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Kiprono D, Thagun C, Kodama Y. Light-dependent chloroplast relocation in wild strawberry ( Fragaria vesca). PLANT SIGNALING & BEHAVIOR 2024; 19:2342744. [PMID: 38630633 PMCID: PMC11028000 DOI: 10.1080/15592324.2024.2342744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Chloroplast photorelocation is a vital organellar response that optimizes photosynthesis in plants amid fluctuating environmental conditions. Chloroplasts exhibit an accumulation response, in which they move toward weak light to enhance photoreception, and an avoidance response, in which they move away from strong light to avoid photodamage. Although chloroplast photorelocation has been extensively studied in model plants such as Arabidopsis thaliana, little is known about this process in the economically important crop strawberry. Here, we investigated chloroplast photorelocation in leaf mesophyll cells of wild strawberry (Fragaria vesca), a diploid relative of commercially cultivated octoploid strawberry (F. × ananassa). Microscopy observation revealed that the periclinal area of leaf mesophyll cells in F. vesca is considerably smaller than that of A. thaliana. Given this small cell size, we investigated chloroplast photorelocation in F. vesca by measuring light transmittance in leaves. Weak blue light induced the accumulation response, whereas strong blue light induced the avoidance response. Unexpectedly, strong red light also induced the accumulation response in F. vesca. These findings shed light on chloroplast photorelocation as an intracellular response, laying the foundation for enhancing photosynthesis and productivity in Fragaria.
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Affiliation(s)
- Daisy Kiprono
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
- Department of Biological Sciences, School of Pure and Applied Sciences, Meru University of Science and Technology, Meru, Kenya
| | - Chonprakun Thagun
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
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2
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Hirano S, Noguchi M, Thagun C, Nishio H, Kodama Y. Levels of photoactivated phototropin modulate signal transmission during the chloroplast accumulation response. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38736289 DOI: 10.1111/pce.14948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
Chloroplasts accumulate in regions of plant cells exposed to irradiation to maximize light reception for efficient photosynthesis. This response is mediated by the blue-light receptor phototropin. Upon the perception of blue light, phototropin is photoactivated, an unknown signal is transmitted from the photoactivated phototropin to distant chloroplasts, and the chloroplasts begin their directional movement. How activated phototropin initiates this signal transmission is unknown. Here, using the liverwort Marchantia polymorpha, we analysed whether increased photoactive phototropin levels mediate signal transmission and chloroplast behaviour during the accumulation response. The signal transmission rate was higher in transgenic cells overexpressing phototropin than in wild-type cells. However, the chloroplast directional movement was similar between wild-type and transgenic cells. Consistent with the observation, increasing the amount of photoactivated phototropin through higher blue-light intensity also accelerated signal transmission but did not affect chloroplast behaviour in wild-type cells. Photoactivation of phototropin under weak blue-light led to the greater protein level of phosphorylated phototropin in cells overexpressing phototropin than in wild-type cells, whereas the autophosphorylation level within each phototropin molecule was similar. These results indicate that the abundance of photoactivated phototropin modulates the signal transmission rate to distant chloroplasts but does not affect chloroplast behaviour during the accumulation response.
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Affiliation(s)
- Satoyuki Hirano
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
- Graduate School of Regional Development and Creativity, Utsunomiya University, Tochigi, Japan
| | - Minoru Noguchi
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
- Graduate School of Regional Development and Creativity, Utsunomiya University, Tochigi, Japan
| | - Chonprakun Thagun
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
| | - Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga, Japan
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, Japan
- Graduate School of Regional Development and Creativity, Utsunomiya University, Tochigi, Japan
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3
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Gu X, Li L, Zhong X, Su Y, Wang T. The size diversity of the Pteridaceae family chloroplast genome is caused by overlong intergenic spacers. BMC Genomics 2024; 25:396. [PMID: 38649816 PMCID: PMC11036588 DOI: 10.1186/s12864-024-10296-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND While the size of chloroplast genomes (cpDNAs) is often influenced by the expansion and contraction of inverted repeat regions and the enrichment of repeats, it is the intergenic spacers (IGSs) that appear to play a pivotal role in determining the size of Pteridaceae cpDNAs. This provides an opportunity to delve into the evolution of chloroplast genomic structures of the Pteridaceae family. This study added five Pteridaceae species, comparing them with 36 published counterparts. RESULTS Poor alignment in the non-coding regions of the Pteridaceae family was observed, and this was attributed to the widespread presence of overlong IGSs in Pteridaceae cpDNAs. These overlong IGSs were identified as a major factor influencing variations in cpDNA size. In comparison to non-expanded IGSs, overlong IGSs exhibited significantly higher GC content and were rich in repetitive sequences. Species divergence time estimations suggest that these overlong IGSs may have already existed during the early radiation of the Pteridaceae family. CONCLUSIONS This study reveals new insights into the genetic variation, evolutionary history, and dynamic changes in the cpDNA structure of the Pteridaceae family, providing a fundamental resource for further exploring its evolutionary research.
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Affiliation(s)
- Xiaolin Gu
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Lingling Li
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Xiaona Zhong
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China.
- Research Institute of Sun Yat-sen University in Shenzhen, 518057, Shenzhen, China.
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, 510642, Guangzhou, China.
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Kimura I, Kanegae T. A phytochrome/phototropin chimeric photoreceptor promotes growth of fern gametophytes under limited light conditions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2403-2416. [PMID: 38189579 DOI: 10.1093/jxb/erae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/06/2024] [Indexed: 01/09/2024]
Abstract
Many ferns thrive even in low-light niches such as under an angiosperm forest canopy. However, the shade adaptation strategy of ferns is not well understood. Phytochrome 3/neochrome (phy3/neo) is an unconventional photoreceptor, found in the fern Adiantum capillus-veneris, that controls both red and blue light-dependent phototropism and chloroplast photorelocation, which are considered to improve photosynthetic efficiency in ferns. Here we show that phy3/neo localizes not only at the plasma membrane but also in the nucleus. Since both phototropism and chloroplast photorelocation are mediated by membrane-associated phototropin photoreceptors, we speculated that nucleus-localized phy3/neo possesses a previously undescribed biological function. We reveal that phy3/neo directly interacts with Adiantum cryptochrome 3 (cry3) in the nucleus. Plant cryptochromes are blue light receptors that transcriptionally regulate photomorphogenesis; therefore, phy3/neo may function via cry3 to synchronize light-mediated development with phototropism and chloroplast photorelocation to promote fern growth under low-light conditions. Furthermore, we demonstrate that phy3/neo regulates the expression of the Cyclin-like gene AcCyc1 and promotes prothallium expansion growth. These findings provide insight into the shade adaptation strategy of ferns and suggest that phy3/neo plays a substantial role in the survival and growth of ferns during the tiny gametophytic stage under low-light conditions, such as those on the forest floor.
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Affiliation(s)
- Izumi Kimura
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Takeshi Kanegae
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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5
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Shi Y, Feng Y, Wang Q, Dong G, Xia W, Jiang F. The Role of tRNA-Centered Translational Regulatory Mechanisms in Cancer. Cancers (Basel) 2023; 16:77. [PMID: 38201505 PMCID: PMC10778012 DOI: 10.3390/cancers16010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. While numerous factors have been identified as contributing to the development of malignancy, our understanding of the mechanisms involved remains limited. Early cancer detection and the development of effective treatments are therefore critical areas of research. One class of molecules that play a crucial role in the transmission of genetic information are transfer RNAs (tRNAs), which are the most abundant RNA molecules in the human transcriptome. Dysregulated synthesis of tRNAs directly results in translation disorders and diseases, including cancer. Moreover, various types of tRNA modifications and the enzymes responsible for these modifications have been implicated in tumor biology. Furthermore, alterations in tRNA modification can impact tRNA stability, and impaired stability can prompt the cleavage of tRNAs into smaller fragments known as tRNA fragments (tRFs). Initially believed to be random byproducts lacking any physiological function, tRFs have now been redefined as non-coding RNA molecules with distinct roles in regulating RNA stability, translation, target gene expression, and other biological processes. In this review, we present recent findings on translational regulatory models centered around tRNAs in tumors, providing a deeper understanding of tumorigenesis and suggesting new directions for cancer treatment.
