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  1. Article ; Online: Diving into the Water: Amphibious Plants as a Model for Investigating Plant Adaptations to Aquatic Environments.

    Koga, Hiroyuki / Ikematsu, Shuka / Kimura, Seisuke

    Annual review of plant biology

    2024  

    Abstract: Amphibious plants can grow and survive in both aquatic and terrestrial environments. This review explores the diverse adaptations that enable them to thrive in such contrasting habitats. Plants with amphibious lifestyles possess fascinating traits, and ... ...

    Abstract Amphibious plants can grow and survive in both aquatic and terrestrial environments. This review explores the diverse adaptations that enable them to thrive in such contrasting habitats. Plants with amphibious lifestyles possess fascinating traits, and their phenotypic plasticity plays an important role in adaptations. Heterophylly, the ability to produce different leaf forms, is one such trait, with submerged leaves generally being longer, narrower, and thinner than aerial leaves. In addition to drastic changes in leaf contours, amphibious plants display significant anatomical and physiological changes, including a reduction in stomatal number and cuticle thickness and changes in photosynthesis mode. This review summarizes and compares the regulatory mechanisms and evolutionary origins of amphibious plants based on molecular biology studies actively conducted in recent years using novel model amphibious plant species. Studying amphibious plants will enhance our understanding of plant adaptations to aquatic environments. Expected final online publication date for the
    Language English
    Publishing date 2024-02-29
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2098209-4
    ISSN 1545-2123 ; 1543-5008
    ISSN (online) 1545-2123
    ISSN 1543-5008
    DOI 10.1146/annurev-arplant-062923-024919
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  2. Article: Diversity of tomato leaf form provides novel insights into breeding.

    Nakayama, Hokuto / Ichihashi, Yasunori / Kimura, Seisuke

    Breeding science

    2023  Volume 73, Issue 1, Page(s) 76–85

    Abstract: Tomato ( ...

    Abstract Tomato (
    Language English
    Publishing date 2023-01-20
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 1190370-3
    ISSN 1344-7610 ; 0536-3683
    ISSN 1344-7610 ; 0536-3683
    DOI 10.1270/jsbbs.22061
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia

    Suetsugu, Kenji / Fukushima, Kenji / Makino, Takashi / Ikematsu, Shuka / Sakamoto, Tomoaki / Kimura, Seisuke

    New Phytologist. 2023 Jan., v. 237, no. 1 p.323-338

    2023  

    Abstract: Cleistogamy, in which plants can reproduce via self‐fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy – the production of only ... ...

    Abstract Cleistogamy, in which plants can reproduce via self‐fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy – the production of only cleistogamous flowers – has rarely been recognized. Thus far, the achlorophyllous orchid genus, Gastrodia, is the only known genus with several plausible completely cleistogamous species. Here, we analyzed the floral developmental transcriptomes of two recently evolved, completely cleistogamous Gastrodia species and their chasmogamous sister species to elucidate the possible changes involved in producing common cleistogamous traits. The ABBA‐BABA test did not support introgression and protein sequence convergence as evolutionary mechanisms leading to cleistogamy, leaving convergence in gene expression as a plausible mechanism. Regarding transcriptomic differentiation, the two cleistogamous species had common modifications in the expression of developmental regulators, exhibiting a gene family‐wide signature of convergent expression changes in MADS‐box genes. Our transcriptomic pseudotime analysis revealed a prolonged juvenile state and eventual maturation, a heterochronic pattern consistent with partial neoteny, in cleistogamous flower development. These findings indicate that transcriptomic partial neoteny, arising from changes in the expression of conserved developmental regulators, might have contributed to the rapid and repeated evolution of cleistogamous flowers in Gastrodia.
    Keywords Gastrodia ; amino acid sequences ; cleistogamy ; flowering ; gene expression ; genes ; introgression ; juveniles ; neoteny ; selfing ; symbiosis ; transcriptome ; transcriptomics
    Language English
    Dates of publication 2023-01
    Size p. 323-338.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.18495
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  4. Article ; Online: Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control.

