ( 6 ) page: 1337 - 1349   2022.11

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    Structure-based high-throughput screening of chemical compounds that target protein-protein interactions (PPI) is a promising technology for gaining insight into how plant development is regulated, leading to many potential agricultural applications. At present, there are no examples of using high-throughput screening to identify chemicals that target plant transcriptional complexes, some of which are responsible for regulating multiple physiological functions. Florigen, a protein encoded by FLOWERING LOCUS T (FT), was initially identified as molecule that promotes flowering and has since been shown to regulate flowering and other developmental phenomena such as tuber formation in potato. FT functions as a component of the florigen activation complex (FAC) with a scaffold protein 14-3-3 and FD, a bZIP transcription factor that activates downstream gene expression. Although 14-3-3 is an important component of FAC, there are little functional analysis of the 14-3-3 itself. Here, we report the results of a high-throughput in vitro fluorescence resonance energy transfer (FRET) screening of chemical libraries that enabled us to identify small molecules capable of inhibiting FAC formation. These molecules abrogate the in vitro interaction between 14-3-3 and OsFD1 peptide, a rice FD, by directly binding to 14-3-3. Treatment with S4, a specific hit molecule, strongly inhibited FAC activity and flowering in duckweed, tuber formation in potato and branching in rice in a dose-dependent manner. Our results demonstrate that the high-throughput screening approach based on three-dimensional structure of PPI is possible in plants. In this study, we have proposed good candidate compounds for future modification to obtain inhibitors of florigen-dependent processes through inhibition of FAC formation.

    DOI: 10.1111/tpj.16008

    PubMed

    researchmap

    Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1111/tpj.16008

  4. Circadian-period variation underlies the local adaptation of photoperiodism in the short-day plant Lemna aequinoctialis. Reviewed International journal

    Tomoaki Muranaka, Shogo Ito, Hiroshi Kudoh, Tokitaka Oyama

    iScience   Vol. 25 ( 7 ) page: 104634 - 104634   2022.7

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)  

    Phenotypic variation is the basis for trait adaptation via evolutionary selection. However, the driving forces behind quantitative trait variations remain unclear owing to their complexity at the molecular level. This study focused on the natural variation of the free-running period (FRP) of the circadian clock because FRP is a determining factor of the phase phenotype of clock-dependent physiology. Lemna aequinoctialis in Japan is a paddy field duckweed that exhibits a latitudinal cline of critical day length (CDL) for short-day flowering. We collected 72 strains of L. aequinoctialis and found a significant correlation between FRPs and locally adaptive CDLs, confirming that variation in the FRP-dependent phase phenotype underlies photoperiodic adaptation. Diel transcriptome analysis revealed that the induction timing of an FT gene is key to connecting the clock phase to photoperiodism at the molecular level. This study highlights the importance of FRP as a variation resource for evolutionary adaptation.

    DOI: 10.1016/j.isci.2022.104634

    PubMed

    researchmap

  5. Characterization of Frond and Flower Development and Identification of FT and FD Genes From Duckweed Lemna aequinoctialis Nd Reviewed International journal

    Akiko Yoshida, Ken-ichiro Taoka, Aoi Hosaka, Keisuke Tanaka, Hisato Kobayashi, Tomoaki Muranaka, Kiminori Toyooka, Tokitaka Oyama, Hiroyuki Tsuji

    Frontiers in Plant Science   Vol. 12   page: 697206 - 697206   2021.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Frontiers Media {SA}  

    <jats:p>Duckweeds (<jats:italic>Araceae: Lemnoideae</jats:italic>) are aquatic monocotyledonous plants that are characterized by their small size, rapid growth, and wide distribution. Developmental processes regulating the formation of their small leaf-like structures, called fronds, and tiny flowers are not well characterized. In many plant species, flowering is promoted by the florigen activation complex, whose major components are florigen FLOWERING LOCUS T (FT) protein and transcription factor FD protein. How this complex is regulated at the molecular level during duckweed flowering is also not well understood. In this study, we characterized the course of developmental changes during frond development and flower formation in <jats:italic>Lemna aequinoctialis</jats:italic> Nd, a short-day plant. Detailed observations of frond and flower development revealed that cell proliferation in the early stages of frond development is active as can be seen in the separate regions corresponding to two budding pouches in the proximal region of the mother frond. <jats:italic>L. aequinoctialis</jats:italic> produces two stamens of different lengths with the longer stamen growing more rapidly. Using high-throughput RNA sequencing (RNA-seq) and <jats:italic>de novo</jats:italic> assembly of transcripts from plants induced to flower, we identified the <jats:italic>L. aequinoctialis FT</jats:italic> and <jats:italic>FD</jats:italic> genes, whose products in other angiosperms form a transcriptional complex to promote flowering. We characterized the protein-protein interaction of duckweed FT and FD in yeast and examined the functions of the two gene products by overexpression in <jats:italic>Arabidopsis</jats:italic>. We found that <jats:italic>L. aequinoctialis</jats:italic> FTL1 promotes flowering, whereas FTL2 suppresses flowering.</jats:p>