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Affiliation(s)
- Yuanjian Shi
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Qinglin Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
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6
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Veljović Jovanović S, Kasalica B, Miletić K, Vidović M, Šušić N, Jeremić D, Belča I. Red-Light Transmittance Changes in Variegated Pelargonium zonale-Diurnal Variation in Chloroplast Movement and Photosystem II Efficiency. Int J Mol Sci 2023; 24:14265. [PMID: 37762566 PMCID: PMC10532150 DOI: 10.3390/ijms241814265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Chloroplast movement rapidly ameliorates the effects of suboptimal light intensity by accumulating along the periclinal cell walls, as well as the effects of excess light by shifting to the anticlinal cell walls. These acclimation responses are triggered by phototropins located at the plasma membrane and chloroplast envelope. Here, we used a recently developed non-invasive system sensitive to very small changes in red light leaf transmittance to perform long-term continuous measurements of dark-light transitions. As a model system, we used variegated Pelargonium zonale leaves containing green sectors (GS) with fully developed chloroplasts and achlorophyllous, white sectors (WS) with undifferentiated plastids, and higher phototropin expression levels. We observed biphasic changes in the red-light transmittance and oscillations triggered by medium intensities of white light, described by a transient peak preceded by a constant decrease in transmittance level. A slight change in red-light transmittance was recorded even in WS. Furthermore, the chloroplast position at lower light intensities affected the rapid light curves, while high light intensity decreased saturated electron transport, maximum quantum efficiency of photosystem II, and increased non-photochemical quenching of chlorophyll fluorescence and epidermal flavonoids. Our results extend the knowledge of light-dependent chloroplast movements and thus contribute to a better understanding of their role in regulating photosynthesis under fluctuating light conditions.
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Affiliation(s)
| | - Bećko Kasalica
- Faculty of Physics, University of Belgrade, 11001 Belgrade, Serbia; (B.K.); (K.M.); (I.B.)
| | - Katarina Miletić
- Faculty of Physics, University of Belgrade, 11001 Belgrade, Serbia; (B.K.); (K.M.); (I.B.)
| | - Marija Vidović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia;
| | - Nikola Šušić
- Institute for Multidisciplinary Research, University of Belgrade, 11030 Belgrade, Serbia;
| | - Dejan Jeremić
- Innovation Center of the Faculty of Chemistry, University of Belgrade, 11001 Belgrade, Serbia;
| | - Ivan Belča
- Faculty of Physics, University of Belgrade, 11001 Belgrade, Serbia; (B.K.); (K.M.); (I.B.)
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7
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Nishio H, Hirano S, Kodama Y. Statistical analysis of organelle movement using state-space models. PLANT METHODS 2023; 19:67. [PMID: 37407985 DOI: 10.1186/s13007-023-01038-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/12/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Organelle motility is essential for the correct cellular function of various eukaryotic cells. In plant cells, chloroplasts move towards the intracellular area irradiated by a weak light to maximise photosynthesis. To initiate this process, an unknown signal is transferred from the irradiated area to distant chloroplasts. Quantification of this chloroplast movement has been performed using visual estimations that are analyst-dependent and labour-intensive. Therefore, an objective and faster method is required. RESULTS In this study, we developed the cellssm package of R ( https://github.com/hnishio/cellssm.git ), which is a user-friendly tool for state-space modelling to statistically analyse the directional movement of cells or organelles. Our method showed a high accuracy in estimating the start time of chloroplast movement in the liverwort Marchantia polymorpha over a short period. The tool indicated that chloroplast movement accelerates during transport to the irradiated area and that signal transfer speed is uneven within a cell. We also developed a method to estimate the common dynamics among multiple chloroplasts in each cell, which clarified different characteristics among cells. CONCLUSIONS We demonstrated that state-space modelling is a powerful method to understand organelle movement in eukaryotic cells. The cellssm package can be applied to various directional movements (both accumulation and avoidance) at cellular and subcellular levels to estimate the true transition of states behind the time-series data.
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Affiliation(s)
- Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga, 522‑8522, Japan.
- Center for Ecological Research, Kyoto University, Shiga, 520‑2113, Japan.
| | - Satoyuki Hirano
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
- Graduate School of Regional Development and Creativity, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan.
- Graduate School of Regional Development and Creativity, Utsunomiya University, Tochigi, 321-8505, Japan.
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8
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Cannon AE, Sabharwal T, Salmi ML, Chittari GK, Annamalai V, Leggett L, Morris H, Slife C, Clark G, Roux SJ. Two distinct light-induced reactions are needed to promote germination in spores of Ceratopteris richardii. FRONTIERS IN PLANT SCIENCE 2023; 14:1150199. [PMID: 37332704 PMCID: PMC10272463 DOI: 10.3389/fpls.2023.1150199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]
Abstract
Germination of Ceratopteris richardii spores is initiated by light and terminates 3-4 days later with the emergence of a rhizoid. Early studies documented that the photoreceptor for initiating this response is phytochrome. However, completion of germination requires additional light input. If no further light stimulus is given after phytochrome photoactivation, the spores do not germinate. Here we show that a crucial second light reaction is required, and its function is to activate and sustain photosynthesis. Even in the presence of light, blocking photosynthesis with DCMU after phytochrome photoactivation blocks germination. In addition, RT-PCR showed that transcripts for different phytochromes are expressed in spores in darkness, and the photoactivation of these phytochromes results in the increased transcription of messages encoding chlorophyll a/b binding proteins. The lack of chlorophyll-binding protein transcripts in unirradiated spores and their slow accumulation makes it unlikely that photosynthesis is required for the initial light reaction. This conclusion is supported by the observation that the transient presence of DCMU, only during the initial light reaction, had no effect on germination. Additionally, the [ATP] in Ceratopteris richardii spores increased coincidentally with the length of light treatment during germination. Overall, these results support the conclusion that two distinct light reactions are required for the germination of Ceratopteris richardii spores.
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9
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Hanba YT, Nishida K, Tsutsui Y, Matsumoto M, Yasui Y, Sizhe Y, Matsuura T, Kawaguchi Akitsu T, Kume A. Leaf optical properties and photosynthesis of fern species with a wide range of divergence time in relation to mesophyll anatomy. ANNALS OF BOTANY 2023; 131:437-450. [PMID: 36749684 PMCID: PMC10072100 DOI: 10.1093/aob/mcad025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS For a comprehensive understanding of the mechanisms of changing plant photosynthetic capacity during plant evolutionary history, knowledge of leaf gas exchange and optical properties are essential, both of which relate strongly to mesophyll anatomy. Although ferns are suitable for investigating the evolutionary history of photosynthetic capacity, comprehensive research of fern species has yet to be undertaken in this regard. METHODS We investigated leaf optical properties, gas exchange and mesophyll anatomy of fern species with a wide range of divergence time, using 66 ferns from natural habitats and eight glasshouse-grown ferns. We used a spectroradiometer and an integrating sphere to measure light absorptance and reflectance by the leaves. KEY RESULTS The more newly divergent fern species had a thicker mesophyll, a larger surface area of chloroplasts facing the intercellular airspaces (Sc), thicker cell walls and large light absorptance. Although no trend with divergence time was obtained in leaf photosynthetic capacity on a leaf-area basis, when the traits were expressed on a mesophyll-thickness basis, trends in leaf photosynthetic capacity became apparent. On a mesophyll-thickness basis, the more newly divergent species had a low maximum photosynthesis rate, accompanied by a low Sc. CONCLUSIONS We found a strong link between light capture, mesophyll anatomy and photosynthesis rate in fern species for the first time. The thick mesophyll of the more newly divergent ferns does not necessarily relate to the high photosynthetic capacity on a leaf-area basis. Rather, the thick mesophyll accompanied by thick cell walls allowed the ferns to adapt to a wider range of environments through increasing leaf toughness, which would contribute to the diversification of fern species.
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Affiliation(s)
- Yuko T Hanba
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Keisuke Nishida
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yuuri Tsutsui
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Mayu Matsumoto
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yutarou Yasui
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Yang Sizhe
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Takumi Matsuura
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Tomoko Kawaguchi Akitsu
- Earth Observation Research Center, Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba 305-8505, Japan
| | - Atsushi Kume
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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10
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Frangedakis E, Marron AO, Waller M, Neubauer A, Tse SW, Yue Y, Ruaud S, Waser L, Sakakibara K, Szövényi P. What can hornworts teach us? FRONTIERS IN PLANT SCIENCE 2023; 14:1108027. [PMID: 36968370 PMCID: PMC10030945 DOI: 10.3389/fpls.2023.1108027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.