    Mishima, Yuichiro / Han, Peixun / Ishibashi, Kota / Kimura, Seisuke / Iwasaki, Shintaro

    The EMBO journal

    2022  Volume 41, Issue 5, Page(s) e109256

    Abstract: The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame determines mRNA stability in multiple organisms. Based on genome-wide correlation ... ...

    Abstract The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame determines mRNA stability in multiple organisms. Based on genome-wide correlation approaches, this previously unrecognized role for the genetic code is attributable to the kinetics of the codon-decoding process by the ribosome. However, complementary experimental analyses are required to clarify the codon effects on mRNA stability and the related cotranslational mRNA decay pathways, for example, those triggered by aberrant ribosome stalling. In the current study, we performed a set of reporter-based analyses to define codon-mediated mRNA decay and ribosome stall-dependent mRNA decay in zebrafish embryos. Our analysis showed that the effect of codons on mRNA stability stems from the decoding process, independent of the ribosome quality control factor Znf598 and stalling-dependent mRNA decay. We propose that codon-mediated mRNA decay is rather triggered by transiently slowed ribosomes engaging in a productive translation cycle in zebrafish embryos.
    MeSH term(s) Amino Acid Sequence ; Animals ; Codon/genetics ; Open Reading Frames/genetics ; Protein Biosynthesis/genetics ; Quality Control ; RNA Stability/genetics ; RNA, Messenger/genetics ; Ribosomes/genetics ; Zebrafish/genetics
    Chemical Substances Codon ; RNA, Messenger
    Language English
    Publishing date 2022-01-18
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 586044-1
    ISSN 1460-2075 ; 0261-4189
    ISSN (online) 1460-2075
    ISSN 0261-4189
    DOI 10.15252/embj.2021109256
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1808: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 100: Show issues

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  5. Article ; Online: Plant Temperature Sensors.

    Sakamoto, Tomoaki / Kimura, Seisuke

    Sensors (Basel, Switzerland)

    2018  Volume 18, Issue 12

    Abstract: Temperature is one of the most important environmental signals for plants. High and low temperatures have a variety of effects that affect plant growth and development profoundly. Further, temperature is an indication of seasonal change. Plants must ... ...

    Abstract Temperature is one of the most important environmental signals for plants. High and low temperatures have a variety of effects that affect plant growth and development profoundly. Further, temperature is an indication of seasonal change. Plants must survive under severe conditions in winter and prepare to resume growth and reach their reproductive stage in the following spring. Recent studies have focused on plant mechanisms responsible for sensing temperature and the molecular systems underlying plant reactions in response to this signal. In this review, we describe how plants sense ambient temperature to adapt to ambient-temperature changes.
    Language English
    Publishing date 2018-12-10
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2052857-7
    ISSN 1424-8220 ; 1424-8220
    ISSN (online) 1424-8220
    ISSN 1424-8220
    DOI 10.3390/s18124365
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  6. Article ; Online: Leaf Cell Morphology Alternation in Response to Environmental Signals in

    Sakamoto, Tomoaki / Ikematsu, Shuka / Namie, Kazuki / Hou, Hongwei / Li, Gaojie / Kimura, Seisuke

    International journal of molecular sciences

    2022  Volume 23, Issue 18

    Abstract: Heterophylly, the phenomenon by which plants alter leaf forms to adapt to surrounding conditions, is apparent in amphibious plant species. In response to submergence, they emerge leaves with narrower blade areas. The pathway that receives the submergence ...

    Abstract Heterophylly, the phenomenon by which plants alter leaf forms to adapt to surrounding conditions, is apparent in amphibious plant species. In response to submergence, they emerge leaves with narrower blade areas. The pathway that receives the submergence signals and the mechanism regulating leaf form via cell proliferation and/or expansion systems have not yet been fully identified yet. Our anatomical study of
    MeSH term(s) Adaptation, Physiological ; Gene Expression Regulation, Plant ; Mesophyll Cells ; Plant Leaves/metabolism ; Plants ; Rorippa/metabolism
    Language English
    Publishing date 2022-09-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms231810401
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  7. Article ; Online: Transcriptomic heterochrony and completely cleistogamous flower development in the mycoheterotrophic orchid Gastrodia.