    DOI: 10.3389/fpls.2021.697206

    PubMed

    researchmap

  6. Detection of uncoupled circadian rhythms in individual cells of Lemna minor using a dual-color bioluminescence monitoring system. Reviewed

    Emiri Watanabe, Minako Isoda, Tomoaki Muranaka, Shogo Ito, Tokitaka Oyama

    Plant & cell physiology   Vol. 62 ( 5 ) page: 815 - 826   2021.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    The plant circadian oscillation system is based on the circadian clock of individual cells. Circadian behavior of cells has been observed by monitoring the circadian reporter activity such as bioluminescence of AtCCA1::LUC+. To deeply analyze different circadian behaviors in individual cells, we developed the dual-color bioluminescence monitoring system that automatically measured the luminescence of two luciferase reporters simultaneously at a single-cell level. We selected a yellow-green-emitting firefly luciferase (LUC+) and a red-emitting luciferase (PtRLUC) that is a mutant form of Brazilian click beetle ELUC. We used AtCCA1::LUC+ and CaMV35S::PtRLUC. CaMV35S::LUC+ was previously reported as a circadian reporter with a low amplitude rhythm. These bioluminescent reporters were introduced into the cells of a duckweed, Lemna minor, by particle bombardment. Time series of the bioluminescence of individual cells in a frond were obtained using a dual-color bioluminescence monitoring system with a green-pass- and red-pass filter. Luminescence intensities from the LUC+ and PtRLUC of each cell were calculated from the filtered luminescence intensities. We succeeded in reconstructing the bioluminescence behaviors of AtCCA1::LUC+ and CaMV35S::PtRLUC in the same cells. Under prolonged constant light conditions, AtCCA1::LUC+ showed a robust circadian rhythm in individual cells in an asynchronous state in the frond, as previously reported. In contrast, CaMV35S::PtRLUC stochastically showed circadian rhythms in a synchronous state. These results strongly suggested the uncoupling of cellular behavior between these circadian reporters. This dual-color bioluminescence monitoring system is a powerful tool to analyze various stochastic phenomena accompanying large cell-to-cell variation in gene expression.

    DOI: 10.1093/pcp/pcab037

    PubMed

    researchmap

  7. Toward a Practical Theory of Timing: Upbeat and E-Series Time for Organisms Reviewed

    Naoki Nomura, Koichiro Matsuno, Tomoaki Muranaka, Jun Tomita

    Biosemiotics     2020.11

     More details

    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    <title>Abstract</title>Timing adjustment is an important ability for living organisms. Wild animals need to act at the right moment to catch prey or escape a predator. Land plants, although limited in their movement, need to decide the right time to grow and bloom. Humans also need to decide the right moment for social actions. Although scientists can pinpoint the timing of such behaviors by observation, we know extremely little about how living organisms as actors or players decide when to act – such as the exact moment to dash or pounce. The time measurements of an outsider-observer and the insider-participants are utterly different. We explain how such essential operations of timing adjustment and temporal spanning, both of which constitute a single regulated set, can be carried out among organisms. For this purpose, we have to reexamine the ordinary conception of time. Our specific explanatory tools include the natural movement known as the upbeat (<italic>anacrusis</italic>) in music, a rhythmic push for the downbeat that follows, which predicts future moves as an anticipatory lead-in. The scheme is situated in and is the extension of our formulation of E-series time, i.e., timing co-adjusted through interaction, which is derived from the semiotic/communicative perspectives. We thereby demonstrate that a prediction-based timing system is not mechanical but communicative and entails meanings for future anticipation.