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Affiliation(s)
| | - Alan O. Marron
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Anna Neubauer
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Sze Wai Tse
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Yuling Yue
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Stephanie Ruaud
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Lucas Waser
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | | | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
- Zurich-Basel Plant Science Center, Zurich, Switzerland
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11
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Tian K, Chai P, Wang Y, Chen L, Qian H, Chen S, Mi X, Ren H, Ma K, Chen J. Species diversity pattern and its drivers of the understory herbaceous plants in a Chinese subtropical forest. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1113742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Understory herbaceous plants are an important component of forest ecosystems, playing important roles in species diversity and forest dynamics in forests. However, the current understanding of the biodiversity of forest communities is mostly from woody plants, and knowledge of community structure and species diversity for understory herbaceous plants remains scarce. In a subtropical forest in China, we investigated understory vascular herbaceous diversity from 300 plots (5 × 5 m) in the main growing season. In this study, we analyzed the community structure and diversity pattern of the understory herbaceous community and linked the species diversity pattern to both abiotic and biotic environments. We found a rich diversity of understory herbaceous communities in this forest (81 species belonging to 55 genera), and floristic elements at the genus level were dominated by tropical elements, followed by temperate elements. The diversity pattern of the understory herbaceous showed a significant habitat preference, with the highest diversity in the lowland valleys and then followed by in middle slopes. In addition, herbaceous diversity was significantly affected by both abiotic factors (such as terrain convexity) and biotic factors (such as the diversity of surrounding woody plants). Our study indicated that species diversity of understory herbaceous showed a remarkable habitat preference, such as lowland valleys, and highlighted the importance of both abiotic and biotic environments in driving herbaceous diversity patterns in the subtropical forest understory.
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12
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Łabuz J, Sztatelman O, Hermanowicz P. Molecular insights into the phototropin control of chloroplast movements. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6034-6051. [PMID: 35781490 DOI: 10.1093/jxb/erac271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Chloroplast movements are controlled by ultraviolet/blue light through phototropins. In Arabidopsis thaliana, chloroplast accumulation at low light intensities and chloroplast avoidance at high light intensities are observed. These responses are controlled by two homologous photoreceptors, the phototropins phot1 and phot2. Whereas chloroplast accumulation is triggered by both phototropins in a partially redundant manner, sustained chloroplast avoidance is elicited only by phot2. Phot1 is able to trigger only a small, transient chloroplast avoidance, followed by the accumulation phase. The source of this functional difference is not fully understood at either the photoreceptor or the signalling pathway levels. In this article, we review current understanding of phototropin functioning and try to dissect the differences that result in signalling to elicit two distinct chloroplast responses. First, we focus on phototropin structure and photochemical and biochemical activity. Next, we analyse phototropin expression and localization patterns. We also summarize known photoreceptor systems controlling chloroplast movements. Finally, we focus on the role of environmental stimuli in controlling phototropin activity. All these aspects impact the signalling to trigger chloroplast movements and raise outstanding questions about the mechanism involved.
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Affiliation(s)
- Justyna Łabuz
- Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego, Warszawa, Poland
| | - Paweł Hermanowicz
- Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa, Kraków, Poland
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13
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Hong Y, Wang Z, Li M, Su Y, Wang T. First Multi-Organ Full-Length Transcriptome of Tree Fern Alsophila spinulosa Highlights the Stress-Resistant and Light-Adapted Genes. Front Genet 2022; 12:784546. [PMID: 35186007 PMCID: PMC8854977 DOI: 10.3389/fgene.2021.784546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Alsophila spinulosa, a relict tree fern, is a valuable plant for investigating environmental adaptations. Its genetic resources, however, are scarce. We used the PacBio and Illumina platforms to sequence the polyadenylated RNA of A. spinulosa root, rachis, and pinna, yielding 125,758, 89,107, and 89,332 unigenes, respectively. Combining the unigenes from three organs yielded a non-redundant reference transcriptome with 278,357 unigenes and N50 of 4141 bp, which were further reconstructed into 38,470 UniTransModels. According to functional annotation, pentatricopeptide repeat genes and retrotransposon-encoded polyprotein genes are the most abundant unigenes. Clean reads mapping to the full-length transcriptome is used to assess the expression of unigenes. The stress-induced ASR genes are highly expressed in all three organs, which is validated by qRT-PCR. The organ-specific upregulated genes are enriched for pathways involved in stress response, secondary metabolites, and photosynthesis. Genes for five types of photoreceptors, CRY signaling pathway, ABA biosynthesis and transduction pathway, and stomatal movement-related ion channel/transporter are profiled using the high-quality unigenes. The gene expression pattern coincides with the previously identified stomatal characteristics of fern. This study is the first multi-organ full-length transcriptome report of a tree fern species, the abundant genetic resources and comprehensive analysis of A. spinulosa, which provides the groundwork for future tree fern research.
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Affiliation(s)
- Yongfeng Hong
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
| | - Ting Wang
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- *Correspondence: Yingjuan Su, ; Ting Wang,
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14
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Makita Y, Suzuki S, Fushimi K, Shimada S, Suehisa A, Hirata M, Kuriyama T, Kurihara Y, Hamasaki H, Okubo-Kurihara E, Yoshitake K, Watanabe T, Sakuta M, Gojobori T, Sakami T, Narikawa R, Yamaguchi H, Kawachi M, Matsui M. Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. Nat Commun 2021; 12:3593. [PMID: 34135337 PMCID: PMC8209157 DOI: 10.1038/s41467-021-23741-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
Photoreceptors are conserved in green algae to land plants and regulate various developmental stages. In the ocean, blue light penetrates deeper than red light, and blue-light sensing is key to adapting to marine environments. Here, a search for blue-light photoreceptors in the marine metagenome uncover a chimeric gene composed of a phytochrome and a cryptochrome (Dualchrome1, DUC1) in a prasinophyte, Pycnococcus provasolii. DUC1 detects light within the orange/far-red and blue spectra, and acts as a dual photoreceptor. Analyses of its genome reveal the possible mechanisms of light adaptation. Genes for the light-harvesting complex (LHC) are duplicated and transcriptionally regulated under monochromatic orange/blue light, suggesting P. provasolii has acquired environmental adaptability to a wide range of light spectra and intensities.
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Setsuko Shimada
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Aya Suehisa
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Manami Hirata
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tomoko Kuriyama
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidefumi Hamasaki
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan
| | - Emiko Okubo-Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Watanabe
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido, Japan
| | - Masaaki Sakuta
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tomoko Sakami
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan.
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15
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Chater CCC. Light in the darkness: how ferns flourished in the ancestral angiosperm forest. THE NEW PHYTOLOGIST 2021; 230:886-888. [PMID: 33725385 DOI: 10.1111/nph.17273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Caspar C C Chater
- Department of Natural Capital and Plant Health, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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16
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Cai S, Huang Y, Chen F, Zhang X, Sessa E, Zhao C, Marchant DB, Xue D, Chen G, Dai F, Leebens‐Mack JH, Zhang G, Shabala S, Christie JM, Blatt MR, Nevo E, Soltis PS, Soltis DE, Franks PJ, Wu F, Chen Z. Evolution of rapid blue-light response linked to explosive diversification of ferns in angiosperm forests. THE NEW PHYTOLOGIST 2021; 230:1201-1213. [PMID: 33280113 PMCID: PMC8048903 DOI: 10.1111/nph.17135] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/21/2020] [Indexed: 05/23/2023]
Abstract
Ferns appear in the fossil record some 200 Myr before angiosperms. However, as angiosperm-dominated forest canopies emerged in the Cretaceous period there was an explosive diversification of modern (leptosporangiate) ferns, which thrived in low, blue-enhanced light beneath angiosperm canopies. A mechanistic explanation for this transformative event in the diversification of ferns has remained elusive. We used physiological assays, transcriptome analysis and evolutionary bioinformatics to investigate a potential connection between the evolution of enhanced stomatal sensitivity to blue light in modern ferns and the rise of angiosperm-dominated forests in the geological record. We demonstrate that members of the largest subclade of leptosporangiate ferns, Polypodiales, have significantly faster stomatal response to blue light than more ancient fern lineages and a representative angiosperm. We link this higher sensitivity to levels of differentially expressed genes in blue-light signaling, particularly in the cryptochrome (CRY) signaling pathway. Moreover, CRYs of the Polypodiales examined show gene duplication events between 212.9-196.9 and 164.4-151.8 Ma, when angiosperms were emerging, which are lacking in other major clades of extant land plants. These findings suggest that evolution of stomatal blue-light sensitivity helped modern ferns exploit the shady habitat beneath angiosperm forest canopies, fueling their Cretaceous hyperdiversification.