    Suetsugu, Kenji / Fukushima, Kenji / Makino, Takashi / Ikematsu, Shuka / Sakamoto, Tomoaki / Kimura, Seisuke

    The New phytologist

    2022  Volume 237, Issue 1, Page(s) 323–338

    Abstract: Cleistogamy, in which plants can reproduce via self-fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy - the production of only ... ...

    Abstract Cleistogamy, in which plants can reproduce via self-fertilization within permanently closed flowers, has evolved in > 30 angiosperm lineages; however, consistent with Darwin's doubts about its existence, complete cleistogamy - the production of only cleistogamous flowers - has rarely been recognized. Thus far, the achlorophyllous orchid genus, Gastrodia, is the only known genus with several plausible completely cleistogamous species. Here, we analyzed the floral developmental transcriptomes of two recently evolved, completely cleistogamous Gastrodia species and their chasmogamous sister species to elucidate the possible changes involved in producing common cleistogamous traits. The ABBA-BABA test did not support introgression and protein sequence convergence as evolutionary mechanisms leading to cleistogamy, leaving convergence in gene expression as a plausible mechanism. Regarding transcriptomic differentiation, the two cleistogamous species had common modifications in the expression of developmental regulators, exhibiting a gene family-wide signature of convergent expression changes in MADS-box genes. Our transcriptomic pseudotime analysis revealed a prolonged juvenile state and eventual maturation, a heterochronic pattern consistent with partial neoteny, in cleistogamous flower development. These findings indicate that transcriptomic partial neoteny, arising from changes in the expression of conserved developmental regulators, might have contributed to the rapid and repeated evolution of cleistogamous flowers in Gastrodia.
    Language English
    Publishing date 2022-10-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.18495
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    In stock of ZB MED Bonn / Germany

    Z 868: Show issues

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  8. Article ; Online: Non-cell-autonomous regulation of petal initiation in Arabidopsis thaliana.

    Takeda, Seiji / Hamamura, Yuki / Sakamoto, Tomoaki / Kimura, Seisuke / Aida, Mitsuhiro / Higashiyama, Tetsuya

    Development (Cambridge, England)

    2022  Volume 149, Issue 17

    Abstract: In many flowering plants, petals initiate in alternate positions from first whorl sepals, suggesting possible signaling between sepal boundaries and petal initiation sites. PETAL LOSS (PTL) and RABBIT EARS (RBE) regulate petal initiation in Arabidopsis ... ...

    Abstract In many flowering plants, petals initiate in alternate positions from first whorl sepals, suggesting possible signaling between sepal boundaries and petal initiation sites. PETAL LOSS (PTL) and RABBIT EARS (RBE) regulate petal initiation in Arabidopsis thaliana and their transcripts are expressed in sepal boundary and petal initiation sites, respectively, suggesting that PTL acts in a non-cell-autonomous manner. Here, we determined that cells expressing PTL and RBE fusion proteins did not overlap but were adjacent, confirming the non-cell-autonomous function of PTL. Genetic ablation of intersepal cells by expressing the diphtheria toxin-A chain gene driven by the PTL promoter resulted in flowers lacking petals, suggesting these cells are required for petal initiation. Transcriptome analysis combined with a PTL induction system revealed 42 genes that were upregulated under PTL activation, including UNUSUAL FLORAL ORGANS (UFO), which likely plays an important role in petal initiation. These findings suggest a molecular mechanism in which PTL indirectly regulates petal initiation and UFO mediates positional signaling between the sepal boundary and petal initiation sites.
    MeSH term(s) Arabidopsis/metabolism ; Arabidopsis Proteins/metabolism ; Flowers/genetics ; Flowers/metabolism ; Gene Expression Regulation, Plant/genetics ; Promoter Regions, Genetic/genetics ; Transcription Factors/metabolism
    Chemical Substances Arabidopsis Proteins ; Transcription Factors
    Language English
    Publishing date 2022-09-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 90607-4
    ISSN 1477-9129 ; 0950-1991
    ISSN (online) 1477-9129
    ISSN 0950-1991
    DOI 10.1242/dev.200684
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    Ub I Zs.183: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
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  9. Article: Heterophylly: Phenotypic Plasticity of Leaf Shape in Aquatic and Amphibious Plants