    DOI: 10.1007/s12304-020-09398-5

    researchmap

    Other Link: http://link.springer.com/article/10.1007/s12304-020-09398-5/fulltext.html

  8. Application of Single-Cell Bioluminescent Imaging to Monitor Circadian Rhythms of Individual Plant Cells. Invited Reviewed International journal

    Tomoaki Muranaka, Tokitaka Oyama

    Methods in molecular biology (Clifton, N.J.)   Vol. 2081   page: 231 - 242   2020

     More details

    Authorship:Lead author   Language:English  

    The bioluminescent reporter system is a powerful tool for the long-term monitoring of gene expression because of its noninvasive nature. Furthermore, in combination with high-sensitive imaging technology, spatiotemporal analysis on regulation and heterogeneity in gene expression is possible. We developed a single-cell bioluminescent imaging system for plants through a transient gene transfection by particle bombardment. By applying this system to a duckweed species, we succeeded in monitoring circadian rhythms of individual cells in an intact plant for over a week. Here we describe methods for gene transfection by particle bombardment and single-cell bioluminescence monitoring by a high-sensitive camera. This technique provides a platform for characterizing gene expression patterns of individual cells in the same tissue.

    DOI: 10.1007/978-1-4939-9940-8_17

    PubMed

    researchmap

  9. How Does Time Flow in Living Systems? Retrocausal Scaffolding and E-series Time Reviewed

    Nomura, Naoki, Matsuno, Koichiro, Muranaka, Tomoaki, Tomita, Jun

    BIOSEMIOTICS   Vol. 12 ( 2 ) page: 267 - 287   2019.8

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:SPRINGER  

    Anticipatory acts or predictive behavior are prerequisites for living organisms to sustain their survival when escaping from a predator, catching prey, or schooling. For example, catching prey requires that the predator perform some procedures that are equivalent to estimating the directional movement of the prey, its speed and its distance relative to the predator. Underlying these procedures is time experience, which does not adhere to man-made mechanical clocks. Living organisms keep time based on the local activities of each participant and form ecological clocks together. The timekeeping of ecological clocks has been called E-series time, which is interactive in character and consists of mutual alignment of timing that is co-adjusted to each other's movements and rhythms. A main objective of our current work is to illustrate how E-series time is used for flows of anticipatory acts. To explain such predictive moves and their efforts based on how the perspective of the immediate future affects the present, we resort to the organismic activity of revising the preceding acts in retrospect and semiotic scaffolding that extends beyond simple linear causality. Special attention is paid to the construction of the notion of retrocausal scaffolding, which is a series of dialogical punctuations or mutual coordination of rhythms for the joint production of the present moment of now. Retrocausal scaffolding is synonymous with negotiated anticipation, which is a semiotic/communicative account of revising the preceding acts in the present moment.

    DOI: 10.1007/s12304-019-09363-x

    Web of Science

    researchmap

  10. Circadian Regulation of the Plant Transcriptome Under Natural Conditions. Reviewed International journal

    Paige E Panter, Tomoaki Muranaka, David Cuitun-Coronado, Calum A Graham, Aline Yochikawa, Hiroshi Kudoh, Antony N Dodd

    Frontiers in genetics   Vol. 10   page: 1239 - 1239   2019

     More details

    Language:English  

    Circadian rhythms produce a biological measure of the time of day. In plants, circadian regulation forms an essential adaptation to the fluctuating environment. Most of our knowledge of the molecular aspects of circadian regulation in plants is derived from laboratory experiments that are performed under controlled conditions. However, it is emerging that the circadian clock has complex roles in the coordination of the transcriptome under natural conditions, in both naturally occurring populations of plants and in crop species. In this review, we consider recent insights into circadian regulation under natural conditions. We examine how circadian regulation is integrated with the acute responses of plants to the daily and seasonally fluctuating environment that also presents environmental stresses, in order to coordinate the transcriptome and dynamically adapt plants to their continuously changing environment.