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Affiliation(s)
- Shengguan Cai
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
| | - Yuqing Huang
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
| | - Fei Chen
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Xin Zhang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Emily Sessa
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
| | - Chenchen Zhao
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - D. Blaine Marchant
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- Department of BiologyStanford UniversityStanfordCA94305USA
| | - Dawei Xue
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Guang Chen
- Collaborative Innovation Centre for Grain IndustryCollege of AgricultureYangtze UniversityJingzhou434025China
| | - Fei Dai
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | | | - Guoping Zhang
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Sergey Shabala
- Tasmanian Institute of AgricultureUniversity of TasmaniaHobartTAS7004Australia
- International Research Centre for Environmental Membrane BiologyFoshan UniversityFoshan528041China
| | - John M. Christie
- Laboratory of Plant Physiology and BiophysicsUniversity of GlasgowGlasgowG12 8QQUK
| | - Michael R. Blatt
- Laboratory of Plant Physiology and BiophysicsUniversity of GlasgowGlasgowG12 8QQUK
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaMount CarmelHaifa34988384Israel
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
| | - Douglas E. Soltis
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
| | - Peter J. Franks
- School of Life and Environmental SciencesThe University of SydneySydneyNSW2006Australia
| | - Feibo Wu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Zhong‐Hua Chen
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
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17
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Frangedakis E, Shimamura M, Villarreal JC, Li FW, Tomaselli M, Waller M, Sakakibara K, Renzaglia KS, Szövényi P. The hornworts: morphology, evolution and development. THE NEW PHYTOLOGIST 2021; 229:735-754. [PMID: 32790880 PMCID: PMC7881058 DOI: 10.1111/nph.16874] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species, Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plant A. agrestis to highlight its potential in answering key questions of land plant biology and evolution.
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Affiliation(s)
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 739-8528, Japan
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, G1V 0A6, Canada
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panamá
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853-1801, USA
- Plant Biology Section, Cornell University, Ithaca, New York, 14853-1801, USA
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB3 EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Karen S. Renzaglia
- Department of Plant Biology, Southern Illinois University, Illinois, 62901, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
- Zurich-Basel Plant Science Center, Zurich, 8092, Switzerland
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18
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Krzeszowiec W, Novokreshchenova M, Gabryś H. Chloroplasts in C3 grasses move in response to blue-light. PLANT CELL REPORTS 2020; 39:1331-1343. [PMID: 32661816 PMCID: PMC7497455 DOI: 10.1007/s00299-020-02567-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/08/2020] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Brachypodium distachyon is a good model for studying chloropla st movements in the crop plants, wheat, rye and barley. The movements are activated only by blue light, similar to Arabidopsis. Chloroplast translocations are ubiquitous in photosynthetic organisms. On the one hand, they serve to optimize energy capture under limiting light, on the other hand, they minimize potential photodamage to the photosynthetic apparatus in excess light. In higher plants chloroplast movements are mediated by phototropins (phots), blue light receptors that also control other light acclimation responses. So far, Arabidopsis thaliana has been the main model for studying the mechanism of blue light signaling to chloroplast translocations in terrestrial plants. Here, we propose Brachypodium distachyon as a model in research into chloroplast movements in C3 cereals. Brachypodium chloroplasts respond to light in a similar way to those in Arabidopsis. The amino acid sequence of Brachypodium PHOT1 is 79.3% identical, and that of PHOT2 is 73.6% identical to the sequence of the corresponding phototropin in Arabidopsis. Both phototropin1 and 2 are expressed in Brachypodium, as shown using quantitative real-time PCR. Intriguingly, the light-expression pattern of BradiPHOT1 and BradiPHOT2 is the opposite of that for Arabidopsis phototropins, suggesting potential unique light signaling in C3 grasses. To investigate if Brachypodium is a good model for studying grass chloroplast movements we analyzed these movements in the leaves of three C3 crop grasses, namely wheat, rye and barley. Similarly to Brachypodium, chloroplasts only respond to blue light in all these species.
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Affiliation(s)
- Weronika Krzeszowiec
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Maria Novokreshchenova
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Halina Gabryś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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19
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Lkhamkhuu E, Zikihara K, Katsura H, Tokutomi S, Hosokawa T, Usami Y, Ichihashi M, Yamaguchi J, Monde K. Effect of circularly polarized light on germination, hypocotyl elongation and biomass production of arabidopsis and lettuce: Involvement of phytochrome B. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:57-67. [PMID: 32362749 PMCID: PMC7193831 DOI: 10.5511/plantbiotechnology.19.1219a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/19/2019] [Indexed: 06/11/2023]
Abstract
Circular dichroism (CD), defined as the differential absorption of left- and right-handed circularly polarized light (CPL), is a useful spectroscopic technique for structural studies of biological systems composed of chiral molecules. The present study evaluated the effects of CPL on germination, hypocotyl elongation and biomass production of Arabidopsis and lettuce. Higher germination rates were observed when Arabidopsis and lettuce seedlings were irradiated with red right-handed CPL (R-CPL) than with red left-handed CPL (L-CPL). Hypocotyl elongation was effectively inhibited when Arabidopsis and lettuce seedlings were irradiated with red R-CPL than with red L-CPL. This difference was not observed when a phytochrome B (phyB) deficient mutant of Arabidopsis was irradiated, suggesting that inhibition of elongation by red R-CPL was mediated by phyB. White R-CPL induced greater biomass production by adult Arabidopsis plants, as determined by their fresh shoot weight, than white L-CPL. To determine the molecular basis of these CPL effects, CD spectra and the effect of CPL on the photoreaction of a sensory module of Arabidopsis phyB were measured. The red light-absorbing form of phyB showed a negative CD in the red light-absorbing region, consistent with the results of germination, inhibition of hypocotyl elongation and biomass production. L-CPL and R-CPL, however, did not differ in their ability to induce the interconversion of the red light-absorbing and far-red light-absorbing forms of phyB. These findings suggest that these CPL effects involve phyB, along with other photoreceptors and the photosynthetic process.
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Affiliation(s)
- Enkhsukh Lkhamkhuu
- Graduate School of Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Kazunori Zikihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531
| | - Hitomi Katsura
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531
- Botanical Gardens, Tohoku University, Sendai, Miyagi 980-0862, Japan
| | - Takafumi Hosokawa
- Research and Development Management Headquarters, Fuji Film Corporation, Kanagawa 258-8577, Japan
| | - Yoshihisa Usami
- Research and Development Management Headquarters, Fuji Film Corporation, Kanagawa 258-8577, Japan
| | - Mitsuyoshi Ichihashi
- Research and Development Management Headquarters, Fuji Film Corporation, Kanagawa 258-8577, Japan
| | - Junji Yamaguchi
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenji Monde
- Graduate School of Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
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20
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Wickell DA, Li FW. On the evolutionary significance of horizontal gene transfers in plants. THE NEW PHYTOLOGIST 2020; 225:113-117. [PMID: 31347197 DOI: 10.1111/nph.16022] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/04/2019] [Indexed: 05/05/2023]
Abstract
Horizontal gene transfer (HGT) has long been seen as a crucial process in the evolution of prokaryotic species, but until recently it was thought to have little, if any, effect on the evolution of eukaryotic life forms. Detecting and describing HGT events in eukaryotes is difficult, making this phenomenon at times controversial. However, modern advances in genomics and bioinformatics have radically altered our view of HGT in eukaryotes, especially in plants. It now appears that HGT to and from plant lineages is more common than previously suspected. Importantly, the transfer of functional nuclear genes with adaptive significance has been reported in numerous taxa. Here we review several recent studies that have found evidence of the horizontal transfer of nuclear genes, and argue that HGT has undoubtedly had profound impacts on plant evolution as a whole.
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Affiliation(s)
- David A Wickell
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, Cornell University, New York, NY, 14853, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, Cornell University, New York, NY, 14853, USA
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21
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Hermanowicz P, Banaś AK, Sztatelman O, Gabryś H, Łabuz J. UV-B Induces Chloroplast Movements in a Phototropin-Dependent Manner. FRONTIERS IN PLANT SCIENCE 2019; 10:1279. [PMID: 31681376 PMCID: PMC6804469 DOI: 10.3389/fpls.2019.01279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/12/2019] [Indexed: 05/07/2023]
Abstract
We examined the impact of UV-B irradiation on chloroplast movements in Arabidopsis leaves. Directional chloroplast movements induced by blue light have been described in multiple plant species. In weak light, chloroplasts accumulate at periclinal cell walls to increase light capture. In strong light, chloroplasts exhibit the avoidance response, as they move towards anticlinal walls to protect the photosynthetic apparatus from light-induced damage. In Arabidopsis, chloroplast movements are triggered by phototropins, phot1 and phot2, which are known as blue/UV-A photoreceptors. We found that irradiation with UV-B of 3.3 µmol·m-2·s-1 induced chloroplast accumulation in wild-type plants. UV-B-triggered accumulation was dependent on the presence of phototropins, especially phot1, but not on UVR8 (the canonical UV-B photoreceptor). Irradiation with strong UV-B of 20 µmol·m-2·s-1 did not induce substantial chloroplast relocations in wild-type leaves. However, in the jac1 mutant, which is defective in chloroplast accumulation, strong UV-B elicited chloroplast avoidance. This indicated that UV-B can also activate signaling to the avoidance response. To assess the possibility of indirect effects of UV-B on chloroplast movements, we examined the impact of UV-B on the actin cytoskeleton, which serves as the motile system for chloroplast movements. While irradiation with UV-B of 3.3 µmol·m-2·s-1 did not affect the actin cytoskeleton, strong UV-B disrupted its structure as shown using an Arabidopsis line expressing Lifeact-green fluorescent protein (GFP). In wild-type plants, pretreatment with strong UV-B attenuated chloroplast responses triggered by subsequent blue light irradiation, further indicating that this UV-B intensity also indirectly affects chloroplast movements. Taken together, our results suggest that the effect of UV-B on chloroplast movement is twofold: it directly induces phototropin-mediated movements; however, at higher intensities, it attenuates the movements in a nonspecific manner.