    Li, Gaojie / Hu, Shiqi / Hou, Hongwei / Kimura, Seisuke

    Plants. 2019 Oct. 16, v. 8, no. 10

    2019  

    Abstract: Leaves show great diversity in shape, size, and color in nature. Interestingly, many plant species have the ability to alter their leaf shape in response to their surrounding environment. This phenomenon is termed heterophylly, and is thought to be an ... ...

    Abstract Leaves show great diversity in shape, size, and color in nature. Interestingly, many plant species have the ability to alter their leaf shape in response to their surrounding environment. This phenomenon is termed heterophylly, and is thought to be an adaptive feature to environmental heterogeneity in many cases. Heterophylly is widespread among land plants, and is especially dominant in aquatic and amphibious plants. Revealing the mechanisms underlying heterophylly would provide valuable insight into the interaction between environmental conditions and plant development. Here, we review the history and recent progress of research on heterophylly in aquatic and amphibious plants.
    Keywords color ; embryophytes ; environmental factors ; leaves ; phenotypic plasticity ; plant development
    Language English
    Dates of publication 2019-1016
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants8100420
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: SOG1, a plant‐specific master regulator of DNA damage responses, originated from nonvascular land plants

    Sakamoto, Ayako N. / Sakamoto, Tomoaki / Yokota, Yuichiro / Teranishi, Mika / Yoshiyama, Kaoru O. / Kimura, Seisuke

    Plant direct. 2021 Dec., v. 5, no. 12

    2021  

    Abstract: The suppressor of gamma response 1 (SOG1), a NAM, ATAF1, 2, and CUC2 (NAC)‐type transcription factor found in seed plants, is a master regulator of DNA damage responses (DDRs). Upon DNA damage, SOG1 regulates the expression of downstream DDR genes. To ... ...

    Abstract The suppressor of gamma response 1 (SOG1), a NAM, ATAF1, 2, and CUC2 (NAC)‐type transcription factor found in seed plants, is a master regulator of DNA damage responses (DDRs). Upon DNA damage, SOG1 regulates the expression of downstream DDR genes. To know the origin of the DDR network in land plants, we searched for a homolog(s) of SOG1 in a moss Physcomitrium (Physcomitrella) patens and identified PpSOG1a and PpSOG1b. To assess if either or both of them function(s) in DDR, we knocked out the PpSOG1s using CRISPR/Cas9‐mediated gene editing and analyzed the responses to DNA‐damaging treatments. The double‐knockout (KO) sog1a sog1b plants showed resistance to γ‐rays, bleomycin, and ultraviolet B (UVB) treatments similarly seen in Arabidopsis sog1 plants. Next, we irradiated wild‐type (WT) and KO plants with γ‐rays and analyzed the whole transcriptome to examine the effect on the expression of DDR genes. The results revealed that many P. patens genes involved in the checkpoint, DNA repair, replication, and cell cycle‐related genes were upregulated after γ‐irradiation, which was not seen in sog1a sog1b plant. These results suggest that PpSOG1a and PpSOG1b work redundantly on DDR response in P. patens; in addition, plant‐specific DDR systems had been established before the emergence of vascular plants.
    Keywords Arabidopsis ; CRISPR-Cas systems ; DNA damage ; DNA repair ; Physcomitrella ; Physcomitrium ; genes ; mosses and liverworts ; transcription factors ; transcriptome ; ultraviolet radiation
    Language English
    Dates of publication 2021-12
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ISSN 2475-4455
    DOI 10.1002/pld3.370
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