    DOI: 10.3389/fgene.2019.01239

    PubMed

    researchmap

  11. Time from Semiosis: E-series Time for Living Systems Reviewed

    Naoki Nomura, Tomoaki Muranaka, Jun Tomita, Koichiro Matsuno

    Biosemiotics   Vol. 11 ( 1 ) page: 65 - 83   2018.4

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Netherlands  

    We develop a semiotic scheme of time, in which time precipitates from the repeated succession of punctuating the progressive tense by the perfect tense. The underlying principle is communication among local participants. Time can thus be seen as a meaning-making, semiotic system in which different time codes are delineated, each having its own grammar and timekeeping. The four time codes discussed are the following: the subjective time having tense, the objective time without tense, the static time without timekeeping, and the inter-subjective time of the E-series. Living organisms adopt a time code called the E-series, which emerges through the local synchronization among organisms or parts of organisms. The inter-subjective time is a new theoretical dimension resulting from the time-aligning activities of interacting agents. Such synchronization in natural settings consists of incessant mutual corrections and adjustments to one’s own punctuation, which is then constantly updated. Unlike the third-person observer keeping the objective time while sitting outside a clock, the second-person negotiators participate in forming the E-series time by punctuating and updating the interface through which different tenses meet at the moment of “now.” Although physics allows physicists to be the only interpreters, the semiotic perspective upends the physical perspective by letting local participants be involved in the interpretation of their mutual negotiations to precipitate that which is called time.

    DOI: 10.1007/s12304-018-9316-0

    Scopus

    PubMed

    researchmap

  12. Monitoring circadian rhythms of individual cells in plants Invited Reviewed

    Tomoaki Muranaka, Tokitaka Oyama

    Journal of Plant Research   Vol. 131 ( 1 ) page: 15 - 21   2018.1

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Tokyo  

    The circadian clock is an endogenous timing system based on the self-sustained oscillation in individual cells. These cellular circadian clocks compose a multicellular circadian system working at respective levels of tissue, organ, plant body. However, how numerous cellular clocks are coordinated within a plant has been unclear. There was little information about behavior of circadian clocks at a single-cell level due to the difficulties in monitoring circadian rhythms of individual cells in an intact plant. We developed a single-cell bioluminescence imaging system using duckweed as the plant material and succeeded in observing behavior of cellular clocks in intact plants for over a week. This imaging technique quantitatively revealed heterogeneous and independent manners of cellular clock behaviors. Furthermore, these quantitative analyses uncovered the local synchronization of cellular circadian rhythms that implied phase-attractive interactions between cellular clocks. The cell-to-cell interaction looked to be too weak to coordinate cellular clocks against their heterogeneity under constant conditions. On the other hand, under light–dark conditions, the heterogeneity of cellular clocks seemed to be corrected by cell-to-cell interactions so that cellular clocks showed a clear spatial pattern of phases at a whole plant level. Thus, it was suggested that the interactions between cellular clocks was an adaptive trait working under day–night cycles to coordinate cellular clocks in a plant body. These findings provide a novel perspective for understanding spatio-temporal architectures in the plant circadian system.

    DOI: 10.1007/s10265-017-1001-x

    Scopus

    PubMed

    researchmap

  13. Early evolution of the land plant circadian clock Reviewed

    Anna-Malin Linde, D. Magnus Eklund, Akane Kubota, Eric R. A. Pederson, Karl Holm, Niclas Gyllenstrand, Ryuichi Nishihama, Nils Cronberg, Tomoaki Muranaka, Tokitaka Oyama, Takayuki Kohchi, Ulf Lagercrantz

    NEW PHYTOLOGIST   Vol. 216 ( 2 ) page: 576 - 590   2017.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY  

    While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis.
    Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants.
    Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha.
    Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.

    DOI: 10.1111/nph.14487

    Web of Science

    PubMed

    researchmap

  14. Synchrony of plant cellular circadian clocks with heterogeneous properties under light/dark cycles Reviewed

    Masaaki Okada, Tomoaki Muranaka, Shogo Ito, Tokitaka Oyama

    SCIENTIFIC REPORTS   Vol. 7 ( 1 ) page: 317   2017.3

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    Individual cells in a plant can work independently as circadian clocks, and their properties are the basis of various circadian phenomena. The behaviour of individual cellular clocks in Lemna gibba was orderly under 24-h light/dark cycles despite their heterogeneous free-running periods (FRPs). Here, we reveal the entrainment habits of heterogeneous cellular clocks using non-24-h light/dark cycles (T-cycles). The cellular rhythms of AtCCA1:: LUC under T = 16 h cycles showed heterogeneous entrainment that was associated with their heterogeneous FRPs. Under T = 12 h cycles, most cells showed rhythms having similar to 24-h periods. This suggested that the lower limit of entrainment to the light/dark cycles of heterogeneous cellular circadian clocks is set to a period longer than 12 h, which enables them to be synchronous under similar to 24-h daily cycles without being perturbed by short light/dark cycles. The entrainment habits of individual cellular clocks are likely to be the basis of the circadian behaviour of plant under the natural day-night cycle with noisy environmental fluctuations. We further suggest that modifications of EARLY FLOWERING3 (ELF3) in individual cells deviate the entrainability to shorter T-cycles possibly by altering both the FRPs and light responsiveness.