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Affiliation(s)
- Paweł Hermanowicz
- Laboratory of Photobiology, Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Halina Gabryś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Justyna Łabuz
- Laboratory of Photobiology, Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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22
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Babla M, Cai S, Chen G, Tissue DT, Cazzonelli CI, Chen ZH. Molecular Evolution and Interaction of Membrane Transport and Photoreception in Plants. Front Genet 2019; 10:956. [PMID: 31681411 PMCID: PMC6797626 DOI: 10.3389/fgene.2019.00956] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/06/2019] [Indexed: 12/20/2022] Open
Abstract
Light is a vital regulator that controls physiological and cellular responses to regulate plant growth, development, yield, and quality. Light is the driving force for electron and ion transport in the thylakoid membrane and other membranes of plant cells. In different plant species and cell types, light activates photoreceptors, thereby modulating plasma membrane transport. Plants maximize their growth and photosynthesis by facilitating the coordinated regulation of ion channels, pumps, and co-transporters across membranes to fine-tune nutrient uptake. The signal-transducing functions associated with membrane transporters, pumps, and channels impart a complex array of mechanisms to regulate plant responses to light. The identification of light responsive membrane transport components and understanding of their potential interaction with photoreceptors will elucidate how light-activated signaling pathways optimize plant growth, production, and nutrition to the prevailing environmental changes. This review summarizes the mechanisms underlying the physiological and molecular regulations of light-induced membrane transport and their potential interaction with photoreceptors in a plant evolutionary and nutrition context. It will shed new light on plant ecological conservation as well as agricultural production and crop quality, bringing potential nutrition and health benefits to humans and animals.
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Affiliation(s)
- Mohammad Babla
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Shengguan Cai
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guang Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - David T. Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | | | - Zhong-Hua Chen
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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Chen Q, Sun J, Song L, Liu W, Yu F, Li S, Gong H, Lu H. Trait acclimation of the clonal fern
Selliguea griffithiana
to forest epiphytic and terrestrial habitats. Ecol Res 2019. [DOI: 10.1111/1440-1703.12002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Quan Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Mengla China
- College of Life Sciences, University of the Chinese Academy of Sciences Beijing China
| | - Jing‐Qi Sun
- School of GeographySouthwest Forestry University Kunming China
| | - Liang Song
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Mengla China
| | - Wen‐Yao Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Mengla China
| | - Fei‐Hai Yu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and ConservationTaizhou University Taizhou China
| | - Su Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Mengla China
| | - He‐De Gong
- School of GeographySouthwest Forestry University Kunming China
| | - Hua‐Zheng Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of Sciences Mengla China
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24
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Pathmanathan JS, Lopez P, Lapointe FJ, Bapteste E. CompositeSearch: A Generalized Network Approach for Composite Gene Families Detection. Mol Biol Evol 2019; 35:252-255. [PMID: 29092069 PMCID: PMC5850286 DOI: 10.1093/molbev/msx283] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genes evolve by point mutations, but also by shuffling, fusion, and fission of genetic fragments. Therefore, similarity between two sequences can be due to common ancestry producing homology, and/or partial sharing of component fragments. Disentangling these processes is especially challenging in large molecular data sets, because of computational time. In this article, we present CompositeSearch, a memory-efficient, fast, and scalable method to detect composite gene families in large data sets (typically in the range of several million sequences). CompositeSearch generalizes the use of similarity networks to detect composite and component gene families with a greater recall, accuracy, and precision than recent programs (FusedTriplets and MosaicFinder). Moreover, CompositeSearch provides user-friendly quality descriptions regarding the distribution and primary sequence conservation of these gene families allowing critical biological analyses of these data.
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Affiliation(s)
| | - Philippe Lopez
- Institut de Biologie Paris-Seine (IBPS), UPMC Université Paris 06, Sorbonne Universités, Paris, France
| | | | - Eric Bapteste
- Institut de Biologie Paris-Seine (IBPS), UPMC Université Paris 06, Sorbonne Universités, Paris, France
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25
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Jabeen A, Reeder B, Svistunenko D, Hisaindee S, Ashraf S, Al-Zuhair S, Battah S. Effect of the Photodynamic Therapy Applications with Potent Microalgae Constituents on Several Types of Tumor. Ing Rech Biomed 2019. [DOI: 10.1016/j.irbm.2018.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Wada M. Light-dependent spatiotemporal control of plant cell development and organelle movement in fern gametophytes. Microscopy (Oxf) 2019; 68:13-36. [PMID: 30576547 DOI: 10.1093/jmicro/dfy143] [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: 09/18/2018] [Revised: 10/30/2018] [Accepted: 11/24/2018] [Indexed: 11/12/2022] Open
Abstract
The haploid gametophyte generation of ferns is an excellent experimental material for cell biology studies because of its simple structure and high sensitivity to light. Each step of the developmental process, such as cell growth, cell cycle and the direction of cell division, is controlled, step by step, by light, unlike what happens in complex seed plant tissues. To perform analyses at the cell or organelle level, we have developed special tools, instruments and techniques, such as a cuvette suitable for repeated centrifugation in particular directions, microbeam irradiators for partial cell irradiation and single-cell ligation technique to create enucleated cells. Some of our main discoveries are as follows: (1) changes in the intracellular position of the nucleus in long protonemal cells by centrifugation revealed that the nuclear position or a factor(s) that is/are co-centrifuged with the nucleus is important for the decision regarding the place of the formation of preprophase bands and the timing of their disappearance, which determines the position where the new cell wall attaches to the mother cell wall; (2) even within a single cell, various phenomena could be induced by blue or red light, with the localization of the blue or red light receptors being different depending on the phenomenon; (3) de novo mRNA synthesis is not involved in the signal transduction pathways underlying light-induced chloroplast movements. In this review article, various microscopic techniques, in addition to the results of physiology studies in fern gametophytes, are described.
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Affiliation(s)
- Masamitsu Wada
- Department of Biological science, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
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27
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Determination of Phototropism and Polarotropism in Fern Protonemal Cells. Methods Mol Biol 2019. [PMID: 30694464 DOI: 10.1007/978-1-4939-9015-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fern protonemal cells grow at their apices as long, undivided filamentous cells toward red (or weak white) light and change their growth direction if the light direction is changed (i.e., phototropism). When protonemata growing between an agar surface and cover glass are irradiated with polarized red light through the glass on the protonemal side, they start growing at the point where the direction of the vibration plane of polarized light and the transition moment of the photoreceptor, which is parallel to the plasma membrane of the cell's apical part, are equal (i.e., polarotropism). Herein, the methods on how to induce and observe this protonemal phototropism and polarotropism are described.
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28
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Wada M. Cytoskeleton Observation in Phototropism and Polarotropism of Adiantum Protonema. Methods Mol Biol 2019; 1924:191-198. [PMID: 30694476 DOI: 10.1007/978-1-4939-9015-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The distribution patterns of the cytoskeleton, i.e., microtubules and actin filaments, in the apical part of protonemal cells are unique and differ from those of other apical growing cells, such as moss and liverwort protonemata, fungal hyphae, and angiosperm pollen tubes. A ring structure composed of microtubules and actin filaments exists at the basal part of the apical dome of protonemal cells. The structure may control the protonemal diameter and growth direction. Herein, the methods of staining of both microtubules and actin filaments are described.
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Affiliation(s)
- Masamitsu Wada
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
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29
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Watson AK, Lannes R, Pathmanathan JS, Méheust R, Karkar S, Colson P, Corel E, Lopez P, Bapteste E. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution. Methods Mol Biol 2019; 1910:271-308. [PMID: 31278668 DOI: 10.1007/978-1-4939-9074-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the post genomic era, large and complex molecular datasets from genome and metagenome sequencing projects expand the limits of what is possible for bioinformatic analyses. Network-based methods are increasingly used to complement phylogenetic analysis in studies in molecular evolution, including comparative genomics, classification, and ecological studies. Using network methods, the vertical and horizontal relationships between all genes or genomes, whether they are from cellular chromosomes or mobile genetic elements, can be explored in a single expandable graph. In recent years, development of new methods for the construction and analysis of networks has helped to broaden the availability of these approaches from programmers to a diversity of users. This chapter introduces the different kinds of networks based on sequence similarity that are already available to tackle a wide range of biological questions, including sequence similarity networks, gene-sharing networks and bipartite graphs, and a guide for their construction and analyses.
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Affiliation(s)
- Andrew K Watson
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Romain Lannes
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Jananan S Pathmanathan
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Raphaël Méheust
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Slim Karkar
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
- Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of NJ, New Brunswick, NJ, USA
| | - Philippe Colson
- Fondation Institut Hospitalo-Universitaire Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Tione, Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM U1095, Aix-Marseille University, Marseille, France
| | - Eduardo Corel
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Philippe Lopez
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France
| | - Eric Bapteste
- Sorbonne Universités, Institut de Biologie Paris-Seine, UPMC Université Paris 6, Paris, France.
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30
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Colson P, Levasseur A, La Scola B, Sharma V, Nasir A, Pontarotti P, Caetano-Anollés G, Raoult D. Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes. Front Microbiol 2018; 9:2668. [PMID: 30538677 PMCID: PMC6277510 DOI: 10.3389/fmicb.2018.02668] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022] Open
Abstract
Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named ‘TRUC’ (for “Things Resisting Uncompleted Classifications”) alongside Bacteria, Archaea, and Eukarya. Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs). Hierarchical clustering analysis was performed based on a binary presence/absence matrix constructed using 727 informational COGs from cellular organisms. The presence/absence of ‘universal’ FSF domains was used to generate an unrooted maximum parsimony phylogenomic tree. Comparison of the gene content of a giant virus with those of a bacterium, an archaeon, and a eukaryote with small genomes was also performed. Overall, both cladistic analyses based on gene sequences of very central and ancient proteins and on highly conserved protein fold structures as well as phenetic analyses were congruent regarding the delineation of a fourth branch of microbes comprised by giant viruses. Giant viruses appeared as a basal group in the tree of all proteomes. A pangenome and core genome determined for Rickettsia bellii (bacteria), Methanomassiliicoccus luminyensis (archaeon), Encephalitozoon intestinalis (eukaryote), and Tupanvirus (giant virus) showed a substantial proportion of Tupanvirus genes that overlap with those of the cellular microbes. In addition, a substantial genome mosaicism was observed, with 51, 11, 8, and 0.2% of Tupanvirus genes best matching with viruses, eukaryota, bacteria, and archaea, respectively. Finally, we found that genes themselves may be subject to lateral sequence transfers. In summary, our data highlight the quantum leap between classical and giant viruses. Phylogenetic and phyletic analyses and the study of protein fold superfamilies confirm previous evidence of the existence of a fourth TRUC of life that includes giant viruses, and highlight its ancestrality and mosaicism. They also point out that best evolutionary representations for giant viruses and cellular microorganisms are rhizomes, and that sequence transfers rather than gene transfers have to be considered.
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Affiliation(s)
- Philippe Colson
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Vikas Sharma
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Pierre Pontarotti
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
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Wu SZ, Yamada M, Mallett DR, Bezanilla M. Cytoskeletal discoveries in the plant lineage using the moss Physcomitrella patens. Biophys Rev 2018; 10:1683-1693. [PMID: 30382556 DOI: 10.1007/s12551-018-0470-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/21/2018] [Indexed: 12/16/2022] Open
Abstract
Advances in cell biology have been largely driven by pioneering work in model systems, the majority of which are from one major eukaryotic lineage, the opisthokonts. However, with the explosion of genomic information in many lineages, it has become clear that eukaryotes have incredible diversity in many cellular systems, including the cytoskeleton. By identifying model systems in diverse lineages, it may be possible to begin to understand the evolutionary origins of the eukaryotic cytoskeleton. Within the plant lineage, cell biological studies in the model moss, Physcomitrella patens, have over the past decade provided key insights into how the cytoskeleton drives cell and tissue morphology. Here, we review P. patens attributes that make it such a rich resource for cytoskeletal cell biological inquiry and highlight recent key findings with regard to intracellular transport, microtubule-actin interactions, and gene discovery that promises for many years to provide new cytoskeletal players.
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Affiliation(s)
- Shu-Zon Wu
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Moe Yamada
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Darren R Mallett
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA.
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32
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Nuclear movement and positioning in plant cells. Semin Cell Dev Biol 2018; 82:17-24. [DOI: 10.1016/j.semcdb.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022]
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33
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Kimura Y, Kimura I, Kanegae T. Phototropins of the moss Physcomitrella patens function as blue-light receptors for phototropism in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2018; 13:e1525995. [PMID: 30265188 PMCID: PMC6204831 DOI: 10.1080/15592324.2018.1525995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Four phototropin genes (PHOTA1, PHOTA2, PHOTB1, PHOTB2) have been isolated in the moss Physcomitrella patens. These genes encode phototropins that mediate blue-light-induced chloroplast movement. However, the individual functions of these phototropins, including the function of mediating blue-light-induced phototropism, remain unclear. To elucidate the individual functions of P. patens phototropins, each of these phototropin genes was expressed in a phototropin-deficient mutant of Arabidopsis (phot1-5 phot2-1). In addition, fluorescence of GFP fused to these phototropins was examined to determine the subcellular localization of each phototropin. Our results demonstrate that all four P. patens phototropins mediate blue-light-induced phototropism and are associated with the plasma membrane in Arabidopsis. Abbreviations GFP: green fluorescent protein; Pp_phot: Physcomitrella patens phototropin.
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Affiliation(s)
- Yuki Kimura
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Izumi Kimura
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Takeshi Kanegae
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
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34
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Jones MA. Using light to improve commercial value. HORTICULTURE RESEARCH 2018; 5:47. [PMID: 30181887 PMCID: PMC6119199 DOI: 10.1038/s41438-018-0049-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/24/2018] [Accepted: 05/02/2018] [Indexed: 05/20/2023]
Abstract
The plasticity of plant morphology has evolved to maximize reproductive fitness in response to prevailing environmental conditions. Leaf architecture elaborates to maximize light harvesting, while the transition to flowering can either be accelerated or delayed to improve an individual's fitness. One of the most important environmental signals is light, with plants using light for both photosynthesis and as an environmental signal. Plants perceive different wavelengths of light using distinct photoreceptors. Recent advances in LED technology now enable light quality to be manipulated at a commercial scale, and as such opportunities now exist to take advantage of plants' developmental plasticity to enhance crop yield and quality through precise manipulation of a crops' lighting regime. This review will discuss how plants perceive and respond to light, and consider how these specific signaling pathways can be manipulated to improve crop yield and quality.
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Affiliation(s)
- Matthew Alan Jones
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex, Colchester, CO4 3SQ UK
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35
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Méheust R, Bhattacharya D, Pathmanathan JS, McInerney JO, Lopez P, Bapteste E. Formation of chimeric genes with essential functions at the origin of eukaryotes. BMC Biol 2018. [PMID: 29534719 PMCID: PMC5851275 DOI: 10.1186/s12915-018-0500-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Eukaryotes evolved from the symbiotic association of at least two prokaryotic partners, and a good deal is known about the timings, mechanisms, and dynamics of these evolutionary steps. Recently, it was shown that a new class of nuclear genes, symbiogenetic genes (S-genes), was formed concomitant with endosymbiosis and the subsequent evolution of eukaryotic photosynthetic lineages. Understanding their origins and contributions to eukaryogenesis would provide insights into the ways in which cellular complexity has evolved. RESULTS Here, we show that chimeric nuclear genes (S-genes), built from prokaryotic domains, are critical for explaining the leap forward in cellular complexity achieved during eukaryogenesis. A total of 282 S-gene families contributed solutions to many of the challenges faced by early eukaryotes, including enhancing the informational machinery, processing spliceosomal introns, tackling genotoxicity within the cell, and ensuring functional protein interactions in a larger, more compartmentalized cell. For hundreds of S-genes, we confirmed the origins of their components (bacterial, archaeal, or generally prokaryotic) by maximum likelihood phylogenies. Remarkably, Bacteria contributed nine-fold more S-genes than Archaea, including a two-fold greater contribution to informational functions. Therefore, there is an additional, large bacterial contribution to the evolution of eukaryotes, implying that fundamental eukaryotic properties do not strictly follow the traditional informational/operational divide for archaeal/bacterial contributions to eukaryogenesis. CONCLUSION This study demonstrates the extent and process through which prokaryotic fragments from bacterial and archaeal genes inherited during eukaryogenesis underly the creation of novel chimeric genes with important functions.