    DOI: 10.1038/s41598-017-00454-8

    Web of Science

    PubMed

    researchmap

  15. Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles Reviewed

    Tomoaki Muranaka, Tokitaka Oyama

    SCIENCE ADVANCES   Vol. 2 ( 7 ) page: e1600500   2016.7

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER ASSOC ADVANCEMENT SCIENCE  

    Recent advances in single-cell analysis have revealed the stochasticity and nongenetic heterogeneity inherent to cellular processes. However, our knowledge of the actual cellular behaviors in a living multicellular organism is still limited. By using a single-cell bioluminescence imaging technique on duckweed, Lemna gibba, we demonstrate that, under constant conditions, cells in the intact plant work as individual circadian clocks that oscillate with their own frequencies and respond independently to external stimuli. Quantitative analysis uncovered the heterogeneity and instability of cellular clocks and partial synchronization between neighboring cells. Furthermore, we found that cellular clocks in the plant body under light-dark cycles showed a centrifugal phase pattern in which the effect of cell-to-cell heterogeneity in period lengths was almost masked. The inherent heterogeneity in the properties of cellular clocks observed under constant conditions is corrected under light-dark cycles to coordinate the daily rhythms of the plant body. These findings provide a novel perspective of spatiotemporal architectures in the plant circadian system.

    DOI: 10.1126/sciadv.1600500

    Web of Science

    PubMed

    researchmap

  16. Characterisation of circadian rhythms of various duckweeds Reviewed

    T. Muranaka, M. Okada, J. Yomo, S. Kubota, T. Oyama

    PLANT BIOLOGY   Vol. 17 ( s1 ) page: 66 - 74   2015.1

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-BLACKWELL  

    The plant circadian clock controls various physiological phenomena that are important for adaptation to natural day-night cycles. Many components of the circadian clock have been identified in Arabidopsis thaliana, the model plant for molecular genetic studies. Recent studies revealed evolutionary conservation of clock components in green plants. Homologues of clock-related genes have been isolated from Lemna gibba and Lemna aequinoctialis, and it has been demonstrated that these homologues function in the clock system in a manner similar to their functioning in Arabidopsis. While clock components are widely conserved, circadian phenomena display diversity even within the Lemna genus. In order to survey the full extent of diversity in circadian rhythms among duckweed plants, we characterised the circadian rhythms of duckweed by employing a semi-transient bioluminescent reporter system. Using a particle bombardment method, circadian bioluminescent reporters were introduced into nine strains representing five duckweed species: Spirodela polyrhiza, Landoltia punctata, Lemna gibba, L.aequinoctialis and Wolffia columbiana. We then monitored luciferase (luc+) reporter activities driven by AtCCA1, ZmUBQ1 or CaMV35S promoters under entrainment and free-running conditions. Under entrainment, AtCCA1::luc+ showed similar diurnal rhythms in all strains. This suggests that the mechanism of biological timing under day-night cycles is conserved throughout the evolution of duckweeds. Under free-running conditions, we observed circadian rhythms of AtCCA1::luc+, ZmUBQ1::luc+ and CaMV35S::luc+. These circadian rhythms showed diversity in period length and sustainability, suggesting that circadian clock mechanisms are somewhat diversified among duckweeds.