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Affiliation(s)
- Raphaël Méheust
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005, Paris, France
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Jananan S Pathmanathan
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005, Paris, France
| | - James O McInerney
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, M13 9PL, Manchester, UK
| | - Philippe Lopez
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005, Paris, France
| | - Eric Bapteste
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), 75005, Paris, France.
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36
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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Suetsugu N, Higa T, Wada M. Ferns, mosses and liverworts as model systems for light-mediated chloroplast movements. PLANT, CELL & ENVIRONMENT 2017; 40:2447-2456. [PMID: 27859339 DOI: 10.1111/pce.12867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 05/05/2023]
Abstract
Light-induced chloroplast movement is found in most plant species, including algae and land plants. In land plants with multiple small chloroplasts, under weak light conditions, the chloroplasts move towards the light and accumulate on the periclinal cell walls to efficiently perceive light for photosynthesis (the accumulation response). Under strong light conditions, chloroplasts escape from light to avoid photodamage (the avoidance response). In most plant species, blue light induces chloroplast movement, and phototropin receptor kinases are the blue light receptors. Molecular mechanisms for photoreceptors, signal transduction and chloroplast motility systems are being studied using the model plant Arabidopsis thaliana. However, to further understand the molecular mechanisms and evolutionary history of chloroplast movement in green plants, analyses using other plant systems are required. Here, we review recent works on chloroplast movement in green algae, liverwort, mosses and ferns that provide new insights on chloroplast movement.
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Affiliation(s)
- Noriyuki Suetsugu
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Takeshi Higa
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Masamitsu Wada
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
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Inoue K, Nishihama R, Kohchi T. Evolutionary origin of phytochrome responses and signaling in land plants. PLANT, CELL & ENVIRONMENT 2017; 40:2502-2508. [PMID: 28098347 DOI: 10.1111/pce.12908] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 06/06/2023]
Abstract
Phytochromes comprise one of the major photoreceptor families in plants, and they regulate many aspects of plant growth and development throughout the plant life cycle. A canonical land plant phytochrome originated in the common ancestor of streptophytes. Phytochromes have diversified in seed plants and some basal land plants because of lineage-specific gene duplications that occurred during the course of land plant evolution. Molecular genetic analyses using Arabidopsis thaliana suggested that there are two types of phytochromes in angiosperms, light-labile type I and light-stable type II, which have different signaling mechanisms and which regulate distinct responses. In basal land plants, little is known about molecular mechanisms of phytochrome signaling, although red light/far-red photoreversible physiological responses and the distribution of phytochrome genes are relatively well documented. Recent advances in molecular genetics using the moss Physcomitrella patens and the liverwort Marchantia polymorpha revealed that basal land plants show far-red-induced responses and that the establishment of phytochrome-mediated transcriptional regulation dates back to at least the common ancestor of land plants. In this review, we summarize our knowledge concerning functions of land plant phytochromes, especially in basal land plants, and discuss subfunctionalization/neofunctionalization of phytochrome signaling during the course of land plant evolution.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
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Ganesan M, Lee HY, Kim JI, Song PS. Development of transgenic crops based on photo-biotechnology. PLANT, CELL & ENVIRONMENT 2017; 40:2469-2486. [PMID: 28010046 DOI: 10.1111/pce.12887] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 06/06/2023]
Abstract
The phenotypes associated with plant photomorphogenesis such as the suppressed shade avoidance response and de-etiolation offer the potential for significant enhancement of crop yields. Of many light signal transducers and transcription factors involved in the photomorphogenic responses of plants, this review focuses on the transgenic overexpression of the photoreceptor genes at the uppermost stream of the signalling events, particularly phytochromes, crytochromes and phototropins as the transgenes for the genetic engineering of crops with improved harvest yields. In promoting the harvest yields of crops, the photoreceptors mediate the light regulation of photosynthetically important genes, and the improved yields often come with the tolerance to abiotic stresses such as drought, salinity and heavy metal ions. As a genetic engineering approach, the term photo-biotechnology has been coined to convey the idea that the greater the photosynthetic efficiency that crop plants can be engineered to possess, the stronger the resistance to biotic and abiotic stresses. Development of GM crops based on photoreceptor transgenes (mainly phytochromes, crytochromes and phototropins) is reviewed with the proposal of photo-biotechnology that the photoreceptors mediate the light regulation of photosynthetically important genes, and the improved yields often come with the added benefits of crops' tolerance to environmental stresses.
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Affiliation(s)
- Markkandan Ganesan
- Subtropical Horticulture Research Institute and Faculty of Biotechnology, Jeju National University, Jeju, 63243, Korea
- Department of Life Sciences, Presidency University, Kolkata, 700073, India
| | - Hyo-Yeon Lee
- Subtropical Horticulture Research Institute and Faculty of Biotechnology, Jeju National University, Jeju, 63243, Korea
| | - Jeong-Il Kim
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186, Korea
| | - Pill-Soon Song
- Subtropical Horticulture Research Institute and Faculty of Biotechnology, Jeju National University, Jeju, 63243, Korea
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40
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41
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Higa T, Hasegawa S, Hayasaki Y, Kodama Y, Wada M. Temperature-dependent signal transmission in chloroplast accumulation response. JOURNAL OF PLANT RESEARCH 2017; 130:779-789. [PMID: 28421371 DOI: 10.1007/s10265-017-0938-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/02/2017] [Indexed: 06/07/2023]
Abstract
Chloroplast photorelocation movement, well-characterized light-induced response found in various plant species from alga to higher plants, is an important phenomenon for plants to increase photosynthesis efficiency and avoid photodamage. The signal for chloroplast accumulation movement connecting the blue light receptor, phototropin, and chloroplasts remains to be identified, although the photoreceptors and the mechanism of movement via chloroplast actin filaments have now been revealed in land plants. The characteristics of the signal have been found; the speed of signal transfer is about 1 µm min-1 and that the signal for the accumulation response has a longer life and is transferred a longer distance than that of the avoidance response. Here, to collect the clues of the unknown signal substances, we studied the effect of temperature on the speed of signal transmission using the fern Adiantum capillus-veneris and found the possibility that the mechanism of signal transfer was not dependent on the simple diffusion of a substance; thus, some chemical reaction must also be involved. We also found new insights of signaling substances, such that microtubules are not involved in the signal transmission, and that the signal could even be transmitted through the narrow space between chloroplasts and the plasma membrane.
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Affiliation(s)
- Takeshi Higa
- Department of Biological Sciences, Tokyo Metropolitan University, Minamiosawa, Tokyo, 192-0397, Japan
| | - Satoshi Hasegawa
- Center for Optical Research and Education, Utsunomiya University, Tochigi, 321-8585, Japan
| | - Yoshio Hayasaki
- Center for Optical Research and Education, Utsunomiya University, Tochigi, 321-8585, Japan
| | - Yutaka Kodama
- Center for Bioscience Research and Education, Utsunomiya University, Tochigi, 321-8505, Japan
| | - Masamitsu Wada
- Department of Biological Sciences, Tokyo Metropolitan University, Minamiosawa, Tokyo, 192-0397, Japan.
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42
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Allorent G, Petroutsos D. Photoreceptor-dependent regulation of photoprotection. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:102-108. [PMID: 28472717 DOI: 10.1016/j.pbi.2017.03.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/26/2017] [Accepted: 03/28/2017] [Indexed: 05/05/2023]
Abstract
In photosynthetic organisms, proteins in the light-harvesting complex (LHC) harvest light energy to fuel photosynthesis, whereas photoreceptor proteins are activated by the different wavelengths of the light spectrum to regulate cellular functions. Under conditions of excess light, blue-light photoreceptors activate chloroplast avoidance movements in sessile plants, and blue- and green-light photoreceptors cause motile algae to swim away from intense light. Simultaneously, LHCs switch from light-harvesting mode to energy-dissipation mode, which was thought to be independent of photoreceptor-signaling up until recently. Recent advances, however, indicate that energy dissipation in green algae is controlled by photoreceptors activated by blue and UV-B light, and new molecular links have been established between photoreception and photoprotection.
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Affiliation(s)
- Guillaume Allorent
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Grenoble Alpes, Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France
| | - Dimitris Petroutsos
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Grenoble Alpes, Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France.