    DOI: 10.1111/plb.12202

    Web of Science

    PubMed

    researchmap

  17. A Single-Cell Bioluminescence Imaging System for Monitoring Cellular Gene Expression in a Plant Body Reviewed

    Tomoaki Muranaka, Saya Kubota, Tokitaka Oyama

    PLANT AND CELL PHYSIOLOGY   Vol. 54 ( 12 ) page: 2085 - 2093   2013.12

     More details

    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

    Gene expression is a fundamental cellular process and expression dynamics are of great interest in life science. We succeeded in monitoring cellular gene expression in a duckweed plant, Lemna gibba, using bioluminescent reporters. Using particle bombardment, epidermal and mesophyll cells were transfected with the luciferase gene (luc+) under the control of a constitutive [Cauliflower mosaic virus 35S (CaMV35S)] and a rhythmic [Arabidopsis thaliana CIRCADIAN CLOCK ASSOCIATED 1 (AtCCA1)] promoter. Bioluminescence images were captured using an EM-CCD (electron multiply charged couple device) camera. Luminescent spots of the transfected cells in the plant body were quantitatively measured at the single-cell level. Luminescence intensities varied over a 1,000-fold range among CaMV35S::luc+-transfected cells in the same plant body and showed a log-normal-like frequency distribution. We monitored cellular gene expression under light-dark conditions by capturing bioluminescence images every hour. Luminescence traces of &gt;= 50 individual cells in a frond were successfully obtained in each monitoring procedure. Rhythmic and constitutive luminescence behaviors were observed in cells transfected with AtCCA1::luc+ and CaMV35S::luc+, respectively. Diurnal rhythms were observed in every AtCCA1::luc+-introduced cell with traceable luminescence, and slight differences were detected in their rhythmic waveforms. Thus the single-cell bioluminescence monitoring system was useful for the characterization of cellular gene expression in a plant body.

    DOI: 10.1093/pcp/pct131

    Web of Science

    PubMed

    researchmap

▼display all

KAKENHI (Grants-in-Aid for Scientific Research) 8

  1. 比較オミクスによる光周性花成の獲得・多様化の分子機構の解明

    Grant number:23K14253  2023.4 - 2026.3

    日本学術振興会  科学研究費助成事業 若手研究  若手研究

    村中 智明

      More details

    Authorship:Principal investigator 

    Grant amount:\4680000 ( Direct Cost: \3600000 、 Indirect Cost:\1080000 )

    多くの植物分類群で、長日性(春咲き)・短日性(秋咲き)、中日性(日長非依存)が独立に獲得されているが、日長応答の多様化プロセスは不明な点が多い。本研究では、花成制御が多様化しており、ゲノム情報が充実しているウキクサ植物全5属について、花成ホルモンであるFT遺伝子に着目して比較オミクスを実施し、FT遺伝子の発現パターンの多様性とその分子基盤を解明する。

    researchmap

  2. Chronoproteinology: Protein Properties that Define the Day Length Explored in Unicellular Green Algae

    Grant number:21H05131  2021.8 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Transformative Research Areas (B)

      More details

    Authorship:Coinvestigator(s) 

    researchmap

  3. Chrono-proteinology: principle and design for protein timers

    Grant number:21H05129  2021.8 - 2024.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Transformative Research Areas (B)  Grant-in-Aid for Transformative Research Areas (B)

      More details

    Authorship:Coinvestigator(s) 

    researchmap

  4. 概日時計が概日である意義:水田ウキクサ開花時期の多様化・局所適応からの実証

    Grant number:20J00255  2020.4 - 2023.3

    日本学術振興会  科学研究費助成事業 特別研究員奨励費  特別研究員奨励費

    村中 智明

      More details

  5. アオウキクサ属を用いた光周性花成の多様化プロセスの解明

    Grant number:20K15861  2020.4 - 2023.3

    日本学術振興会  科学研究費助成事業 若手研究  若手研究

    村中 智明

      More details

    Authorship:Principal investigator 

    Grant amount:\4160000 ( Direct Cost: \3200000 、 Indirect Cost:\960000 )

    植物の生活史において開花・結実は最重要イベントである。そのため、花成時期は分類学・生態学の双方に重要な形質となる。花成時期の決定要因に、概日時計を基盤とした日長計測による光周性がある。多くの分類群で、長日性(春咲き)・短日性(秋咲き)の両方が見られるが、日長応答の多様化プロセスは不明である。本研究では、古くから光周性の解析に用いられてきたアオウキクサ属のイボウキクサ(長日)・アオウキクサ(短日)の純系株についてゲノムを決定し、ゲノムから表現型まで多階層での比較解析を行う。古くて新しいモデル植物として分子遺伝学の基盤を整備し、光周性花成を中心に種分化プロセスを分子レベルで解明する。
    アオウキクサで見出した花成ホルモンFTのホモログについて、シロイヌナズナでの過剰発現により機能を解析した。過剰発現により花成が著しく促進し、フロリゲンとしての機能が確認された。本ホモログをLaFTh1と命名した。LaFTh1は消灯後11時間後に発現が誘導されるため、夜が11時間以上、つまり日長13時間以下で花成が誘導されると考えられる。昨年度に得たイボウキクサのRNA-seqデータの解析から、LaFTh1のホモログが同定された。発現パターンもアオウキクサと同様であり、短日条件においてのみ夜の後半に発現がみられた。イボウキクサでは長日植物であり、LaFTh1のホモログが発現する短日条件では花成がみられない。イボウキクサのLaFTh1ホモログにはフロリゲン活性がない可能性があり、シロイヌナズナの過剰発現による機能解析を計画している。一方で、イボウキクサが開花する長日条件においてのみ発現が見られる別のFTホモログも検出された。本研究で同定したイボウキクサ、アオウキクサのFTのホモログのタンパク配列情報に加えて、公開データベースに登録されているFT配列のデータを用いて、アミノ酸配列の系統解析を行った。その結果、イボウキクサにおいて長日条件で誘導されるFTホモログがシロイヌナズナのFT、イネのHd3aと同じクレードに入り、アオウキクサのLaFTh1はミナトカモジグサやトウモロコシで報告されているFTホモログと同じクレードに入った。ミナトカモジグサのFTホモログはLaFTh1と同じく、短日条件において夜の後半で誘導されることが報告されている。LaFTh1は単子葉植物で広く保存された、短日条件において夜の後半で誘導されるFTホモログである可能性がある。
    本研究の目的は長日植物と短日植物において日長応答が逆転するメカニズムを明らかとすることである。長日植物であるイボウキクサと、短日植物であるアオウキクサにおいて、花成に関与するFTホモログが異なることが示唆されたことは、日長応答の逆転を理解する上で重要であり、予想以上の成果が得られたと考えている。一方で、当初予定していた光周性を示さないイボウキクサ系統との掛け合わせによる原因変異の同定については、掛け合わせ手法の確立ができず、進んでいない。また、RNA-seqやゲノム解読についても実験条件の検討に手間取り年度内に実施することができなかった。これらを次の年度のはじめに実施し、遅れを取り戻す予定である。全体としては順調に進展していると考えている。
    アオウキクサにおいて光質により光周性応答が異なることが報告されているため、光質を変えてRNA-seqを実施する。また、LaFTh1の発現タイミングを変化させる分子機構を解明するために、限界日長が異なるアオウキクサ系統について、比較RNA-seqを実施する。
    イボウキクサについては、ゲノム配列決定と光周性を示さない系統でのRNA-seqおよびリシーケンスを行う。また、掛け合わせによるQTL-seqを行う。

    researchmap

  6. イネ人為突然変異白葉枯病抵抗性遺伝子の同定と抵抗性機構の解明

    Grant number:19H02934  2019.4 - 2023.3

    日本学術振興会  科学研究費助成事業 基盤研究(B)  基盤研究(B)

    一谷 勝之, 内海 俊樹, 岡本 繁久, 清水 圭一, 志水 勝好, 鈴木 章弘, 村中 智明, 穴井 豊昭, 田浦 悟, 内海 俊樹, 岡本 繁久, 清水 圭一, 志水 勝好, 鈴木 章弘, 村中 智明, 穴井 豊昭, 田浦 悟

      More details

    Authorship:Coinvestigator(s) 

    白葉枯病はイネの最重要病害の一つである.インド型イネ品種IR24はフィリピンの白葉枯病菌6レースと日本の6レースすべてに罹病性であるが,人為突然変異処理によりそれらすべてに抵抗性を示す系統XM5, XM6, XM14が得られている.各系統は劣性の1抵抗性遺伝子を持ち,それぞれxa19, xa20, xa42と命名された. 2021年度の実績を以下に示す.
    (1)イネ品種 日本晴に野生型のXa42遺伝子で形質転換した個体とXM14を交配し,得られたF1個体を自殖させてF2となる種子を得た.また,日本晴にゲノム編集を行い、野生型Xa42遺伝子が変異型遺伝子ホモ接合に変換された個体を複数得た。
    (2)XM14の擬似病斑の組織構造および発達経過を観察した.走査電子顕微鏡で観察したところ表面における異常は観察できなかった.病斑を表皮組織よりも深く分析できるX線解析顕微鏡で観察したところK,Si, CaおよびClについて分布に粗密が見られる試料が見られた.
    (3)通常栽培で播種後25日のXM14, IR24ではROSとNOの両方とも、XM14の方が有意に多かった。擬似病班が出現する条件で栽培して比較したところ、両系統ともに、NO量は通常栽培より有意に高い値を示した。PR1a、PR1b遺伝子の発現は、擬似病斑が出現したXM14で非常に高かった。
    (4)xa19, xa20の候補染色体領域におけるSNPを検出できるようなDNAマーカーを設計し,白葉枯病抵抗性とDNAマーカー遺伝子型の関係を調査した. xa19, xa20, xa42遺伝子 の日本型品種台中65号背景の準同質遺伝子系統,長稈遺伝子と3抵抗性遺伝子を組み合わせたIR24背景の準同質遺伝子系統作りを進め,BC3F1となる種子を得た.