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Kong SG, Wada M. Molecular basis of chloroplast photorelocation movement. JOURNAL OF PLANT RESEARCH 2016; 129:159-66. [PMID: 26794773 DOI: 10.1007/s10265-016-0788-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 01/03/2016] [Indexed: 05/05/2023]
Abstract
Chloroplast photorelocation movement is an essential physiological response for sessile plant survival and the optimization of photosynthetic ability. Simple but effective experiments on the physiological, cell biological and molecular genetic aspects have been widely used to investigate the signaling components of chloroplast photorelocation movement in Arabidopsis for the past few decades. Although recent knowledge on chloroplast photorelocation movement has led us to a deeper understanding of its physiological and molecular basis, the biochemical roles of the downstream factors remain largely unknown. In this review, we briefly summarize recent advances regarding chloroplast photorelocation movement and propose that a new high-resolution approach is necessary to investigate the molecular mechanism underlying actin-based chloroplast photorelocation movement.
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Affiliation(s)
- Sam-Geun Kong
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan.
- Research Center for Live-Protein Dynamics, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Masamitsu Wada
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
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44
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Kong SG, Okajima K. Diverse photoreceptors and light responses in plants. JOURNAL OF PLANT RESEARCH 2016; 129:111-4. [PMID: 26860414 DOI: 10.1007/s10265-016-0792-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Sam-Geun Kong
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan.
- Research Center for Live-Protein Dynamics, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Koji Okajima
- Department of Physics, Keio University, Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
- RIKEN Harima Institute, Spring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
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45
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Li FW, Mathews S. Evolutionary aspects of plant photoreceptors. JOURNAL OF PLANT RESEARCH 2016; 129:115-22. [PMID: 26843269 DOI: 10.1007/s10265-016-0785-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 12/27/2015] [Indexed: 05/04/2023]
Abstract
Plant photoreceptors link environmental light cues with physiological responses, determining how individual plants complete their life cycles. Structural and functional evolution of photoreceptors has co-occurred as plants diversified and faced the challenge of new light environments, during the transition of plants to land and as substantial plant canopies evolved. Large-scale comparative sequencing projects allow us for the first time to document photoreceptor evolution in understudied clades, revealing some surprises. Here we review recent progress in evolutionary studies of three photoreceptor families: phytochromes, phototropins and neochromes.
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Affiliation(s)
- Fay-Wei Li
- Department of Biology, Duke University, Durham, NC, 27708, USA.
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
| | - Sarah Mathews
- CSIRO National Research Collections Australia, Australian National Herbarium, Canberra, ACT, 2601, Australia.
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46
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Abstract
In response to low or high intensities of light, the chloroplasts in the mesophyll cells of the leaf are able to increase or decrease their exposure to light by accumulating at the upper and lower sides or along the side walls of the cell respectively. This movement, regulated by the phototropin blue light photoreceptors phot1 and phot2, results in a decreased or increased transmission of light through the leaf. This way the plant is able to optimize harvesting of the incoming light or avoid damage caused by excess light. Here we describe a method that indirectly measures the movement of chloroplasts by taking advantage of the resulting change in leaf transmittance. By using a microplate reader, quantitative measurements of chloroplast accumulation or avoidance can be monitored over time, for multiple samples with relatively little hands-on time.
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47
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WADA M. Chloroplast and nuclear photorelocation movements. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2016; 92:387-411. [PMID: 27840388 PMCID: PMC5328789 DOI: 10.2183/pjab.92.387] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/24/2016] [Indexed: 05/18/2023]
Abstract
Chloroplasts move toward weak light to increase photosynthetic efficiency, and migrate away from strong light to protect chloroplasts from photodamage and eventual cell death. These chloroplast behaviors were first observed more than 100 years ago, but the underlying mechanism has only recently been identified. Ideal plant materials, such as fern gametophytes for photobiological and cell biological approaches, and Arabidopsis thaliana for genetic analyses, have been used along with sophisticated methods, such as partial cell irradiation and time-lapse video recording under infrared light to study chloroplast movement. These studies have revealed precise chloroplast behavior, and identified photoreceptors, other relevant protein components, and novel actin filament structures required for chloroplast movement. In this review, our findings regarding chloroplast and nuclear movements are described.
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Affiliation(s)
- Masamitsu WADA
- Department Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa, Tokyo, Japan
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48
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Sullivan S, Hart JE, Rasch P, Walker CH, Christie JM. Phytochrome A Mediates Blue-Light Enhancement of Second-Positive Phototropism in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:290. [PMID: 27014313 PMCID: PMC4786545 DOI: 10.3389/fpls.2016.00290] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/23/2016] [Indexed: 05/05/2023]
Abstract
Hypocotyl phototropism of etiolated Arabidopsis seedlings is primarily mediated by the blue-light receptor kinase phototropin 1 (phot1). Phot1-mediated curvature to continuous unilateral blue light irradiation (0.5 μmol m(-2) s(-1)) is enhanced by overhead pre-treatment with red light (20 μmol m(-2) s(-1) for 15 min) through the action of phytochrome (phyA). Here, we show that pre-treatment with blue light is equally as effective in eliciting phototropic enhancement and is dependent on phyA. Although blue light pre-treatment was sufficient to activate early phot1 signaling events, phot1 autophosphorylation in vivo was not found to be saturated, as assessed by subsequently measuring phot1 kinase activity in vitro. However, enhancement effects by red and blue light pre-treatment were not observed at higher intensities of phototropic stimulation (10 μmol m(-2) s(-1)). Phototropic enhancement by red and blue light pre-treatments to 0.5 μmol m(-2) s(-1) unilateral blue light irradiation was also lacking in transgenic Arabidopsis where PHOT1 expression was restricted to the epidermis. Together, these findings indicate that phyA-mediated effects on phot1 signaling are restricted to low intensities of phototropic stimulation and originate from tissues other than the epidermis.
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49
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Wang D, Wagner M, Butt HJ, Wu S. Supramolecular hydrogels constructed by red-light-responsive host-guest interactions for photo-controlled protein release in deep tissue. SOFT MATTER 2015; 11:7656-7662. [PMID: 26292617 DOI: 10.1039/c5sm01888a] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a novel red-light-responsive supramolecule. The tetra-ortho-methoxy-substituted azobenzene (mAzo) and β-cyclodextrin (β-CD) spontaneously formed a supramolecular complex. The substituted methoxy groups shifted the responsive wavelength of the azo group to the red light region, which is in the therapeutic window and desirable for biomedical applications. Red light induced the isomerization of mAzo and the disassembly of the mAzo/β-CD supramolecular complex. We synthesized a mAzo-functionalized polymer and a β-CD-functionalized polymer. Mixing the two polymers in an aqueous solution generated a supramolecular hydrogel. Red light irradiation induced a gel-to-sol transition as a result of the disassembly of the mAzo/β-CD complexes. Proteins were loaded in the hydrogel. Red light could control protein release from the hydrogel in tissue due to its deep penetration depth in tissue. We envision the use of red-light-responsive supramolecules for deep-tissue biomedical applications.
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Affiliation(s)
- Dongsheng Wang
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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Kanegae T, Kimura I. A phytochrome/phototropin chimeric photoreceptor of fern functions as a blue/far-red light-dependent photoreceptor for phototropism in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:480-8. [PMID: 26095327 DOI: 10.1111/tpj.12903] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 05/07/2023]
Abstract
In the fern Adiantum capillus-veneris, the phototropic response of the protonemal cells is induced by blue light and partially inhibited by subsequent irradiation with far-red light. This observation strongly suggests the existence of a phytochrome that mediates this blue/far-red reversible response; however, the phytochrome responsible for this response has not been identified. PHY3/NEO1, one of the three phytochrome genes identified in Adiantum, encodes a chimeric photoreceptor composed of both a phytochrome and a phototropin domain. It was demonstrated that phy3 mediates the red light-dependent phototropic response of Adiantum, and that phy3 potentially functions as a phototropin. These findings suggest that phy3 is the phytochrome that mediates the blue/far-red response in Adiantum protonemata. In the present study, we expressed Adiantum phy3 in a phot1 phot2 phototropin-deficient Arabidopsis line, and investigated the ability of phy3 to induce phototropic responses under various light conditions. Blue light irradiation clearly induced a phototropic response in the phy3-expressing transgenic seedlings, and this effect was fully inhibited by simultaneous irradiation with far-red light. In addition, experiments using amino acid-substituted phy3 indicated that FMN-cysteinyl adduct formation in the light, oxygen, voltage (LOV) domain was not necessary for the induction of blue light-dependent phototropism by phy3. We thus demonstrate that phy3 is the phytochrome that mediates the blue/far-red reversible phototropic response in Adiantum. Furthermore, our results imply that phy3 can function as a phototropin, but that it acts principally as a phytochrome that mediates both the red/far-red and blue/far-red light responses.
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Affiliation(s)
- Takeshi Kanegae
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Minami Osawa, Hachioji, Tokyo, 192-0397, Japan
| | - Izumi Kimura
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Minami Osawa, Hachioji, Tokyo, 192-0397, Japan
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