    researchmap

  7. Local adaptation of the critical day length for flowering based on robust and flexible circadian system

    Grant number:16H06864  2016.8 - 2018.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Research Activity start-up  Grant-in-Aid for Research Activity start-up

    Muranaka Tomoaki

      More details

    Authorship:Principal investigator 

    Grant amount:\2990000 ( Direct Cost: \2300000 、 Indirect Cost:\690000 )

    Organisms on the earth detect variation in day-length and anticipate upcoming seasonal changes. The critical day-lengths of photoperiodic responses often show a latitudinal cline due to the local adaptation. In plants, it is well known that the photoperiodic flowering is based on the day-length measurement by the circadian clock. However, the modulation mechanisms of the critical day-length is unclear. Using a short-day duckweed, Lemna aequinoctialis, we found the significant correlation between critical day-lengths and circadian periods. This suggests that the local adaptation of critical day-lengths is likely to involve the modulation of circadian periods.

    researchmap

  8. 1細胞発光イメージングを用いた植物個体内における概日時計ネットワークの解析

    Grant number:12J01530  2012.4 - 2015.3

    日本学術振興会  科学研究費助成事業 特別研究員奨励費  特別研究員奨励費

    村中 智明

      More details

    概日時計は約24時間周期の振動を生成し、それを外環境の昼夜変動へと同調させることで日周的な環境変動への適応を可能としている。植物においても概日時計は光合成や、成長、花成などの主要な生理現象の制御に関与している。植物細胞ではその多くで時計遺伝子が発現しており、細胞一つ一つが細胞時計として振る舞う。しかしながら植物個体中における細胞概日時計の挙動は、その観測の困難さから不明な点が多かった。研究員は自身が開発した一細胞発光イメージングシステムを用いて細胞レベルでの概日時計の解析に取り組んできた。昨年度までに、イボウキクサを材料に解析を行い、昼夜のない定常条件において細胞リズムが脱同期すること、近傍細胞間には位相を近づけようとする相互作用が示唆されるが、その強度は細胞が示す周期のばらつき、不安定性を抑えるほど強くないこと、を明らかとしてきた。
    本年度ではリズム解析手法を改良し、これまでに得られたデータを再評価することで、細胞間における周期のばらつき、及び、周期変動を定量的に記述することに成功した。また、脱同期時の細胞振動子リズムに明暗条件を与え、位相の異なる細胞振動子が外部明暗周期に同調していく過程を観察した。同調過程における細胞概日リズムの挙動は明暗条件前の位相にのみ依存したことから、個体上の細胞は各々の時間情報に従い、独立に明暗条件に同調すると結論づけた。さらに、同調後の明暗条件下において細胞リズムの位相には空間的なパターンが存在することを発見した。このパターンには、同調前のリズムデータから推定された細胞の周期・位相とも明瞭な相関がなく、明暗条件下において細胞の位置情報に基づき新たに形成されたパターンだと考えられた。以上の結果は、これまで知見の乏しかった植物個体内における細胞概日時計の基本的性質を明らかにし、新たな問題設定を可能にする先駆的なものだと考えている。

    researchmap

▼display all

 

Teaching Experience (Off-campus) 2

  1. 環境計測学

    2021.4 - 2022.9 鹿児島大学農学部)

     More details

    前期15回(1コマ)。3年生配当。集合授業形式。必修授業

    researchmap

  2. 計算機基礎実習II

    2018.9 - 2020.3 龍谷大学先端理工学部)

     More details

    非常勤講師として担当。後期15コマ。Rについての解説・実習指導。選択授業。

    researchmap